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Sample records for abcc8 dna variations

  1. Complex ABCC8 DNA variations in congenital hyperinsulinism: lessons from functional studies

    DEFF Research Database (Denmark)

    Muzyamba, Morris; Farzaneh, Tabasum; Behe, Phillip;

    2007-01-01

    singly or in combination led to intracellular retention of the channel complex and loss of function. By contrast, V1572I is trafficked appropriately and is functional, consistent with a mechanism of reduction to hemizygosity of paternal ABCC8 in focal disease. V1572I is likely to be a benign DNA variant...

  2. Familial mild hyperglycemia associated with a novel ABCC8-V84I mutation within three generations

    DEFF Research Database (Denmark)

    Gonsorcikova, Lucie; Vaxillaire, Martine; Pruhova, Stepanka;

    2011-01-01

    We present a unique case of a 19-year-old man with a positive family history of persistent mild hyperglycemia and a novel V84I mutation in ABCC8. The proband was initially detected to have fasting hyperglycemia (ranging 6.1-6.4 mmol/L) at the age of 12 years. Increased fasting blood glucose was a...

  3. Hyperinsulinaemic hypoglycaemia and diabetes mellitus due to dominant ABCC8/KCNJ11 mutations.

    LENUS (Irish Health Repository)

    Kapoor, R R

    2011-10-01

    Dominantly acting loss-of-function mutations in the ABCC8\\/KCNJ11 genes can cause mild medically responsive hyperinsulinaemic hypoglycaemia (HH). As controversy exists over whether these mutations predispose to diabetes in adulthood we investigated the prevalence of diabetes in families with dominantly inherited ATP-sensitive potassium (K(ATP)) channel mutations causing HH in the proband.

  4. The spectrum of ABCC8 mutations in Norwegian patients with congenital hyperinsulinism of infancy

    DEFF Research Database (Denmark)

    Sandal, T; Laborie, L B; Brusgaard, K;

    2009-01-01

    channel KIR6.2, which are encoded by the genes ABCC8 and KCNJ11, respectively. Activating mutations in the subunit genes can result in monogenic diabetes, whereas inactivating mutations are the most common cause of congenital hyperinsulinism of infancy (CHI). Twenty-six Norwegian probands with CHI were...... focal disease. One patient had a de novo mutation likely to cause a milder, dominant form of CHI. Altogether, 16 different ABCC8 mutations (including the novel alterations W231R, C267X, IVS6-3C>G, I462V, Q917X and T1531A) were identified. The mutations IVS10+1G>T, R1493W and V21D occurred in five, three...... and two families, respectively. KCNJ11 mutations were not found in any patients. Based on our mutation screening, we estimate the minimum birth prevalence of ABCC8-CHI in Norway to 1:70,000 during the past decade. Our results considerably extend the knowledge of the molecular genetics behind CHI...

  5. ABCC8-Related Maturity-Onset Diabetes of the Young (MODY12): Clinical Features and Treatment Perspective.

    Science.gov (United States)

    Ovsyannikova, Alla K; Rymar, Oksana D; Shakhtshneider, Elena V; Klimontov, Vadim V; Koroleva, Elena A; Myakina, Natalya E; Voevoda, Mikhail I

    2016-09-01

    Maturity-onset diabetes of the young (MODY) is a heterogeneous group of diseases associated with gene mutations leading to dysfunction of pancreatic β-cells. Thirteen identified MODY variants differ from each other by the clinical course and treatment requirement. Currently, MODY subtypes 1-5 are best-studied, descriptions of the other forms are sporadic. This article reports a MODY12 clinical case, caused by a mutation in the gene of the ATP-binding cassette transporter sub-family C member 8 (ABCC8), encoding sulfonylurea receptor 1. Diabetes manifested in a 27-year-old non-obese man with epilepsy in anamnesis. No evidence of ketosis was present, pancreatic antibodies were undetectable, and C-peptide remained within the reference range. During the initial investigation, non-proliferative diabetic retinopathy and elevated albumin excretion rate was revealed. After 4 months, diabetes was complicated by pre-proliferative retinopathy and diabetic macular edema. Recurrent hypoglycemia and an increase in body weight was observed on moderate and even small insulin doses. Taking into account the clinical features and the presence of diabetes in four generations on the maternal side, screening for all MODY subtypes was performed. A mutation in the ABCC8 gene was found in proband and in his mother. After the insulin discontinuation, gliclazide modified release combined with sodium/glucose cotransporter 2 (SGLT2) inhibitors was started. This treatment eliminated hypoglycemia and improved glycemic variability parameters. A decrease in the amplitude of glucose excursions was documented by continuous glucose monitoring. After 3 months of treatment, glycemic control was still optimal, and no hypoglycemic episodes were observed. The case report demonstrates the clinical features of ABCC8-associated MODY and the therapeutic potential of a combination of sulfonylurea with SGLT2 inhibitor in this disease. PMID:27538677

  6. Effect of genetic variants in KCNJ11, ABCC8, PPARG and HNF4A loci on the susceptibility of type 2 diabetes in Chinese Han population

    Institute of Scientific and Technical Information of China (English)

    WANG Fang; HAN Xue-yao; REN Qian; ZHANG Xiu-ying; HAN Ling-chuan; LUO Ying-ying; ZHOU Xiang-hai; JI Li-nong

    2009-01-01

    Background KCNJ11, ABCC8, PPARG, and HNF4A have been found to be associated with type 2 diabetes in populations with different genetic backgrounds. The aim of this study was to test, in a Chinese Han population from Beijing, whether the genetic variants in these four genes were associated with genetic predisposition to type 2 diabetes.Methods We studied the association of four representative SNPs in KCNJ11, ABCC8, PPARG and HNF4A by genotyping them using ABI SnaPshot(R) Multiplex System in 400 unrelated type 2 diabetic patients and 400 unrelated normoglycaemic subjects. Results rs5219(E23K) in KCNJ11 was associated with genetic susceptibility to type 2 diabetes (OR=1.400 with 95% Cl 1.117 1.755, P=0.004 under an additive model, OR=-1.652 with 95% Cl 1.086 2.513, P=0.019 under a recessive model,and OR=1.521 with 95% Cl 1.089 2.123, P=0.014 under a dominant model) after adjusting for sex and body mass index (BMI). We did not find evidence of association for ABCC8 rs1799854, PPARG rs1801282 (Pro12Ala) and HNF4A rs2144908. Genotype-phenotype correlation analysis revealed that rs1799854 in ABCC8 was associated with 2-hour postprandial insulin secretion (P=0.005) after adjusting for sex, age and BMI. Although no interactions between the four variants on the risk of type 2 diabetes were detected, the multiplicative interaction between PPARG Pro12Ala and HNF4A rs2144908 was found to be associated with 2-hour postprandial insulin (P=-0.004 under an additive model for rs2144908;and P=0.001 under a dominant model for rs2144908) after adjusting for age, sex and BMI, assuming a dominant model for PPARG Pro12Ala.Conclusions Our study replicated the association of rs5219 in KCNJ11 with type 2 diabetes in Chinese Han population in Beijing. And we also observed that ABCC8 as well as the interaction between PPARG and HNF4A may contribute to post-challenge insulin secretion.

  7. Lack of association between KCNJ11 (rs5219 and ABCC8 (rs757110 polymorphisms and sulphonylurea treatment response in type 2 diabetes patients in Novosibirsk region

    Directory of Open Access Journals (Sweden)

    Irina Arkadyevna Bondar

    2015-03-01

    Full Text Available AimSulfonylureas (SU are widely used in everyday clinical practice in treatment of patients with type 2 diabetes mellitus (T2DM. There is a considerable variability in SU effects, which may be caused by psychological, social, biological and genetic factors. The aim of the study was to investigate the association between rs5219 KCNJ11 gene and rs757110 ABCC8 gene polymorphism and long-term response to SU-drugs of second and third generation in the Novosibirsk region.Materials and Methods326 patients with type 2 diabetes in the Novosibirsk region were examined. Patients were divided into 2 groups, depending on HbA1c level. The first group included patients with target HbA1c levels on SU monotherapy. The second group included patients who did not reach target HbA1c levels on the highest dose of SU. Genotyping of KCNJ11 (rs5219 and ABCC8 (rs757110 was performed by TaqMan real-time PCR (ICBFM SB RAS, Novosibirsk, Russia.ResultsPatients with type 2 diabetes with a good response to SU-therapy compared to the group of patients with a poor response to SU-therapy were older (65.8±9.1 years vs. 61.6±7.9 years, p<0.01, had later onset of type 2 diabetes (59.7±9.2 years vs. 48.3±9.3 years, p <0.01, shorter duration of type 2 diabetes (6.1±4.8 years vs. 13.2±7.3 years, p<0.01 and weak insulin resistance: fasting insulin 9.7±6.9 mU/ml vs. 13.6±12.7 mU/ml (p<0.05, HOMA-IR 3.1±2.2 vs. 6.2±6.0 (p<0.01, triglycerides 1.76±0.83 mmol/l vs. 2.42±1.97 mmol/l (p <0.01. Statistically significant differences between KCNJ11 (rs5219 and ABCC8 (rs757110 genotypes and response to SU-therapy was not found. The frequency of risk allele T polymorphism rs5219 KCNG11 gene in patients with a good response to SU was 0.38 and in the patients with a poor response to SU -0.38 (χ2=0.02, р=0.89. The frequency of the risk allele G polymorphism rs757110 ABCC8 gene in patients with a good response to SU was 0.40 and in the patients with poor response to SU -0.37 (χ2

  8. Physical activity modifies the effect of SNPs in the SLC2A2 (GLUT2) and ABCC8 (SUR1) genes on the risk of developing type 2 diabetes

    DEFF Research Database (Denmark)

    Oskari Kilpeläinen, Tuomas; Lakka, T A; Laaksonen, D E;

    2007-01-01

    whether physical activity (PA), assessed annually with a questionnaire, modified the association of SNPs in SLC2A2 and ABCC8 with the conversion to T2D in the combined intervention and control groups of the DPS. Finnish overweight subjects with IGT (N = 479) were followed for an average of 4.1 yr...

  9. Common variants in the ATP-sensitive K channel genes KCNJ11 (Kir6.2) and ABCC8 (SUR1) in relation to glucose intolerance: population-based studies and meta-analyses

    NARCIS (Netherlands)

    Dam, van R.M.; Hoebee, B.; Seidell, J.C.; Schaap, M.M.; Bruin, de T.W.; Feskens, E.J.M.

    2005-01-01

    Abstract Aims To evaluate the relation between common variants in the ATP-sensitive K(+) channel genes and glucose intolerance. Methods We conducted a meta-analysis of reported association studies in Caucasian populations for common variants in the ABCC8 (exons 16 and 18) and the KCNJ11 (E23K) gene

  10. Mitochondrial DNA sequence variation in Greeks.

    Science.gov (United States)

    Kouvatsi, A; Karaiskou, N; Apostolidis, A; Kirmizidis, G

    2001-12-01

    Mitochondrial DNA (mtDNA) control region sequences were determined in 54 unrelated Greeks, coming from different regions in Greece, for both segments HVR-I and HVR-II. Fifty-two different mtDNA haplotypes were revealed, one of which was shared by three individuals. A very low heterogeneity was found among Greek regions. No one cluster of lineages was specific to individuals coming from a certain region. The average pairwise difference distribution showed a value of 7.599. The data were compared with that for other European or neighbor populations (British, French, Germans, Tuscans, Bulgarians, and Turks). The genetic trees that were constructed revealed homogeneity between Europeans. Median networks revealed that most of the Greek mtDNA haplotypes are clustered to the five known haplogroups and that a number of haplotypes are shared among Greeks and other European and Near Eastern populations.

  11. Mitochondrial DNA sequence variation in single cells from leukemia patients

    OpenAIRE

    Yao, Yong-Gang; Ogasawara, Yoji; Kajigaya, Sachiko; Molldrem, Jeffrey J.; Falcão, Roberto P; Pintão, Maria-Carolina; McCoy, J. Philip; Rizzatti, Edgar Gil; Young, Neal S

    2007-01-01

    A high frequency of mtDNA somatic mutation has been observed in many tumors as well as in aging tissues. In this study, we analyzed the mtDNA control region sequence variation in 3534 single normal cells and individual blasts from 18 patients with leukemia and 10 healthy donors, to address the mutation process in leukemic cells. We found significant differences in mtDNA sequence, as represented by the number of haplotypes and the mean number of cells with each nonaggregate haplotype in a popu...

  12. DNA template dependent accuracy variation of nucleotide selection in transcription.

    Directory of Open Access Journals (Sweden)

    Harriet Mellenius

    Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  13. DNA Methylation Variation Trends during the Embryonic Development of Chicken.

    Directory of Open Access Journals (Sweden)

    Shizhao Li

    Full Text Available The embryogenesis period is critical for epigenetic reprogramming and is thus of great significance in the research field of poultry epigenetics for elucidation of the trends in DNA methylation variations during the embryonic development of birds, particularly due to differences in embryogenesis between birds and mammals. Here, we first examined the variations in genomic DNA methylation during chicken embryogenesis through high-performance liquid chromatography using broilers as the model organism. We then identified the degree of DNA methylation of the promoters and gene bodies involved in two specific genes (IGF2 and TNF-α using the bisulfite sequencing polymerase chain reaction method. In addition, we measured the expression levels of IGF2, TNF-α and DNA methyltransferase (DNMT 1, 3a and 3b. Our results showed that the genomic DNA methylation levels in the liver, heart and muscle increased during embryonic development and that the methylation level of the liver was significantly higher in mid-anaphase. In both the muscle and liver, the promoter methylation levels of TNF-α first increased and then decreased, whereas the gene body methylation levels remained lower at embryonic ages E8, 11 and 14 before increasing notably at E17. The promoter methylation level of IGF2 decreased persistently, whereas the methylation levels in the gene body showed a continuous increase. No differences in the expression of TNF-α were found among E8, 11 and 14, whereas a significant increase was observed at E17. IGF2 showed increasing expression level during the examined embryonic stages. In addition, the mRNA and protein levels of DNMTs increased with increasing embryonic ages. These results suggest that chicken shows increasing genomic DNA methylation patterns during the embryonic period. Furthermore, the genomic DNA methylation levels in tissues are closely related to the genes expression levels, and gene expression may be simultaneously regulated by promoter

  14. Plant genome size variation: bloating and purging DNA.

    Science.gov (United States)

    Michael, Todd P

    2014-07-01

    Plant genome size variation is a dynamic process of bloating and purging DNA. While it was thought plants were on a path to obesity through continual DNA bloating, recent research supports that most plants activity purge DNA. Plant genome size research has greatly benefited from the cataloguing of genome size estimates at the Kew Plant DNA C-values Database, and the recent availability of over 50 fully sequenced and published plant genomes. The emerging trend is that plant genomes bloat due to the copy-and-paste proliferation of a few long terminal repeat retrotransposons (LTRs) and aggressively purge these proliferating LTRs through several mechanisms including illegitimate and incomplete recombination, and double-strand break repair through non-homologous end joining. However, ultra-small genomes such as Utricularia gibba (Bladderwort), which is 82 megabases (Mb), purge excess DNA through genome fractionation and neofunctionalization during multiple rounds of whole genome duplication (WGD). In contrast, the largest published genome, Picea abies (Norway Spruce) at 19 800 Mb, has no detectable WGD but has bloated with diverse and diverged LTRs that either have evaded purging mechanisms or these purging mechanism are absent in gymnosperms. Finally, advances in DNA methylation studies suggest that smaller genomes have a more aggressive epigenomic surveillance system to purge young LTR retrotransposons, which is less active or missing in larger genomes like the bloated gymnosperms. While genome size may not reflect genome complexity, evidence is mounting that genome size may reflect evolutionary status. PMID:24651721

  15. Patterns of DNA Barcode Variation in Canadian Marine Molluscs

    Science.gov (United States)

    Layton, Kara K.S.; Martel, André L.; Hebert, Paul DN.

    2014-01-01

    Background Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. Methodology/Principal Findings This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0–26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%–46.5%), and showed a significant positive correlation with nearest neighbour distances. Conclusions/Significance DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad

  16. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure.

    Science.gov (United States)

    Han, Bingshe; Li, Wenhao; Chen, Zuozhou; Xu, Qiongqiong; Luo, Juntao; Shi, Yingdi; Li, Xiaoxia; Yan, Xiaonan; Zhang, Junfang

    2016-01-01

    DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure. PMID:27494266

  17. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

    Science.gov (United States)

    Xu, Qiongqiong; Luo, Juntao; Shi, Yingdi; Li, Xiaoxia; Yan, Xiaonan; Zhang, Junfang

    2016-01-01

    DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure. PMID:27494266

  18. Mitochondrial DNA T4216C and A4917G variations in multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Talebi, Mahnaz; Sakhinia, Ebrahim;

    2015-01-01

    focuses on the neurogenetics of the complex pathogenesis of MS in relation to factors such as mitochondrial DNA (mtDNA) variations. T4216C and A4917G are common mitochondrial gene variations associated with MS. The present study tested whether mtDNA T4216C variation in the NADH Dehydrogenase 1 (ND1) mt...

  19. Mitochondrial DNA sequence variation in the Anatolian Peninsula (Turkey)

    Indian Academy of Sciences (India)

    Hatice Mergen; Reyhan Öner; Cihan Öner

    2004-04-01

    Throughout human history, the region known today as the Anatolian peninsula (Turkey) has served as a junction connecting the Middle East, Europe and Central Asia, and, thus, has been subject to major population movements. The present study is undertaken to obtain information about the distribution of the existing mitochondrial D-loop sequence variations in the Turkish population of Anatolia. A few studies have previously reported mtDNA sequences in Turks. We attempted to extend these results by analysing a cohort that is not only larger, but also more representative of the Turkish population living in Anatolia. In order to obtain a descriptive picture for the phylogenetic distribution of the mitochondrial genome within Turkey, we analysed mitochondrial D-loop region sequence variations in 75 individuals from different parts of Anatolia by direct sequencing. Analysis of the two hypervariable segments within the noncoding region of the mitochondrial genome revealed the existence of 81 nucleotide mutations at 79 sites. The neighbour-joining tree of Kimura’s distance matrix has revealed the presence of six main clusters, of which H and U are the most common. The data obtained are also compared with several European and Turkic Central Asian populations.

  20. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy.

    Science.gov (United States)

    Silva, Gonçalo; Lima, Fernando P; Martel, Paulo; Castilho, Rita

    2014-10-01

    Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy. PMID:25143035

  1. Effects of Wolbachia on mitochondrial DNA variation in populations of Athetis lepigone (Lepidoptera: Noctuidae) in China

    Science.gov (United States)

    Wolbachia are endosymbiotic bacteria that infect arthropods and incompatibility among strains can affect gene flow within host insect populations, that can result in significant host mitochondrial DNA (MtD) variation. The effects of Wolbachia infection on mtDNA variation was studied in Athetis lepi...

  2. Variation of DNA damage levels in peripheral blood mononuclear cells isolated in different laboratories

    DEFF Research Database (Denmark)

    Godschalk, Roger W L; Ersson, Clara; Stępnik, Maciej;

    2014-01-01

    collected in the same way and processed using the same blood isolation procedure. The inter-laboratory variation was the prominent contributor to the overall variation. The inter-laboratory coefficient of variation decreased for both DNA strand breaks (from 68 to 26%) and FPG sensitive sites (from 57 to 12...... to as 'centre') collected and cryopreserved PBMC samples from three donors, using a standardised cell isolation protocol. The samples were analysed in 13 different laboratories for DNA damage, which is measured by the comet assay. The study aim was to assess variation in DNA damage in PBMC samples that were...

  3. Genomic profiling of plastid DNA variation in the Mediterranean olive tree

    OpenAIRE

    Dorado Gabriel; Khadari Bouchaib; Hernández Pilar; Besnard Guillaume; Savolainen Vincent

    2011-01-01

    Abstract Background Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid...

  4. Genomic profiling of plastid DNA variation in the Mediterranean olive tree

    Directory of Open Access Journals (Sweden)

    Dorado Gabriel

    2011-05-01

    Full Text Available Abstract Background Characterisation of plastid genome (or cpDNA polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L. by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs of cpDNA haplotypes in the Mediterranean olive tree. Results Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels. They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals. Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations. Conclusions We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.

  5. Mitochondrial DNA Variation in Southeastern Pre-Columbian Canids.

    Science.gov (United States)

    Brzeski, Kristin E; DeBiasse, Melissa B; Rabon, David R; Chamberlain, Michael J; Taylor, Sabrina S

    2016-05-01

    The taxonomic status of the red wolf (Canis rufus) is heavily debated, but could be clarified by examining historic specimens from the southeastern United States. We analyzed mitochondrial DNA (mtDNA) from 3 ancient (350-1900 year olds) putative wolf samples excavated from middens and sinkholes within the historic red wolf range. We detected 3 unique mtDNA haplotypes, which grouped with the coyote mtDNA clade, suggesting that the canids inhabiting southeastern North America prior to human colonization from Europe were either coyotes, which would vastly expand historic coyote distributions, an ancient coyote-wolf hybrid, or a North American evolved red wolf lineage related to coyotes. Should the red wolf prove to be a distinct species, our results support the idea of either an ancient hybrid origin for red wolves or a shared common ancestor between coyotes and red wolves. PMID:26774058

  6. Inter-laboratory variation in DNA damage using a standard comet assay protocol

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Ersson, Clara; Loft, Steffen;

    2012-01-01

    There are substantial inter-laboratory variations in the levels of DNA damage measured by the comet assay. The aim of this study was to investigate whether adherence to a standard comet assay protocol would reduce inter-laboratory variation in reported values of DNA damage. Fourteen laboratories...... determined the baseline level of DNA strand breaks (SBs)/alkaline labile sites and formamidopyrimidine DNA glycosylase (FPG)-sensitive sites in coded samples of mononuclear blood cells (MNBCs) from healthy volunteers. There were technical problems in seven laboratories in adopting the standard protocol......, which were not related to the level of experience. Therefore, the inter-laboratory variation in DNA damage was only analysed using the results from laboratories that had obtained complete data with the standard comet assay protocol. This analysis showed that the differences between reported levels...

  7. Fully Streched Single DNA Molecules in a Nanofluidic Chip Show Large-Scale Structural Variation

    DEFF Research Database (Denmark)

    Pedersen, Jonas Nyvold; Marie, Rodolphe; Bauer, D. L.;

    2013-01-01

    When stretching and imaging DNA molecules in nanofluidic devices, it is important to know the relation between the physical length as measured in the lab and the distance along the contour of the DNA. Here a single DNA molecule longer than 1 Mbp is loaded into a nanofluidic device consisting of two...... the contour length of the DNA, and (iii) without having the full DNA molecule inside the field-of-view. The analysis is based on the transverse motion of the DNA due its Brownian motion, i.e. the DNA's response to the thermal fluctuations of the liquid surrounding it. The parameter values obtained by fitting...... reflects the local AT/GC-content. Single molecules are loaded into the chip and imaged. Due to the almost complete stretching of the DNA, structural variations in the size range from kbp to Mbp can be detected and quantified from the melting pattern alone....

  8. Length Variation, Heteroplasmy and Sequence Divergence in the Mitochondrial DNA of Four Species of Sturgeon (Acipenser)

    OpenAIRE

    Brown, J R; Beckenbach, K.; Beckenbach, A. T.; Smith, M.J

    1996-01-01

    The extent of mtDNA length variation and heteroplasmy as well as DNA sequences of the control region and two tRNA genes were determined for four North American sturgeon species: Acipenser transmontanus, A. medirostris, A. fulvescens and A. oxyrhnychus. Across the Continental Divide, a division in the occurrence of length variation and heteroplasmy was observed that was concordant with species biogeography as well as with phylogenies inferred from restriction fragment length polymorphisms (RFL...

  9. Chloroplast DNA variation of oaks in western Central Europe and genetic consequences of human influences

    NARCIS (Netherlands)

    König, A.O.; Ziegenhagen, B.; Dam, van B.C.; Csaikl, U.M.; Coart, E.; Degen, B.; Burg, K.; Vries, de S.M.G.; Petit, R.J.

    2002-01-01

    Oak chloroplast DNA (cpDNA) variation was studied in a grid-based inventory in western Central Europe, including Belgium, The Netherlands, Luxembourg, Germany, the Czech Republic, and the northern parts of Upper and Lower Austria. A total of 2155 trees representing 426 populations of Quercus robur L

  10. Interindividual variation in binding of benzo[a]pyrene to DNA in cultured human Bronchi

    DEFF Research Database (Denmark)

    Harris, C.C.; Autrup, Herman; Connor, R.;

    1976-01-01

    The binding of benzo[a]pyrene to DNA in cultured human bronchus was measured in specimens from 37 patients. The binding values ranged from 2 to 151 picomoles of benzo[a]pyrene per milligram of DNA with an overall mean +/- standard error of 34.2 +/- 5.2. This 75-fold interindividual variation in t...

  11. Human longevity and variation in DNA damage response and repair

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette; Flachsbart, Friederike;

    2014-01-01

    others. Data were applied on 592 SNPs from 77 genes involved in nine sub-processes: DNA-damage response, base excision repair (BER), nucleotide excision repair, mismatch repair, non-homologous end-joining, homologous recombinational repair (HRR), RecQ helicase activities (RECQ), telomere functioning...... and mitochondrial DNA processes. The study population was 1089 long-lived and 736 middle-aged Danes. A self-contained set-based test of all SNPs displayed association with longevity (P-value=9.9 × 10-5), supporting that the overall pathway could affect longevity. Investigation of the nine sub-processes using...

  12. Mitochondrial DNA control region variation in Dubai, United Arab Emirates.

    Science.gov (United States)

    Alshamali, Farida; Brandstätter, Anita; Zimmermann, Bettina; Parson, Walther

    2008-01-01

    249 entire mtDNA control region sequences were generated and analyzed in a population sample from Dubai, one of the seven United Arab Emirates. The control region was amplified in one piece and sequenced with different sequencing primers. Sequence evaluation was performed twice and validated by a third senior mtDNA scientist. Phylogenetic analyses were used for quality assurance purposes and for the determination of the haplogroup affiliation of the samples. Upon publication, the population data are going to be available in the EMPOP database (www.empop.org).

  13. Algorithm of detecting structural variations in DNA sequences

    Science.gov (United States)

    Nałecz-Charkiewicz, Katarzyna; Nowak, Robert

    2014-11-01

    Whole genome sequencing enables to use the longest common subsequence algorithm to detect genetic structure variations. We propose to search position of short unique fragments, genetic markers, to achieve acceptable time and space complexity. The markers are generated by algorithms searching the genetic sequence or its Fourier transformation. The presented methods are checked on structural variations generated in silico on bacterial genomes giving the comparable or better results than other solutions.

  14. Mitochondrial DNA HV1 and HV2 variation in Danes

    DEFF Research Database (Denmark)

    Mikkelsen, Martin; Sørensen, Erik; Rasmussen, Erik Michael;

    2010-01-01

    Sequences from the two hypervariable regions (HV1 and HV2) of the control region of the mitochondrial DNA were obtained from a total of 201 Danes and five individuals who later were recognized to be of non-West European origin. Two fractions of each region were amplified separately and sequenced...

  15. Mitochondrial DNA variation in the Viking age population of Norway.

    Science.gov (United States)

    Krzewińska, Maja; Bjørnstad, Gro; Skoglund, Pontus; Olason, Pall Isolfur; Bill, Jan; Götherström, Anders; Hagelberg, Erika

    2015-01-19

    The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.

  16. Geographic variation of chloroplast DNA in Platycarya strobilacea (Juglandaceae)

    Institute of Scientific and Technical Information of China (English)

    Shi-Chao CHEN; Li ZHANG; Jie ZENG; Fei SHI; Hong YANG; Yun-Rui MAO; Cheng-Xin FU

    2012-01-01

    The monotypic genus Platycarya (Juglandaceae) is one of the most widespread temperate tree species in East Asia.In this research,we implemented a phylogeographical study using chloroplast DNA (cpDNA) (psbA-trnH and atpB-rbcL intergenic spacer) sequences on Platycarya strobilacea,in order to identify the locations of the species' main refugia and migration routes.A total of 180 individuals of P.stobilacea from 27 populations from China and Jeju Island (Korea) were collected.The results revealed that P.strobilacea had 35 haplotypes for the two intergenic spacers and high genetic diversity (hT =0.926).This surprisingly high diversity ofhaplotypes indicates its long evolutionary history,which is in agreement with previous phylogenetic analyses and fossil records.Significant cpDNA population subdivision was detected (GST =0.720; NST =0.862),suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (NST > GST,P < 0.05).The construction of phylogenetic relationships of the 35 chlorotypes detected four major cpDNA clades.Divergence dating analyses using BEAST suggest that the divergence of the major cpDNA clades occurred before the Miocene.Demographic analysis indicated that the Eastern clade underwent localized demographic expansions.The molecular phylogenetic data,together with the geographic distribution of the haplotypes,suggest the existence of multiple glacial refugia in most of its current range in China through Quaternary climatic oscillations.

  17. Epigenetic Variation in Monozygotic Twins: A Genome-Wide Analysis of DNA Methylation in Buccal Cells

    Directory of Open Access Journals (Sweden)

    Jenny van Dongen

    2014-05-01

    Full Text Available DNA methylation is one of the most extensively studied epigenetic marks in humans. Yet, it is largely unknown what causes variation in DNA methylation between individuals. The comparison of DNA methylation profiles of monozygotic (MZ twins offers a unique experimental design to examine the extent to which such variation is related to individual-specific environmental influences and stochastic events or to familial factors (DNA sequence and shared environment. We measured genome-wide DNA methylation in buccal samples from ten MZ pairs (age 8–19 using the Illumina 450k array and examined twin correlations for methylation level at 420,921 CpGs after QC. After selecting CpGs showing the most variation in the methylation level between subjects, the mean genome-wide correlation (rho was 0.54. The correlation was higher, on average, for CpGs within CpG islands (CGIs, compared to CGI shores, shelves and non-CGI regions, particularly at hypomethylated CpGs. This finding suggests that individual-specific environmental and stochastic influences account for more variation in DNA methylation in CpG-poor regions. Our findings also indicate that it is worthwhile to examine heritable and shared environmental influences on buccal DNA methylation in larger studies that also include dizygotic twins.

  18. Patterns of DNA Barcode Variation in Canadian Marine Molluscs

    OpenAIRE

    Layton, Kara K. S.; Martel, André L.; Hebert, Paul D. N.

    2014-01-01

    BACKGROUND: Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonst...

  19. Large scale variation in DNA copy number in chicken breeds

    NARCIS (Netherlands)

    Crooijmans, R.P.M.A.; Fife, M.; FitzGerald, R.J.; strickland, S.; Groenen, M.

    2013-01-01

    Background Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, c

  20. Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

    OpenAIRE

    Silva, Gonçalo; Lima, Fernando P.; Martel, Paulo; Castilho, Rita

    2014-01-01

    Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as...

  1. DNA methylation mediates genetic variation for adaptive transgenerational plasticity.

    Science.gov (United States)

    Herman, Jacob J; Sultan, Sonia E

    2016-09-14

    Environmental stresses experienced by individual parents can influence offspring phenotypes in ways that enhance survival under similar conditions. Although such adaptive transgenerational plasticity is well documented, its transmission mechanisms are generally unknown. One possible mechanism is environmentally induced DNA methylation changes. We tested this hypothesis in the annual plant Polygonum persicaria, a species known to express adaptive transgenerational plasticity in response to parental drought stress. Replicate plants of 12 genetic lines (sampled from natural populations) were grown in dry versus moist soil. Their offspring were exposed to the demethylating agent zebularine or to control conditions during germination and then grown in dry soil. Under control germination conditions, the offspring of drought-stressed parents grew longer root systems and attained greater biomass compared with offspring of well-watered parents of the same genetic lines. Demethylation removed these adaptive developmental effects of parental drought, but did not significantly alter phenotypic expression in offspring of well-watered parents. The effect of demethylation on the expression of the parental drought effect varied among genetic lines. Differential seed provisioning did not contribute to the effect of parental drought on offspring phenotypes. These results demonstrate that DNA methylation can mediate adaptive, genotype-specific effects of parental stress on offspring phenotypes. PMID:27629032

  2. Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya.

    Science.gov (United States)

    Resende, Adriana; Gonçalves, Joana; Muigai, Anne W T; Pereira, Filipe

    2016-06-01

    The history of domestic sheep (Ovis aries) in Africa remains largely unknown. After being first introduced from the Near East, sheep gradually spread through the African continent with pastoral societies. The eastern part of Africa was important either for the first diffusion of sheep southward or for putative secondary introductions from the Arabian Peninsula or southern Asia. We analysed mitochondrial DNA control region sequences of 91 domestic sheep from Kenya and found a high diversity of matrilines from the widespread haplogroup B, whereas only a single individual from haplogroup A was detected. Our phylogeography analyses of more than 500 available mitochondrial DNA sequences also identified ancestral haplotypes that were probably first introduced in Africa and are now widely distributed. Moreover, we found no evidence of an admixture between East and West African sheep. The presence of shared haplotypes in eastern and ancient southern African sheep suggests the possible southward movement of sheep along the eastern part of Africa. Finally, we found no evidence of an extensive introduction of sheep from southern Asia into Africa via the Indian Ocean trade. The overall findings on the phylogeography of East African domestic sheep set the grounds for understanding the origin and subsequent movements of sheep in Africa. The richness of maternal lineages in Kenyan breeds is of prime importance for future conservation and breeding programmes. PMID:26765790

  3. Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Richards Eric J

    2008-09-01

    Full Text Available Abstract Background DNA methylation is an important biochemical mark that silences repetitive sequences, such as transposons, and reinforces epigenetic gene expression states. An important class of repetitive genes under epigenetic control in eukaryotic genomes encodes ribosomal RNA (rRNA transcripts. The ribosomal genes coding for the 45S rRNA precursor of the three largest eukaryotic ribosomal RNAs (18S, 5.8S, and 25–28S are found in nucleolus organizer regions (NORs, comprised of hundreds to thousands of repeats, only some of which are expressed in any given cell. An epigenetic switch, mediated by DNA methylation and histone modification, turns rRNA genes on and off. However, little is known about the mechanisms that specify and maintain the patterns of NOR DNA methylation. Results Here, we explored the extent of naturally-occurring variation in NOR DNA methylation among accessions of the flowering plant Arabidopsis thaliana. DNA methylation in coding regions of rRNA genes was positively correlated with copy number of 45S rRNA gene and DNA methylation in the intergenic spacer regions. We investigated the inheritance of NOR DNA methylation patterns in natural accessions with hypomethylated NORs in inter-strain crosses and defined three different categories of inheritance in F1 hybrids. In addition, subsequent analysis of F2 segregation for NOR DNA methylation patterns uncovered different patterns of inheritance. We also revealed that NOR DNA methylation in the Arabidopsis accession Bor-4 is influenced by the vim1-1 (variant in methylation 1-1 mutation, but the primary effect is specified by the NORs themselves. Conclusion Our results indicate that the NORs themselves are the most significant determinants of natural variation in NOR DNA methylation. However, the inheritance of NOR DNA methylation suggests the operation of a diverse set of mechanisms, including inheritance of parental methylation patterns, reconfiguration of parental NOR DNA

  4. DNA Conformational Variations Induced by Stretching 3'5'-Termini Studied by Molecular Dynamics Simulations

    Institute of Scientific and Technical Information of China (English)

    QI Wen-Peng; LEI Xiao-Ling

    2011-01-01

    @@ Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction.The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA.We study the conformational variations of a 22-mer DNA caused by stretching both 3'-and 5'-termini by molecular dynamics simulations.It requires 250kJ/mol to stretch the DNA molecule by 3'5'-termini for 3.5 run and the force plateau is at 123.8 pN.The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34°to 20°and the successive base pairs rolls to the side of the DNA major groove.The distances between successive base pairs increases from 3.2.(A) to 5.6(A).%Investigating the interaction between protein and stretched DNA molecules has become a new way to study the protein DNA interaction. The conformations from different stretching methods give us a further understanding of the interaction between protein and DNA. We study the conformational variations of a 22-met DNA caused by stretching both 3'- and 5'-termini by molecular dynamics simulations. It requires 250k J/mol to stretch the DNA molecule by 3'5'-termini for 3.5nm and the force plateau is at 123.8pN. The stretching 3'5'-termini leads to large values of the angle opening and the dihedral propeller between bases in one base pair, the double helix untwists from 34° to 20° and the successive base pairs rolls to the side of the DNA major groove. The distances between successive base pairs increases from 3.2 (A) to 5.6 (A).

  5. Terminal region sequence variations in variola virus DNA.

    Science.gov (United States)

    Massung, R F; Loparev, V N; Knight, J C; Totmenin, A V; Chizhikov, V E; Parsons, J M; Safronov, P F; Gutorov, V V; Shchelkunov, S N; Esposito, J J

    1996-07-15

    Genome DNA terminal region sequences were determined for a Brazilian alastrim variola minor virus strain Garcia-1966 that was associated with an 0.8% case-fatality rate and African smallpox strains Congo-1970 and Somalia-1977 associated with variola major (9.6%) and minor (0.4%) mortality rates, respectively. A base sequence identity of > or = 98.8% was determined after aligning 30 kb of the left- or right-end region sequences with cognate sequences previously determined for Asian variola major strains India-1967 (31% death rate) and Bangladesh-1975 (18.5% death rate). The deduced amino acid sequences of putative proteins of > or = 65 amino acids also showed relatively high identity, although the Asian and African viruses were clearly more related to each other than to alastrim virus. Alastrim virus contained only 10 of 70 proteins that were 100% identical to homologs in Asian strains, and 7 alastrim-specific proteins were noted. PMID:8661439

  6. Mitochondrial DNA sequence variation in Finnish patients with matrilineal diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Soini Heidi K

    2012-07-01

    Full Text Available Abstract Background The genetic background of type 2 diabetes is complex involving contribution by both nuclear and mitochondrial genes. There is an excess of maternal inheritance in patients with type 2 diabetes and, furthermore, diabetes is a common symptom in patients with mutations in mitochondrial DNA (mtDNA. Polymorphisms in mtDNA have been reported to act as risk factors in several complex diseases. Findings We examined the nucleotide variation in complete mtDNA sequences of 64 Finnish patients with matrilineal diabetes. We used conformation sensitive gel electrophoresis and sequencing to detect sequence variation. We analysed the pathogenic potential of nonsynonymous variants detected in the sequences and examined the role of the m.16189 T>C variant. Controls consisted of non-diabetic subjects ascertained in the same population. The frequency of mtDNA haplogroup V was 3-fold higher in patients with diabetes. Patients harboured many nonsynonymous mtDNA substitutions that were predicted to be possibly or probably damaging. Furthermore, a novel m.13762 T>G in MTND5 leading to p.Ser476Ala and several rare mtDNA variants were found. Haplogroup H1b harbouring m.16189 T > C and m.3010 G > A was found to be more frequent in patients with diabetes than in controls. Conclusions Mildly deleterious nonsynonymous mtDNA variants and rare population-specific haplotypes constitute genetic risk factors for maternally inherited diabetes.

  7. An improved method for detecting genetic variation in DNA using denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    We have examined the feasibility of denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes to detect variations in genomic and cloned DNAs. The result has demonstrated that use of RNA:DNA duplexes makes DGGE much more practical for screening a large number of samples than use of DNA:DNA heteroduplexes, because preparation of RNA probes is easier than that of DNA probes. Three different 32P-labeled RNA probes were produced. Genomic or cloned DNAs were digested with restriction enzymes and hybridized to labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. The presence of a mismatch(es) was detected as a difference in the mobility of bands on the gel. The experimental conditions were determined using DNA segments from cloned normal and three thalassemic human β-globin genes. The results from experiments on the cloned DNAs suggest that DGGE of RNA:DNA duplexes will detect nucleotide substitutions and deletions in DNA. In the course of these studies, a polymorphism due to a single-base substitution at position 666 of IVS2 (IVS2-666) of the human β-globin gene was directly identified using genomic DNA samples. A study of 59 unrelated Japanese from Hiroshima was undertaken in which the frequency of the allele with C at IVS2-666 was 0.48 and that of the allele with T was 0.52. This approach was found to be very effective for detecting heritable variation and should be a powerful tool for detecting fresh mutations in DNA, which occur outside the known restriction sites. (author)

  8. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

    Science.gov (United States)

    Dressman, Devin; Yan, Hai; Traverso, Giovanni; Kinzler, Kenneth W.; Vogelstein, Bert

    2003-01-01

    Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single magnetic particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently labeled particles via flow cytometry. This approach is called BEAMing on the basis of four of its principal components (beads, emulsion, amplification, and magnetics). Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and used for further experimentation. BEAMing can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues. PMID:12857956

  9. Genetic Variation in DNA of Coho Salmon from the Lower Columbia River : Final Report 1993.

    Energy Technology Data Exchange (ETDEWEB)

    Fobes, Stephen; Knudsen, Kathy; Allendorf, Fred

    1993-04-01

    The goal of this project was to develop techniques to provide the information needed to determine if Lower Columbia River coho salmon represent a 'species' under the Endangered Species Act. Our report features two new nuclear DNA approaches to the improved detection of genetic variation: (1) Studies of DNA-level genetic variation for two nuclear growth hormone genes; (2) Use of arbitrary DNA primers (randomly amplified polymorphic DNA, or 'RAPD' primers) to detect variation at large numbers of nuclear genes. We used the polymerase chain reaction (PCR) to amplify variable sections (introns) of two growth hormone genes (GH-I and G/f-Z) in several salmonid species. Coho salmon had three DNA length variants for G/-I intron C. Restriction analysis and sequencing provided valuable information about the mode of evolution of these DNA sequences. We tested segregation of the variants in captive broods of coho salmon, and demonstrated that they are alleles at a single Mendelian locus. Population studies using the GH-1 alleles showed highly significant frequency differences between Lower Columbia River and Oregon Coast coho salmon, and marginal differences among stocks within these regions. These new markers are adequately defined and tested to use in coho salmon population studies of any size. The nature of the variation at GH-1 (Variable Number Tandem Repeats, or 'VNTRs') suggests that more genetic variants will be found in coho salmon from other areas. GH-2 intron C also showed length variation in coho salmon, and this variation was found to be sex-linked. Because PCR methods require minute amounts of tissue, this discovery provides a technique to determine the gender of immature coho salmon without killing them. Chinook salmon had restriction patterns and sequence divergences similar to coho salmon. Thus, we expect that sex linkage of GH-2 alleles predates the evolutionary divergence of Pacific salmon species, and that gender testing with

  10. Inheritance and Variation of Genomic DNA Methylation in Diploid and Triploid Pacific Oyster (Crassostrea gigas).

    Science.gov (United States)

    Jiang, Qun; Li, Qi; Yu, Hong; Kong, Lingfeng

    2016-02-01

    DNA methylation is an important epigenetic mechanism that could be responsive to environmental changes indicating a potential role in natural selection and adaption. In order to evaluate an evolutionary role of DNA methylation, it is essential to first gain a better insight into inheritability. To address this question, this study investigated DNA methylation variation from parents to offspring in the Pacific oyster Crassostrea gigas using fluorescent-labeled methylation-sensitive amplified polymorphism (F-MSAP) analysis. Most of parental methylated loci were stably transmitted to offspring segregating following Medelian expectation. However, methylated loci deviated more often than non-methylated loci and offspring showed a few de novo methylated loci indicating DNA methylation changes from parents to offspring. Interestingly, some male-specific methylated loci were found in this study which might help to explore sex determination in oyster. Despite environmental stimuli, genomic stresses such as polyploidization also can induce methylation changes. This study also compared global DNA methylation level and individual methylated loci between diploid and triploid oysters. Results showed no difference in global methylation state but a few ploidy-specific loci were detected. DNA methylation variation during polyploidization was less than autonomous methylation variation from parents to offspring.

  11. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion

    DEFF Research Database (Denmark)

    Saillard, J; Forster, P; Lynnerup, N;

    2000-01-01

    characterization of Eskimos in general and Greenlanders in particular, we have sequenced hypervariable segment I (HVS-I) of the mitochondrial DNA (mtDNA) control region and typed relevant RFLP sites in the mtDNA of 82 Eskimos from Greenland. A comparison of our data with published sequences demonstrates major mtDNA...... types shared between Na Dene and Eskimo, indicating a common Beringian history within the Holocene. We further confirm the presence of an Eskimo-specific mtDNA subgroup characterized by nucleotide position 16265G within mtDNA group A2. This subgroup is found in all Eskimo groups analyzed so far and is...... estimated to have originated <3,000 years ago. A founder analysis of all Eskimo and Chukchi A2 types indicates that the Siberian and Greenland ancestral mtDNA pools separated around the time when the Neo-Eskimo culture emerged. The Greenland mtDNA types are a subset of the Alaskan mtDNA variation: they lack...

  12. Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes.

    Directory of Open Access Journals (Sweden)

    Joseph Evans

    Full Text Available Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19(th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09 and dw3 (SBI-07 had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.

  13. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula.

    Science.gov (United States)

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies. PMID

  14. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula

    Science.gov (United States)

    Barral-Arca, Ruth; Pischedda, Sara; Gómez-Carballa, Alberto; Pastoriza, Ana; Mosquera-Miguel, Ana; López-Soto, Manuel; Martinón-Torres, Federico; Álvarez-Iglesias, Vanesa; Salas, Antonio

    2016-01-01

    The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies. PMID

  15. Mitochondrial DNA variation of the common hippopotamus: evidence for a recent population expansion

    DEFF Research Database (Denmark)

    Okello, John Bosco A.; Nyakaana, Silvester; Masembe, C.;

    2005-01-01

    Mitochondrial DNA control region sequence variation was obtained and the population history of the common hippopotamus was inferred from 109 individuals from 13 localities covering six populations in sub-Saharan Africa. In all, 100 haplotypes were defined, of which 98 were locality specific...

  16. Estimation Of The Proportion Of Variation Accounted For By DNA Tests. II: Phenotypic Variance

    Science.gov (United States)

    The proportion of phenotypic variation accounted for (Rp2) is an important characteristic of a DNA test. Therefore, several estimators of this quantity were evaluated by simulation of 500 replicates of a population of 1000 progeny of 100 sires (3 levels of narrow sense heritability and 4 levels of ...

  17. Estimation of the Proportion of Variation Accounted for by DNA Tests. I: Genetic Variance

    Science.gov (United States)

    The proportion of genetic variation accounted for (Rg2) is an important characteristic of a DNA test. For each of 3 levels of narrow sense heritability of the observed trait (h2gy) and 4 levels of Rg2, 500 independent replicates of an observed trait and a molecular breeding value (MBV) for 1000 offs...

  18. Estimation of the Proportion of Genetic Variation Accounted for by DNA Tests

    Science.gov (United States)

    An increasingly relevant question in evaluating commercial DNA tests is "What proportion of the additive genetic variation in the target trait is accounted for by the test?" Therefore, several estimators of this quantity were evaluated by simulation of a population of 1000 animals with 100 sires, ea...

  19. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    1995-01-01

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  20. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations.

    Directory of Open Access Journals (Sweden)

    Hyang-Min Byun

    Full Text Available BACKGROUND: DNA methylation is an epigenetic mechanism that has been increasingly investigated in observational human studies, particularly on blood leukocyte DNA. Characterizing the degree and determinants of DNA methylation stability can provide critical information for the design and conduction of human epigenetic studies. METHODS: We measured DNA methylation in 12 gene-promoter regions (APC, p16, p53, RASSF1A, CDH13, eNOS, ET-1, IFNγ, IL-6, TNFα, iNOS, and hTERT and 2 of non-long terminal repeat elements, i.e., L1 and Alu in blood samples obtained from 63 healthy individuals at baseline (Day 1 and after three days (Day 4. DNA methylation was measured by bisulfite-PCR-Pyrosequencing. We calculated intraclass correlation coefficients (ICCs to measure the within-individual stability of DNA methylation between Day 1 and 4, subtracted of pyrosequencing error and adjusted for multiple covariates. RESULTS: Methylation markers showed different temporal behaviors ranging from high (IL-6, ICC = 0.89 to low stability (APC, ICC = 0.08 between Day 1 and 4. Multiple sequence and marker characteristics were associated with the degree of variation. Density of CpG dinucleotides nearby the sequence analyzed (measured as CpG(o/e or G+C content within ±200 bp was positively associated with DNA methylation stability. The 3' proximity to repeat elements and range of DNA methylation on Day 1 were also positively associated with methylation stability. An inverted U-shaped correlation was observed between mean DNA methylation on Day 1 and stability. CONCLUSIONS: The degree of short-term DNA methylation stability is marker-dependent and associated with sequence characteristics and methylation levels.

  1. Varietal tracing of virgin olive oils based on plastid DNA variation profiling.

    Directory of Open Access Journals (Sweden)

    Marga Pérez-Jiménez

    Full Text Available Olive oil traceability remains a challenge nowadays. DNA analysis is the preferred approach to an effective varietal identification, without any environmental influence. Specifically, olive organelle genomics is the most promising approach for setting up a suitable set of markers as they would not interfere with the pollinator variety DNA traces. Unfortunately, plastid DNA (cpDNA variation of the cultivated olive has been reported to be low. This feature could be a limitation for the use of cpDNA polymorphisms in forensic analyses or oil traceability, but rare cpDNA haplotypes may be useful as they can help to efficiently discriminate some varieties. Recently, the sequencing of olive plastid genomes has allowed the generation of novel markers. In this study, the performance of cpDNA markers on olive oil matrices, and their applicability on commercial Protected Designation of Origin (PDO oils were assessed. By using a combination of nine plastid loci (including multi-state microsatellites and short indels, it is possible to fingerprint six haplotypes (in 17 Spanish olive varieties, which can discriminate high-value commercialized cultivars with PDO. In particular, a rare haplotype was detected in genotypes used to produce a regional high-value commercial oil. We conclude that plastid haplotypes can help oil traceability in commercial PDO oils and set up an experimental methodology suitable for organelle polymorphism detection in the complex olive oil matrices.

  2. Exploration of methods to identify polymorphisms associated with variation in DNA repair capacity phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Jones, I M; Thomas, C B; Xi, T; Mohrenweiser, H W; Nelson, D O

    2006-07-03

    Elucidating the relationship between polymorphic sequences and risk of common disease is a challenge. For example, although it is clear that variation in DNA repair genes is associated with familial cancer, aging and neurological disease, progress toward identifying polymorphisms associated with elevated risk of sporadic disease has been slow. This is partly due to the complexity of the genetic variation, the existence of large numbers of mostly low frequency variants and the contribution of many genes to variation in susceptibility. There has been limited development of methods to find associations between genotypes having many polymorphisms and pathway function or health outcome. We have explored several statistical methods for identifying polymorphisms associated with variation in DNA repair phenotypes. The model system used was 80 cell lines that had been resequenced to identify variation; 191 single nucleotide substitution polymorphisms (SNPs) are included, of which 172 are in 31 base excision repair pathway genes, 19 in 5 anti-oxidation genes, and DNA repair phenotypes based on single strand breaks measured by the alkaline Comet assay. Univariate analyses were of limited value in identifying SNPs associated with phenotype variation. Of the multivariable model selection methods tested: the easiest that provided reduced error of prediction of phenotype was simple counting of the variant alleles predicted to encode proteins with reduced activity, which led to a genotype including 52 SNPs; the best and most parsimonious model was achieved using a two-step analysis without regard to potential functional relevance: first SNPs were ranked by importance determined by Random Forests Regression (RFR), followed by cross-validation in a second round of RFR modeling that included ever more SNPs in declining order of importance. With this approach 6 SNPs were found to minimize prediction error. The results should encourage research into utilization of multivariate

  3. Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.

    Science.gov (United States)

    Li, Jing; Li, Jing-Wen; Feng, Zhixing; Wang, Juanjuan; An, Haoran; Liu, Yanni; Wang, Yang; Wang, Kailing; Zhang, Xuegong; Miao, Zhun; Liang, Wenbo; Sebra, Robert; Wang, Guilin; Wang, Wen-Ching; Zhang, Jing-Ren

    2016-07-01

    DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life. We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae, a leading human pathogen. We here report that the epigenetic diversity is caused by extensive DNA inversions among hsdSA, hsdSB, and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdSA alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this HsdSA1-dependent phase variation requires intact DNA methylase activity encoded by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus, the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and resulting epigenetic switch dictate the phase variation between the opaque and transparent phenotypes. Phase variation has been well documented for its importance in pneumococcal carriage and invasive infection, but its molecular basis remains unclear. Our work has discovered a novel epigenetic cause for this significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings broadly represents a significant advancement in our understanding of bacterial R-M systems and their potential in shaping epigenetic and phenotypic diversity of the prokaryotic organisms because similar site-specific recombination systems widely exist in many archaeal and bacterial species. PMID:27427949

  4. Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae

    Science.gov (United States)

    Wang, Juanjuan; An, Haoran; Liu, Yanni; Wang, Kailing; Miao, Zhun; Liang, Wenbo; Sebra, Robert; Wang, Guilin; Wang, Wen-Ching; Zhang, Jing-Ren

    2016-01-01

    DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life. We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae, a leading human pathogen. We here report that the epigenetic diversity is caused by extensive DNA inversions among hsdSA, hsdSB, and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdSA alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this HsdSA1-dependent phase variation requires intact DNA methylase activity encoded by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus, the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and resulting epigenetic switch dictate the phase variation between the opaque and transparent phenotypes. Phase variation has been well documented for its importance in pneumococcal carriage and invasive infection, but its molecular basis remains unclear. Our work has discovered a novel epigenetic cause for this significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings broadly represents a significant advancement in our understanding of bacterial R-M systems and their potential in shaping epigenetic and phenotypic diversity of the prokaryotic organisms because similar site-specific recombination systems widely exist in many archaeal and bacterial species. PMID:27427949

  5. Variation in rDNA locus number and position among legume species and detection of 2 linked rDNA loci in the model Medicago truncatula by FISH.

    Science.gov (United States)

    Abirached-Darmency, Mona; Prado-Vivant, Emilce; Chelysheva, Liudmila; Pouthier, Thomas

    2005-06-01

    Within Fabaceae, legume species have a variable genome size, chromosome number, and ploidy level. The genome distribution of ribosomal genes, easily detectable by fluorescent in situ hybridization (FISH), is a good tool for anchoring physical and genetic comparative maps. The organisation of 45S rDNA and 5S loci was analysed by FISH in the 4 closely related species: Pisum sativum, Medicago truncatula, Medicago sativa (2 diploid taxa), and Lathyrus sativus. The 2 types of rDNA arrays displayed interspecific variation in locus number and location, but little intraspecific variation was detected. In the model legume, M. truncatula, the presence of 2 adjacent 45S rDNA loci was demonstrated, and the location of the rDNA loci was independent of the general evolution of the genome DNA. The different parameters relative to clustering of the rDNA loci in specific chromosome regions and the possible basis of rDNA instability are discussed. PMID:16121252

  6. Variation in Ribosomal DNA among Isolates of the Mycorrhizal Fungus Cenococcum Geophilum FR.

    Science.gov (United States)

    Lobuglio, Katherine Frances

    1990-01-01

    Cenococcum geophilum Fr., a cosmopolitan mycorrhizal fungus, is well-known for its extremely wide host and habitat range. The ecological diversity of C. geophilum sharply contrasts its present taxonomic status as a monotypic form -genus. Restriction fragment length polymorphisms (RFLPs) in nuclear ribosomal DNA (rDNA) was used to assess the degree of genetic variation among 72 isolates of C. geophilum. The probe used in this study was the rDNA repeat cloned from C. geophilum isolate A145 (pCG15). Length of the rDNA repeat was approximately 9 kb. The rDNA clone was mapped for 5 restriction endonucleases. Hybridization with cloned Saccharomyces cerevisiae rDNA (pSR118, and pSR125 containing the 18S, and 5.8-25S rRNA genes respectively), and alignment of restriction endonuclease sites conserved in the rDNA genes of other fungi, were used to position the corresponding rDNAs of C. geophilum. Southern hybridizations with EcoRI, HindIII, XhoI, and PstI digested DNAs indicated extensive variation among the C. geophilum isolates, greater than has been previously reported to occur within a fungal species. Most of the rDNA polymorphisms occurred in the IGS region. Restriction endonuclease site and length polymorphisms were also observed in the 5.8S-26S genic regions. Sixteen size categories of length mutations, 6 restriction endonuclease site additions, and 4 restriction endonuclease site deletions were determined using isolate A145 as a reference. The rDNA repeat length among the isolates varied from approximately 8.5 to 10.2 kb. RFLPs were also observed in the mitochondrial (mt) 24S rRNA gene and flanking regions of HindIII digested DNAs of C. geophilum isolates representing both geographically distinct and similar origins. Among the C. geophilum isolates analyzed there were fewer RFLPs in mt-DNA than in nuclear rDNA. EcoRI rDNA phenotypes between C. geophilum and Elaphomyces anthracinus, its proposed teleomorph or sexual state, did not correspond. In addition, the four

  7. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

    Directory of Open Access Journals (Sweden)

    B. Bennetts

    2014-09-01

    Full Text Available Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA in collaboration with the Human Genetics Society of Australasia (HGSA, and the Human Variome Project (HVP is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

  8. Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies.

    Directory of Open Access Journals (Sweden)

    Zalman Vaksman

    Full Text Available Microsatellites (MST, tandem repeats of 1-6 nucleotide motifs, are mutational hot-spots with a bias for insertions and deletions (INDELs rather than single nucleotide polymorphisms (SNPs. The majority of MST instability studies are limited to a small number of loci, the Bethesda markers, which are only informative for a subset of colorectal cancers. In this paper we evaluate non-haplotype alleles present within next-gen sequencing data to evaluate somatic MST variation (SMV within DNA repair proficient and DNA repair defective cell lines. We confirm that alleles present within next-gen data that do not contribute to the haplotype can be reliably quantified and utilized to evaluate the SMV without requiring comparisons of matched samples. We observed that SMV patterns found in DNA repair proficient cell lines without DNA repair defects, MCF10A, HEK293 and PD20 RV:D2, had consistent patterns among samples. Further, we were able to confirm that changes in SMV patterns in cell lines lacking functional BRCA2, FANCD2 and mismatch repair were consistent with the different pathways perturbed. Using this new exome sequencing analysis approach we show that DNA instability can be identified in a sample and that patterns of instability vary depending on the impaired DNA repair mechanism, and that genes harboring minor alleles are strongly associated with cancer pathways. The MST Minor Allele Caller used for this study is available at https://github.com/zalmanv/MST_minor_allele_caller.

  9. A genetic basis for the variation in the vulnerability of cancer to DNA damage

    OpenAIRE

    Yard, Brian D.; Adams, Drew J.; Chie, Eui Kyu; Tamayo, Pablo; Battaglia, Jessica S.; Gopal, Priyanka; Rogacki, Kevin; Pearson, Bradley E.; Phillips, James; Raymond, Daniel P.; Pennell, Nathan A.; Almeida, Francisco; Cheah, Jaime H.; Clemons, Paul A.; Shamji, Alykhan

    2016-01-01

    Radiotherapy is not currently informed by the genetic composition of an individual patient's tumour. To identify genetic features regulating survival after DNA damage, here we conduct large-scale profiling of cellular survival after exposure to radiation in a diverse collection of 533 genetically annotated human tumour cell lines. We show that sensitivity to radiation is characterized by significant variation across and within lineages. We combine results from our platform with genomic featur...

  10. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia

    OpenAIRE

    Trejaut, Jean A; Poloni, Estella S.; Yen, Ju-Chen; Lai, Ying-Hui; Loo, Jun-Hun; Lee, Chien-Liang; He, Chun-Lin; Lin, Marie

    2014-01-01

    BACKGROUND: Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent ...

  11. Application of the adductome approach to assess intertissue DNA damage variations in human lung and esophagus

    International Nuclear Information System (INIS)

    Methods for determining the differential susceptibility of human organs to DNA damage have not yet been explored to any large extent due to technical constraints. The development of comprehensive analytical approaches by which to detect intertissue variations in DNA damage susceptibility may advance our understanding of the roles of DNA adducts in cancer etiology and as exposure biomarkers at least. A strategy designed for the detection and comparison of multiple DNA adducts from different tissue samples was applied to assess esophageal and peripherally- and centrally-located lung tissue DNA obtained from the same person. This adductome approach utilized LC/ESI-MS/MS analysis methods designed to detect the neutral loss of 2'-deoxyribose from positively ionized 2'-deoxynucleoside adducts transmitting the [M+H]+ > [M+H-116]+ transition over 374 transitions. In the final analyses, adductome maps were produced which facilitated the visualization of putative DNA adducts and their relative levels of occurrence and allowed for comprehensive comparisons between samples, including a calf thymus DNA negative control. The largest putative adducts were distributed similarly across the samples, however, differences in the relative amounts of putative adducts in lung and esophagus tissue were also revealed. The largest-occurring lung tissue DNA putative adducts were 90% similar (n = 50), while putative adducts in esophagus tissue DNA were shown to be 80 and 84% similar to central and peripheral lung tissue DNA respectively. Seven DNA adducts, N2-ethyl-2'-deoxyguanosine (N2-ethyl-dG), 1,N6-etheno-2'-deoxyadenosine (εdA), α-S- and α-R-methyl-γ-hydroxy-1,N2-propano-2'-deoxyguanosine (1,N2-PdG1, 1,N2-PdG2), 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-8-hydroxy-pyrimido[1,2-a] purine-(3H)-one (8-OH-PdG) and the two stereoisomers of 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxypyrimido[1,2-a] purine-(3H)-one (6-OH-PdG) were unambiguously detected in all tissue DNA samples by

  12. A genetic basis for the variation in the vulnerability of cancer to DNA damage

    Science.gov (United States)

    Yard, Brian D.; Adams, Drew J.; Chie, Eui Kyu; Tamayo, Pablo; Battaglia, Jessica S.; Gopal, Priyanka; Rogacki, Kevin; Pearson, Bradley E.; Phillips, James; Raymond, Daniel P.; Pennell, Nathan A.; Almeida, Francisco; Cheah, Jaime H.; Clemons, Paul A.; Shamji, Alykhan; Peacock, Craig D.; Schreiber, Stuart L.; Hammerman, Peter S.; Abazeed, Mohamed E.

    2016-01-01

    Radiotherapy is not currently informed by the genetic composition of an individual patient's tumour. To identify genetic features regulating survival after DNA damage, here we conduct large-scale profiling of cellular survival after exposure to radiation in a diverse collection of 533 genetically annotated human tumour cell lines. We show that sensitivity to radiation is characterized by significant variation across and within lineages. We combine results from our platform with genomic features to identify parameters that predict radiation sensitivity. We identify somatic copy number alterations, gene mutations and the basal expression of individual genes and gene sets that correlate with the radiation survival, revealing new insights into the genetic basis of tumour cellular response to DNA damage. These results demonstrate the diversity of tumour cellular response to ionizing radiation and establish multiple lines of evidence that new genetic features regulating cellular response after DNA damage can be identified. PMID:27109210

  13. Population genetic structure of Indian shad, Tenualosa ilisha inferred from variation in mitochondrial DNA sequences.

    Science.gov (United States)

    Behera, B K; Singh, N S; Paria, P; Sahoo, A K; Panda, D; Meena, D K; Das, P; Pakrashi, S; Biswas, D K; Sharma, A P

    2015-09-01

    Indian shad, Tenualosa ilisha, is a commercially important anadromous fish representing major catch in Indo-pacific region. The present study evaluated partial Cytochrome b (Cyt b) gene sequence of mtDNA in T. ilisha for determining genetic variation from Bay of Bengal and Arabian Sea origins. The genomic DNA extracted from T. ilisha samples representing two distant rivers in the Indian subcontinent, the Bhagirathi (lower stretch of Ganges) and the Tapi was analyzed. Sequencing of 307 bp mtDNA Cytochrome b gene fragment revealed the presence of 5 haplotypes, with high haplotype diversity (Hd) of 0.9048 with variance 0.103 and low nucleotide diversity (π) of 0.14301. Three population specific haplotypes were observed in river Ganga and two haplotypes in river Tapi. Neighbour-joining tree based on Cytochrome b gene sequences of T. ilisha showed that population from Bay of Bengal and Arabian Sea origins belonged to two distinct clusters. PMID:26521565

  14. Confocal 3D DNA Cytometry: Assessment of Required Coefficient of Variation by Computer Simulation

    Directory of Open Access Journals (Sweden)

    Lennert S. Ploeger

    2004-01-01

    Full Text Available Background: Confocal Laser Scanning Microscopy (CLSM provides the opportunity to perform 3D DNA content measurements on intact cells in thick histological sections. So far, sample size has been limited by the time consuming nature of the technology. Since the power of DNA histograms to resolve different stemlines depends on both the sample size and the coefficient of variation (CV of histogram peaks, interpretation of 3D CLSM DNA histograms might be hampered by both a small sample size and a large CV. The aim of this study was to analyze the required CV for 3D CLSM DNA histograms given a realistic sample size. Methods: By computer simulation, virtual histograms were composed for sample sizes of 20000, 10000, 5000, 1000, and 273 cells and CVs of 30, 25, 20, 15, 10 and 5%. By visual inspection, the histogram quality with respect to resolution of G0/1 and G2/M peaks of a diploid stemline was assessed. Results: As expected, the interpretability of DNA histograms deteriorated with decreasing sample sizes and higher CVs. For CVs of 15% and lower, a clearly bimodal peak pattern with well distinguishable G0/1 and G2/M peaks were still seen at a sample size of 273 cells, which is our current average sample size with 3D CLSM DNA cytometry. Conclusions: For unambiguous interpretation of DNA histograms obtained using 3D CLSM, a CV of at most 15% is tolerable at currently achievable sample sizes. To resolve smaller near diploid stemlines, a CV of 10% or better should be aimed at. With currently available 3D imaging technology, this CV is achievable.

  15. Sequence-length variation of mtDNA HVS-IC-stretch in Chinese ethnic groups

    Institute of Scientific and Technical Information of China (English)

    Feng CHEN; Yong-hui DANG; Chun-xia YAN; Yan-ling LIU; Ya-jun DENG; David J. R. FULTON; Teng CHEN

    2009-01-01

    The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing ap-proaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=-0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of up-stream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics.

  16. Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia

    Directory of Open Access Journals (Sweden)

    Eagle Shannon HC

    2012-03-01

    Full Text Available Abstract Background Despite their ubiquity and high diversity in eukaryotic genomes, DNA transposons are rarely encountered in ribosomal DNA (rDNA. In contrast, R-elements, a diverse group of non-LTR retrotransposons, specifically target rDNA. Pokey is a DNA transposon that targets a specific rDNA site, but also occurs in many other genomic locations, unlike R-elements. However, unlike most DNA transposons, Pokey has been a stable component of Daphnia genomes for over 100 million years. Here we use qPCR to estimate the number of 18S and 28S ribosomal RNA genes and Pokey elements in rDNA (rPokey, as well as other genomic locations (gPokey in two species of Daphnia. Our goals are to estimate the correlation between (1 the number of 18S and 28S rRNA genes, (2 the number of 28S genes and rPokey, and (3 the number of rPokey and gPokey. In addition, we ask whether Pokey number and distribution in both genomic compartments are affected by differences in life history between D. pulex and D. pulicaria. Results We found differences in 18S and 28S gene number within isolates that are too large to be explained by experimental variation. In general, Pokey number within isolates is modest (Pokey. There is no correlation between the number of rRNA genes and rPokey, or between rPokey and gPokey. However, we identified three isolates with unusually high numbers of both rPokey and gPokey, which we infer is a consequence of recent transposition. We also detected other rDNA insertions (rInserts that could be degraded Pokey elements, R- elements or the divergent PokeyB lineage recently detected in the Daphnia genome sequence. Unlike rPokey, rInserts are positively correlated with rRNA genes, suggesting that they are amplified by the same mechanisms that amplify rDNA units even though rPokey is not. Overall, Pokey frequency and distribution are similar in D. pulex and D. pulicaria suggesting that differences in life history have no impact on Pokey. Conclusions The

  17. Genetic variation in Opisthorchis viverrini (Trematoda: Opisthorchiidae) from northeast Thailand and Laos PDR based on random amplified polymorphic DNA analyses

    OpenAIRE

    Sithithaworn, Paiboon; Nuchjungreed, Chadaporn; Srisawangwong, Tuanchai; Ando, Katsuhiko; Petney, Trevor N.; Neil B. Chilton; Andrews, Ross H.

    2006-01-01

    Genetic variation in Opisthorchis viverrini adults originating from different locations in northeast Thailand and Laos, People’s Democratic Republic (PDR), was examined using random amplified polymorphic DNA (RAPD) analyses. In an initial analysis, the genomic DNA of one fluke from each of ten localities was amplified using 15 random primers (10-mers); however, genetic variation among O. viverrini specimens was detected reliably for only four primers. A more detailed RAPD analysis using these...

  18. High Sequence Variations in Mitochondrial DNA Control Region among Worldwide Populations of Flathead Mullet Mugil cephalus

    Directory of Open Access Journals (Sweden)

    Brian Wade Jamandre

    2014-01-01

    Full Text Available The sequence and structure of the complete mtDNA control region (CR of M. cephalus from African, Pacific, and Atlantic populations are presented in this study to assess its usefulness in phylogeographic studies of this species. The mtDNA CR sequence variations among M. cephalus populations largely exceeded intraspecific polymorphisms that are generally observed in other vertebrates. The length of CR sequence varied among M. cephalus populations due to the presence of indels and variable number of tandem repeats at the 3′ hypervariable domain. The high evolutionary rate of the CR in this species probably originated from these mutations. However, no excessive homoplasic mutations were noticed. Finally, the star shaped tree inferred from the CR polymorphism stresses a rapid radiation worldwide, in this species. The CR still appears as a good marker for phylogeographic investigations and additional worldwide samples are warranted to further investigate the genetic structure and evolution in M. cephalus.

  19. Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands.

    Science.gov (United States)

    Delfin, Frederick; Myles, Sean; Choi, Ying; Hughes, David; Illek, Robert; van Oven, Mannis; Pakendorf, Brigitte; Kayser, Manfred; Stoneking, Mark

    2012-02-01

    Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomons ∼9,200 years ago and is the most frequent NRY haplogroup there. There are no consistent genetic differences between Austronesian-speaking and Papuan-speaking groups, suggesting extensive genetic contact between them. Santa Cruz, which is located in Remote Oceania, shows unusually low frequencies of mtDNA and NRY haplogroups of recent Asian ancestry. This is in apparent contradiction with expectations based on archaeological and linguistic evidence for an early (∼3,200 years ago), direct colonization of Santa Cruz by Lapita people from the Bismarck Archipelago, via a migration that "leapfrogged" over the rest of the Solomons. Polynesian Outliers show dramatic island-specific founder events involving various NRY haplogroups. We also find that NRY, but not mtDNA, genetic distance is correlated with the geographic distance between Solomons groups and that historically attested spheres of cultural interaction are associated with the recent genetic structure of Solomons groups, as revealed by mtDNA HV1 sequence and Y-STR haplotype diversity. Our results fill an important lacuna in human genetic studies of Oceania and aid in understanding the colonization and genetic history of

  20. Regional Variation in mtDNA of the Lesser Prairie-Chicken

    Science.gov (United States)

    Hagen, Christian A.; Pitman, James C.; Sandercock, Brett K.; Wolfe, Don H.; Robel, Robel J.; Applegate, Roger D.; Oyler-McCance, Sara J.

    2010-01-01

    Cumulative loss of habitat and long-term decline in the populations of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) have led to concerns for the species' viability throughout its range in the southern Great Plains. For more efficient conservation past and present distributions of genetic variation need to be understood. We examined the distribution of mitochondrial DNA (mtDNA) variation in the Lesser Prairie-Chicken across Kansas, Colorado, Oklahoma, and New Mexico. Throughout the range we found little genetic differentiation except for the population in New Mexico, which was significantly different from most other publications. We did, however, find significant isolation by distance at the rangewide scale (r=0.698). We found no relationship between haplotype phylogeny and geography, and our analyses provide evidence for a post-glacial population expansion within the species that is consistent with the idea that speciation within Tympanuchus is recent. Conservation actions that increase the likelihood of genetically viable populations in the future should be evaluated for implementation.

  1. Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific.

    Science.gov (United States)

    Baker, C S; Medrano-Gonzalez, L; Calambokidis, J; Perry, A; Pichler, F; Rosenbaum, H; Straley, J M; Urban-Ramirez, J; Yamaguchi, M; von Ziegesar, O

    1998-06-01

    The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR-RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (phi ST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (phi ST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall FST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long-term migration rates suggested that male-mediated gene flow was several-fold greater than female gene flow. These results

  2. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events.

    Directory of Open Access Journals (Sweden)

    Stéphane Buhler

    Full Text Available Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model. However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used

  3. Investigation of the effect of ionizing radiation on gene expression variation by the 'DNA chips': feasibility of a biological dosimeter

    International Nuclear Information System (INIS)

    After having described the different biological effects of ionizing radiation and the different approaches to biological dosimetry, and introduced 'DNA chips' or DNA micro-arrays, the author reports the characterization of gene expression variations in the response of cells to a gamma irradiation. Both main aspects of the use DNA chips are investigated: fundamental research and diagnosis. This research thesis thus proposes an analysis of the effect of ionizing radiation using DNA chips, notably by comparing gene expression modifications measured in mouse irradiated lung, heart and kidney. It reports a feasibility study of bio-dosimeter based on expression profiles

  4. Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

    Directory of Open Access Journals (Sweden)

    Elodie Caboux

    Full Text Available The European Prospective Investigation into Cancer and nutrition (EPIC is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88% performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

  5. Genetic Variation Among Vegetative Compatibility Groups of Fusarium oxysporum f. sp. cubense Analyzed by DNA Fingerprinting.

    Science.gov (United States)

    Bentley, S; Pegg, K G; Moore, N Y; Davis, R D; Buddenhagen, I W

    1998-12-01

    ABSTRACT Genetic variation within a worldwide collection of 208 isolates of Fu-sarium oxysporum f. sp. cubense, representing physiological races 1, 2, 3, and 4 and the 20 reported vegetative compatibility groups (VCGs), was analyzed using modified DNA amplification fingerprinting. Also characterized were 133 isolates that did not belong to any of the reported VCGs of F. oxysporum f. sp. cubense including race 3 isolates from a Heliconia species and isolates from a symptomatic wild banana species growing in the jungle in peninsular Malaysia. The DNA fingerprint patterns were generally VCG specific, irrespective of geographic or host origin. A total of 33 different genotypes were identified within F. oxysporum f. sp. cu-bense; 19 genotypes were distinguished among the isolates that belonged to the 20 reported VCGs, and 14 new genotypes were identified among the isolates that did not belong to any of the existing VCGs. DNA fingerprinting analysis also allowed differentiation of nine clonal lineages within F. oxysporum f. sp. cubense. Five of these lineages each contained numerous closely related VCGs and genotypes, and the remaining four lineages each contained a single genotype. The genetic diversity and geographic distribution of several of these lineages of F. oxysporum f. sp. cubense suggests that they have coevolved with edible bananas and their wild diploid progenitors in Asia. DNA fingerprinting analysis of isolates from the wild pathosystem provides further evidence for the coevolution hypothesis. The genetic isolation and limited geographic distribution of four of the lineages of F. oxysporum f. sp. cubense suggests that the pathogen has also arisen independently, both within and outside of the center of origin of the host.

  6. Genetic Variation Among Vegetative Compatibility Groups of Fusarium oxysporum f. sp. cubense Analyzed by DNA Fingerprinting.

    Science.gov (United States)

    Bentley, S; Pegg, K G; Moore, N Y; Davis, R D; Buddenhagen, I W

    1998-12-01

    ABSTRACT Genetic variation within a worldwide collection of 208 isolates of Fu-sarium oxysporum f. sp. cubense, representing physiological races 1, 2, 3, and 4 and the 20 reported vegetative compatibility groups (VCGs), was analyzed using modified DNA amplification fingerprinting. Also characterized were 133 isolates that did not belong to any of the reported VCGs of F. oxysporum f. sp. cubense including race 3 isolates from a Heliconia species and isolates from a symptomatic wild banana species growing in the jungle in peninsular Malaysia. The DNA fingerprint patterns were generally VCG specific, irrespective of geographic or host origin. A total of 33 different genotypes were identified within F. oxysporum f. sp. cu-bense; 19 genotypes were distinguished among the isolates that belonged to the 20 reported VCGs, and 14 new genotypes were identified among the isolates that did not belong to any of the existing VCGs. DNA fingerprinting analysis also allowed differentiation of nine clonal lineages within F. oxysporum f. sp. cubense. Five of these lineages each contained numerous closely related VCGs and genotypes, and the remaining four lineages each contained a single genotype. The genetic diversity and geographic distribution of several of these lineages of F. oxysporum f. sp. cubense suggests that they have coevolved with edible bananas and their wild diploid progenitors in Asia. DNA fingerprinting analysis of isolates from the wild pathosystem provides further evidence for the coevolution hypothesis. The genetic isolation and limited geographic distribution of four of the lineages of F. oxysporum f. sp. cubense suggests that the pathogen has also arisen independently, both within and outside of the center of origin of the host. PMID:18944830

  7. Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers

    Directory of Open Access Journals (Sweden)

    Wales Richard

    2001-07-01

    Full Text Available Abstract Analysis of the genetic variation of an endangered population is an important component for the success of conservation. Animals from two local Romanian pig breeds, the Mangalitsa and Bazna, were analysed for variation at a number of genetic loci using PCR-based DNA tests. Polymorphism was assessed at loci which 1 are known to cause phenotypic variation, 2 are potentially involved in trait differences or 3 are putative candidate genes. The traits considered are disease resistance, growth, coat colour, meat quality and prolificacy. Even though the populations are small and the markers are limited to specific genes, we found significant differences in five of the ten characterised loci. In some cases the observed allele frequencies were interesting in relation to gene function and the phenotype of the breed. These breeds are part of a conservation programme in Romania and marker information may be useful in preserving a representative gene pool in the populations. The use of polymorphisms in type 1 (gene markers may be a useful complement to analysis based on anonymous markers.

  8. The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

    Institute of Scientific and Technical Information of China (English)

    WEN; Bo; SHI; Hong; REN; Ling; XI; Huifeng; LI; Kaiyuan; ZHA

    2004-01-01

    The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the genetic relationship between the Mosuo and five other ethnic groups currently residing in northwest Yunnan, i.e. Naxi, Tibetan, Bai, Yi and Pumi, by typing the genetic variations in mtDNA HVS1 and 21 Y chromosome markers (13 SNPs & 8 STR markers). We showed that the maternal lineages of the Mosuo bear the strongest resemblance with those found in Naxi while its paternal lineages are more similar to those that are prevalent in Yunnan Tibetan. The marked difference between paternal and maternal lineages may be attributable to the genetic history, matriarchal structure, and visiting marriage.

  9. Variations of SOST mRNA expression in human bone are associated with DNA polymorphism and DNA methylation in the SOST gene

    DEFF Research Database (Denmark)

    Lhaneche, Leila; Domingues, Aline; Hannouche, Didier;

    2016-01-01

    SOST encodes sclerostin, an inhibitor of bone formation that antagonizes canonical Wnt signaling. Variations of SOST expression have an impact on bone mineral density (BMD) and bone strength. We hypothesized that genetic and epigenetic DNA modifications have an impact on SOST gene expression. By ...

  10. Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

    Directory of Open Access Journals (Sweden)

    P. K. Rout

    2012-01-01

    Full Text Available Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the

  11. mtDNA variation in Inuit populations of Greenland and Canada: migration history and population structure.

    Science.gov (United States)

    Helgason, Agnar; Pálsson, Gísli; Pedersen, Henning Sloth; Angulalik, Emily; Gunnarsdóttir, Ellen Dröfn; Yngvadóttir, Bryndís; Stefánsson, Kári

    2006-05-01

    We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.

  12. Seasonal variations in levels of DNA adducts and X-spots in human populations living in different parts of Poland.

    OpenAIRE

    Grzybowska, E; Hemminki, K; Choraźy, M

    1993-01-01

    White blood cell DNA adducts were measured in coke oven workers, in residents from the area next to the coke oven in Silesia, Poland (highly industrialized region), and in residents from the rural area of Poland using the 32P-postlabeling technique. This method detected aromatic adducts including adducts formed by polycyclic aromatic hydrocarbons (PAHs). Highest levels of adducts in DNA were seen in the group of coke battery workers (6.9 adducts/10(8) nucleotides). Seasonal variations in leve...

  13. Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

    Science.gov (United States)

    Delgado, Ana M; Cook, James M

    2009-01-01

    Background Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306) of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may reflect a bottleneck during

  14. Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

    Directory of Open Access Journals (Sweden)

    Cook James M

    2009-03-01

    Full Text Available Abstract Background Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306 of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may

  15. Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography.

    Science.gov (United States)

    Cerezo, María; Gusmão, Leonor; Černý, Viktor; Uddin, Nabeel; Syndercombe-Court, Denise; Gómez-Carballa, Alberto; Göbel, Tanja; Schneider, Peter M; Salas, Antonio

    2016-03-20

    Africa is the cradle of all human beings, and although it has been the focus of a number of genetic studies, there are many questions that remain unresolved. We have performed one of the largest and most comprehensive meta-analyses of mitochondrial DNA (mtDNA) lineages carried out in the African continent to date. We generated high-throughput mtDNA single nucleotide polymorphism (SNP) data (230 SNPs) from 2024 Africans, where more than 500 of them were additionally genotyped for the control region. These data were analyzed together with over 12,700 control region profiles collected from the literature, representing more than 300 population samples from Africa. Insights into the African homeland of humans are discussed. Phylogeographic patterns for the African continent are shown at a high phylogeographic resolution as well as at the population and regional levels. The deepest branch of the mtDNA tree, haplogroup L0, shows the highest sub-haplogroup diversity in Southeast and East Africa, suggesting this region as the homeland for modern humans. Several demographic estimates point to the coast as a facilitator of human migration in Africa, but the data indicate complex patterns, perhaps mirroring the effect of recent continental-scaled demographic events in re-shaping African mtDNA variability. PMID:27020033

  16. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation

    NARCIS (Netherlands)

    Colomé Tatché, Maria; Cortijo, Sandra; Wardenaar, Rene; Monteiro Morgado, Lionel; Lahouze, Benoit; Sarazin, Alexis; Etcheverry, Mathilde; Martin, Antoine; Feng, Suhua; Duvernois-Berthet, Evelyne; Labadie, Karine; Wincker, Patrick; Jacobsen, Steven E.; Jansen, Ritsert C.; Colot, Vincent; Johannes, Frank

    2012-01-01

    The rate of meiotic crossing over (CO) varies considerably along chromosomes, leading to marked distortions between physical and genetic distances. The causes underlying this variation are being unraveled, and DNA sequence and chromatin states have emerged as key factors. However, the extent to whic

  17. Genetic variation and species identification of Thai Boesenbergia (Zingiberaceae) analyzed by chloroplast DNA polymorphism.

    Science.gov (United States)

    Techaprasan, Jiranan; Ngamriabsakul, Chatchai; Klinbunga, Sirawut; Chusacultanachai, Sudsanguan; Jenjittikul, Thaya

    2006-07-31

    Genetic variation and molecular phylogeny of 22 taxa representing 14 extant species and 3 unidentified taxa of Boesenbergia in Thailand and four outgroup species (Cornukaempferia aurantiflora, Hedychium biflorum, Kaempferia parviflora, and Scaphochlamys rubescens) were examined by sequencing of 3 chloroplast (cp) DNA regions (matK, psbA-trnH and petA-psbJ). Low interspecific genetic divergence (0.25-1.74%) were observed in these investigated taxa. The 50% majority-rule consensus tree constructed from combined chloroplast DNA sequences allocated Boesenbergia in this study into 3 different groups. Using psbA-1F/psbA-3R primers, an insertion of 491 bp was observed in B. petiolata. Restriction analysis of the amplicon (380-410 bp) from the remaining species with Rsa I further differentiated Boesenbergia to 2 groupings; I (B. basispicata, B. longiflora, B. longipes, B. plicata, B.pulcherrima, B. tenuispicata, B. thorelii, B. xiphostachya, Boesenbergia sp.1 and Boesenbergia sp.3; phylogenetic clade A) that possesses a Rsa I restriction site and II (B.curtisii, B. regalis, B. rotunda and Boesenbergia sp.2; phylogenetic clade B and B. siamensis; phylogenetic clade C) that lacks a restriction site of Rsa I. Single nucleotide polymorphism (SNP) and indels found can be unambiguously applied to authenticate specie-origin of all investigated samples and revealed that Boesenbergia sp.1, Boesenbergia sp.2 and B. pulcherrima (Mahidol University, Kanchanaburi), B. cf. pulcherrima1 (Prachuap Khiri Khan) and B. cf. pulcherrima2 (Thong Pha Phum, Kanchanaburi) are B. plicata, B. rotunda and B. pulcherrima, respectively. In addition, molecular data also suggested that Boesenbergia sp.3 should be further differentiated from B. longiflora and regarded as a newly unidentified Boesenbergia species. PMID:16889678

  18. Variation in assessment of oxidatively damaged DNA in mononuclear blood cells by the comet assay with visual scoring

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Bräuner, Elvira Vaclavik; Folkmann, Janne Kjaersgaard;

    2008-01-01

    The comet assay is popular for assessments of genotoxicity, but the comparison of results between studies is challenging because of differences in experimental procedures and reports of DNA damage in different units. We investigated the variation of DNA damage in mononuclear blood cells (MNBCs......) measured by the comet assay with focus on the variation related to alkaline unwinding and electrophoresis time, number of cells scored, as well as the putative benefits of transforming the primary end points to common units by the use of reference standards and calibration curves. Eight experienced...... conclusion, our results indicate that inter-investigator difference in scoring is a strong determinant of DNA damage levels measured by the comet assay....

  19. Assessment and reduction of comet assay variation in relation to DNA damage: studies from the European Comet Assay Validation Group

    DEFF Research Database (Denmark)

    Møller, Peter; Möller, Lennart; Godschalk, Roger W L;

    2010-01-01

    The alkaline single cell gel electrophoresis (comet) assay has become a widely used method for the detection of DNA damage and repair in cells and tissues. Still, it has been difficult to compare results from different investigators because of differences in assay conditions and because the data...... are reported in different units. The European Comet Assay Validation Group (ECVAG) was established for the purpose of validation of the comet assay with respect to measures of DNA damage formation and its repair. The results from this inter-laboratory validation trail showed a large variation in...... substantial reliability for the measurement of DNA damage by the comet assay but there is still a need for further validation to reduce both assay and inter-laboratory variation....

  20. Genetic Variation and Diversity of Japanese Loach Inferred from Mitochondrial DNA

    Science.gov (United States)

    Koizumi, Noriyuki; Takemura, Takeshi; Watabe, Keiji; Mori, Atsushi

    We conducted a phylogenetic analysis of the cytochrome b gene sequences (1,131-bp) in mitochondrial DNA, to elucidate genetic variation and diversity of the loach Misgurnus anguillicaudatus population in Japan. There were 147 haplotypes that were identified from 444 specimens collected from 123 sites. The phylogenetic tree based on the maximum parsimony method indicated three clades (A, B and C). Clade A resembled genetically the European loach M. fossilis, and the haplotypes were distributed from the North Kanto region northward. Clade B was closely related to the Chinese loach M. anguillicaudatus, and the haplotypes were distributed over the South Tohoku region westward. Clade C that composed of seven subclades seemed to be endemic to Japan, and the haplotypes of these subclades indicated regional or nationwide distribution. Distribution of Clade A and B in Japan appeared to derive from not only artificial release of individuals imported recently from China or Korea, but also diastrophism related to formation processes of the Japanese Islands. Also the estimated divergence time for evolutionary separations between clades was from the upper Miocene to the lower Pliocene (7.4 to 3.8 mya).

  1. Genetic architecture of trout from Albania as revealed by mtDNA control region variation

    Directory of Open Access Journals (Sweden)

    Shumka Spase

    2009-02-01

    Full Text Available Abstract To determine the genetic architecture of trout in Albania, 87 individuals were collected from 19 riverine and lacustrine sites in Albania, FYROM and Greece. All individuals were analyzed for sequence variation in the mtDNA control region. Among fourteen haplotypes detected, four previously unpublished haplotypes, bearing a close relationship to haplotypes of the Adriatic and marmoratus lineages of Salmo trutta, were revealed. Ten previously described haplotypes, characteristic of S. ohridanus, S. letnica and the Adriatic and Mediterranean lineages of S. trutta, were also detected. Haplotypes detected in this study were placed in a well supported branch of S. ohridanus, and a cluster of Mediterranean – Adriatic – marmoratus haplotypes, which were further delimited into three subdivisions of Mediterranean, marmoratus, and a previously non-described formation of four Adriatic haplotypes (Balkan cluster. Haplotypes of the Balkan cluster and the other Adriatic haplotypes, do not represent a contiguous haplotype lineage and appear not to be closely related, indicating independent arrivals into the Adriatic drainage and suggesting successive colonization events. Despite the presence of marmoratus haplotypes in Albania, no marbled phenotype was found, confirming previously reported findings that there is no association between this phenotype and marmoratus haplotypes.

  2. Jagged1 DNA Copy Number Variation Is Associated with Poor Outcome in Liver Cancer.

    Science.gov (United States)

    Kawaguchi, Kazunori; Honda, Masao; Yamashita, Taro; Okada, Hikari; Shirasaki, Takayoshi; Nishikawa, Masashi; Nio, Kouki; Arai, Kuniaki; Sakai, Yoshio; Yamashita, Tatsuya; Mizukoshi, Eishiro; Kaneko, Shuichi

    2016-08-01

    Notch signaling abnormalities are reported to be involved in the acceleration of malignancy in solid tumors and stem cell formation or regeneration in various organs. We analyzed specific genes for DNA copy number variations in liver cancer cells and investigated whether these factors relate to clinical outcome. Chromosome 20p, which includes the ligand for Notch pathways, Jagged1, was found to be amplified in several types of hepatoma cells, and its mRNA was up-regulated according to α-fetoprotein gene expression levels. Notch inhibition using Jagged1 shRNA and γ-secretase inhibitors produced significant suppression of cell growth in α-fetoprotein-producing cells with suppression of downstream genes. Using in vivo hepatoma models, the administration of γ-secretase inhibitors resulted in reduced tumor sizes and effective Notch inhibition with widespread apoptosis and necrosis of viable tumor cells. The γ-secretase inhibitors suppressed cell growth of the epithelial cell adhesion molecule-positive fraction in hepatoma cells, indicating that Notch inhibitors could suppress the stem cell features of liver cancer cells. Even in clinical liver cancer samples, the expression of α-fetoprotein and Jagged1 showed significant correlation, and amplification of the copy number of Jagged1 was associated with Jagged1 mRNA expression and poor survival after liver cancer surgical resection. In conclusion, amplification of Jagged1 contributed to mRNA expression that activates the Jagged1-Notch signaling pathway in liver cancer and led to poor outcome.

  3. Phylogenetic Relationships and Genetic Variation in Longidorus and Xiphinema Species (Nematoda: Longidoridae) Using ITS1 Sequences of Nuclear Ribosomal DNA.

    Science.gov (United States)

    Ye, Weimin; Szalanski, Allen L; Robbins, R T

    2004-03-01

    Genetic analyses using DNA sequences of nuclear ribosomal DNA ITS1 were conducted to determine the extent of genetic variation within and among Longidorus and Xiphinema species. DNA sequences were obtained from samples collected from Arkansas, California and Australia as well as 4 Xiphinema DNA sequences from GenBank. The sequences of the ITS1 region including the 3' end of the 18S rDNA gene and the 5' end of the 5.8S rDNA gene ranged from 1020 bp to 1244 bp for the 9 Longidorus species, and from 870 bp to 1354 bp for the 7 Xiphinema species. Nucleotide frequencies were: A = 25.5%, C = 21.0%, G = 26.4%, and T = 27.1%. Genetic variation between the two genera had a maximum divergence of 38.6% between X. chambersi and L. crassus. Genetic variation among Xiphinema species ranged from 3.8% between X. diversicaudatum and X. bakeri to 29.9% between X. chambersi and X. italiae. Within Longidorus, genetic variation ranged from 8.9% between L. crassus and L. grandis to 32.4% between L. fragilis and L. diadecturus. Intraspecific genetic variation in X. americanum sensu lato ranged from 0.3% to 1.9%, while genetic variation in L. diadecturus had 0.8% and L. biformis ranged from 0.6% to 10.9%. Identical sequences were obtained between the two populations of L. grandis, and between the two populations of X. bakeri. Phylogenetic analyses based on the ITS1 DNA sequence data were conducted on each genus separately using both maximum parsimony and maximum likelihood analysis. Among the Longidorus taxa, 4 subgroups are supported: L. grandis, L. crassus, and L. elongatus are in one cluster; L. biformis and L. paralongicaudatus are in a second cluster; L. fragilis and L. breviannulatus are in a third cluster; and L. diadecturus is in a fourth cluster. Among the Xiphinema taxa, 3 subgroups are supported: X. americanum with X. chambersi, X. bakeri with X. diversicaudatum, and X. italiae and X. vuittenezi forming a sister group with X. index. The relationships observed in this study

  4. Genetic variation and population differentiation of Michelia formosana (Magnoliaceae) based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene recolonization.

    Science.gov (United States)

    Lu, Sheng-You; Hong, Kuo-Hsiang; Liu, Show-Ling; Cheng, Yu-Pin; Wu, Wen-Luan; Chiang, Tzen-Yuh

    2002-06-01

    We used sequence variation of the atpB- rbcL intergenic spacer of cpDNA and nested clade analysis to assess the phylogeographic pattern of Michelia formosana, a species restricted to Taiwan and the Ryukyus. In total, 31 haplotypes were identified and clustered into four major chlorotypes. Genetic composition of nearly all populations was heterogeneous and paraphyletic phylogenetically. Although the apportionment of cpDNA variation hardly revealed a geographic pattern due to the coancestry of dominant sequences, some chlorotypes were restrictedly distributed. According to the patterns of clade dispersion and displacement, a reconstructed minimum spanning network revealed that historical events of past fragmentation and range expansion, associated with glaciation, may have shaped the phylogeographic patterns of M. formosana. Four possible refugia were identified: the Iriomote and Ishigaki Islands (the southern Ryukyus), Wulai (northern Taiwan), and Nanjen (southern Taiwan), on the basis of the interior positions of their haplotypes in the network and the high level of nucleotide diversity. Given insufficient time for coalescence at the cpDNA locus since the late Pleistocene recolonization, lineage sorting led to low levels of genetic differentiation among populations. In contrast, hierarchical examination of the random amplified polymorphic DNA (RAPD) data scored from six populations across three geographical regions, using an analysis of molecular variance (AMOVA), indicated high genetic differentiation both among populations (Phi(ST) = 0.471) and among regions (Phi(CT) = 0.368). An unweighted pair group method with arithmetic mean (UPGMA) tree of the RAPD fingerprints revealed that populations of two offshore islands of eastern Taiwan ( M. formosana var. kotoensis) were clustered with geographically remote populations of the Ryukyus instead of those in southern Taiwan, suggesting some historical division due to geographic barriers of the central mountain range. In

  5. Linearisation of λDNA molecules by instantaneous variation of the trapping electrode voltage inside a micro-channel

    International Nuclear Information System (INIS)

    Because long DNA molecules usually exist in random coil states due to the entropic effect, linearisation is required for devices equipped with nanopores where electrical sequencing is necessary during single-file translocation. We present a novel technique for linearising DNA molecules in a micro-channel. In our device, electrodes are embedded in the bottom surface of the channel. The application of a voltage induces the trapping of λDNA molecules on the positive electrode. An instantaneous voltage drop is used to put the λDNA molecules in a partly released state and the hydrodynamic force of the solution induces linearisation. Phenomena were directly observed using an optical microscopy system equipped with a high-speed camera and the linearisation principle was explored in detail. Furthermore, we estimate the tensile characteristics produced by the flow of the solution through a numerical model of a tethered polymer subject to a Poiseuille flow. The mean tensile force is in the range of 0.1–1 pN. This is sufficiently smaller than the structural transition point of λDNA but counterbalances the entropic elasticity that causes the random coil shape of λDNA molecules in solution. We show the important role of thermal fluctuation in the manipulation of molecules in solution and clarify the tensile conditions required for DNA linearisation using a combination of solution flow and voltage variation in a microchannel. (paper)

  6. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes.

    Science.gov (United States)

    Wood, Elizabeth T; Stover, Daryn A; Ehret, Christopher; Destro-Bisol, Giovanni; Spedini, Gabriella; McLeod, Howard; Louie, Leslie; Bamshad, Mike; Strassmann, Beverly I; Soodyall, Himla; Hammer, Michael F

    2005-07-01

    To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.

  7. Mitochondrial DNA variation within P-type cytoplasmic male sterility of Plantago lanceolata L

    NARCIS (Netherlands)

    Groenendijk, C.F.M.; Sandbrink, J.M.; Van Brederode, J.; Van Damme, J.M.M.

    1997-01-01

    MtDNA restriction fragment polymorphisms were found between cytoplasmic male-sterility types P and R of Plantago lanceolata with the homologous probe pPl311 and maize mtDNA fragments derived from the regions of atp1, cox1 and cox2. No mtDNA differences were observed between male-sterile and restored

  8. Study of genetic variation at the level of DNA between normal and sterilized potato tuber moth males (phthorimaea operculella, zeller)

    International Nuclear Information System (INIS)

    The main objective of current study was to determine the genetic variation at the level of DNA between the normal and sterilized potato tuber moth males. The required mating experiments were carried out to obtain partially sterilized males at 150 Gy and their offspring. Some biological factors of these males were estimated and compared to their unirradiated siblings. To acquire good quality and quantity of DNA for the AFLP technique, several methods were undertaken to isolate DNA of potato tuber moth male from different developmental stages especially from adult stage. However, a method called Modified M5 was used. By Modified M5, which required phenol for the isolation of DNA, in some samples 8 to 12 μg were obtained from one insect with 95-100% purity. In our study, AFLP technique was used to analyze the DNA samples of irradiated and unirradiated males from required mating. The result analysis showed that there was a clear genetic variability between examined individuals. However, the relationship between unirradiated F1 and F2 males was stronger than that between irradiated males. Thus, our result demonstrates that the AFLP could be efficiently utilized for studying genetic variation between insect species or between individuals of the same line which have biological differences induced by several factors such as irradiation. Moreover, this technique could enhance the effectiveness of sterile insect technique by using the AFLP in the monitoring system of released insects. (author)

  9. Study Of Genetic Variation At The Level Of DNA Between Normal And Steriled Potato Tuber Moth Males (Phthorimaea operculella, Zeller)

    International Nuclear Information System (INIS)

    The main objective of current study was to determine the genetic variation at the level of DNA between the normal and sterilized potato tuber moth males. The required mating experiments were carried out to obtain partially sterilize males at 150 Gy and their offspring. Some biological factors of these males were estimated and compared to their unirradiated siblings. To acquire good quality and quantity of DNA for the AFLP technique, several methods were undertaken to isolate DNA of potato tuber moth male from different developmental stages especially from adult stage. However, a method called Modified M5 was used. By Modified M5, which required phenol for the isolation of DNA, in some samples 8 to 12 Mg were obtained from one insect with 95-100% purity. In our study, AFLP technique was used to analyze the DNA samples of irradiated and unirradiated males from required mating. The result analysis showed that there was a clear genetic variability between examined individuals. However, the relationship between unirradiated F1 and F2 males was stronger than that between irradiated males. Thus, our result demonstrates that the AFLP could be efficiently utilized for studying genetic variation between insect species or between individuals of the same line which have biological differences induced by several factors such as irradiation. Moreover, this technique could enhance the effectiveness of sterile insect technique by using the AFLP in the monitoring system of released insects. (author)

  10. Sequence-dependent Structural Variation in DNA Undergoing Intrahelical Inspection by the DNA glycosylase MutM

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Rou-Jia; Zhang, Michael; Qi, Yan; Verdine, Gregory L. (Harvard-Med); (Harvard)

    2012-08-31

    MutM, a bacterial DNA-glycosylase, plays a critical role in maintaining genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions to initiate base excision DNA repair. The task faced by MutM of locating rare oxoG residues embedded in an overwhelming excess of undamaged bases is especially challenging given the close structural similarity between oxoG and its normal progenitor, guanine (G). MutM actively interrogates the DNA to detect the presence of an intrahelical, fully base-paired oxoG, whereupon the enzyme promotes extrusion of the target nucleobase from the DNA duplex and insertion into the extrahelical active site. Recent structural studies have begun to provide the first glimpse into the protein-DNA interactions that enable MutM to distinguish an intrahelical oxoG from G; however, these initial studies left open the important question of how MutM can recognize oxoG residues embedded in 16 different neighboring sequence contexts (considering only the 5'- and 3'-neighboring base pairs). In this study we set out to understand the manner and extent to which intrahelical lesion recognition varies as a function of the 5'-neighbor. Here we report a comprehensive, systematic structural analysis of the effect of the 5'-neighboring base pair on recognition of an intrahelical oxoG lesion. These structures reveal that MutM imposes the same extrusion-prone ('extrudogenic') backbone conformation on the oxoG lesion irrespective of its 5'-neighbor while leaving the rest of the DNA relatively free to adjust to the particular demands of individual sequences.

  11. Molecular DNA variation among Triturus vittatus vittatus (Urodela from different breeding sites at the southern limit of its distribution

    Directory of Open Access Journals (Sweden)

    Oren Pearlson

    2007-11-01

    Full Text Available Molecular DNA variation among Triturus vittatus vittatus (striped newt from different breeding sites at the southern limit of the species distribution (where environmental conditions are most extreme was studied by the random amplification of polymorphic DNA (RAPD method that has been found to be appropriate for other Triturus species. Altitudes of the localities ranged between 15-740 m a.s.l. Of the 20 primers employed, OPA-16 was the only one suitable for T. vittatus, revealing a different band pattern for different populations. Genetic similarity was calculated by band sharing, which demonstrated a high similarity among the Israeli populations.

  12. Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation.

    Science.gov (United States)

    Marková, Silvia; Dufresne, France; Rees, David J; Cerný, Martin; Kotlík, Petr

    2007-07-01

    The water fleas of the Daphnia pulex complex play a key role in freshwater ecosystems throughout the northern hemisphere. Despite the fact that they have been the subject of study for numerous biological disciplines, their phylogeny and species delimitation remain controversial. We used DNA sequence variation of the mitochondrial ND5 gene to reconstruct the phylogenetic relationships of D. pulicaria Forbes, a widespread member of this complex from North America and Europe. Populations from the two continents respectively split into two evolutionary lineages, Eastern Nearctic and European, which each belong to another main clade within the D. pulex complex (the pulicaria and tenebrosa groups, respectively). Unexpectedly, melanin and carotenoid pigmented D. pulicaria populations from European high-mountain lakes were not allied with the transparent populations inhabiting the same lakes and the lowland ponds and reservoirs throughout Europe, but were included with the samples from Canada and Greenland in the Eastern Nearctic lineage. Until now populations belonging to this lineage were known only from Canada and North Atlantic islands, but not from mainland Europe. Independent data from microsatellite markers supported the genetic distinctiveness of the sympatric carotenoid pigmented and transparent populations and suggested that they may have undergone transition to obligate parthenogenesis, possibly as a consequence of past introgressive hybridization. Two different taxa are therefore confused under the name D. pulicaria in Europe. The close phylogenetic relationships of European populations with those from Canada and Greenland suggest that the Nearctic lineage is of recent origin in Europe via intercontinental dispersal from the North America. It has evolved melanin and carotenoid pigmentation as adaptations against the UV light stress, which enable it to share habitat occupied by the transparent European species. The Nearctic D. pulicaria thus provides a new model

  13. MitoLSDB: a comprehensive resource to study genotype to phenotype correlations in human mitochondrial DNA variations.

    Directory of Open Access Journals (Sweden)

    Shamnamole K

    Full Text Available Human mitochondrial DNA (mtDNA encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease association studies on mtDNA (http://mitolsdb.igib.res.in. The main goal of MitoLSDB is to provide a central platform for direct submissions of novel variants that can be curated by the Mitochondrial Research Community. MitoLSDB provides access to standardized and annotated data from literature and databases encompassing information from 5231 individuals, 675 populations and 27 phenotypes. This platform is developed using the Leiden Open (source Variation Database (LOVD software. MitoLSDB houses information on all 37 genes in each population amounting to 132397 variants, 5147 unique variants. For each variant its genomic location as per the Revised Cambridge Reference Sequence, codon and amino acid change for variations in protein-coding regions, frequency, disease/phenotype, population, reference and remarks are also listed. MitoLSDB curators have also reported errors documented in literature which includes 94 phantom mutations, 10 NUMTs, six documentation errors and one artefactual recombination. MitoLSDB is the largest repository of mtDNA variants systematically standardized and presented using the LOVD platform. We believe that this is a good starting resource to curate mtDNA variants and will facilitate direct submissions enhancing data coverage, annotation in context of pathogenesis and quality control by ensuring non-redundancy in reporting novel disease associated variants.

  14. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life

    OpenAIRE

    Wang, Deli; Liu, Xin; Zhou, Ying; Xie, Hehuang; Hong, Xiumei; Tsai, Hui-Ju; Wang, Guoying; Liu, Rong; Wang, Xiaobin

    2012-01-01

    Prenatal development and early childhood are critical periods for establishing the tissue-specific epigenome, and may have a profound impact on health and disease in later life. However, epigenomic profiles at birth and in early childhood remain largely unexplored. The focus of this report is to examine the individual variation and longitudinal pattern of genome-wide DNA methylation levels from birth through the first two years of life in 105 Black children (59 males and 46 females) enrolled ...

  15. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

    OpenAIRE

    Beleza Sandra; Luiselli Donata; Sequeira Fernando; Coelho Margarida; Rocha Jorge

    2009-01-01

    Abstract Background Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyanek...

  16. Analysis of domestic dog mitochondrial DNA sequence variation for forensic investigations

    OpenAIRE

    Angleby, Helen

    2005-01-01

    The first method for DNA analysis in forensics was presented in 1985. Since then, the introduction of the polymerase chain reaction (PCR) has rendered possible the analysis of small amounts of DNA and automated sequencing and fragment analysis techniques have facilitated the analyses. In most cases short tandemly repeated regions (STRs) of nuclear DNA are analysed in forensic investigations, but all samples cannot be successfully analysed using this method. For samples containing minute amoun...

  17. Developmental activity variations of DNA polymerase α,δ,ε in mouse forebrains and spleens

    Institute of Scientific and Technical Information of China (English)

    杨荣武; 陆长德

    1995-01-01

    The levels of DNA polymerase α,δ,ε were examined in the neonatal mouse forebrains andspleens.The levels of DNA polymerase α were determined by the difference of polymerase activity in theabsence and the presence of α specific inhibitor,BuPdGTP,or its monoclonal antibody.The levels of DNApolymerase δ were determined in H · A fractions after separating it from the other two enzymes.The levelsof DNA polymerase ε were identified in H · A fractions by the use of α-monoclonal antibody or BuPdGTP.Results showed that in the mouse forebrain DNA polymerase α,δ,ε activities are the highest before birth,decline sharply following birth and are very low on the 8th day and hardly detectable on the 17th day;as forthe mouse spleen,however,DNA polymerase α,δ,ε activities are the lowest at birth,increase rapidly afterbirth and reach their maxima on the 8th day and then decline gradually but remain in higher levels.Theseresults not only prove that DNA polymerase α and δ take part in cell DNA replication but also suggest thatDNA polymerase ε is involved in DNA replication.

  18. The use of high-throughput DNA sequencing in the investigation of antigenic variation: application to Neisseria species.

    Directory of Open Access Journals (Sweden)

    John K Davies

    Full Text Available Antigenic variation occurs in a broad range of species. This process resembles gene conversion in that variant DNA is unidirectionally transferred from partial gene copies (or silent loci into an expression locus. Previous studies of antigenic variation have involved the amplification and sequencing of individual genes from hundreds of colonies. Using the pilE gene from Neisseria gonorrhoeae we have demonstrated that it is possible to use PCR amplification, followed by high-throughput DNA sequencing and a novel assembly process, to detect individual antigenic variation events. The ability to detect these events was much greater than has previously been possible. In N. gonorrhoeae most silent loci contain multiple partial gene copies. Here we show that there is a bias towards using the copy at the 3' end of the silent loci (copy 1 as the donor sequence. The pilE gene of N. gonorrhoeae and some strains of Neisseria meningitidis encode class I pilin, but strains of N. meningitidis from clonal complexes 8 and 11 encode a class II pilin. We have confirmed that the class II pili of meningococcal strain FAM18 (clonal complex 11 are non-variable, and this is also true for the class II pili of strain NMB from clonal complex 8. In addition when a gene encoding class I pilin was moved into the meningococcal strain NMB background there was no evidence of antigenic variation. Finally we investigated several members of the opa gene family of N. gonorrhoeae, where it has been suggested that limited variation occurs. Variation was detected in the opaK gene that is located close to pilE, but not at the opaJ gene located elsewhere on the genome. The approach described here promises to dramatically improve studies of the extent and nature of antigenic variation systems in a variety of species.

  19. Ureaplasma antigenic variation beyond MBA phase variation: DNA inversions generating chimeric structures and switching in expression of the MBA N-terminal paralogue UU172.

    Science.gov (United States)

    Zimmerman, Carl-Ulrich R; Rosengarten, Renate; Spergser, Joachim

    2011-02-01

    Phase variation of the major ureaplasma surface membrane protein, the multiple-banded antigen (MBA), with its counterpart, the UU376 protein, was recently discussed as a result of DNA inversion occurring at specific inverted repeats. Two similar inverted repeats to the ones within the mba locus were found in the genome of Ureaplasma parvum serovar 3; one within the MBA N-terminal paralogue UU172 and another in the adjacent intergenic spacer region. In this report, we demonstrate on both genomic and protein level that DNA inversion at these inverted repeats leads to alternating expression between UU172 and the neighbouring conserved hypothetical ORF UU171. Sequence analysis of this phase-variable 'UU172 element' from both U. parvum and U. urealyticum strains revealed that it is highly conserved among both species and that it also includes the orthologue of UU144. A third inverted repeat region in UU144 is proposed to serve as an additional potential inversion site from which chimeric genes can evolve. Our results indicate that site-specific recombination events in the genome of U. parvum serovar 3 are dynamic and frequent, leading to a broad spectrum of antigenic variation by which the organism may evade host immune responses.

  20. Mitochondrial DNA variation and virologic and immunological HIV outcomes in African Americans

    Science.gov (United States)

    Aissani, Brahim; Shrestha, Sadeep; Wiener, Howard W.; Tang, Jianming; Kaslow, Richard A.; Wilson, Craig M.

    2016-01-01

    Objective To evaluate the impact of mitochondrial DNA (mtDNA) haplogroups on virologic and immunological outcomes of HIV infection. Design HAART-naive African American adolescent participants to the Reaching for Excellence in Adolescent Care and Health study. Methods The mtDNA haplogroups were inferred from sequenced mtDNA hypervariable regions HV1 and HV2 and their predictive value on HIV outcomes were evaluated in linear mixed models, controlled for human leukocyte antigen (HLA)-B27, HLA-B57 and HLA-B35-Px alleles and other covariates. Results We report data showing that the mtDNA L2 lineage, a group composed of L2a, L2b and L2e mtDNA haplogroups in the studied population, is significantly associated (beta=−0.08; Bonferroni-adjusted P=0.004) with decline of CD4+ T cells (median loss of 8 ± 1 cells per month) in HAART-naive HIV-infected individuals of African American descent (n=133). No significant association (PHIV infection, its phylogenetic divergence from J and U5a, two lineages associated with accelerated HIV progression in European Americans, raises the possibility that interactions with common nucleus-encoded variants drive HIV progression. Disentangling the effects of mitochondrial and nuclear gene variants on the outcomes of HIV infection is an important step to be taken toward a better understanding of HIV/AIDS pathogenesis and pharmacogenomics. PMID:24932613

  1. Occupational solvent exposure, genetic variation of DNA repair genes, and the risk of non-Hodgkin's lymphoma.

    Science.gov (United States)

    Jiao, Jie; Zheng, Tongzhang; Lan, Qing; Chen, Yingtai; Deng, Qian; Bi, Xiaofeng; Kim, Christopher; Holford, Theodore; Leaderer, Brian; Boyle, Peter; Ba, Yue; Xia, Zhaolin; Chanock, Stephen J; Rothman, Nathaniel; Zhang, Yawei

    2012-11-01

    The main objective of this study was to test the hypothesis that genetic variations in DNA repair genes may modify the association between occupational exposure to solvents and the risk of non-Hodgkin's lymphoma (NHL). A population-based case-control study was conducted on Connecticut women including 518 histologically confirmed incident NHL cases and 597 controls. Unconditional logistic regression models were used to estimate the odds ratios and effect modification from the 30 single nucleotide polymorphisms in 16 DNA repair genes of the association between solvent exposure and the risk of NHL overall and subtypes. Single nucleotide polymorphisms in MGMT (rs12917) and NBS1 (rs1805794) significantly modified the association between exposure to chlorinated solvents and the risk of NHL (Pfor interaction=0.0003 and 0.0048, respectively). After stratification by major NHL histological subtypes, MGMT (rs12917) modified the association between chlorinated solvents and the risk of diffuse large B-cell lymphoma (Pfor interaction=0.0027) and follicular lymphoma (Pfor interaction=0.0024). A significant interaction was also observed between occupational exposure to benzene and BRCA2 (rs144848) for NHL overall (Pfor interaction=0.0042). Our study results suggest that genetic variations in DNA repair genes modify the association between occupational exposure to solvents and the risk of NHL. PMID:22430443

  2. Geographic variation and taxonomy of crested newts (Triturus cristatus superspecies): morphological and mitochondrial DNA data

    NARCIS (Netherlands)

    Arntzen, J.W.; Wallis, Graham P.

    1999-01-01

    Within the newt genus Triturus, the large-bodied species in the T. cristatus (crested newt) superspecies show an unusual degree of variation in relative trunk length as a result of among-taxon variation in interlimb vertebral count. Here we examine the systematic value of this feature as assessed by

  3. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

    DEFF Research Database (Denmark)

    Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

    2008-01-01

    Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary u...

  4. Variations in the Processing of DNA Double-Strand Breaks Along 60-MeV Therapeutic Proton Beams

    Science.gov (United States)

    Chaudhary, Pankaj; Marshall, Thomas I.; Currell, Frederick J.; Kacperek, Andrzej; Schettino, Giuseppe; Prise, Kevin M.

    2016-01-01

    Purpose To investigate the variations in induction and repair of DNA damage along the proton path, after a previous report on the increasing biological effectiveness along clinically modulated 60-MeV proton beams. Methods and Materials Human skin fibroblast (AG01522) cells were irradiated along a monoenergetic and a modulated spread-out Bragg peak (SOBP) proton beam used for treating ocular melanoma at the Douglas Cyclotron, Clatterbridge Centre for Oncology, Wirral, Liverpool, United Kingdom. The DNA damage response was studied using the 53BP1 foci formation assay. The linear energy transfer (LET) dependence was studied by irradiating the cells at depths corresponding to entrance, proximal, middle, and distal positions of SOBP and the entrance and peak position for the pristine beam. Results A significant amount of persistent foci was observed at the distal end of the SOBP, suggesting complex residual DNA double-strand break damage induction corresponding to the highest LET values achievable by modulated proton beams. Unlike the directly irradiated, medium-sharing bystander cells did not show any significant increase in residual foci. Conclusions The DNA damage response along the proton beam path was similar to the response of X rays, confirming the low-LET quality of the proton exposure. However, at the distal end of SOBP our data indicate an increased complexity of DNA lesions and slower repair kinetics. A lack of significant induction of 53BP1 foci in the bystander cells suggests a minor role of cell signaling for DNA damage under these conditions. PMID:26452569

  5. PRIMARILY RESULTS OF PHYTOPLANKTON DNA AND VARIATION TO ENVIRONMENTAL FACTORS IN DURRES`S BAY COASTAL WATERS (ALBANIA

    Directory of Open Access Journals (Sweden)

    Laura Gjyli

    2013-10-01

    Full Text Available After isolation of phytoplankton DNA in coastal waters of Durres Bay, Albania, quantification and analysis of quality were investigated with spectrophotometric analysis. Analysis of UV absorption by the nucleotides provides a simple and accurate estimation of the concentration of nucleic acids in a sample. This method is however limited by the quantity of DNA and the purity of the preparation. Also biotic environment factors as Chlorophyll a and abiotic environment factors as temperature, salinity, pH, dissolved oxygen, turbidity, nitrate, phosphate were investigated to assess DNA quantities in different environment conditions. The Chlorophyll a was studied also to access the level of trophy. The sample stations were: Golem Beach (GB, Channel of Plepa (ChP, Hekurudha Beach (HB, Ex-Fuel Quay in Marine Durres Harbour (EFQ, Water Channel of Durres City (WChDC and Currila Beach (CB. Samples are taken in one meter depth from the water surface. Water samples were collected monthly from April to October 2011. The most abundant stations with phytoplankton DNA are Channel of Plepa and Water Channel of Durres City. This confirms that there are spills of fresh waters, sewage or agricultural water spills, often discharge in coastal waters. Referring Mutliple Regression Analysis and single regression analysis, the association between phytoplankton DNA and environment factors was strong (R2 = 0.75. Basing in single correlation and statistically significance (p-value ≤ 0.05, the enviroment factors that correlated to phytoplankton DNA were pH, salinity and phosphate; explaining thus the variation of total phytoplankton in Durres Bay coastal waters.

  6. Probing the functional impact of sequence variation on p53-DNA interactions using a novel microsphere assay for protein-DNA binding with human cell extracts.

    Directory of Open Access Journals (Sweden)

    Maher A Noureddine

    2009-05-01

    Full Text Available The p53 tumor suppressor regulates its target genes through sequence-specific binding to DNA response elements (REs. Although numerous p53 REs are established, the thousands more identified by bioinformatics are not easily subjected to comparative functional evaluation. To examine the relationship between RE sequence variation -- including polymorphisms -- and p53 binding, we have developed a multiplex format microsphere assay of protein-DNA binding (MAPD for p53 in nuclear extracts. Using MAPD we measured sequence-specific p53 binding of doxorubicin-activated or transiently expressed p53 to REs from established p53 target genes and p53 consensus REs. To assess the sensitivity and scalability of the assay, we tested 16 variants of the p21 target sequence and a 62-multiplex set of single nucleotide (nt variants of the p53 consensus sequence and found many changes in p53 binding that are not captured by current computational binding models. A group of eight single nucleotide polymorphisms (SNPs was examined and binding profiles closely matched transactivation capability tested in luciferase constructs. The in vitro binding characteristics of p53 in nuclear extracts recapitulated the cellular in vivo transactivation capabilities for eight well-established human REs measured by luciferase assay. Using a set of 26 bona fide REs, we observed distinct binding patterns characteristic of transiently expressed wild type and mutant p53s. This microsphere assay system utilizes biologically meaningful cell extracts in a multiplexed, quantitative, in vitro format that provides a powerful experimental tool for elucidating the functional impact of sequence polymorphism and protein variation on protein/DNA binding in transcriptional networks.

  7. Multiple origins of cultivated radishes as evidenced by a comparison of the structural variations in mitochondrial DNA of Raphanus.

    Science.gov (United States)

    Yamagishi, Hiroshi; Terachi, Toru

    2003-02-01

    Configurations of mitochondrial coxI and orfB gene regions were analysed by polymerase chain reaction (PCR) in three wild and one cultivated species of Raphanus. A total of 207 individual plants from 60 accessions were used. PCR with five combinations of primers identified five different amplification patterns both in wild and cultivated radishes. While the mitochondrial DNA (mtDNA) type of Ogura male-sterile cytoplasm was distinguishable from the normal type, the mtDNAs of normal radishes were further classified into four types. The variations were common to wild and cultivated radishes, although contrasting features were found depending on the region of cultivation. These results provide evidence that cultivated radishes have multiple origins from various wild plants of Raphanus.

  8. Evaluating the role of mitochondrial DNA variation to the genetic predisposition to radiation-induced toxicity

    International Nuclear Information System (INIS)

    Background and purpose: Mitochondrial DNA common variants have been reported to be associated with the development of radiation-induced toxicity. Using a large cohort of patients, we aimed to validate these findings by investigating the potential role of common European mitochondrial DNA SNPs (mtSNPs) to the development of radio-toxicity. Material and methods: Overall acute and late toxicity data were assessed in a cohort of 606 prostate cancer patients by means of Standardized Total Average Toxicity (STAT) score. We carried out association tests between radiation toxicity and a selection of 15 mtSNPs (and the haplogroups defined by them). Results: Statistically significant association between mtSNPs and haplogroups with toxicity could not be validated in our Spanish cohort. Conclusions: The present study suggests that the mtDNA common variants analyzed are not associated with clinically relevant increases in risk of overall radiation-induced toxicity in prostate cancer patients

  9. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola

    Directory of Open Access Journals (Sweden)

    Beleza Sandra

    2009-04-01

    Full Text Available Abstract Background Current information about the expansion of Bantu-speaking peoples is hampered by the scarcity of genetic data from well identified populations from southern Africa. Here, we fill an important gap in the analysis of the western edge of the Bantu migrations by studying for the first time the patterns of Y-chromosome, mtDNA and lactase persistence genetic variation in four representative groups living around the Namib Desert in southwestern Angola (Ovimbundu, Ganguela, Nyaneka-Nkumbi and Kuvale. We assessed the differentiation between these populations and their levels of admixture with Khoe-San groups, and examined their relationship with other sub-Saharan populations. We further combined our dataset with previously published data on Y-chromosome and mtDNA variation to explore a general isolation with migration model and infer the demographic parameters underlying current genetic diversity in Bantu populations. Results Correspondence analysis, lineage sharing patterns and admixture estimates indicate that the gene pool from southwestern Angola is predominantly derived from West-Central Africa. The pastoralist Herero-speaking Kuvale people were additionally characterized by relatively high frequencies of Y-chromosome (12% and mtDNA (22% Khoe-San lineages, as well as by the presence of the -14010C lactase persistence mutation (6%, which likely originated in non-Bantu pastoralists from East Africa. Inferred demographic parameters show that both male and female populations underwent significant size growth after the split between the western and eastern branches of Bantu expansions occurring 4000 years ago. However, males had lower population sizes and migration rates than females throughout the Bantu dispersals. Conclusion Genetic variation in southwestern Angola essentially results from the encounter of an offshoot of West-Central Africa with autochthonous Khoisan-speaking peoples from the south. Interactions between the Bantus

  10. Mitochondrial DNA sequence variation and haplogroup distribution in Chinese patients with LHON and m.14484T>C.

    Directory of Open Access Journals (Sweden)

    Dandan Yu

    Full Text Available BACKGROUND: Leber hereditary optic neuropathy (LHON, MIM 535000 is one of the most common mitochondrial genetic disorders caused by three primary mtDNA mutations (m.3460G>A, m.11778G>A and m. 14484T>C. The clinical expression of LHON is affected by many additional factors, e.g. mtDNA background, nuclear genes, and environmental factors. Hitherto, there is no comprehensive study of Chinese LHON patients with m.14484T>C. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we analyzed the mtDNA sequence variations and haplogroup distribution pattern of the largest number of Chinese LHON patients with m.14484T>C to date. We first determined the complete mtDNA sequences in eleven LHON probands with m.14484T>C, to discern the potentially pathogenic mutations that co-segregate with m.14484T>C. We then dissected the matrilineal structure of 52 patients with m.14484T>C (including 14 from unrelated families and 38 sporadic cases and compared it with the reported Han Chinese from general populations. Complete mtDNA sequencing showed that the eleven matrilines belonged to nine haplogroups including Y2, C4a, M8a, M10a1a, G1a1, G2a1, G2b2, D5a2a1, and D5c. We did not identify putatively pathogenic mutation that was co-segregated with m.14484T>C in these lineages based on the evolutionary analysis. Compared with the reported Han Chinese from general populations, the LHON patients with m.14484T>C had significantly higher frequency of haplogroups C, G, M10, and Y, but a lower frequency of haplogroup F. Intriguingly, we also observed a lower prevalence of F lineages in LHON subjects with m.11778G>A in our previous study, suggesting that this haplogroup may enact similar role during the onset of LHON in the presence of m.14484T>C or m.11778G>A. CONCLUSIONS/SIGNIFICANCE: Our current study provided a comprehensive profile regarding the mtDNA variation and background of Chinese patients with LHON and m.14484T>C. Matrilineal background might affect the expression of LHON

  11. Discovery and genotyping of existing and induced DNA sequence variation in potato

    NARCIS (Netherlands)

    Uitdewilligen, J.G.A.M.L.

    2012-01-01

    In this thesis natural and induced DNA sequence diversity in potato (Solanum tuberosum) for use in marker-trait analysis and potato breeding is assessed. The study addresses the challenges of reliable, high-throughput identification and genotyping of sequence variants in existing tetraploid potato c

  12. Validation and Estimation of Additive Genetic Variation Associated with DNA Tests for Quantitative Beef Cattle Traits

    Science.gov (United States)

    The U.S. National Beef Cattle Evaluation Consortium (NBCEC) has been involved in the validation of commercial DNA tests for quantitative beef quality traits since their first appearance on the U.S. market in the early 2000s. The NBCEC Advisory Council initially requested that the NBCEC set up a syst...

  13. Methodological variations in the isolation of genomic DNA from Streptococcus bacteria

    Directory of Open Access Journals (Sweden)

    Mônica Moreira

    2010-08-01

    Full Text Available In this work, genomic DNA of Streptococcus pyogenes, S. mutans and S. sobrinus was isolated using two methods: either using the detergent cetyltrimethylammonium bromide (CTAB at 65ºC; or by applying ultrasound to a mixture of silica and celite in CTAB. The composite method that used ultrasound was the more efficient, allowing the straightforward extraction of genomic DNA from Gram-positive bacteria with good quality and reproducibility.O gênero Streptococcus encontra-se amplamente distribuído na natureza e algumas espécies constituem a microbiota humana da cavidade bucal, como Streptococcus pyogenes, que pode estar associado a importantes doenças humanas, Streptococcus mutans e Streptococcus sobrinus, relacionados à cárie dental. O DNA genômico destas três espécies foi isolado utilizando-se dois métodos, o primeiro utilizando o detergente brometo de cetiltrimetilamônio (CTAB à 65ºC e outro associando ultra-som a uma mistura de sílica e celite em CTAB. O método que possibilitou a extração do DNA genômico das bactérias Gram positivas, com qualidade, boa reprodutibilidade fácil execução foi aquele que utilizou ultra-som associado à sílica e celite em CTAB.

  14. Phylogeography of mitochondrial DNA variation in brown bears and polar bears

    Science.gov (United States)

    Shields, Gerald F.; Adams, Deborah; Garner, Gerald; Labelle, Martine; Pietsch, Jacy; Ramsay, Malcolm; Schwartz, Charles; Titus, Kimberly; Williamson, Scott

    2000-01-01

    We analyzed 286 nucleotides of the middle portion of the mitochondrial cytochrome b gene of 61 brown bears from three locations in Alaska and 55 polar bears from Arctic Canada and Arctic Siberia to test our earlier observations of paraphyly between polar bears and brown bears as well as to test the extreme uniqueness of mitochondrial DNA types of brown bears on Admiralty, Baranof, and Chichagof (ABC) islands of southeastern Alaska. We also investigated the phylogeography of brown bears of Alaska's Kenai Peninsula in relation to other Alaskan brown bears because the former are being threatened by increased human development. We predicted that: (1) mtDNA paraphyly between brown bears and polar bears would be upheld, (2) the mtDNA uniqueness of brown bears of the ABC islands would be upheld, and (3) brown bears of the Kenai Peninsula would belong to either clade II or clade III of brown bears of our earlier studies of mtDNA. All of our predictions were upheld through the analysis of these additional samples.

  15. Relationships in Ananas and other related genera using chloroplast DNA restriction site variation.

    Science.gov (United States)

    Duval, M F; Buso, G S C; Ferreira, F R; Noyer, J L; Coppens d'Eeckenbrugge, G; Hamon, P; Ferreira, M E

    2003-12-01

    Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera. One hundred fifteen accessions representing the seven Ananas species and seven other Bromelioideae including the neighboring monospecific genus Pseudananas, two Pitcairnioideae, and one Tillandsioideae were included in the study. Eight primers designed from cpDNA were used for generating fragments. Restriction by 18 endonucleases generated 255 variable fragments. Dissimilarities were calculated from the resulting matrix using the Sokal and Michener index and the neighbor-joining method was used to reconstruct the diversity tree. Phylogenetic reconstruction was attempted using Wagner parsimony. Phenetic and cladistic analyses gave consistent results. They confirm the basal position of Bromelia in the Bromelioideae. Ananas and Pseudananas form a monophyletic group, with three strongly supported sub-groups, two of which are geographically consistent. The majority of Ananas parguazensis accessions constitute a northern group restricted to the Rio Negro and Orinoco basins in Brazil. The tetraploid Pseudananas sagenarius joins the diploid Ananas fritzmuelleri to constitute a southern group. The third and largest group, which includes all remaining species plus some accessions of A. parguazensis and intermediate phenotypes, is the most widespread and its distribution overlaps those of the northern and southern groups. Ananas ananassoides is dominant in this sub-group and highly variable. Its close relationship to all cultivated species supports the hypothesis that this species is the wild ancestor of the domesticated pineapple. The data indicate that gene flow is common within this group and scarcer with both the first and second groups. Comparison of cpDNA data with published genomic DNA data point to the hybrid origin of Ananas bracteatus and support the autopolyploidy of Pseudananas. The Ananas-Pseudananas group structure and distribution are

  16. Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

    Science.gov (United States)

    Guo, Guo-Ye; Chen, Fang; Shi, Xiao-Dong; Tian, Yin-Shuai; Yu, Mao-Qun; Han, Xue-Qin; Yuan, Li-Chun; Zhang, Ying

    2016-01-01

    Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia. PMID:27461559

  17. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.

    Science.gov (United States)

    Labrie, Viviane; Buske, Orion J; Oh, Edward; Jeremian, Richie; Ptak, Carolyn; Gasiūnas, Giedrius; Maleckas, Almantas; Petereit, Rūta; Žvirbliene, Aida; Adamonis, Kęstutis; Kriukienė, Edita; Koncevičius, Karolis; Gordevičius, Juozas; Nair, Akhil; Zhang, Aiping; Ebrahimi, Sasha; Oh, Gabriel; Šikšnys, Virginijus; Kupčinskas, Limas; Brudno, Michael; Petronis, Arturas

    2016-06-01

    The inability to digest lactose, due to lactase nonpersistence, is a common trait in adult mammals, except in certain human populations that exhibit lactase persistence. It is not known how the lactase gene is dramatically downregulated with age in most individuals but remains active in some individuals. We performed a comprehensive epigenetic study of human and mouse small intestines, by using chromosome-wide DNA-modification profiling and targeted bisulfite sequencing. Epigenetically controlled regulatory elements accounted for the differences in lactase mRNA levels among individuals, intestinal cell types and species. We confirmed the importance of these regulatory elements in modulating lactase mRNA levels by using CRISPR-Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, because lactase-persistence and lactase-nonpersistence DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors enable a gradual accumulation of epigenetic changes with age, thereby influencing phenotypic outcome. PMID:27159559

  18. Tracking an invasive honey bee pest: mitochondrial DNA variation in North American small hive beetles

    OpenAIRE

    Jay. D. Evans,; Jeff. S. Pettis,; Michael Hood, W.; Shimanuki, Hachiro

    2003-01-01

    International audience We describe the current and past distributions of North American small hive beetles (Aethina tumida) having two distinct mitochondrial DNA haplotypes. A collection of 539 hive beetles showed irregular distributions of these haplotypes across the southeastern US. Beetles from the first collections made in coastal South Carolina showed haplotype NA1, exclusively. This haplotype is less common in Georgia and was not observed in North Carolina. Later collections from thi...

  19. Searching for the Optimal Sampling Solution: Variation in Invertebrate Communities, Sample Condition and DNA Quality.

    Directory of Open Access Journals (Sweden)

    Martin M Gossner

    Full Text Available There is a great demand for standardising biodiversity assessments in order to allow optimal comparison across research groups. For invertebrates, pitfall or flight-interception traps are commonly used, but sampling solution differs widely between studies, which could influence the communities collected and affect sample processing (morphological or genetic. We assessed arthropod communities with flight-interception traps using three commonly used sampling solutions across two forest types and two vertical strata. We first considered the effect of sampling solution and its interaction with forest type, vertical stratum, and position of sampling jar at the trap on sample condition and community composition. We found that samples collected in copper sulphate were more mouldy and fragmented relative to other solutions which might impair morphological identification, but condition depended on forest type, trap type and the position of the jar. Community composition, based on order-level identification, did not differ across sampling solutions and only varied with forest type and vertical stratum. Species richness and species-level community composition, however, differed greatly among sampling solutions. Renner solution was highly attractant for beetles and repellent for true bugs. Secondly, we tested whether sampling solution affects subsequent molecular analyses and found that DNA barcoding success was species-specific. Samples from copper sulphate produced the fewest successful DNA sequences for genetic identification, and since DNA yield or quality was not particularly reduced in these samples additional interactions between the solution and DNA must also be occurring. Our results show that the choice of sampling solution should be an important consideration in biodiversity studies. Due to the potential bias towards or against certain species by Ethanol-containing sampling solution we suggest ethylene glycol as a suitable sampling solution when

  20. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

    OpenAIRE

    Maurano, Matthew T.; Humbert, Richard; Rynes, Eric; Thurman, Robert E; Haugen, Eric; Wang, Hao; Reynolds, Alex P.; Sandstrom, Richard; Qu, Hongzhu; Brody, Jennifer; Shafer, Anthony; Neri, Fidencio; Lee, Kristen; Kutyavin, Tanya; Stehling-Sun, Sandra

    2012-01-01

    Genome-wide association studies (GWAS) have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by DNase I hypersensitive sites (DHSs). 88% of such DHSs are active during fetal development, and are enriched for gestational exposure-related phenotypes. We identify distant gene targets for hundreds of DHSs that may explain phenotype associations. Disease-associated variants systematically perturb tr...

  1. Genetic diversity of Albanian goat breeds revealed by mtDNA sequence variation

    OpenAIRE

    Hoda, Anila; Biçoku, Ylli; Dobi, Petrit

    2014-01-01

    Albanian farmers have a long tradition in goat farming. Recently, several studies were carried out to determine genetic diversity of local goat populations, using molecular markers such as SNP (Single Nucleotide Polymorphisms), microsatellites and AFLP (Amplified Fragment Length Polymorphism). In the present study 77 mtDNA D-loop sequences from six different goat breeds were analysed. The results revealed 67 different haplotypes, with haplotype diversity ranging from 0.864 to 1 and nucleotide...

  2. Variation of karyotype and nuclear DNA content among four species of Plectranthus L’ Héritier, 1788 (Lamiaceae) from Brazil

    Science.gov (United States)

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Abstract Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus. PMID:26753074

  3. Variation of karyotype and nuclear DNA content among four species of Plectranthus L' Héritier, 1788 (Lamiaceae) from Brazil.

    Science.gov (United States)

    Nani, Thaís Furtado; Mesquita, Amanda Teixeira; Bustamante, Fernanda de Oliveira; Barbosa, Sandro; Barbosa, João Vítor Calvelli; Davide, Lisete Chamma

    2015-01-01

    Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus. PMID:26753074

  4. Low variation in ribosomal DNA and internal transcribed spacers of the symbiotic fungi of leaf-cutting ants (Attini: Formicidae

    Directory of Open Access Journals (Sweden)

    Silva-Pinhati A.C.O.

    2004-01-01

    Full Text Available Leaf-cutting ants of the genera Atta and Acromyrmex (tribe Attini are symbiotic with basidiomycete fungi of the genus Leucoagaricus (tribe Leucocoprineae, which they cultivate on vegetable matter inside their nests. We determined the variation of the 28S, 18S, and 5.8S ribosomal DNA (rDNA gene loci and the rapidly evolving internal transcribed spacers 1 and 2 (ITS1 and ITS2 of 15 sympatric and allopatric fungi associated with colonies of 11 species of leafcutter ants living up to 2,600 km apart in Brazil. We found that the fungal rDNA and ITS sequences from different species of ants were identical (or nearly identical to each other, whereas 10 GenBank Leucoagaricus species showed higher ITS variation. Our findings suggest that Atta and Acromyrmex leafcutters living in geographic sites that are very distant from each other cultivate a single fungal species made up of closely related lineages of Leucoagaricus gongylophorus. We discuss the strikingly high similarity in the ITS1 and ITS2 regions of the Atta and Acromyrmex symbiotic L. gongylophorus studied by us, in contrast to the lower similarity displayed by their non-symbiotic counterparts. We suggest that the similarity of our L. gongylophorus isolates is an indication of the recent association of the fungus with these ants, and propose that both the intense lateral transmission of fungal material within leafcutter nests and the selection of more adapted fungal strains are involved in the homogenization of the symbiotic fungal stock.

  5. Analysis of DNA methylation variation in wheat genetic background after alien chromatin introduction based on methylation-sensitive amplification polymorphism

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    During the process of alien germplasm introduced into wheat genome by chromosome engineering,extensive genetic variations of genome structure and gene expression in recipient could be induced.In this study,we performed GISH(genome in situ hybridization)and AFLP(amplified fragment length polymorphism) on wheat-rye chromosome transIocation lines and their parents to detect the identity in genomic structure of different translocation lines.The results showed that the genome primary structure variations were not obviously detected in different translocation lines except the same 1RS chromosome translocation.Methylation sensitive amplification polymorphism(MSAP)analyses on genomic DNA showed that the ratios of fully-methylated sites were significantly increased in translocation lines(CN12,20.15%;CN17,20.91%;CN18,22.42%),but the ratios of hemimethylated sites were significantly lowered(CN12,21.41%;CN17,23.43%;CN18,22.42%),whereas 16.37%were fully-methylated and 25.44%were hemimethylated in case of their wheat parent.Twenty-nine classes of methylation patterns were identified in a comparative assay of cytosine methylation patterns between wheat-rye translocation lines and their wheat parent,including 13 hypermethylation patterns(33.74%),9 demethylation patterns(22.76%)and 7 uncertain patterns(4.07%).In further sequence analysis,the alterations of methylation pattern affected both repetitive DNA sequences,such as retrotransposons and tandem repetitive sequences,and low-copy DNA.

  6. Intraspecific DNA variation in nuclear genes of the mosquito Aedes aegypti.

    Science.gov (United States)

    Morlais, I; Severson, D W

    2003-12-01

    Single nucleotide polymorphisms (SNPs) are an abundant source of genetic variation among individual organisms. To assess the usefulness of SNPs for genome analysis in the yellow fever mosquito, Aedes aegypti, we sequenced 25 nuclear genes in each of three strains and analysed nucleotide diversity. The average frequency of nucleotide variation was 12 SNPs per kilobase, indicating that nucleotide variation in Ae. aegypti is similar to that in other organisms, including Drosophila and the malaria vector Anopheles gambiae. Transition polymorphisms outnumbered transversion polymorphisms, at a ratio of about 2:1. We examined codon usage and confirmed that mutational bias favours G and C ending codons. Codon bias was most pronounced in highly expressed genes. Nucleotide diversity estimates indicated that substitution rates are positively correlated in coding and non-coding regions. Nucleotide diversity varied from one gene to another. The unequal distribution of SNPs among Ae. aegypti nuclear genes suggests that single base variations are non-neutral and are subject to selective constraints. Our analysis showed that ubiquitously expressed genes have lower polymorphism rates and are likely under strong purifying selection, whereas tissue specific genes and genes with a putative role in parasite defence exhibit higher levels of polymorphism that may be associated with diversifying selection. PMID:14986924

  7. Analysis of genetic variation within clonal lineages of grape phylloxera (Daktulosphaira vitifoliae Fitch) using AFLP fingerprinting and DNA sequencing.

    Science.gov (United States)

    Vorwerk, S; Forneck, A

    2007-07-01

    Two AFLP fingerprinting methods were employed to estimate the potential of AFLP fingerprints for the detection of genetic diversity within single founder lineages of grape phylloxera (Daktulosphaira vitifoliae Fitch). Eight clonal lineages, reared under controlled conditions in a greenhouse and reproducing asexually throughout a minimum of 15 generations, were monitored and mutations were scored as polymorphisms between the founder individual and individuals of succeeding generations. Genetic variation was detected within all lineages, from early generations on. Six to 15 polymorphic loci (from a total of 141 loci) were detected within the lineages, making up 4.3% of the total amount of genetic variation. The presence of contaminating extra-genomic sequences (e.g., viral material, bacteria, or ingested chloroplast DNA) was excluded as a source of intraclonal variation. Sequencing of 37 selected polymorphic bands confirmed their origin in mostly noncoding regions of the grape phylloxera genome. AFLP techniques were revealed to be powerful for the identification of reproducible banding patterns within clonal lineages. PMID:17893744

  8. [Nucleotide variation in the mitochondrial DNA cytochrome oxidase 1 gene in the Siberian sucker (Catostomus catostomus rostratus) from Kolyma River].

    Science.gov (United States)

    Bachevskaja, L T; Pereverzeva, V V; Ivanova, G D; Agapova, G A

    2014-10-01

    This study presents the data of the first molecular genetic analysis of the Siberian sucker from Kolyma River. Polymorphism of the mtDNA cytochrome oxidase 1 gene was established. Comparative sequence analysis of the gene examined and the GenBank variants characterizing suckers from the rivers of Canada enabled the suggestion that the sucker penetrated to Asia from North America approximately at the end of Early and the beginning of the Middle Pleistocene. It was demonstrated that intrapopulation genetic variation in the Siberian sucker accounted for 11.63% of total variation, while the proportion of the intergroup, component (Fst) constituted 88.37%. It seems likely that a considerable proportion of intergroup variation was caused by the long period of isolation of the Siberian sucker in Kolyma River. The prevalence of one common haplotype, CH-COI 1, in the sample examined indicates that the founder effect played an importaht role in the history of the formation of the Kolyma population. PMID:25720253

  9. A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process

    Directory of Open Access Journals (Sweden)

    Yiğiter Ayten

    2010-01-01

    Full Text Available To study chromosomal aberrations that may lead to cancer formation or genetic diseases, the array-based Comparative Genomic Hybridization (aCGH technique is often used for detecting DNA copy number variants (CNVs. Various methods have been developed for gaining CNVs information based on aCGH data. However, most of these methods make use of the log-intensity ratios in aCGH data without taking advantage of other information such as the DNA probe (e.g., biomarker positions/distances contained in the data. Motivated by the specific features of aCGH data, we developed a novel method that takes into account the estimation of a change point or locus of the CNV in aCGH data with its associated biomarker position on the chromosome using a compound Poisson process. We used a Bayesian approach to derive the posterior probability for the estimation of the CNV locus. To detect loci of multiple CNVs in the data, a sliding window process combined with our derived Bayesian posterior probability was proposed. To evaluate the performance of the method in the estimation of the CNV locus, we first performed simulation studies. Finally, we applied our approach to real data from aCGH experiments, demonstrating its applicability.

  10. Genetic structure of Xiphinema pachtaicum and X. index populations based on mitochondrial DNA variation.

    Science.gov (United States)

    Gutiérrez-Gutiérrez, Carlos; Castillo, Pablo; Cantalapiedra-Navarrete, Carolina; Landa, Blanca B; Derycke, Sofie; Palomares-Rius, Juan E

    2011-10-01

    The dagger nematodes Xiphinema pachtaicum and X. index are two of the most widespread and frequently occurring Xiphinema spp. co-infesting vineyards and other crops and natural habitats worldwide. Sexual reproduction is rare in these species. The primary objective of this study was to determine the genetic structure of X. pachtaicum and X. index populations using eight and seven populations, respectively, from different "wine of denomination of origin (D.O.) zones" in Spain and Sardinia (Italy), by studying mitochondrial (cytochrome oxidase c subunit 1 or COI) and nuclear (D2-D3 expansion segments of 28S rDNA) markers. Both Xiphinema spp. showed low intraspecific divergence among COI sequences, ranging from 0.2% (1 base substitution) to 2.3% (10 substitutions) in X. pachtaicum and from 0.2% (1 base substitution) to 0.4% (2 substitutions) in X. index. Population genetic structure was strong for both species. Nevertheless, molecular differences among grapevine-growing areas were not significant, and intrapopulation diversity was very low. It is hypothesized that this genetic homogeneity in the nematode populations reflects their predominant parthenogenetic reproduction mode and low dispersal abilities. Our results also show that X. pachtaicum populations in Spain have possibly been established from two different populations of origin. Results also demonstrated that the two DNA regions studied are suitable diagnostic markers for X. index and X. pachtaicum.

  11. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

    Full Text Available Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb and 7 (1.1 Mb from an individual from the International HapMap Project (NA12872. We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

  12. Variation induced by DNA rearrangement in a transgenic Bt+CpTI cotton strain

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In the development of transgenic Bt + CpTI cotton cultivars, one male and female sterile mutant has been found in a homozygous T4 strain in our laboratory. The mutant plant, as well as its leaves, buds and flowers, is only 1/2-1/3 as large as that of the wild transgenic Bt + CpTI bivalant cotton plants. Cytological observation found that the chromosome number of the mutant is 2n = 52; however, there are 4 - 8 univalents observed in meiosis Ⅰ of pollen mother cells. Laboratory bioassay indicated that the mutant was highly resistant to bollworm as the wild plants. PCR amplification revealed that Bt and CpTI genes in the mutant were still intactly inserted. However, small deletion of flanked area had been observed in the mutant by Southern blotting analysis. So it is proposed that the mutant phenotype might result from either the DNA deletion or T-DNA trans-ferring in plant genome. No such report has been presented that the rearrangement of chromosome structure in a homo-zygous transgenic line occurred. Further analysis is ongoing.

  13. Mitochondrial DNA sequence variation and phylogeography of Neotropic pumas (Puma concolor).

    Science.gov (United States)

    Caragiulo, Anthony; Dias-Freedman, Isabela; Clark, J Alan; Rabinowitz, Salisa; Amato, George

    2014-08-01

    Pumas occupy the largest latitudinal range of any New World terrestrial mammal. Human population growth and associated habitat reduction has reduced their North American range by nearly two-thirds, but the impact of human expansion in Central and South America on puma populations is not clear. We examined mitochondrial DNA diversity of pumas across the majority of their range, with a focus on Central and South America. Four mitochondrial gene regions (1140 base pairs) revealed 16 unique haplotypes differentiating pumas into three geographic groupings: North America, Central America and South America. These groups were highly differentiated as indicated by significant pairwise FST values. North American samples were genetically homogenous compared to Central and South American samples, and South American pumas were the most diverse and ancestral. These findings support an earlier hypothesis that North America was recolonized by founding pumas from Central and South America.

  14. Estimation of genetic variation of Amorphophallus titanum Becc. based on Random Amplified Polymorphic DNA

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    YUYU SURYASARI POERBA

    2008-04-01

    Full Text Available Amorphophallus titanum Becc. (Araceae, is known by titan arum (western or bunga bangkai (Indonesian, is the bulkiest inflorescence in the world. The species is valued for its unique character of their inflorescence. The species has been overexploited and is considered as vulnerable plant species. The present study is carried out to assess genetic diversity and to estimate genetic relationship among 22 accessions collected from two different populations in Sumatra using Random Amplified Polymorphic DNA (RAPD. Nine RAPD primers generated 143 scorable bands which 137 (95.84% of them were polymorphic. Clustering analysis was performed based on RAPD profiles using the UPGMA method. The range of genetic dissimilarity value among accessions was from 0.14 to 0.59, while the range of genetic dissimilarity among populations was from 0.67 and 0.77. These values showed that A. titanum from Sumatra were more genetically diverse among genotypes than that of among populations.

  15. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens).

    Science.gov (United States)

    Kakou, Bidénam; Angers, Bernard; Glémet, Hélène

    2016-03-01

    The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish. PMID:26841134

  16. Chloroplast DNA variation and phylogeography of Ligularia tongolensis (Asteraceae), a species endemic to the Hengduan Mountains region of China

    Institute of Scientific and Technical Information of China (English)

    Jin-Feng WANG; Yue-Zhi PAN; Xun GONG; Yu-Chung CHIANG; Chiaki KURODA

    2011-01-01

    In this research, we aimed to study the genetic variation and phylogeographic pattern of Ligularia tongolensis, a perennial herb endemic to the Hengduan Mountains region of China. We sequenced two chloroplast DNA (cpDNA) intergenic spacers (trnQ-5'rps 16, trnL-rpl32) in 140 individuals from 14 populations of three groups (Jinshajiang vs. Yalongjiang vs. Wumeng) within this species range. High levels of haplotype diversity (Hd= 0.814)and total genetic diversity (Ht = 0.862) were detected at the species level, based on a total of 12 haplotypes identified.Low levels of intrapopulation diversity (Hs = 0.349), high levels of genetic divergence (Gst = 0.595, Nst = 0.614,Fst = 0.597), and the absence of isolation by distance tests were also found in L. tongolensis. Furthermore, H2 and H5, the dominant haplotypes that located at internal nodes and deviated from extinct ancestral haplotype in the network, were found to be shared between Jinshajiang and Yalongjiang groups. These results indicate that past fragmentation may be the important factor responsible for the present phylogeographical pattern of L. tongolensis.Meanwhile, the locations occupied by each group might have served as independent refugia for L. tongolensis during the Quaternary glaciation. Unimodal mismatch distribution and star-like genealogies indicated this species underwent past demographic expansion events, with expansion ages of 274 ka BP.

  17. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans

    Energy Technology Data Exchange (ETDEWEB)

    Torroni, A.; Schurr, T.G.; Cabell, M.F.; Wallace, D.C. (Emory Univ., Atlanta, GA (United States)); Sukernik, R.I.; Starikovskaya, Y.B. (Institute of Cytology and Genetics, Novosibirsk (Russian Federation)); Crawford, M.H.; Comuzzie, A.G. (Univ. of Kansas, Lawrence, KS (United States))

    1993-09-01

    The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analysis and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. These findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present. 61 refs., 5 figs., 7 tabs.

  18. Phylogeography of Cyananthus delavayi (Campanulaceae) in Hengduan Mountains inferred from variation in nuclear and chloroplast DNA sequences

    Institute of Scientific and Technical Information of China (English)

    Guo-Dong LI; Liang-Liang YUE; Hang SUN; Zi-Gang QIAN

    2012-01-01

    Phylogeographic studies on alpine plants endemic to the Hengduan Mountains of the southeastern Qinghai-Tibet Plateau are still limited in number.In this study,we used sequence variation of one nuclear gene (ncpGS,which encodes the chloroplastic glutamine synthetase) and in two chloroplast DNA segments to investigate the phylogeographic structure and population demographic history of Cyananthus delavayi,a narrow-range species endemic to this region.We identified eight chlorotypes and 16 nuclear genotypes in a survey of 10 populations sampled throughout the range of the species.The results of both phylogenetic and network analyses suggested that the genealogical relationships of both chlorotypes and nuclear genotypes showed a clear geographical correlation.High total genetic diversity,low levels of within-population diversity,and strong population differentiation (chloroplast DNA:hT =0.827,hS =0.087,NST =0.899,GST =0.895; nuclear DNA:hT =0.910,hS =0.348,NST =0719,GST =0.618) were identified.Based on the mismatch distribution analyses,no evidence of recent demographic population expansion was found for this species.Nested clade analyses of both chlorotypes and nuclear genotypes indicated that restricted gene flow resulting from isolation by distance and allopatrc fragmentation were likely to have been the major processes that shaped their present-day spatial distribution.Our dating of the genetic divergences between three major geographic lineages suggested that the largest glaciation of the early Quaternary developed in the Qinghai-Tibet Plateau and mountainous isolation may have together led to deep intraspecific vicariance within this species.

  19. Molecular DNA variation among Triturus vittatus vittatus (Urodela) from different breeding sites at the southern limit of its distribution

    OpenAIRE

    Oren Pearlson; Gad Degani

    2007-01-01

    Molecular DNA variation among Triturus vittatus vittatus (striped newt) from different breeding sites at the southern limit of the species distribution (where environmental conditions are most extreme) was studied by the random amplification of polymorphic DNA (RAPD) method that has been found to be appropriate for other Triturus species. Altitudes of the localities ranged between 15-740 m a.s.l. Of the 20 primers employed, OPA-16 was the only one suitable for T. vittatus, revealing a differe...

  20. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region.

    Science.gov (United States)

    Kim, Jae-Hwan; Lee, Seong-Su; Kim, Seung Chang; Choi, Seong-Bok; Kim, Su-Hyun; Lee, Chang Woo; Jung, Kyoung-Sub; Kim, Eun Sung; Choi, Young-Sun; Kim, Sung-Bok; Kim, Woo Hyun; Cho, Chang-Yeon

    2016-05-01

    Many studies have reported the frequency and distribution of haplogroups among various cattle breeds for verification of their origins and genetic diversity. In this study, 318 complete sequences of the mtDNA control region from four Korean cattle breeds were used for haplogroup classification. 71 polymorphic sites and 66 haplotypes were found in these sequences. Consistent with the genetic patterns in previous reports, four haplogroups (T1, T2, T3, and T4) were identified in Korean cattle breeds. In addition, T1a, T3a, and T3b sub-haplogroups were classified. In the phylogenetic tree, each haplogroup formed an independent cluster. The frequencies of T3, T4, T1 (containing T1a), and T2 were 66%, 16%, 10%, and 8%, respectively. Especially, the T1 haplogroup contained only one haplotype and a sample. All four haplogroups were found in Chikso, Jeju black and Hanwoo. However, only the T3 and T4 haplogroups appeared in Heugu, and most Chikso populations showed a partial of four haplogroups. These results will be useful for stable conservation and efficient management of Korean cattle breeds. PMID:26954229

  1. Genetic variation in Labeo fimbriatus (Cypriniformes: Cyprinidae) populations as revealed by partial cytochrome b sequences of mitochondrial DNA.

    Science.gov (United States)

    Swain, Subrat Kumar; Bej, Dillip; Das, Sofia Priyadarsani; Sahoo, Lakshman; Jayasankar, Pallipuram; Das, Pratap Chandra; Das, Paramananda

    2016-05-01

    Labeo fimbriatus, a medium sized carp is assessed as a commercially important aquaculture species in Indian subcontinent. In the present study, the genetic diversity and population structure of four Indian riverine populations of L. fimbriatus have been evaluated using partial cytochrome b sequences of mitochondrial DNA. Sequencing and analysis of this gene from 108 individuals defined 7 distinct haplotypes. Haplotype diversity (Hd) and nucleotide diversity (π) ranged from 0.067 to 0.405 and 0.00023 to 0.03231, respectively. The Mahanadi population had the highest π level. Analysis of molecular variance (AMOVA) indicated that 47.36% of genetic variation contained within population and 53.76% of genetic variation among groups. Pairwise FST analysis indicated that there was little or no genetic differentiation among populations (-0.0018 to 04572) from different geographical regions except Mahanadi population. The Mahanadi population can be considered as a separate stock from rest three riverine populations. Accordingly, the genetic information generated from this study can be implemented while taking decision in formulating base population for the sustainable selective breeding programs of this species. PMID:25329277

  2. Genetic variations of Lansium domesticum Corr. accessions from Java, Sumatra and Ceram based on Random Amplified Polymorphic DNA fingerprints

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    KUSUMADEWI SRI YULITA

    2011-07-01

    Full Text Available Yulita KS (2011 Genetic variations of Lansium domesticum Corr. accessions from Java, Bengkulu and Ceram based on Random Amplified Polymorphic DNA fingerprints. Biodiversitas 12: 125-130. Duku (Lansium domesticum Corr. is one of popular tropical fruits in SE Asia. The spesies has three varieties, known as duku, langsat and kokosan; and duku is the most popular one for being the sweetiest fruit. Indonesia has several local varieties of duku, such as duku Condet, duku Sumber and duku Palembang. This present study aimed to assess genetic diversity of 47 accessions of duku from Java, Sumatra, and Ceram based on RAPD fingerprints. Ten RAPD’s primers were initially screened and five were selected for the analysis. These five primers (OPA 7, 13, 18, OPB 7, and OPN 12 generated 53 scorable bands with an average of 10.6 polymorphic fragment per primer. Percentage of polymorphism ranged from 16.89% (OPA 7 and OPN 12 to 24.54% (OPB 7 with an average of 20.16% polymorphism. OPB 7 at 450 bp was exclusively possessed by accession 20 (Java, OPA 18 at 500 bp was by accession 6 (Java, 550 bp by 3 clones from Bengkulu. While OPN 12 at 300 bp and OPA 13 at 450 bp were shared among the accessions. Clustering analysis was performed based on RAPD profiles using the UPGMA method. The range of genetic similarity value among accessions was 0.02-0.65 suggesting high variation of gene pool existed among accessions.

  3. Investigating the potential role of genetic and epigenetic variation of DNA methyltransferase genes in hyperplastic polyposis syndrome.

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    Musa Drini

    Full Text Available BACKGROUND: Hyperplastic Polyposis Syndrome (HPS is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC. At least half of CRCs arising in HPS show a CpG island methylator phenotype (CIMP, potentially linked to aberrant DNA methyltransferase (DNMT activity. CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT, and negative regulators of Wnt signaling (such as WIF1. In this study, we investigated the potential for interaction of genetic and epigenetic variation in DNMT genes, in the aetiology of HPS. METHODS: We utilized high resolution melting (HRM analysis to screen 45 cases with HPS for novel sequence variants in DNMT1, DNMT3A, DNMT3B, and DNMT3L. 21 polyps from 13 patients were screened for BRAF and KRAS mutations, with assessment of promoter methylation in the DNMT1, DNMT3A, DNMT3B, DNMT3L MLH1, MGMT, and WIF1 gene promoters. RESULTS: No pathologic germline mutations were observed in any DNA-methyltransferase gene. However, the T allele of rs62106244 (intron 10 of DNMT1 gene was over-represented in cases with HPS (p<0.01 compared with population controls. The DNMT1, DNMT3A and DNMT3B promoters were unmethylated in all instances. Interestingly, the DNMT3L promoter showed low levels of methylation in polyps and normal colonic mucosa relative to matched disease free cells with methylation level negatively correlated to expression level in normal colonic tissue. DNMT3L promoter hypomethylation was more often found in polyps harbouring KRAS mutations (p = 0.0053. BRAF mutations were common (11 out of 21 polyps, whilst KRAS mutations were identified in 4 of 21 polyps. CONCLUSIONS: Genetic or epigenetic alterations in DNMT genes do not appear to be associated with HPS, but further investigation of genetic variation at rs62106244 is justified given the high frequency of the minor allele in this case series.

  4. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life.

    Science.gov (United States)

    Wang, Deli; Liu, Xin; Zhou, Ying; Xie, Hehuang; Hong, Xiumei; Tsai, Hui-Ju; Wang, Guoying; Liu, Rong; Wang, Xiaobin

    2012-06-01

    Prenatal development and early childhood are critical periods for establishing the tissue-specific epigenome, and may have a profound impact on health and disease in later life. However, epigenomic profiles at birth and in early childhood remain largely unexplored. The focus of this report is to examine the individual variation and longitudinal pattern of genome-wide DNA methylation levels from birth through the first two years of life in 105 Black children (59 males and 46 females) enrolled at the Boston Medical Center. We performed epigenomic mapping of cord blood at birth and venous blood samples from the same set of children within the first two years of life using Illumina Infinium Humanmethylation27 BeadChip. We observed a wide range of inter-individual variations in genome-wide methylation at each time point including lower levels at CpG islands, TSS200, 5'UTR and 1st Exon locations, but significantly higher levels in CpG shores, shelves, TSS1500, gene body and 3'UTR. We identified CpG sites with significant intra-individual longitudinal changes in the first two years of life throughout the genome. Specifically, we identified 159 CpG sites in males and 149 CpG sites in females with significant longitudinal changes defined by both statistical significance and magnitude of changes. These significant CpG sites appeared to be located within genes with important biological functions including immunity and inflammation. Further studies are needed to replicate our findings, including analysis by specific cell types, and link those individual variations and longitudinal changes with specific health outcomes in early childhood and later life. PMID:22522910

  5. Tissue-specific variation in DNA methylation levels along human chromosome 1

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    De Bustos Cecilia

    2009-06-01

    Full Text Available Abstract Background DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different tissues for differentially methylated sites have focused on the methylation of CpGs in CpG islands, which are concentrations of CpGs often associated with gene promoters. Results Here, we use a methylation profiling strategy that is predominantly responsive to methylation differences outside of CpG islands. The method compares the yield from two samples of size-selected fragments generated by a methylation-sensitive restriction enzyme. We then profile nine different normal tissues from two human donors relative to spleen using a custom array of genomic clones covering the euchromatic portion of human chromosome 1 and representing 8% of the human genome. We observe gross regional differences in methylation states across chromosome 1 between tissues from the same individual, with the most striking differences detected in the comparison of cerebellum and spleen. Profiles of the same tissue from different donors are strikingly similar, as are the profiles of different lobes of the brain. Comparing our results with published gene expression levels, we find that clones exhibiting extreme ratios reflecting low relative methylation are statistically enriched for genes with high expression ratios, and vice versa, in most pairs of tissues examined. Conclusion The varied patterns of methylation differences detected between tissues by our methylation profiling method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands.

  6. SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

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    Patel Viren

    2010-09-01

    Full Text Available Abstract Background The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. Results SeqAnt (Sequence Annotator is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. Conclusion SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.

  7. Variations of 18S rDNA Loci Among Six Populations of Paeonia obovata Maxim. (Paeoniaceae) Revealed by Fluorescence In Situ Hybridization

    Institute of Scientific and Technical Information of China (English)

    Rui Luo; Chao Wang; Daming Zhang

    2006-01-01

    The localization of 18S ribosomal RNA genes (rDNA) by fluorescence in situ hybridization (FISH) had been performed for some species of Paeonia. However, the pattern of 18S rDNA loci among populations is indistinct. In the present study, we localized 18S rDNA loci on meiotic or mitotic chromosomes of six populations of Paeonia obovata Maxim. (Paeoniaceae). Different numbers of rDNA loci were found with different diploid (2n=10) populations, namely eight (Lushi and Mt. Jiuhua populations), 10 (Mt. Taibai population), and seven (Mt. Guandi population), whereas tetraploid (2n=20) populations were all found with 16 loci. All rDNA loci were mapped near telomeres of mitotic chromosomes and there was no chromosome with two loci. The present results show that molecular cytological polymorphism exists among P. obovata diploid populations, indicating that structural variations occurred frequently during the evolutionary history of this species, accompanied with differentiation among populations.

  8. [Genuineness of Morinda officinalis How germplasm inferred from ITS sequences variation of nuclear ribosomal DNA].

    Science.gov (United States)

    Ding, Ping; Liu, Jin; Qiu, Jin-Ying; Lai, Xiao-Ping

    2012-04-01

    PCR sequencing ITS genes methods were used to assess the genetic diversity of Morinda officinalis How different populations. The sequence of Morinda officinalis ITS gene was 567 bp in length, and the content of G/C was 64.5%. In this study, 17 haplotypes were obtained, which were at a high level of branching, and the haplotypes of Guangdong population showed to be the expansion origin. The result of the analysis of molecular variance (AMOVA) also showed that the percentage of variation among populations (56.65%) was greater than that within a population (43.35%). The F(ST) value was 0.566 5, and the genetic divergence among populations was significant. Mantel test results also indicated that the level of geneflow was positively correlated with geographic distances (R2 = 0.721 1). The result showed a good correlation between genotype and geographic distribution of Morinda officinalis, and ITS gene sequencing could be useful molecular method for the genuineness and phylogeography of Morinda officinalis. PMID:22799040

  9. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa.

    Science.gov (United States)

    Zaitlin, David; Pierce, Andrew J

    2010-12-01

    The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10⁶ base pairs, which is approximately 40% of the previously published estimate. PMID:21164539

  10. Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya.

    Science.gov (United States)

    Kibegwa, F M; Githui, K E; Jung'a, J O; Badamana, M S; Nyamu, M N

    2016-06-01

    Phylogenetic relationships among and genetic variability within 60 goats from two different indigenous breeds in Narok and Isiolo counties in Kenya and 22 published goat samples were analysed using mitochondrial control region sequences. The results showed that there were 54 polymorphic sites in a 481-bp sequence and 29 haplotypes were determined. The mean haplotype diversity and nucleotide diversity were 0.981 ± 0.006 and 0.019 ± 0.001, respectively. The phylogenetic analysis in combination with goat haplogroup reference sequences from GenBank showed that all goat sequences were clustered into two haplogroups (A and G), of which haplogroup A was the commonest in the two populations. A very high percentage (99.90%) of the genetic variation was distributed within the regions, and a smaller percentage (0.10%) distributed among regions as revealed by the analysis of molecular variance (amova). This amova results showed that the divergence between regions was not statistically significant. We concluded that the high levels of intrapopulation diversity in Isiolo and Narok goats and the weak phylogeographic structuring suggested that there existed strong gene flow among goat populations probably caused by extensive transportation of goats in history. PMID:26459231

  11. DNA variation in the phenotypically-diverse brown alga Saccharina japonica

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    Balakirev Evgeniy S

    2012-07-01

    Full Text Available Abstract Background Saccharina japonica (Areschoug Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS, plastid (rbcLS and mitochondrial (COI DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP and its two common morphological varieties, known as the “longipes” (LON and “shallow-water” (SHA forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica. Results The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions. The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5’- and 3’- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5’- or 3’- used for tree reconstruction. Consequently, the 5’-COI “barcoding” region (~ 650 bp can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events. Conclusion Taking into account

  12. Mitochondrial DNA Variation Among Populations of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) From Pakistan

    Science.gov (United States)

    Yasin, Muhammad; Rugman-Jones, Paul F.; Wakil, Waqas; Stouthamer, Richard

    2016-01-01

    The Red Palm Weevil (RPW) Rhynchophorus ferrugineus (Olivier) is a voracious pest of palm species. In recent decades its range has expanded greatly, particularly impacting the date palm industry in the Middle East. This has led to conjecture regarding the origins of invasive RPW populations. For example, in parts of the Middle East, RPW is commonly referred to as the “Pakistani weevil” in the belief that it originated there. We sought evidence to support or refute this belief. First reports of RPW in Pakistan were from the Punjab region in 1918, but it is unknown whether it is native or invasive there. We estimated genetic variation across five populations of RPW from two provinces of Pakistan, using sequences of the mitochondrial cytochrome oxidase subunit I gene. Four haplotypes were detected; two (H1 and H5) were abundant, accounting for 88% of specimens across the sampled populations, and were previously known from the Middle East. The remaining haplotypes (H51 and H52) were newly detected (in global terms) and there was no geographic overlap in their distribution within Pakistan. Levels of haplotype diversity were much lower than those previously recorded in accepted parts of the native range of RPW, suggesting that the weevil may be invasive in Pakistan. The affinity of Pakistani haplotypes to those reported from India (and the geographical proximity of the two countries), make the latter a likely “native” source. With regards the validity of the name “Pakistani weevil”, we found little genetic evidence to justify it. PMID:27651423

  13. DNA-sequence variation among Schistosoma mekongi populations and related taxa; phylogeography and the current distribution of Asian schistosomiasis.

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    Stephen W Attwood

    Full Text Available BACKGROUND: Schistosomiasis in humans along the lower Mekong River has proven a persistent public health problem in the region. The causative agent is the parasite Schistosoma mekongi (Trematoda: Digenea. A new transmission focus is reported, as well as the first study of genetic variation among S. mekongi populations. The aim is to confirm the identity of the species involved at each known focus of Mekong schistosomiasis transmission, to examine historical relationships among the populations and related taxa, and to provide data for use (a priori in further studies of the origins, radiation, and future dispersal capabilities of S. mekongi. METHODOLOGY/PRINCIPAL FINDINGS: DNA sequence data are presented for four populations of S. mekongi from Cambodia and southern Laos, three of which were distinguishable at the COI (cox1 and 12S (rrnS mitochondrial loci sampled. A phylogeny was estimated for these populations and the other members of the Schistosoma sinensium group. The study provides new DNA sequence data for three new populations and one new locus/population combination. A Bayesian approach is used to estimate divergence dates for events within the S. sinensium group and among the S. mekongi populations. CONCLUSIONS/SIGNIFICANCE: The date estimates are consistent with phylogeographical hypotheses describing a Pliocene radiation of the S. sinensium group and a mid-Pleistocene invasion of Southeast Asia by S. mekongi. The date estimates also provide Bayesian priors for future work on the evolution of S. mekongi. The public health implications of S. mekongi transmission outside the lower Mekong River are also discussed.

  14. Seasonal changes in markers of oxidative damage to lipids and DNA; correlations with seasonal variation in diet.

    Science.gov (United States)

    Smolková, Bozena; Dusinská, Mária; Raslová, Katarína; McNeill, Geraldine; Spustová, Viera; Blazícek, Pavol; Horská, Alexandra; Collins, Andrew

    2004-07-13

    We have addressed the question whether the relatively high incidence of cardiovascular disease and certain cancers in countries of central/eastern Europe might be associated with nutritional imbalance, in particular a lack of fresh fruit and vegetables in the diet in winter months. Nutritional parameters and markers of oxidative stress were studied in three Slovak population groups: 46 survivors of myocardial infarction (MI group) and 48 healthy, normolipidemic subjects (NL), living in or near Bratislava; and 70 rural controls (RC group) living a more traditional life style in a country town. Data were collected in February/March and September/October of two consecutive years, representing times of minimum and maximum local availability of fresh fruits and vegetables. Oxidative stress was monitored using two biomarkers; plasma malondialdehyde (MDA, a product of lipid peroxidation), and oxidation of lymphocyte DNA. Dietary antioxidants, folic acid, homocysteine, total antioxidant status (FRAP) and uric acid were measured in plasma. Food frequency questionnaires were administered. Vegetable consumption in summer/autumn was twice as high as in winter/spring. DNA damage did not vary consistently across the seasons. Mean plasma MDA levels for the MI and NL groups showed a clear pattern, with high levels in winter/spring and low levels in summer/autumn. Folic acid showed a reciprocal pattern, similar to the pattern of vegetable consumption. The RC group had the smallest seasonal variations in vegetable consumption, folic acid levels, and MDA. High winter MDA levels are seen in those individuals with relatively low folic acid; they never occur in subjects with high plasma folic acid, implying that folic acid might directly protect against lipid oxidation. This study illustrates the value of the molecular epidemiological approach, while emphasising the need for well characterised population groups and valid biomarkers.

  15. Assessment of Genetic Variation Within Indian Mustard(Brassica juncea) Germplasm Using Random Amplified Polymorphic DNA Markers

    Institute of Scientific and Technical Information of China (English)

    Muhammad Ayub Khan; Malik Ashiq Rabbani; Muharnmad Munir; Saifullah Khan Ajmal; Muhammad Azim Malik

    2008-01-01

    Genetic diversity among 45 Indian mustard (Brassica Juncea L.) genotypes comprising 37 germplasm collections, five advance breeding lines and three improved cultivars was investigated at the DNA level using the random amplified polymorphic DNA (RAPD) technique. Fifteen primers used generated a total of 92 RAPD fragments, of which 81 (88%) were polymorphic. Of these, 13 were unique to accession 'Pak85559'. Each primer produced four to nine amplified products with an average of 6.13 bands per primer. Based on pairwise comparisons of RAPD amplification products, Nei and Li's similarity coefficients were calculated to evaluate the relationships among the accessions. Pairwise similarity indices were higher among the oilseed accessions and cultivars showing narrow ranges of 0.77-0.99. An unweighted pair-group method with arithmetic averages cluster analysis based on these genetic similarities placed most of the collections and oilseed cultivars close to each other, showing a low level of polymorphism between the accessions used. However, the clusters formed by oilseed collections and cultivars were comparatively distinct from that of advanced breeding lines. Genetically, all of the accessions were classified into a few major groups and a number of individual accessions. Advanced breeding lines were relatively divergent from the rest of the accessions and formed independent clusters. Clustering of the accessions did not show any pattern of association between the RAPD markers and the collection sites. A low level of genetic variability of oilseed mustard was attributed to the selection for similar traits and horticultural uses. Perhaps close parentage of these accessions further contributed towards their little diversity. The study demonstrated that RAPD is a simple and fast technique to compare the genetic relationship and pattern of variation among the gene pool of this crop.

  16. Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood.

    Science.gov (United States)

    Toperoff, Gidon; Aran, Dvir; Kark, Jeremy D; Rosenberg, Michael; Dubnikov, Tatyana; Nissan, Batel; Wainstein, Julio; Friedlander, Yechiel; Levy-Lahad, Ephrat; Glaser, Benjamin; Hellman, Asaf

    2012-01-15

    Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here, we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranking regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (P = 0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence-risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR = 1.061, 95% CI: 1.032-1.090), the odds ratio for decrease of 1 standard deviation of methylation (adjusted to gender) was 1.5856 (95% CI: 1.2824-1.9606) and the sensitivity (area under the curve = 0.638, 95% CI: 0.586-0.690; males = 0.675, females = 0.609) was better than that of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals who stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM and suggests a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM.

  17. Genetic characterization of Kenai brown bears (Ursus arctos): Microsatellite and mitochondrial DNA control region variation in brown bears of the Kenai Peninsula, south central Alaska

    Science.gov (United States)

    Jackson, J.V.; Talbot, S.L.; Farley, S.

    2008-01-01

    We collected data from 20 biparentally inherited microsatellite loci, and nucleotide sequence from the maternally inherited mitochondrial DNA (mtDNA) control region, to determine levels of genetic variation of the brown bears (Ursus arctos L., 1758) of the Kenai Peninsula, south central Alaska. Nuclear genetic variation was similar to that observed in other Alaskan peninsular populations. We detected no significant inbreeding and found no evidence of population substructuring on the Kenai Peninsula. We observed a genetic signature of a bottleneck under the infinite alleles model (IAM), but not under the stepwise mutation model (SMM) or the two-phase model (TPM) of microsatellite mutation. Kenai brown bears have lower levels of mtDNA haplotypic diversity relative to most other brown bear populations in Alaska. ?? 2008 NRC.

  18. Next-Gen phylogeography of rainforest trees: exploring landscape-level cpDNA variation from whole-genome sequencing.

    Science.gov (United States)

    van der Merwe, M; McPherson, H; Siow, J; Rossetto, M

    2014-01-01

    Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next-generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun-based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species-specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape-level studies. As the key laboratory-based steps do not require prior species-specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet-laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.

  19. Genetic variation in scaly hair-fin anchovy Setipinna tenuifilis (Engraulididae) based on the mitochondrial DNA control region.

    Science.gov (United States)

    Xu, Shengyong; Song, Na; Lu, Zhichuang; Wang, Jun; Cai, Shanshan; Gao, Tianxiang

    2014-06-01

    Scaly hair-fin anchovy (Setipinna tenuifilis) is a small, pelagic and economical species and widely distributed in Chinese coastal water. However, resources of S. tenuifilis have been reduced due to overfishing. For better fishery management, it is necessary to understand the pattern of S. tenuifilis's biogeography. Genetic analyses were taken place to detect their population genetic variation. A total of 153 individuals from 7 locations (Dongying, Yantai, Qingdao, Nantong, Wenzhou, Xiamen and Beibu Bay) were sequenced at the 5' end of mtDNA control region. A 39-bp tandem repeated sequence was found at the 5' end of the segment and a polymorphism of tandem repeated sequence was detected among 7 populations. Both mismatch distribution analysis and neutrality tests showed S. tenuifilis had experienced a recent population expansion. The topology of neighbor-joining tree and Bayesian evolutionary tree showed no significant genealogical branches or clusters of samples corresponding to sampling locality. Hierarchical analysis of molecular variance and conventional pairwise population Fst value at group hierarchical level implied that there might have genetic divergence between southern group (population WZ, XM and BB) and northern group (population DY, YT, QD and NT). We concluded that there might have three different fishery management groups of S. tenuifilis and the late Pleistocene glacial event might have a crucial effect on present-day demography of S. tenuifilis in this region.

  20. Genetic Variation of Cassava Mealybug, Phenacoccus manihoti (Hemiptera: Pseudococcidae, Based on DNA Sequences from Mitochondrial and Nuclear Genes

    Directory of Open Access Journals (Sweden)

    Atsalek RATTANAWANNEE

    2016-02-01

    Full Text Available The present study aimed to investigate the genetic variation and genetic structure of the Phenacoccus manihoti Matile-Ferrero, one of the most serious insect pests of cassava worldwide, in populations in Thailand, using mitochondrial and nuclear DNA sequence based analysis. The samples of P. manihoti were collected from 28 major cassava-growing areas within 18 provinces in Thailand. Our field survey results showed that the northeastern and eastern regions of Thailand were widely and highly infested with P. manihoti. Phylogenetic analysis revealed 2 mitochondrial clades and a single nuclear clade, which corresponded to low genetic variability. This suggests that P. manihoti has a high potential to spread aggressively throughout the cassava-growing areas in Thailand that in which it was first found in 2008. In addition, the generally low genetic divergence observed may be due to the highly prevalent parthenogenetic reproduction of this insect pest species. Further research is therefore necessary to develop proportional prevention and surveillance programs for early detection and rapid response. In addition, the genetic structure and variability of P. manihoti populations from neighboring countries should be studied.

  1. Pressure dissociation of integration host factor–DNA complexes reveals flexibility-dependent structural variation at the protein–DNA interface

    OpenAIRE

    Senear, Donald F.; Tretyachenko-Ladokhina, Vira; Opel, Michael L.; Aeling, Kimberly A.; G Wesley Hatfield; Franklin, Laurie M.; Darlington, Reuben C.; Alexander Ross, J. B.

    2007-01-01

    E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236–39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. ...

  2. Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai-Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation

    Institute of Scientific and Technical Information of China (English)

    Jia-Bin ZOU; Xiao-Li PENG; Long LI; Jian-Quan LIU; Georg MIEHE; Lars OPGENOORTH

    2012-01-01

    The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis,a dominant species of the conifer forests in the eastern declivity of the Qinghai-Tibetan Plateau.We collected 422 individuals from 42 natural populations of three major varieties classified under this species.In conifers,mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow.To this end,we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nadl intron b/c) and three cpDNA fragments (trnL-trnF,trnS-trnG and nadhK/C).We found that cpDNA probably introgressed from P.purpurea into remote populations of P.likiangensis through long-distance dispersal.Multiple refugia seem to have been maintained for P.likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions.Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations.However,genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions,which may result from the long-distance dispersal of the cpDNA,as well as its fast lineage sorting during intraspecific divergences.Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers,which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa.Together,the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion,long-distance dispersal,and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.

  3. Use of sequence variation in three highly variable regions of the mitochondrial DNA for the discrimination of allogeneic platelets

    NARCIS (Netherlands)

    Warner, JB; Bruin, EJ; Hannig, H; Hellenkamp, F; Horning, A; Mittmann, K; van der Steege, G; de Leij, LFMH; Garritsen, HSP

    2006-01-01

    BACKGROUND: Human mitochondrial DNA (mtDNA) polymorphisms can be used to detect allogeneic transfused platelets. To increase the number of informative polymorphisms we investigated three hypervariable regions (HVR1, HVR2, and HVR3) within the displacement loop (D-loop) region of the mtDNA. STUDY DES

  4. Cylindrotheca closterium Is a Species Complex as Was Evidenced by the Variations of rbcL Gene and SSU rDNA

    Institute of Scientific and Technical Information of China (English)

    LI Haitao; YANG Guanpin; SUN Ying; WU Suihan; ZHANG Xiufang

    2007-01-01

    The genus Cylindrotheca consists of a small group of marine diatoms with a few species described. Eleven isolates of diatoms identified as Cylindrotheca closterium morphologically were obtained from Jiaozhou Bay with their nuclear-encoded small-subunit ribosomal RNA (SSU rDNA) and chloroplast-encoded rbcL gene sequences determined in this study. Interestingly, very high sequence divergences of SSU rDNA and rbcL gene were found among these isolates, and numerous nucleotide variation of rbcL gene caused relatively few variation of deduced amino acid sequence. Phylogenetic analyses based on SSU rDNA and rbcL gene, respectively, grouped the isolates into 6 clades. Phylogenetic tree of SSU rDNA placed all the Cylindrotheca isolates together, separating them into two lineages clearly. LineageⅠ was composed of the eleven C. closterium isolates obtained in this study together with another C. closterium isolate, but some clades were not well supported. LineageⅡ contained two C. closterium isolates and one C. fusiformis isolate. Phylogenetic analysis of rbcL gene also separated the Cylindrotheca isolates into two well-defined lineages. The eleven C. closterium isolates formed a lineage and all clades were supported strongly. Statistical comparisons of SSU rDNA indicated that the average distance within lineage Ⅰ was significantly higher than that of other microalgae species (P < 0.01). These results suggested the existence of cryptic species within C. closterium.

  5. Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype.

    Science.gov (United States)

    Etemadi, Arash; Islami, Farhad; Phillips, David H; Godschalk, Roger; Golozar, Asieh; Kamangar, Farin; Malekshah, Akbar Fazel-Tabar; Pourshams, Akram; Elahi, Seerat; Ghojaghi, Farhad; Strickland, Paul T; Taylor, Philip R; Boffetta, Paolo; Abnet, Christian C; Dawsey, Sanford M; Malekzadeh, Reza; van Schooten, Frederik J

    2013-06-15

    Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to xenobiotic metabolism and 12 SNPs in eight DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by32P-postlabeling. Multivariable regression models were compared by Akaike's information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 10(8) nucleotides (mean: 5.8 ± 3.1). DNA adduct level was significantly lower in homozygotes for NAT2 slow alleles and ERCC5 non-risk-allele genotype, and was higher in the MPO homozygote risk-allele genotype. The sum of risk alleles in these genes significantly correlated with the log-adduct level (r = 0.4, p studies, with large inter-individual variation which could best be explained by a combination of Phase I genes and NER capacity. PMID:23175176

  6. High regional genetic diversity and lack of host-specificity in Ostrinia nubilalis (Lepidoptera: Crambidae) as revealed by mtDNA variation.

    Science.gov (United States)

    Piwczyński, M; Pabijan, M; Grzywacz, A; Glinkowski, W; Bereś, P K; Buszko, J

    2016-08-01

    The European corn borer (Ostrinia nubilalis) infests a wide array of host plants and is considered one of the most serious pests of maize in Europe. Recent studies suggest that individuals feeding on maize in Europe should be referred to O. nubilalis (sensu nov.), while those infesting dicots as Ostrinia scapulalis (sensu nov.). We test if the clear genetic distinctiveness among individuals of O. nubilalis living on maize vs. dicots is tracked by mitochondrial DNA (mtDNA). We used fragments of COI and COII genes of 32 individuals traditionally recognized as O. nubilalis collected on three host plants, maize, mugwort and hop, growing in different parts of Poland. In addition, we reconstructed the mtDNA phylogeny of Ostrinia species based on our data and sequences retrieved from GenBank to assess host and/or biogeographic patterns. We also compared haplotype variation found in Poland (east-central Europe) with other regions (Anatolia, Eastern Europe, Balkans, Far East, North America). Our study showed high mtDNA diversity of O. nubilalis in Poland in comparison with other regions and revealed rare haplotypes likely of Asian origin. We did not find distinct mtDNA haplotypes in larvae feeding on maize vs. dicotyledonous plants. Phylogenetic analyses showed an apparent lack of mtDNA divergence among putatively distinct lineages belonging to the O. nubilalis group as identical haplotypes are shared by Asian and European individuals. We argue that human-mediated dispersal, hybridization and sporadic host jumps are likely responsible for the lack of a geographic pattern in mtDNA variation. PMID:27019346

  7. Evaluation of Interindividual Human Variation in Bioactivation and DNA Adduct Formation of Estragole in Liver Predicted by Physiologically Based Kinetic/Dynamic and Monte Carlo Modeling.

    Science.gov (United States)

    Punt, Ans; Paini, Alicia; Spenkelink, Albertus; Scholz, Gabriele; Schilter, Benoit; van Bladeren, Peter J; Rietjens, Ivonne M C M

    2016-04-18

    Estragole is a known hepatocarcinogen in rodents at high doses following metabolic conversion to the DNA-reactive metabolite 1'-sulfooxyestragole. The aim of the present study was to model possible levels of DNA adduct formation in (individual) humans upon exposure to estragole. This was done by extending a previously defined PBK model for estragole in humans to include (i) new data on interindividual variation in the kinetics for the major PBK model parameters influencing the formation of 1'-sulfooxyestragole, (ii) an equation describing the relationship between 1'-sulfooxyestragole and DNA adduct formation, (iii) Monte Carlo modeling to simulate interindividual human variation in DNA adduct formation in the population, and (iv) a comparison of the predictions made to human data on DNA adduct formation for the related alkenylbenzene methyleugenol. Adequate model predictions could be made, with the predicted DNA adduct levels at the estimated daily intake of estragole of 0.01 mg/kg bw ranging between 1.6 and 8.8 adducts in 10(8) nucleotides (nts) (50th and 99th percentiles, respectively). This is somewhat lower than values reported in the literature for the related alkenylbenzene methyleugenol in surgical human liver samples. The predicted levels seem to be below DNA adduct levels that are linked with tumor formation by alkenylbenzenes in rodents, which were estimated to amount to 188-500 adducts per 10(8) nts at the BMD10 values of estragole and methyleugenol. Although this does not seem to point to a significant health concern for human dietary exposure, drawing firm conclusions may have to await further validation of the model's predictions. PMID:26952143

  8. Host Plant Mediated Population Variations of Cotton Whitefly Bemisia tabaci Gennadius (Aleyrodidae: Homoptera Characterized with Random DNA Markers

    Directory of Open Access Journals (Sweden)

    Yasodha Perumal

    2009-01-01

    Full Text Available Problem statement: Whitefly, Bemisia tabaci is an important sucking pest of field, horticultural and ornamental plants causing feeding injuries besides spreading disease by acting as a vector of Gemini viruses. The polyphagous nature of the pest makes it as a highly complex species. Approach: The influence of host plants utilized by the species on the population differences at molecular level was attempted using Random Amplified Polymorphic DNA (RAPD markers. Results: Ten RAPD primers out of the total seventeen primers screened produced 236 markers. The total number of bands obtained from each primer ranged from 11-35 with an average of 23.60 bands per primer. Of the pair wise combination among thirteen species, Srivilliputhur population showed the highest similarity index (0.826 while the lowest (0.111 was recorded by Namakkal population. The similarity coefficient based on the 236 RAPD markers generated ranged from 0.111-0.826. Three major clusters were formed from UPGMA dendrogram, which was constructed based on Jaccard’s similarity. PCR screening demarcated the whitefly population based on the host species. The first cluster included population collected from okra and cotton, while second cluster comprised of population from eggplant and cauliflower and the third cluster included population from eggplant. It could be deduced that population from cotton and okra had 50% similarity, while 60-70% similarity was observed for population from eggplant and cauliflower. Conclusion: Our investigation offered the lead that within a narrow geographical region there exits variation based on host plants being utilized by the whitefly population.

  9. The resolution of aneuploid DNA stem lines by flow cytometry: limitations imposed by the coefficient of variation and the percentage of aneuploid nuclei.

    Science.gov (United States)

    Cusick, E L; Milton, J I; Ewen, S W

    1990-04-01

    Factors important in the resolution of cell sub-populations with differing DNA contents were investigated using an EPICS C flow cytometer. Software is available for the EPICS C which permits data from any two histograms to be superimposed or added together before display. Samples of fresh and archival thyroid tissue, stained with propidium iodide, were analysed on the flow cytometer and the peak channel number noted. The photomultiplier (PMT) voltage was increased and the sample analysed again producing a second histogram with a higher peak channel number. The two histograms were added together to simulate a cell suspension with two sub-populations with a different DNA content. By systematically altering the PMT voltage and the number of nuclei included in each analysis, it was possible to examine the importance of DNA index and the percentage of tumor cells with an aneuploid DNA content for both fresh and paraffin-embedded thyroid nuclei. The crucial importance of achieving a low coefficient of variation (CV) was demonstrated and consequently the reservations that pertain when archival material is studied, particularly in tumours where DNA aneuploidy is frequently expressed with a low DNA index.

  10. Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools.

    Directory of Open Access Journals (Sweden)

    Jun Ding

    2015-07-01

    Full Text Available DNA sequencing identifies common and rare genetic variants for association studies, but studies typically focus on variants in nuclear DNA and ignore the mitochondrial genome. In fact, analyzing variants in mitochondrial DNA (mtDNA sequences presents special problems, which we resolve here with a general solution for the analysis of mtDNA in next-generation sequencing studies. The new program package comprises 1 an algorithm designed to identify mtDNA variants (i.e., homoplasmies and heteroplasmies, incorporating sequencing error rates at each base in a likelihood calculation and allowing allele fractions at a variant site to differ across individuals; and 2 an estimation of mtDNA copy number in a cell directly from whole-genome sequencing data. We also apply the methods to DNA sequence from lymphocytes of ~2,000 SardiNIA Project participants. As expected, mothers and offspring share all homoplasmies but a lesser proportion of heteroplasmies. Both homoplasmies and heteroplasmies show 5-fold higher transition/transversion ratios than variants in nuclear DNA. Also, heteroplasmy increases with age, though on average only ~1 heteroplasmy reaches the 4% level between ages 20 and 90. In addition, we find that mtDNA copy number averages ~110 copies/lymphocyte and is ~54% heritable, implying substantial genetic regulation of the level of mtDNA. Copy numbers also decrease modestly but significantly with age, and females on average have significantly more copies than males. The mtDNA copy numbers are significantly associated with waist circumference (p-value = 0.0031 and waist-hip ratio (p-value = 2.4×10-5, but not with body mass index, indicating an association with central fat distribution. To our knowledge, this is the largest population analysis to date of mtDNA dynamics, revealing the age-imposed increase in heteroplasmy, the relatively high heritability of copy number, and the association of copy number with metabolic traits.

  11. In situ labeling of DNA reveals interindividual variation in nuclear DNA breakdown in hair and may be useful to predict success of forensic genotyping of hair

    OpenAIRE

    Szabo, Sandra; Jaeger, Karin; Fischer, Heinz; Tschachler, Erwin; Parson, Walther; Eckhart, Leopold

    2011-01-01

    Hair fibers are formed by keratinocytes of the hair follicle in a process that involves the breakdown of the nucleus including DNA. Accordingly, DNA can be isolated with high yield from the hair bulb which contains living keratinocytes, whereas it is difficult to prepare from the distal portions of hair fibers and from shed hair. Nevertheless, forensic investigations are successful in a fraction of shed hair samples found at crime scenes. Here, we report that interindividual differences in th...

  12. Limited phylogeographic signal in sex-linked and autosomal loci despite geographically, ecologically, and phenotypically concordant structure of mtDNA variation in the Holarctic avian genus Eremophila.

    Directory of Open Access Journals (Sweden)

    Sergei V Drovetski

    Full Text Available Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early-Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris with respect to the Temminck's lark (E. bilopha. In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species.

  13. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

    Directory of Open Access Journals (Sweden)

    Yang An

    Full Text Available A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.

  14. mtDNA G10398A variation provides risk to type 2 diabetes in population group from the Jammu region of India

    Directory of Open Access Journals (Sweden)

    Varun Sharma

    2014-12-01

    Full Text Available Mitochondrion plays an integral role in glucose metabolism and insulin secretion. Mitochondrial electron-transport chain (ETC is involved in adenosine triphosphate (ATP generation and ATP mediated insulin secretion in pancreatic β-cells. β-cell dysfunction is a critical component in the pathogenesis of type 2 diabetes (T2D. The mtDNA G10398A variation (amino acid change: Alanine → Threonine within the NADH dehydrogenase (ND3 subunit of complex I of mtDNA ETC, has emerged as a variation of clinical significance in various disorders including T2D. This variation is supposed to result in altered complex I function, leading to an increased rate of electron leakage and reactive oxygen species (ROS production, which might cause β-cell damage and impaired insulin secretion. The aim of the study was to explore the association of mtDNA G10398A variation with T2D in a total of 439 samples (196 T2D cases and 243 healthy controls belonging to the Jammu region of Jammu and Kashmir (J&K. The candidate gene association analyses showed significant association of mtDNA G10398A variant with T2D and the estimated odds ratio (OR was 2.83 (1.64–4.90 at 95% CI in the studied population group. The extent of genetic heterogeneity in T2D and diversity of the Indian population groups, make such replication studies pertinent to understand the etiology of T2D in these population groups.

  15. Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype

    OpenAIRE

    Etemadi, Arash; Islami, Farhad; Phillips, David H.; Godschalk, Roger; Golozar, Asieh; Kamangar, Farin; Malekshah, Akbar Fazel-Tabar; Pourshams, Akram; Elahi, Seerat; Ghojaghi, Farhad; Strickland, Paul T.; Taylor, Philip R.; Boffetta, Paolo; Abnet, Christian C.; Dawsey, Sanford M.

    2012-01-01

    Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to...

  16. Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli.

    OpenAIRE

    Nou, X; Braaten, B; Kaltenbach, L; Low, D A

    1995-01-01

    Pyelonephritis-associated pili (Pap) expression in Escherichia coli is subject to a phase variation control mechanism that is regulated by the leucine-responsive regulatory protein (Lrp), PapI, and deoxyadenosine methylase (Dam). In previous work, we found that the differential Dam methylation of two target sites in pap regulatory DNA, GATC-I and GATC II, is essential for the transition between active and inactive pap transcriptional states. Here, we identify six Lrp binding sites within the ...

  17. Cytogenetic variation of repetitive DNA elements in Hoplias malabaricus (Characiformes - Erythrinidae) from white, black and clear water rivers of the Amazon basin.

    Science.gov (United States)

    Santos, Fabíola Araújo Dos; Marques, Diego Ferreira; Terencio, Maria Leandra; Feldberg, Eliana; Rodrigues, Luís Reginaldo R

    2016-03-01

    Hoplias malabaricus is a common fish species occurring in white, black and clear water rivers of the Amazon basin. Its large distribution across distinct aquatic environments can pose stressful conditions for dispersal and creates possibilities for the emergence of local adaptive profiles. We investigated the chromosomal localization of repetitive DNA markers (constitutive heterochromatin, rDNA and the transposable element REX-3) in populations from the Amazonas river (white water), the Negro river (black water) and the Tapajós river (clear water), in order to address the variation/association of cytogenomic features and environmental conditions. We found a conserved karyotypic macrostructure with a diploid number of 40 chromosomes (20 metacentrics + 20 submetacentrics) in all the samples. Heteromorphism in pair 14 was detected as evidence for the initial differentiation of an XX/XY system. Minor differences detected in the amount of repetitive DNA markers are interpreted as possible signatures of local adaptations to distinct aquatic environments.

  18. Characterization of variation induced by low-energy N+ and cloning of differentially expressed cDNA of a mutant in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Using Arabidopsis thaliana as experimental materials, the variations induced by low-energy N+ have been investigated. Germination rate of the treated seeds is lower than that of the control, and it decreases with the intensification of the radiation. The phenotypic variations have been observed in M2 plants irradiated with higher doses, such as chlorisis, semilethality, plant morphology, and changes of blooming habit and fertility. In random amplified polymorphic DNA (RAPD) analysis on M2 seedlings, some differences including band deletions or additions are found in treated plants compared to the control and the differences are associated with the radiation doses. One of the M1 plants from the seeds irradiated with the dose of 80×1015 N+/cm2 is a dwarf variant. Its stable M6 generation, mutant T80II, is used to construct subtractive cDNA library and to clone differentially expressed cDNA. A 721 bp cDNA fragment is partly homologous with GRF7 gene.

  19. Variation in the measurement of DNA damage by comet assay measured by the ECVAG dagger inter-laboratory validation trial

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Johansson, Clara; Loft, Steffen;

    2010-01-01

    by the different laboratories as evidenced by an inter-laboratory coefficient of variation (CV) of 47%. Adjustment of the primary comet assay end points by a calibration curve prepared in each laboratory reduced the CV to 28%, a statistically significant reduction (P ... of the inter-laboratory variation originated from differences in image analysis, whereas the intra-laboratory variation was considerably smaller than the variation between laboratories. In summary, adjustment of primary comet assay results by reference standards reduces inter-laboratory variation in the level...

  20. Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation

    DEFF Research Database (Denmark)

    Salas, A; Rasmussen, Erik Michael; Lareu, M V;

    2001-01-01

    The mtDNA analysis (mtDNA) is increasingly being demanded for forensic purposes due to the fact that many times the use of standard nuclear marker fails to analyze degraded samples (such as bones) and specially for the analysis of hair shafts (a common sample in the crime scene). However, analysi...

  1. Diurnal variations in depth profiles of UV-induced DNA damage and inhibition of bacterioplankton production in tropical coastal waters

    NARCIS (Netherlands)

    Visser, PM; Poos, JJ; Scheper, BB; Boelen, P; van Duyl, FC

    2002-01-01

    In this study, diurnal changes in bacterial production and DNA damage in bacterio-plankton (measured as cyclobutane pyrimidine dimers, CPDs) incubated in bags at different depths in tropical coastal waters were investigated. The DNA damage and inhibition of the bacterial production was highest at th

  2. Early mouse embryos exhibit strain variation in radiation-induced sister-chromatid exchange: relationship with DNA repair.

    Science.gov (United States)

    Bennett, J; Pedersen, R A

    1984-04-01

    Although mature mammalian sperm are incapable of DNA repair, repair of damaged sperm DNA can occur after fertilization, as the sperm head decondenses and forms the male pronucleus. To quantify the cytogenetic effects of damage to sperm DNA we adapted the sister-chromatid exchange (SCE) test for use in early mouse embryos. After ultraviolet (UV) irradiation of sperm, eggs were fertilized in vitro and cultured for 2 cell cycles in medium containing fluorodeoxyuridine and bromodeoxyuridine; chromosomes were then prepared for SCE analysis. We found that UV-induced SCEs could be detected at the second cleavage division, and that eggs of different strains showed different frequencies of SCEs when fertilized by damaged sperm of a single strain. These results may indicate strain-specific differences in DNA repair of UV-induced DNA lesions by the early mouse embryo.

  3. Early mouse embryos exhibit strain variation in radiation-induced sister-chromatid exchange: relationship with DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, J. (California Univ., San Francisco (USA). Lab. of Radiobiology); Pedersen, R.A. (California Univ., San Francisco (USA). Dept. of Anatomy)

    1984-04-01

    Although mature mammalian sperm are incapable of DNA repair, repair of damaged sperm DNA can occur after fertilization, as the sperm head decondenses and forms the male pronucleus. To quantify the cytogenetic effects of damage to sperm DNA we adapted the sister-chromatid exchange (SCE) test for use in early mouse embryos. After ultraviolet (UV) irradiation of sperm, eggs were fertilized in vitro and cultured for 2 cell cycles in medium containing fluorodeoxyuridine and bromodeoxyuridine; chromosomes were then prepared for SCE analysis. We found that UV-induced SCEs could be detected at the second cleavage division, and that eggs of different strains showed different frequencies of SCEs when fertilized by damaged sperm of a single strain. These results may indicate strain-specific differences in DNA repair of UV-induced DNA lesions by the early mouse embryo.

  4. Ultraviolet cross-linking of helical oligonucleotides to two monoclonal MRL-1pr/1pr anti-DNA autoantibodies. Variations in H and L chain binding to DNA

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Y.J.; Stollar, B.D. (Tufts Univ., Boston, MA (USA))

    1990-11-15

    Experiments were performed to determine whether both H and L chains of different anti-native DNA autoantibodies are uniformly involved in binding to DNA. Two purified monoclonal mouse (MRL-1pr/1pr) IgG autoantibodies, H241 and 2C10, were tested. They both bound synthetic helical oligonucleotides of 10 to 20 base pairs in a gel electrophoresis retardation assay but differed in their preferences for given base sequences. Exposure of antibody-radiolabeled oligonucleotide mixtures to UV light (254 nm) for 10 min led to specific covalent cross-linking of oligonucleotide to both the H and the L chains of H241 but only to the H chain of 2C10. Single labeling events were detected without higher aggregation. The oligonucleotides were not cross-linked to unrelated IgG, even after 2 h of irradiation. Cross-linked (radioactively labeled) H and L chains of H241 and 2C10 were isolated from denaturing electrophoresis gels and digested with lysyl endopeptidase and/or staphylococcal V8 protease. H241 and 2C10 H chains each yielded a major labeled peptide fragment, but the peptides from the two antibodies were different. These experiments measured only some of the antibody-DNA interactions, probably with bases in the major groove of the DNA. They indicated that two MRL-1pr/1pr IgG anti-native DNA antibodies differ in their H and L chain contacts with DNA and provide an approach to identifying affinity-labeled binding sites in the antibodies.

  5. Mitochondrial DNA variation in the grasshopper Sinipta dalmani: application of long-PCR to the development of a homologous probe.

    Science.gov (United States)

    Pensel, S M; Vilardi, J C; Remis, M I

    2005-12-01

    RFLP analysis of mtDNA in natural populations is a valuable tool for phylogeographic and population genetic studies. The amplification of long DNA fragments using universal primers may contribute to the development of novel homologous probes in species for which no previous genomic information is available. Here we report how we obtained the complete mtDNA genome of Sinipta dalmani (Orthoptera) in 2 fragments (7 and 9 kb) using primers of conserved regions. The specificity of the PCR reactions was ultimately confirmed by several lines of evidence. These fragments were used as a probe for a mtDNA RFLP study in S. dalmani that analyzed the pattern of haplotype distribution and nucleotide diversity within and among chromosomally differentiated natural populations. Our results suggest that the restriction in gene flow detected at the molecular level may explain the chromosome differentiation detected previously and the maintenance of chromosome polymorphism in some areas of S. dalmani geographic distribution.

  6. Assessment and reduction of comet assay variation in relation to DNA damage: studies from the European Comet Assay Validation Group.

    OpenAIRE

    Moller, Peter; Moller, Lennart; Godschalk, Roger W. L.; Jones, George D. D.

    2010-01-01

    The alkaline single cell gel electrophoresis (comet) assay has become a widely used method for the detection of DNA damage and repair in cells and tissues. Still, it has been difficult to compare results from different investigators because of differences in assay conditions and because the data are reported in different units. The European Comet Assay Validation Group (ECVAG) was established for the purpose of validation of the comet assay with respect to measures of DNA damage formation and...

  7. Investigating the Potential Role of Genetic and Epigenetic Variation of DNA Methyltransferase Genes in Hyperplastic Polyposis Syndrome

    OpenAIRE

    Drini, Musa; Nicholas C. Wong; Hamish S Scott; Craig, Jeffrey M; Dobrovic, Alexander; Chelsee A Hewitt; Dow, Christofer; Young, Joanne P; Jenkins, Mark A; Saffery, Richard; Macrae, Finlay A.

    2011-01-01

    Background Hyperplastic Polyposis Syndrome (HPS) is a condition associated with multiple serrated polyps, and an increased risk of colorectal cancer (CRC). At least half of CRCs arising in HPS show a CpG island methylator phenotype (CIMP), potentially linked to aberrant DNA methyltransferase (DNMT) activity. CIMP is associated with methylation of tumor suppressor genes including regulators of DNA mismatch repair (such as MLH1, MGMT), and negative regulators of Wnt signaling (such as WIF1). In...

  8. Quantifying male-biased dispersal among social groups in the collared peccary (Pecari tajacu) using analyses based on mtDNA variation.

    Science.gov (United States)

    Cooper, J D; Vitalis, R; Waser, P M; Gopurenko, D; Hellgren, E C; Gabor, T M; DeWoody, J A

    2010-01-01

    Recent advances in the statistical analysis of microsatellite data permit calculation of sex-specific dispersal rates through sex- and age-specific comparisons of genetic variation. This approach, developed for the analysis of data derived from co-dominant autosomal markers, should be applicable to a sex-specific marker such as mitochondrial DNA. To test this premise, we amplified a 449 bp control region DNA sequence from the mitochondrial genome of the collared peccary (Pecari tajacu), and estimated intra-class correlations among herds sampled from three Texas populations. Analyses on data partitioned by breeding group showed a clear signal of male-biased dispersal; sex-specific fixation indices associated with genetic variation among social groups within populations yielded values for females (F(GP)=0.91), which were significantly larger than values for males (F(GP)=0.24; P=0.0015). The same general pattern emerged when the analyses were conducted on age classes (albeit nonsignificantly), as well as categories of individuals that were predicted a posteriori to be dispersers (adult males) and philopatric (adult females and all immatures). By extending a previously published methodology based on biparentally inherited markers to matrilineally inherited haploid data, we calculated sex-specific rates of contemporary dispersal among social groups within populations (m(male symbol)=0.37). These results support the idea that mitochondrial DNA haplotype frequency data can be used to estimate sex-specific instantaneous dispersal rates in a social species.

  9. Evaluation of Genetic Variations in Maize Seedlings Exposed to Electric Field Based on Protein and DNA Markers

    Directory of Open Access Journals (Sweden)

    Asma A. AL-Huqail

    2015-01-01

    Full Text Available The current study analyzed proteins and nuclear DNA of electric fields (ELF exposed and nonexposed maize seedlings for different exposure periods using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, isozymes, random amplified polymorphic DNA (RAPD, and comet assay, respectively. SDS-PAGE analysis revealed total of 46 polypeptides bands with different molecular weights ranging from 186.20 to 36.00 KDa. It generated distinctive polymorphism value of 84.62%. Leucine-aminopeptidase, peroxidase, and catalase isozymes showed the highest values of polymorphism (100% based on zymograms number, relative front (Rf, and optical intensity while esterase isozyme generated polymorphism value of 83.33%. Amino acids were analyzed using high-performance liquid chromatography, which revealed the presence of 17 amino acids of variable contents ranging from 22.65% to 28.09%. RAPD revealed that 78 amplified DNA products had highly polymorphism value (95.08% based on band numbers, with variable sizes ranging from 120 to 992 base pairs and band intensity. Comet assay recorded the highest extent of nuclear DNA damage as percentage of tailed DNA (2.38% and tail moment unit (5.36 at ELF exposure of maize nuclei for 5 days. The current study concluded that the longer ELF exposing periods had genotoxic stress on macromolecules of maize cells and biomarkers used should be augmented for reliable estimates of genotoxicity after exposure of economic plants to ELF stressors.

  10. An ECVAG inter-laboratory validation study of the comet assay: inter-laboratory and intra-laboratory variations of DNA strand breaks and FPG-sensitive sites in human mononuclear cells.

    Science.gov (United States)

    Ersson, Clara; Møller, Peter; Forchhammer, Lykke; Loft, Steffen; Azqueta, Amaya; Godschalk, Roger W L; van Schooten, Frederik-Jan; Jones, George D D; Higgins, Jennifer A; Cooke, Marcus S; Mistry, Vilas; Karbaschi, Mahsa; Phillips, David H; Sozeri, Osman; Routledge, Michael N; Nelson-Smith, Kirsty; Riso, Patrizia; Porrini, Marisa; Matullo, Giuseppe; Allione, Alessandra; Stepnik, Maciej; Ferlińska, Magdalena; Teixeira, João Paulo; Costa, Solange; Corcuera, Laura-Ana; López de Cerain, Adela; Laffon, Blanca; Valdiglesias, Vanessa; Collins, Andrew R; Möller, Lennart

    2013-05-01

    The alkaline comet assay is an established, sensitive method extensively used in biomonitoring studies. This method can be modified to measure a range of different types of DNA damage. However, considerable differences in the protocols used by different research groups affect the inter-laboratory comparisons of results. The aim of this study was to assess the inter-laboratory, intra-laboratory, sample and residual (unexplained) variations in DNA strand breaks and formamidopyrimidine DNA glycosylase (FPG)-sensitive sites measured by the comet assay by using a balanced Latin square design. Fourteen participating laboratories used their own comet assay protocols to measure the level of DNA strand breaks and FPG-sensitive sites in coded samples containing peripheral blood mononuclear cells (PBMC) and the level of DNA strand breaks in coded calibration curve samples (cells exposed to different doses of ionising radiation) on three different days of analysis. Eleven laboratories found dose-response relationships in the coded calibration curve samples on two or three days of analysis, whereas three laboratories had technical problems in their assay. In the coded calibration curve samples, the dose of ionising radiation, inter-laboratory variation, intra-laboratory variation and residual variation contributed to 60.9, 19.4, 0.1 and 19.5%, respectively, of the total variation. In the coded PBMC samples, the inter-laboratory variation explained the largest fraction of the overall variation of DNA strand breaks (79.2%) and the residual variation (19.9%) was much larger than the intra-laboratory (0.3%) and inter-subject (0.5%) variation. The same partitioning of the overall variation of FPG-sensitive sites in the PBMC samples indicated that the inter-laboratory variation was the strongest contributor (56.7%), whereas the residual (42.9%), intra-laboratory (0.2%) and inter-subject (0.3%) variations again contributed less to the overall variation. The results suggest that the

  11. Inter-individual variation in DNA double-strand break repair in human fibroblasts before and after exposure to low doses of ionizing radiation

    International Nuclear Information System (INIS)

    DNA double-strand breaks (DSB) are generally considered the most critical lesion induced by ionizing radiation (IR) and may initiate carcinogenesis and other disease. Using an immunofluorescence assay to simultaneously detect nuclear foci of the phosphorylated forms of histone H2AX and ATM kinase at sites of DSBs, we examined the response of 25 apparently normal and 10 DNA repair-deficient (ATM, ATR, NBN, LIG1, LIG4, and FANCG) primary fibroblast strains irradiated with low doses of 137Cs γ-rays. Quiescent G0/G1-phase cultures were exposed to 5, 10, and 25 cGy and allowed to repair for 24 h. The maximum level of IR-induced foci (0.15 foci per cGy, at 10 or 30 min) in the normal strains showed much less inter-individual variation (CV ∼ 0.2) than the level of spontaneous foci, which ranged from 0.2-2.6 foci/cell (CV ∼ 0.6; mean ± SD of 1.00 ± 0.57). Significantly slower focus formation post-irradiation was observed in seven normal strains, similar to most mutant strains examined. There was variation in repair efficiency measured by the fraction of IR-induced foci remaining 24 h post-irradiation, curiously with the strains having slower focus formation showing more efficient repair after 25 cGy. Interestingly, the ranges of spontaneous and residual induced foci levels at 24 h in the normal strains were as least as large as those observed for the repair-defective mutant strains. The inter-individual variation in DSB foci parameters observed in cells exposed to low doses of ionizing radiation in this small survey of apparently normal people suggests that hypomorphic genetic variants in genomic maintenance and/or DNA damage signaling and repair genes may contribute to differential susceptibility to cancer induced by environmental mutagens.

  12. Genetic variation of Kaempferia (Zingiberaceae) in Thailand based on chloroplast DNA (psbA-trnH and petA-psbJ) sequences.

    Science.gov (United States)

    Techaprasan, J; Klinbunga, S; Ngamriabsakul, C; Jenjittikul, T

    2010-01-01

    Genetic variation and species authentication of 71 Kaempferia accessions (representing 15 recognized, six new, and four unidentified species) found indigenously in Thailand were examined by determining chloroplast psbA-trnH and partial petA-psbJ spacer sequences. Ten closely related species (Boesenbergia rotunda, Gagnepainia godefroyi, G. thoreliana, Globba substrigosa, Smithatris myanmarensis, S. supraneanae, Scaphochlamys biloba, S. minutiflora, S. rubescens, and Stahlianthus sp) were also included. After sequence alignments, 1010 and 865 bp in length were obtained for the respective chloroplast DNA sequences. Intraspecific sequence variation was not observed in Kaempferia candida, K. angustifolia, K. laotica, K. galanga, K. pardi sp nov., K. bambusetorum sp nov., K. albomaculata sp nov., K. minuta sp nov., Kaempferia sp nov. 1, and G. thoreliana, for which more than one specimen was available. In contrast, intraspecific sequence polymorphisms were observed in various populations of K. fallax, K. filifolia, K. elegans, K. pulchra, K. rotunda, K. marginata, K. parviflora, K. larsenii, K. roscoeana, K. siamensis, and G. godefroyi. A strict consensus tree based on combined psbA-trnH and partial petA-psbJ sequences revealed four major groups of Kaempferia species. We suggest that the genus Kaempferia is a polyphyletic group, as K. candida was distantly related and did not group with other Kaempferia species. Polymorphic sites and indels of psbA-trnH and petA-psbJ can be used as DNA barcodes for species diagnosis of most Kaempferia and outgroup species. Nuclear DNA polymorphism should be examined to determine if there has been interspecific hybridization and chloroplast DNA introgression in these taxa. PMID:20927714

  13. Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey

    Directory of Open Access Journals (Sweden)

    Wang Yanjie

    2010-09-01

    Full Text Available Abstract Background Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation, measuring changes in chromosome number and DNA methylation across multiple generations. Results F1 plants from intergeneric hybridization between Raphanus sativus L. (2n = 18, RR and Brassica alboglabra Bailey (2n = 18, CC were obtained by hand crosses and subsequent embryo rescue. Random amplification of polymorphic DNA (RAPD markers were used to identify the F1 hybrid plants. The RAPD data indicated that the hybrids produced specific bands similar to those of parents and new bands that were not present in either parent. Chromosome number variation of somatic cells from allotetraploids in the F4 to F10 generations showed that intensive genetic changes occurred in the early generations of distant hybridization, leading to the formation of mixopolyploids with different chromosome numbers. DNA methylation variation was revealed using MSAP (methylation-sensitive amplification polymorphism, which showed that cytosine methylation patterns changed markedly in the process of hybridization and amphidiploid formation. Differences in cytosine methylation levels demonstrated an epigenetic instability of the allopolyploid of Raphanobrassica between the genetically stable and unstable generations. Conclusions Our results showed that chromosome instability occurred in the early generations of allopolyploidy and then the plants were reverted to largely euploidy in later generations. During this process, DNA methylation changed markedly. These results suggest that

  14. Sequence variations in DNA repair gene XPC is associated with lung cancer risk in a Chinese population: a case-control study

    International Nuclear Information System (INIS)

    The nucleotide excision repair (NER) protein, xeroderma pigmentosum C (XPC), participates in recognizing DNA lesions and initiating DNA repair in response to DNA damage. Because mutations in XPC cause a high risk of cancer in XP patients, we hypothesized that inherited sequence variations in XPC may alter DNA repair and thus susceptibility to cancer. In this hospital-based case-control study, we investigated five XPC tagging, common single nucleotide polymorphisms (tagging SNPs) in 1,010 patients with newly diagnosed lung cancer and 1,011 matched cancer free controls in a Chinese population. In individual tagging SNP analysis, we found that rs3731055AG+AA variant genotypes were associated with a significantly decreased risk of lung adenocarcinoma [adjusted odds ratio (OR), 0.71; 95% confidence interval (CI), 0.56–0.90] but an increased risk of small cell carcinomas [adjusted OR, 1.79; 95% CI, 1.05–3.07]. Furthermore, we found that haplotype ACCCA was associated with a decreased risk of lung adenocarcinoma [OR, 0.78; 95% CI, 0.62–0.97] but an increased risk of small cell carcinomas [OR, 1.68; 95% CI, 1.04–2.71], which reflected the presence of rs3731055A allele in this haplotype. Further stratified analysis revealed that the protective effect of rs3731055AG+AA on risk of lung adenocarcinoma was more evident among young subjects (age ≤ 60) and never smokers. These results suggest that inherited sequence variations in XPC may modulate risk of lung cancer, especially lung adenocarcinoma, in Chinese populations. However, these findings need to be verified in larger confirmatory studies with more comprehensively selected tagging SNPs

  15. [Genetic structure of the Siberian Sucker (Catostomus catostomus rostratus) according to data on sequence variation of the mtDNA cytochrome B gene].

    Science.gov (United States)

    Bachevskaia, L T; Pereverzeva, V V; Ivanova, G D; Agapova, G A; Primak, A A

    2014-01-01

    Data regarding the structure and variation of the nucleotide sequence of the cytochrome b gene of mitochondrial DNA of the Siberian Sucker from the Kolyma River were obtained. Analysis of the median network revealed that evolutionary lines diverged from a common ancestor. Penetration of the sucker into Asia from Northern America took place between the Early and Middle Pleistocene. Prolonged reproductive isolation of the Siberian and Northern American suckers led to interspecies divergence with the appearance of amino acid substitutions, which, apparently, fixed due to positive selection. The Siberian Sucker appeared to have three modifications of the Cytb protein. PMID:25735175

  16. Lack of association between mitochondrial DNA G15257A and G15812A variations and multiple sclerosis

    DEFF Research Database (Denmark)

    Andalib, Sasan; Talebi, Mahnaz; Sakhinia, Ebrahim;

    2015-01-01

    BACKGROUND: Multiple sclerosis (MS) is a debilitating disease of the central nervous system for which no definitive therapy has yet been developed. The etiology remains uncertain, but there is evidence of genetic susceptibility to the disease, including contributions from mitochondrial DNA (mt...

  17. The analysis of variation of mtDNA hypervariable region 1 suggests that Eastern and Western Pygmies diverged before the Bantu expansion.

    Science.gov (United States)

    Destro-Bisol, Giovanni; Coia, Valentina; Boschi, Ilaria; Verginelli, Fabio; Cagliá, Alessandra; Pascali, Vincenzo; Spedini, Gabriella; Calafell, Francesc

    2004-02-01

    The Eastern Pygmies from Zaire and Western Pygmies from Cameroon, Congo, and the Central African Republic represent the two principal groups of African Pygmies. In the "recent divergence" hypothesis in which Western Pygmies are thought to be the result of hybridization between the ancestors of Eastern Pygmies and Bantu farmers who penetrated the equatorial belt and came into contact with Pygmies around 2-3 kiloyears ago. On the basis of recent archaeological research in the tropical rain forest, we propose a "pre-Bantu divergence" hypothesis, which posits the separation between the ancestors of Eastern and Western Pygmies earlier than 18 kiloyears ago. In order to test the two hypotheses, we analyzed the variation of the hypervariable region 1 of the mitochondrial DNA in the Mbenzele, Western Pygmies of the Central African Republic, and compared our results with those of previous mtDNA and Y chromosome studies. Distribution, sequence variation, and age of haplogroups along with genetic distances among populations, estimates of divergence times, and simulations based on the coalescent approach were found to be congruent with the pre-Bantu divergence but failed to support the recent divergence hypothesis.

  18. Variations in genomic DNA methylation during the long-term in vitro proliferation of oil palm embryogenic suspension cultures

    OpenAIRE

    Rival, A.; Ilbert, P.; Labeyrie, A.; E. Torres; Doulbeau, Sylvie; Personne, A.; Dussert, Stéphane; Beulé, T.; Durand-Gasselin, T.; Tregear, James; Jaligot, E.

    2013-01-01

    The long-term proliferation of embryogenic cell suspensions of oil palm is associated with changes in both genomic methylation rates and embryogenic capacities. In the aim of exploring the relationship between epigenetic stability and the long-term in vitro proliferation of plant tissues, we have studied changes in genomic DNA methylation levels in embryogenic suspensions of oil palm (Elaeis guineensis Jacq.). Five embryogenic callus lines were obtained from selected hybrid seeds and then pro...

  19. Phylogenetic Analysis of a Privately-owned Korean Native Chicken Population Using mtDNA D-loop Variations

    OpenAIRE

    Hoque, M. R.; Choi, N. R.; Sultana, H.; Kang, B. S.; Heo, K. N.; Hong, S K; Jo, C.; Lee, J.H.

    2013-01-01

    The use of Korean native chicken is increasing, and the discovery of new genetic resources is very important from both economic and genetic conservation points of view. In this study, mtDNA D-loop sequences from 272 privately-owned Korean native chickens from a Hyunin farm were investigated. Seventeen nucleotide substitutions were identified from the sequence analysis and they were classified as 6 haplotypes. Previously investigated haplotypes in five Korean native chicken populations have be...

  20. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  1. Genetic variations in DNA repair genes, radiosensitivity to cancer and susceptibility to acute tissue reactions in radiotherapy-treated cancer patients

    Energy Technology Data Exchange (ETDEWEB)

    Chistiakov, Dimitry A. (Dept. of Pathology, Univ. of Pittsburgh, Pittsburgh (US)); Voronova, Natalia V. (Dept. of Molecular Diagnostics, National Research Center GosNIIgenetika, Moscow (RU)); Chistiakov, Pavel A. (Dept. of Radiology, Cancer Research Center, Moscow (RU))

    2008-06-15

    Ionizing radiation is a well established carcinogen for human cells. At low doses, radiation exposure mainly results in generation of double strand breaks (DSBs). Radiation-related DSBs could be directly linked to the formation of chromosomal rearrangements as has been proven for radiation-induced thyroid tumors. Repair of DSBs presumably involves two main pathways, non-homologous end joining (NHEJ) and homologous recombination (HR). A number of known inherited syndromes, such as ataxia telangiectasia, ataxia-telangiectasia like-disorder, radiosensitive severe combined immunodeficiency, Nijmegen breakage syndrome, and LIG4 deficiency are associated with increased radiosensitivity and/or cancer risk. Many of them are caused by mutations in DNA repair genes. Recent studies also suggest that variations in the DNA repair capacity in the general population may influence cancer susceptibility. In this paper, we summarize the current status of DNA repair proteins as potential targets for radiation-induced cancer risk. We will focus on genetic alterations in genes involved in HR- and NHEJ-mediated repair of DSBs, which could influence predisposition to radiation-related cancer and thereby explain interindividual differences in radiosensitivity or radioresistance in a general population

  2. A family of differentially amplified repetitive DNA sequences in the genus Beta reveals genetic variation in Beta vulgaris subspecies and cultivars.

    Science.gov (United States)

    Kubis, S; Heslop-Harrison, J S; Schmidt, T

    1997-03-01

    Members of a highly abundant restriction satellite family have been isolated from the wild beet species Beta nana. The satellite DNA sequence is characterized by a conserved RsaI restriction site and is present in three of four sections of the genus Beta, namely Nanae, Corollinae, and Beta. It was not detected in species of the evolutionary old section Procumbentes, suggesting its amplification after separation of this section. Sequences of eight monomers were aligned revealing a size variation from 209 to 233 bp and an AT content ranging from 56.5% to 60.5%. The similarity between monomers in B. nana varied from 77.7% to 92.2%. Diverged subfamilies were identified by sequence analysis and Southern hybridization. A comparative study of this repetitive DNA element by fluorescent in situ hybridization and Southern analyses in three representative species was performed showing a variable genomic organization and heterogeneous localizations along metaphase chromosomes both within and between species. In B. nana the copy number of this satellite, with some 30,000 per haploid genome, is more than tenfold higher than in Beta lomatogona and up to 200 times higher than in Beta vulgaris, indicating different levels of sequence amplification during evolution in the genus Beta. In sugar beet (B. vulgaris), the large-scale organization of this tandem repeat was examined by pulsed-field gel electrophoresis. Southern hybridization to genomic DNA digested with DraI demonstrated that satellite arrays are located in AT-rich regions and the tandem repeat is a useful probe for the detection of genetic variation in closely related B. vulgaris cultivars, accessions, and subspecies.

  3. Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

    NARCIS (Netherlands)

    Kerstens, H.H.D.; Crooijmans, R.P.M.A.; Dibbits, B.W.; Vereijken, A.; Okimoto, R.; Groenen, M.A.M.

    2011-01-01

    Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and

  4. The historical demography and genetic variation of the endangered Cycas multipinnata (Cycadaceae) in the red river region, examined by chloroplast DNA sequences and microsatellite markers.

    Science.gov (United States)

    Gong, Yi-Qing; Zhan, Qing-Qing; Nguyen, Khang Sinh; Nguyen, Hiep Tien; Wang, Yue-Hua; Gong, Xun

    2015-01-01

    Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species. PMID:25689828

  5. Evaluation of IGFBP-7 DNA methylation changes and serum protein variation in Swedish subjects with and without type 2 diabetes

    OpenAIRE

    Gu, Harvest F; Gu, Tianwei; Hilding, Agneta; Zhu, Yiming; Kärvestedt, Lars; Östenson, Claes-Göran; Lai, Maode; Kutsukake, Masahiko; Frystyk, Jan; Tamura, Kazuhiro; Brismar, Kerstin

    2013-01-01

    Background Insulin-like growth factor-binding protein 7 (IGFBP-7) is able to interact with insulin-like growth factor 1 (IGF-1) as well as insulin. Previous studies have suggested that serum IGFBP-7 levels may be associated with insulin resistance in type 2 diabetes (T2D). This study aimed to evaluate IGFBP-7 serum protein and IGFBP7 DNA methylation levels in the subjects with and without T2D. Results A total of 340 Swedish subjects including 100 newly diagnosed T2D patients (50 women/50 men)...

  6. Variation patterns of mitochondrial DNA of Abies alba Mill. in suture zones of postglacial migration in Europe

    Directory of Open Access Journals (Sweden)

    Duśan Gomory

    2011-04-01

    Full Text Available Thirty silver fir populations originating from the putative suture zones of the postglacial recolonization (Slovenia, Bosnia and Hercegovina, Ukraine were studied using a mitochondrial nad5-4 gene marker. The geographical distribution of mtDNA haplotypes in the Ukrainian Carpathians and their northern foothills indicates a very recent meeting of migration streams arriving from the Romanian Carpathians and Central Europe. In the western part of the Balkan Peninsula, two counterparallel migration streams are the most plausible explanation of the pattern observed. The haplotype typical for the Balkan Peninsula predominates along the Adrian coast, whereas the CentralEuropean haplotype is more represented in the inland.

  7. Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae

    Directory of Open Access Journals (Sweden)

    Smith Samson W

    2011-01-01

    Full Text Available Abstract Background Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the mitochondrial electron transport chain and integral to cellular energy metabolism. Results We quantified significant variation among C. briggsae isolates for all phenotypes measured, only some of which was statistically associated with isolate-specific ND5 deletion frequency. We found that fecundity-related traits and pharyngeal pumping rate were strongly inversely related to ND5 deletion level and that C. briggsae isolates with high ND5 deletion levels experienced a tradeoff between early fecundity and lifespan. Conversely, oxidative stress resistance was only weakly associated with ND5 deletion level while ATP content was unrelated to deletion level. Finally, mean levels of reactive oxygen species measured in vivo showed a significant non-linear relationship with ND5 deletion level, a pattern that may be driven by among-isolate variation in antioxidant or other compensatory mechanisms. Conclusions Our findings suggest that the ND5 deletion may adversely affect fitness and mitochondrial functioning while promoting aging in natural populations, and help to further establish this species as a useful model for explicit tests of hypotheses in aging biology and mitochondrial genetics.

  8. DNA variation and polymorphism in Tunisian plum species (Prunus spp): contribution of flow cytometry and molecular markers.

    Science.gov (United States)

    Ben Tamarzizt, H; Walker, D; Ben Mustapha, S; Abdallah, D; Baraket, G; Salhi Hannachi, A; Zehdi Azzouzi, S

    2015-01-01

    Plums (Prunus spp) are among the most important stone fruit crops in the world. European (Prunus domestica) and Japanese (Prunus salicina) plums are characterized by different levels of ploidy. Because genetic variability is the prerequisite for any plant-breeding program, we aimed to establish the taxonomic status of Tunisian plums and study their genetic variability. The nuclear DNA content of 45 wild and cultivated Tunisian plums was determined by flow cytometry. Two arbitrary primers (AD10, AD17) were used to elaborate SCAR markers useful to identify plum species. Three wild trees, Zenou 1, Zenou 6, and Zenou 3, which had 2C nuclear DNA contents of 1.99, 2.05, and 2.13 pg, were shown to be hexaploid (2n = 6x = 48), whereas the others were diploid (2n = 2x = 16). These results suggest that the three hexaploid wild plums belong to Prunus insititia, and the others belong to Prunus salicina. No SCAR markers were revealed using the AD10 and AD17 RAPD primers in relation to the ploidy of plums. We note also that AD17 primer appears to be the most informative concerning the genetic diversity. Morphological and pomological traits revealed similarity between introduced and Tunisian plum cultivars. Despite the significant morphological differences found, all the cultivars studied belong to P. salicina. The information obtained in this analysis provided on local plum genetic resources will be helpful to establish a core collection, to evaluate genetic diversity, and to initiate an improvement and selection program.

  9. Genetic variation between two Tibetan macaque (Macaca thibetana) populations in the eastern China based on mitochondrial DNA control region sequences.

    Science.gov (United States)

    Yao, Yongfang; Zhong, Lijing; Liu, Bofeng; Li, Jiayi; Ni, Qingyong; Xu, Huailiang

    2013-06-01

    Tibetan macaque (Macaca thibetana) is a threatened primate species endemic to China. Population genetic and phylogenetic analyses were conducted in 66 Tibetan individuals from Sichuan (SC), Huangshan (HS), and Fujian (FJ) based on a 477-bp fragment of mitochondrial DNA control region. Four new haplotypes were defined, and a relatively high level of genetic diversity was first observed in FJ populations (Hd = 0.7661). Notably, a continuous approximately 10 bp-fragment deletion was observed near the 5' end of the mtDNA control region of both HS and FJ populations when compared with that of SC population, and a sharing haplotype was found between the two populations, revealing a closer genetic relationship. However, significant genetic differentiation (FST = 0.8700) and more poor gene exchange (Nm < 1) had occurred among three populations. This study mainly provide a further insight into the genetic relationship between HS and FJ Tibetan macaque populations, but it may be necessary to carry out further study with extra samples from other locations in the geographic coverage of the two subspecies (M. thibetana pullus and M. thibetana huangshanensis).

  10. Mitochondrial DNA variation in the East China Sea and Yellow Sea populations of swimming crab Ovalipes punctatus.

    Science.gov (United States)

    Zheng, Wei; Han, Zhiqiang; Chen, Guobao; Yu, Cungen; Gao, Tianxiang

    2015-08-01

    Swimming crab Ovalipes punctatus is a commercially important species in the East China Sea and Yellow Sea, but there is limited knowledge of its genetic population structure. The population genetic structure of O. punctatus in East China Sea and Yellow Sea was examined with a 658-bp segment of the mtDNA COI gene. A total of 60 individuals were collected from five locations and 48 haplotypes were obtained. Mean haplotype diversity and nucleotide diversity for the five populations were 0.9876 ± 0.0068 and 0.0074 ± 0.0041, respectively. Analysis of molecular variance (AMOVA) detected no significant differences at all hierarchical levels, and all FST values were non-significant, indicating that no significant population genetic structure exists in the East China Sea and Yellow Sea. These results supported the null hypothesis that O. punctatus within the East China Sea and Yellow Sea constitutes a panmictic mtDNA gene pool. Neutrality tests and mismatch distribution supported population expansion in this species, indicating that climate change could play an important role in affecting the demographic history of marine species. Strong dispersal capacity of larvae and adults, and ocean currents in the studied area could be the reasons for genetic homogeneity in this species in the East China Sea and Yellow Sea. Another explanation for the lack of phylogeographic structure in O. punctatus might reflect a recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium.

  11. Host-Associated Population Variations of Bemisia tabaci (Genn. (Hemiptera:Sternorrhyncha: Aleyrodidae Characterized with Random DNA Markers

    Directory of Open Access Journals (Sweden)

    A. Helmi

    2011-01-01

    Full Text Available Whitefly, Bemisia tabaci (Genn. is an important sucking plant sap pest of field, horticultural and ornamental plants causing feeding injuries besides spreading plant diseases by acting as a vector of Gemini-viruses. The polyphagous nature of the pest makes it as a highly complex species. The influence of six host plants belonging to three different plant families utilized by the species on the population differences at molecular level was attempted using Random Amplified Polymorphic DNA (RAPD markers. Fifteen RAPD primers were screened seven of them were produced 218 DNA fragments, 209 of them were polymorphic while the other nine bands could be considered as common for B. tabaci. Total number of bands obtained from each primer ranged from 23-44 with an average of 36.33 bands per primer. RAPD-PCR analysis led to identification of 42 polymorphic markers holding specificity for these hosts' populations. Phylogenetic relationships among the studied populations using this technique clearly separated these six populations into two main clusters with similarity matrix percentage of 88 and 64%. These results indicated that B. tabaci may have different genotypes on adaptations to certain host plant species in Egypt.

  12. In vitro genotypic variation of Campylobacter coli documented by pulsed-field gel electrophoretic DNA profiling, implications for epidemiological studies

    DEFF Research Database (Denmark)

    On, Stephen L.W.

    1998-01-01

    Six isolates of Campylobacter coli from different pig herds were subcultured up to 50 times over a 6-month period and DNA samples suitable for pulsed-field gel electrophoretic (PFGE) profiling prepared at regular (1, 20, 40 and 50 passages) intervals. In 5/6 strains, changes in the banding patterns...... of Sma1, Sal1 and/or BamH1 digests were observed. In one such strain the differences were considered artifactual. However, significant alterations in PFGE profiles between subcultures of four strains were seen, irrespective of the restriction enzyme used. Spontaneous intramolecular genomic rearrangements...... were considered the most likely mechanism for the changes observed. A numerical analysis based upon the combined distribution of Sma1- and Sal1-derived fragments clustered most strain subcultures together, with the exception of those from one isolate which were divided into two clusters. The effect...

  13. Types of variation in DNA-A among isolates of East African cassava mosaic virus from Kenya, Malawi and Tanzania.

    Science.gov (United States)

    Zhou, X; Robinson, D J; Harrison, B D

    1998-11-01

    Complete nucleotide sequences of the DNA-A-like molecules of three East African cassava mosaic virus (EACMV) isolates from Kenya (-K, 2801 nt) and Malawi (-MH and -MK, both 2804 nt) were determined. These sequences were compared with that published for a Tanzanian isolate (-T, 2801 nt) and the partial sequence of a third Malawian isolate. Intergenic region sequences of all isolates, and deduced amino acid sequences of their AC1 (Rep) proteins, each formed a tightly related cluster that was distinct from the comparable components of other begomoviruses. Other complementary-sense genes (AC2, AC3, AC4) differed between EACMV isolates in a way consistent with the accumulation of point mutations. In contrast, virus-sense genes (CP, AV2) of isolates -MH and -MK differed (substantially for AV2) from those of other EACMV isolates but somewhat resembled those of tomato yellow leaf curl virus-Israel, suggesting they had been acquired by recombination with an unidentified begomovirus.

  14. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa.

    Directory of Open Access Journals (Sweden)

    Chiara Barbieri

    Full Text Available Bantu speech communities expanded over large parts of sub-Saharan Africa within the last 4000-5000 years, reaching different parts of southern Africa 1200-2000 years ago. The Bantu languages subdivide in several major branches, with languages belonging to the Eastern and Western Bantu branches spreading over large parts of Central, Eastern, and Southern Africa. There is still debate whether this linguistic divide is correlated with a genetic distinction between Eastern and Western Bantu speakers. During their expansion, Bantu speakers would have come into contact with diverse local populations, such as the Khoisan hunter-gatherers and pastoralists of southern Africa, with whom they may have intermarried. In this study, we analyze complete mtDNA genome sequences from over 900 Bantu-speaking individuals from Angola, Zambia, Namibia, and Botswana to investigate the demographic processes at play during the last stages of the Bantu expansion. Our results show that most of these Bantu-speaking populations are genetically very homogenous, with no genetic division between speakers of Eastern and Western Bantu languages. Most of the mtDNA diversity in our dataset is due to different degrees of admixture with autochthonous populations. Only the pastoralist Himba and Herero stand out due to high frequencies of particular L3f and L3d lineages; the latter are also found in the neighboring Damara, who speak a Khoisan language and were foragers and small-stock herders. In contrast, the close cultural and linguistic relatives of the Herero and Himba, the Kuvale, are genetically similar to other Bantu-speakers. Nevertheless, as demonstrated by resampling tests, the genetic divergence of Herero, Himba, and Kuvale is compatible with a common shared ancestry with high levels of drift, while the similarity of the Herero, Himba, and Damara probably reflects admixture, as also suggested by linguistic analyses.

  15. Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling.

    Science.gov (United States)

    Wasowicz, Pawel; Pauwels, Maxime; Pasierbinski, Andrzej; Przedpelska-Wasowicz, Ewa M; Babst-Kostecka, Alicja A; Saumitou-Laprade, Pierre; Rostanski, Adam

    2016-01-01

    The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest. PMID:26835186

  16. Phylogeography of Arabidopsis halleri (Brassicaceae) in mountain regions of Central Europe inferred from cpDNA variation and ecological niche modelling

    Science.gov (United States)

    Pauwels, Maxime; Pasierbinski, Andrzej; Przedpelska-Wasowicz, Ewa M.; Babst-Kostecka, Alicja A.; Saumitou-Laprade, Pierre; Rostanski, Adam

    2016-01-01

    The present study aimed to investigate phylogeographical patterns present within A. halleri in Central Europe. 1,281 accessions sampled from 52 populations within the investigated area were used in the study of genetic variation based on chloroplast DNA. Over 500 high-quality species occurrence records were used in ecological niche modelling experiments. We evidenced the presence of a clear phylogeographic structure within A. halleri in Central Europe. Our results showed that two genetically different groups of populations are present in western and eastern part of the Carpathians. The hypothesis of the existence of a glacial refugium in the Western Carpathians adn the Bohemian Forest cannot be rejected from our data. It seems, however, that the evidence collected during the present study is not conclusive. The area of Sudetes was colonised after LGM probably by migrants from the Bohemian Forest. PMID:26835186

  17. Intragenomic sequence variation at the ITS1 - ITS2 region and at the 18S and 28S nuclear ribosomal DNA genes of the New Zealand mud snail, Potamopyrgus antipodarum (Hydrobiidae: mollusca)

    Science.gov (United States)

    Hoy, Marshal S.; Rodriguez, Rusty J.

    2013-01-01

    Molecular genetic analysis was conducted on two populations of the invasive non-native New Zealand mud snail (Potamopyrgus antipodarum), one from a freshwater ecosystem in Devil's Lake (Oregon, USA) and the other from an ecosystem of higher salinity in the Columbia River estuary (Hammond Harbor, Oregon, USA). To elucidate potential genetic differences between the two populations, three segments of nuclear ribosomal DNA (rDNA), the ITS1-ITS2 regions and the 18S and 28S rDNA genes were cloned and sequenced. Variant sequences within each individual were found in all three rDNA segments. Folding models were utilized for secondary structure analysis and results indicated that there were many sequences which contained structure-altering polymorphisms, which suggests they could be nonfunctional pseudogenes. In addition, analysis of molecular variance (AMOVA) was used for hierarchical analysis of genetic variance to estimate variation within and among populations and within individuals. AMOVA revealed significant variation in the ITS region between the populations and among clones within individuals, while in the 5.8S rDNA significant variation was revealed among individuals within the two populations. High levels of intragenomic variation were found in the ITS regions, which are known to be highly variable in many organisms. More interestingly, intragenomic variation was also found in the 18S and 28S rDNA, which has rarely been observed in animals and is so far unreported in Mollusca. We postulate that in these P. antipodarum populations the effects of concerted evolution are diminished due to the fact that not all of the rDNA genes in their polyploid genome should be essential for sustaining cellular function. This could lead to a lessening of selection pressures, allowing mutations to accumulate in some copies, changing them into variant sequences.                   

  18. Phylogeography of Spiraea alpina (Rosaceae) in the Qinghai-Tibetan Plateau inferred from chloroplast DNA sequence variations

    Institute of Scientific and Technical Information of China (English)

    Fa-Qi ZHANG; Qing-Bo GAO; De-Jun ZHANG; Yi-Zhong DUAN; Yin-Hu LI; Peng-Cheng FU; Rui XING; Khan GULZAR; Shi-Long CHEN

    2012-01-01

    The aim of the present study was to investigate the phylogeographic patterns of Spiraea alpina (Rosaceae) and clarify its response to past climatic changes in the climate-sensitive Qinghai-Tibetan Plateau (QTP).We sequenced a chloroplast DNA fragment (trnL-trnF) from 528 individuals representing 43 populations.We identified 10 haplotypes,which were tentatively divided into three groups.These haplotypes or groups were distributed in the different regions of the QTP.Only half the populations were fixed by a single haplotype,whereas the others contained two or more.In the central and eastern regions,adjacent populations at the local scale shared the same haplotype.Our phylogeographic analyses suggest that this alpine shrub survived in multiple refugia during the Last Glacial Maximum and that earlier glaciations may have trigged deep intraspecific divergences.Post-glacial expansions occurred only within populations or across multiple populations within a local range.The findings of the present study together with previous phylogeographic reports suggest that evolutionary histories of plants in the QTP are complex and variable depending on the species investigated.

  19. Copy number variations of genes involved in stress responses reflect the redox state and DNA damage in brewing yeasts.

    Science.gov (United States)

    Adamczyk, Jagoda; Deregowska, Anna; Skoneczny, Marek; Skoneczna, Adrianna; Natkanska, Urszula; Kwiatkowska, Aleksandra; Rawska, Ewa; Potocki, Leszek; Kuna, Ewelina; Panek, Anita; Lewinska, Anna; Wnuk, Maciej

    2016-09-01

    The yeast strains of the Saccharomyces sensu stricto complex involved in beer production are a heterogeneous group whose genetic and genomic features are not adequately determined. Thus, the aim of the present study was to provide a genetic characterization of selected group of commercially available brewing yeasts both ale top-fermenting and lager bottom-fermenting strains. Molecular karyotyping revealed that the diversity of chromosome patterns and four strains with the most accented genetic variabilities were selected and subjected to genome-wide array-based comparative genomic hybridization (array-CGH) analysis. The differences in the gene copy number were found in five functional gene categories: (1) maltose metabolism and transport, (2) response to toxin, (3) siderophore transport, (4) cellular aldehyde metabolic process, and (5) L-iditol 2-dehydrogenase activity (p < 0.05). In the Saflager W-34/70 strain (Fermentis) with the most affected array-CGH profile, loss of aryl-alcohol dehydrogenase (AAD) gene dosage correlated with an imbalanced redox state, oxidative DNA damage and breaks, lower levels of nucleolar proteins Nop1 and Fob1, and diminished tolerance to fermentation-associated stress stimuli compared to other strains. We suggest that compromised stress response may not only promote oxidant-based changes in the nucleolus state that may affect fermentation performance but also provide novel directions for future strain improvement. PMID:27299603

  20. Copy number variations of genes involved in stress responses reflect the redox state and DNA damage in brewing yeasts.

    Science.gov (United States)

    Adamczyk, Jagoda; Deregowska, Anna; Skoneczny, Marek; Skoneczna, Adrianna; Natkanska, Urszula; Kwiatkowska, Aleksandra; Rawska, Ewa; Potocki, Leszek; Kuna, Ewelina; Panek, Anita; Lewinska, Anna; Wnuk, Maciej

    2016-09-01

    The yeast strains of the Saccharomyces sensu stricto complex involved in beer production are a heterogeneous group whose genetic and genomic features are not adequately determined. Thus, the aim of the present study was to provide a genetic characterization of selected group of commercially available brewing yeasts both ale top-fermenting and lager bottom-fermenting strains. Molecular karyotyping revealed that the diversity of chromosome patterns and four strains with the most accented genetic variabilities were selected and subjected to genome-wide array-based comparative genomic hybridization (array-CGH) analysis. The differences in the gene copy number were found in five functional gene categories: (1) maltose metabolism and transport, (2) response to toxin, (3) siderophore transport, (4) cellular aldehyde metabolic process, and (5) L-iditol 2-dehydrogenase activity (p < 0.05). In the Saflager W-34/70 strain (Fermentis) with the most affected array-CGH profile, loss of aryl-alcohol dehydrogenase (AAD) gene dosage correlated with an imbalanced redox state, oxidative DNA damage and breaks, lower levels of nucleolar proteins Nop1 and Fob1, and diminished tolerance to fermentation-associated stress stimuli compared to other strains. We suggest that compromised stress response may not only promote oxidant-based changes in the nucleolus state that may affect fermentation performance but also provide novel directions for future strain improvement.

  1. Genetic variation of Chinese and Japanese wild Pacific abalone (Haliotis discus hannai) measured by microsatellite DNA markers

    Institute of Scientific and Technical Information of China (English)

    LI Qi; KIJIMA Akihiro

    2006-01-01

    Population differentiation and relationships among three wild populations of the Pacific abalone Haliotis discus hannai collected from coastal seas around China and Japan were estimated using microsatellite DNA analysis. The results obtained with six microsatellite loci showed a high genetic diversity for China and Japan populations. The mean number of alleles per locus ranged from 11.7 to 23.0, and the average of observed and expected heterozygosity ranged from 0.656 to 0.721, and from 0.721 to 0.793, respectively. The observed genotype frequencies at each locus were mostly in agreement with Hardy-Weinberg expectations with five exceptions. Significant differences were detected between Chinese and Japanese H. discus hannai populations [Weir and Cocker-ham's fixation index(Fst) range: 0.020~0.023; Slatkin's fixation index (Rst) range: 0.016~0.044], and no obvious difference was detected between the samples of Japanese H. discus hannai populations (Fst=0.002; Rst = 0.007). The level of differentiation among populations is further evidenced by the nNeighbor-joining tree topology on which the Japanese samples were closely clustered, and the Chinese population formed a separate cluster. These results suggest that care should be taken in future management of different populations.

  2. Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

    Directory of Open Access Journals (Sweden)

    D. LOUKOVITIS

    2015-01-01

    Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

  3. Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India

    Indian Academy of Sciences (India)

    MANISHA SARSWAT; SAURABH DEWAN; RAJENDRA SINGH FARTYAL

    2016-06-01

    Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 forCOI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes,respectively. Almost all species were represented by 2–3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis , Liodrosophila nitida, Lordiphosa parantillaria , Lordiphosa ayarpathaensis ,Scaptomyza himalayana,Scaptomyza tistai , Zaprionus grandis and Stegana minuta are provided to public domains through this study.

  4. DNA sequence and haplotype variation in two candidate genes for dilated cardiomyopathy in the turkey Meleagris gallopavo.

    Science.gov (United States)

    Lin, Kuan-chin; Xu, Jun; Kamara, Davida; Geng, Tuoyu; Gyenai, Kwaku; Reed, Kent M; Smith, Edward J

    2007-05-01

    Determining variation in genes is fundamental to understanding their function in the disease state. Cardiac troponin T (cTnT) and phospholamban (PLN) genes have been implicated in dilated cardiomyopathy (DCM) in human and model species. To investigate the role of these 2 candidate genes in DCM in the turkey Meleagris gallopavo, understanding sequence variants and map position distribution is necessary. To this end, a total of 1854 and 1771 bp of cTnT and PLN gene sequences, respectively, were scanned for single nucleotide polymorphisms (SNPs) in a randomly bred population. A total of 15 SNPs was identified in the cTnT and PLN genomic sequences. Nine haplotypes, 5 in cTnT and 4 in PLN, were identified. Observed heterozygosities (0.02-0.39) in the turkey population were low for both genes. Within each gene, 1 SNP corresponding to a restriction enzyme site was identified and used to develop a PCR-restriction fragment length polymorphism (RFLP) genotyping assay. The PLN gene was genetically mapped to turkey chromosome 2, equivalent to Gallus gallus chromosome 3, and cTnT mapped to a turkey microchromosome. Although limited because of the relatively small sample size of 55 birds, the data from this SNP analysis of PLN and cTnT provide a foundation from which to evaluate the function of cTnT and PLN in the turkey. Information about the distribution of the SNPs and haplotypes will facilitate future association and linkage studies.

  5. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution

    Directory of Open Access Journals (Sweden)

    Purves Joanne

    2012-09-01

    Full Text Available Abstract Background Staphylococcus aureus Repeat (STAR elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.

  6. Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

    Directory of Open Access Journals (Sweden)

    Thomas Howard

    2007-08-01

    Full Text Available Abstract Background Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences. Results A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass, Zea mays (maize, Hordeum vulgare (barley, Glycine max (soybean and Arabidopsis thaliana (thale cress was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'. Conclusion Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.

  7. Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India.

    Science.gov (United States)

    Roy, Pritesh Sundar; Rao, Gundimeda Jwala Narasimha; Jena, Sudipta; Samal, Rashmita; Patnaik, Ashok; Patnaik, Sasank Sekhar Chyau; Jambhulkar, Nitiprasad Namdeorao; Sharma, Srigopal; Mohapatra, Trilochan

    2016-01-01

    A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei's genetic diversity value (He) was in the range of 0.034-0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93-11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha. PMID:27598392

  8. In search of the genetic footprints of Sumerians: a survey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq

    Directory of Open Access Journals (Sweden)

    Olivieri Anna

    2011-10-01

    Full Text Available Abstract Background For millennia, the southern part of the Mesopotamia has been a wetland region generated by the Tigris and Euphrates rivers before flowing into the Gulf. This area has been occupied by human communities since ancient times and the present-day inhabitants, the Marsh Arabs, are considered the population with the strongest link to ancient Sumerians. Popular tradition, however, considers the Marsh Arabs as a foreign group, of unknown origin, which arrived in the marshlands when the rearing of water buffalo was introduced to the region. Results To shed some light on the paternal and maternal origin of this population, Y chromosome and mitochondrial DNA (mtDNA variation was surveyed in 143 Marsh Arabs and in a large sample of Iraqi controls. Analyses of the haplogroups and sub-haplogroups observed in the Marsh Arabs revealed a prevalent autochthonous Middle Eastern component for both male and female gene pools, with weak South-West Asian and African contributions, more evident in mtDNA. A higher male than female homogeneity is characteristic of the Marsh Arab gene pool, likely due to a strong male genetic drift determined by socio-cultural factors (patrilocality, polygamy, unequal male and female migration rates. Conclusions Evidence of genetic stratification ascribable to the Sumerian development was provided by the Y-chromosome data where the J1-Page08 branch reveals a local expansion, almost contemporary with the Sumerian City State period that characterized Southern Mesopotamia. On the other hand, a more ancient background shared with Northern Mesopotamia is revealed by the less represented Y-chromosome lineage J1-M267*. Overall our results indicate that the introduction of water buffalo breeding and rice farming, most likely from the Indian sub-continent, only marginally affected the gene pool of autochthonous people of the region. Furthermore, a prevalent Middle Eastern ancestry of the modern population of the marshes of

  9. Genetic variation in DNA-repair pathways and response to radiochemotherapy in esophageal adenocarcinoma: a retrospective cohort study of the Eastern Cooperative Oncology Group

    International Nuclear Information System (INIS)

    Recent data in esophageal cancer suggests the variant allele of a single-nucleotide polymorphism (SNP) in XRCC1 may be associated with resistance to radiochemotherapy. However, this SNP has not been assessed in a histologically homogeneous clinical trial cohort that has been treated with a uniform approach. In addition, whether germline DNA may serve as a surrogate for tumor genotype at this locus is unknown in this disease. Our objective was to assess this SNP in relation to the pathologic complete response (pCR) rate in subjects with esophageal adenocarcinoma who received cisplatin-based preoperative radiochemotherapy in a multicenter clinical trial (Eastern Cooperative Oncology Group 1201). As a secondary aim, we investigated the rate of allelic imbalance between germline and tumor DNA. Eighty-one eligible treatment-naïve subjects with newly diagnosed resectable esophageal adenocarcinoma received radiotherapy (45 Gy) concurrent with cisplatin-based chemotherapy, with planned subsequent surgical resection. The primary endpoint was pCR, defined as complete absence of tumor in the surgical specimen after radiochemotherapy. Using germline DNA from 60 subjects, we examined the base-excision repair SNP, XRCC1 Arg399Gln, and 4 other SNPs in nucleotide excision (XPD Lys751Gln and Asp312Asn, ERCC1 3' flank) and double-stranded break (XRCC2 5' flank) repair pathways, and correlated genotype with pCR rate. Paired tumor tissue was used to estimate the frequency of allelic imbalance at the XRCC1 SNP. The variant allele of the XRCC1 SNP (399Gln) was detected in 52% of subjects. Only 6% of subjects with the variant allele experienced a pCR, compared to 28% of subjects without the variant allele (odds ratio 5.37 for failing to achieve pCR, p = 0.062). Allelic imbalance at this locus was found in only 10% of informative subjects, suggesting that germline genotype may reflect tumor genotype at this locus. No significant association with pCR was noted for other SNPs

  10. Genetic variation in DNA-repair pathways and response to radiochemotherapy in esophageal adenocarcinoma: a retrospective cohort study of the Eastern Cooperative Oncology Group

    Directory of Open Access Journals (Sweden)

    Wu Xifeng

    2011-05-01

    Full Text Available Abstract Background Recent data in esophageal cancer suggests the variant allele of a single-nucleotide polymorphism (SNP in XRCC1 may be associated with resistance to radiochemotherapy. However, this SNP has not been assessed in a histologically homogeneous clinical trial cohort that has been treated with a uniform approach. In addition, whether germline DNA may serve as a surrogate for tumor genotype at this locus is unknown in this disease. Our objective was to assess this SNP in relation to the pathologic complete response (pCR rate in subjects with esophageal adenocarcinoma who received cisplatin-based preoperative radiochemotherapy in a multicenter clinical trial (Eastern Cooperative Oncology Group 1201. As a secondary aim, we investigated the rate of allelic imbalance between germline and tumor DNA. Methods Eighty-one eligible treatment-naïve subjects with newly diagnosed resectable esophageal adenocarcinoma received radiotherapy (45 Gy concurrent with cisplatin-based chemotherapy, with planned subsequent surgical resection. The primary endpoint was pCR, defined as complete absence of tumor in the surgical specimen after radiochemotherapy. Using germline DNA from 60 subjects, we examined the base-excision repair SNP, XRCC1 Arg399Gln, and 4 other SNPs in nucleotide excision (XPD Lys751Gln and Asp312Asn, ERCC1 3' flank and double-stranded break (XRCC2 5' flank repair pathways, and correlated genotype with pCR rate. Paired tumor tissue was used to estimate the frequency of allelic imbalance at the XRCC1 SNP. Results The variant allele of the XRCC1 SNP (399Gln was detected in 52% of subjects. Only 6% of subjects with the variant allele experienced a pCR, compared to 28% of subjects without the variant allele (odds ratio 5.37 for failing to achieve pCR, p = 0.062. Allelic imbalance at this locus was found in only 10% of informative subjects, suggesting that germline genotype may reflect tumor genotype at this locus. No significant association

  11. Use of novel DNA fingerprinting techniques for the detection and characterization of genetic variation in vegetatively propagated crops. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    Vegetative propagated crops, such as banana and platain, sweet potato, yam, sugarcane and cassava, represent important sources of food in the developing countries. Although some of these crops may produce seeds, they must for practical purposes be propagated vegetatively. As normal plant breeding strategies based on genetic hybridization are of limited value or not applicable to such crops, it is necessary to assess the genetic diversity already existing in these crops and to design breeding strategies accordingly. If the existing genetic variation is shown to be too narrow for breeding purposes, one promising possibility for the introduction of genetic variability is the use of mutations induced by radiation or chemical mutagens. This CRP focused on: the detection of genetic diversity induced by mutagenic treatment or in vitro culture; the development of crop-specific markers; and increasing co-operation between molecular biologists in advanced laboratories and plant breeders and molecular biologists in the developing countries. The success of this CRP is evidenced by the introduction and application of new molecular methods by laboratories in developing countries, specially for the analysis of local crop genetic diversity. These exciting preliminary results show the potential for applications in crop improvement but much work remains to be done. Many of the vegetatively propagated species are ''orphan crops'', under-investigated on the international level. The development of new uses of transgenesis for the development of edible vaccines should not be overlooked. The challenge that remains is in the application of these new tools for practical end-user oriented improvements in vegetatively propagated crops. The present publication summarizes the third and final Research Co-ordination Meeting on the Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops

  12. A radioimmunoassay of chicken growth hormone using growth hormone produced by recombinant DNA technology: validation and observations of plasma hormone variations in genetically fat and lean chickens

    International Nuclear Information System (INIS)

    A radioimmunoassay (RIA) of chicken growth hormone (c-GH) has been developed using growth hormone produced by recombinant DNA technology. The best rabbit antiserum was used at 1/300,000 final dilution. Hormone labelling by iodine-125, achieved by chloramine T, allowed a specific activity of 3.7 MBq/μg. The equilibrium curves show that optimal conditions of incubation were reached at room temperature for 24h. This RIA used a second sheep antibody which precipitated the whole c-GH bound to the first antibody in the presence of polyethylene glycol solution (6%) at room temperature for 30 min. In our conditions, sensitivity was about 30 pg of c-GH per tube. Coefficient of variation was around 10%. No cross reaction was found with avian LH and prolactin. Thyrotrophin-releasing hormone (TRH) injection to young chickens induced 20-fold higher plasma c-GH concentrations. Simultaneous injection of somatostatin and TRH slightly reduced these concentrations. Hypoglycemia induced by insulin led to a drop of the plasma c-GH concentration. Conversely, refeeding or glucose load induced slight increases of the c-GH level. Genetically fat chickens tended to exhibit higher plasma c-GH concentrations than lean chickens

  13. Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

    Directory of Open Access Journals (Sweden)

    Chen Zuozhou

    2010-11-01

    Full Text Available Abstract Background Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. Results Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms. Conclusions We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.

  14. Genetic structure and phylogeography of a relict tree fern,Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations:Implications for conservation

    Institute of Scientific and Technical Information of China (English)

    Zi-Juan WANG; Kai-Yun GUAN

    2011-01-01

    In this study,we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos.Combining cpDNA trnL-trnF and atpB-rbcL sequence variations,five haplotypes were identified from the 10 investigated populations.Moderate haplotype diversity (h = 0.66580) and low nucleotide diversity (π = 0.23 × 10-3) were detected.The S.brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195,π = 0.35 × 10-3) than that of Hainan-Laos (h = 0.00000,π = 0.00).A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA.Nested clade analysis identified two major clusters of the five haplotypes,one clade in the Yunnan region and the other in Hainan-Laos.The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes.The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations.The Yunnan populations frequently contained an ancestral haplotype,and most of them harbored other descendent haplotypes.Based on the distribution pattern of haplotypes and the nested clade analysis results,the Yunnan region potentially had several refugia of this species during glacial periods,whereas the Hainan populations were probable new colonizations.

  15. Seasonal variation of DNA damage and repair in patients with non-melanoma skin cancer and referents with and without psoriasis

    DEFF Research Database (Denmark)

    Møller, P; Knudsen, Lisbeth E.; Frentz, G;

    1998-01-01

    Quadruples of skin cancer patients with and without psoriasis and referents with and without psoriasis (4 x 20 study persons) were identified and examined for DNA damage by single cell gel electrophoresis (comet-assay) and DNA-repair by UV-induced unscheduled DNA synthesis (UDS) in mononuclear...

  16. Grapes, galls, and geography: the distribution of nuclear and mitochondrial DNA variation across host-plant species and regions in a specialist herbivore.

    Science.gov (United States)

    Downie, D A; Fisher, J R; Granett, J

    2001-07-01

    Studies of patterns of molecular variation in natural populations can provide important insights into a number of evolutionary problems. Among these, the question of whether geographic factors are more important than ecological factors in promoting population differentiation and ultimately speciation has been an important and contentious area in evolutionary biology. Systems involving herbivorous insects have played a leading role in this discussion. This study examined the distribution of molecular variation in a highly specialized gall-forming insect, grape phylloxera (Daktulosphaira vitifoliae Fitch), that is found on both sympatric and allopatric host-plant species of the genus Vitis. In addition, the relationship of insects in the introduced range in the United States to ancestral populations in the native range was examined. Evidence for differentiation along host-plant lines from both nuclear (RAPD) and mitochondrial (COI) DNA was confounded with the effect of geography. Differentiation was found where hosts were allopatric or parapatric, but no evidence was found for such differentiation on two hosts, V. vulpina and V. aestivalis, that are broadly sympatric. The question of population differentiation onto these sympatric hosts can be considered to be resolved--it has not occurred in spite of a long history of association. Evidence was equivocal, but suggestive of a period of divergence in allopatry prior to reestablishment of contact, for insects associated with another host plant species, V. cinerea, found in both sympatric and parapatric populations. A low level of diversity and placement of samples collected from the grape species V. riparia at the tip of a phylogenetic tree supports the hypothesis that this host has been recently colonized from populations from the Mississippi Valley. A polyphyletic origin for biotype B grape phylloxera was supported: Although most samples collected from vineyards in the introduced range in California had similar

  17. Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae in southern Africa

    Directory of Open Access Journals (Sweden)

    Pereira-da-Conceicoa Lyndall L

    2012-02-01

    Full Text Available Abstract Background Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9–10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. Results Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S] and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]. Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4–11.5 mya. Conclusions The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from

  18. How selection fashions morphological variation in Cakile maritima: A comparative analysis of population structure using random amplified polymorphic DNA and quantitative traits

    Institute of Scientific and Technical Information of China (English)

    Gandour MHEMMED; Hessini KAMEL; Abdelly CHEDLY

    2012-01-01

    It is a long-standing debate in evolutionary biology whether natural selection can generate divergence in the face of gene flow.Comparative studies of quantitative genetic and neutral marker differentiation have provided means for detecting the action of selection and random genetic drift in natural populations.We estimated the degree of population divergence in several quantitative traits and compared these estimates with that based on presumably neutral molecular markers (random amplified polymorphic DNA [RAPD]).This approach allowed us to disentangle the effects of divergent selection from that of other evolutionary forces.Nine populations of Cakile maritima,which encompasses the complete range of distribution of this species in Tunisia,were examined.We found a high proportion of total genetic variance to be among populations and among ecoregions for quantitative traits (range of QsT:0.44-0.88) and a moderate one for RAPD markers (GsT:0.081).In addition,almost all characters displayed a significant higher QsT than GsT,indicating occurrence of phenotypic plasticity and local adaptation.The latter is explicable as there is no reason to expect that natural selection would affect in similar fashion all traits and affect all populations at a similar level.We also found a negative and significant correlation between genetic variation in molecular marker loci and quantitative traits at the multitrait scale.This result attests that the evolution of these markers in C.maritima were not paralleled,suggesting that the degree of genetic differentiation in neutral marker loci is closely predictive of the degree of differentiation in loci coding quantitative traits and the majority of these neutral markers negatively controlled the studied quantitative traits.

  19. VARIATION IN MITOCHONDRIAL-DNA LEVELS IN MUSCLE FROM NORMAL CONTROLS - IS DEPLETION OF MTDNA IN PATIENTS WITH MITOCHONDRIAL MYOPATHY A DISTINCT CLINICAL SYNDROME

    NARCIS (Netherlands)

    POULTON, J; SEWRY, C; POTTER, CG; BOUGERON, T; CHRETIEN, D; WIJBURG, FA; MORTEN, KJ; BROWN, G

    1995-01-01

    Recent studies have identified a group of patients with cytochrome oxidase (COX) deficiency presenting in infancy associated with a deficiency of mtDNA in muscle or other affected tissue (Moraes et al 1991). We used a navel approach to compare the level of mitochondrial (mtDNA) compared to nuclear D

  20. Evaluation of Interindividual Human Variation in Bioactivation and DNA Adduct Formation of Estragole in Liver Predicted by Physiologically Based Kinetic/Dynamic and Monte Carlo Modeling

    NARCIS (Netherlands)

    Punt, Ans; Paini, Alicia; Spenkelink, Bert; Scholz, Gabriele; Schilter, Benoit; Bladeren, Van Peter J.; Rietjens, Ivonne M.C.M.

    2016-01-01

    Estragole is a known hepatocarcinogen in rodents at high doses following metabolic conversion to the DNA-reactive metabolite 1′-sulfooxyestragole. The aim of the present study was to model possible levels of DNA adduct formation in (individual) humans upon exposure to estragole. This was done by

  1. Genuineness of Morinda officinalis How germplasm inferred from ITS sequences variation of nuclear ribosomal DNA%基于核糖体rDNA ITS序列变异探讨巴戟天道地性

    Institute of Scientific and Technical Information of China (English)

    丁平; 刘瑾; 邱金英; 赖小平

    2012-01-01

    本文应用PCR测序技术,对不同产地巴戟天(Morinda officinalis How)的rDNA ITS区片段进行检测,ITS全序列为567 bp,G/C含量为64.5%.本研究共获得17个单倍型,各单倍型呈高水平的树状演化,来自广东群体的单倍型显示是扩张的源头.分子变异等级分析(AMOVA)的计算结果显示,群体间变异占变异的比例(56.65%)大于群体内变异(43.35%),FST值为0.566 5,各群体间出现遗传分化.Mantel检验结果也显示基因流水平与地理距离呈正相关关系(R2=0.721 1),表明巴戟天群体间的亲缘关系与地理分布有较好的相关性.本研究为探讨巴戟天道地药材形成的分子机制以及谱系地理学的研究奠定基础.%PCR sequencing ITS genes methods were used to assess the genetic diversity of Morinda officinalis How different populations. The sequence of Morinda officinalis ITS gene was 567 bp in length, and the content of G/C was 64.5%. In this study, 17 haplotypes were obtained, which were at a high level of branching, and the haplotypes of Guangdong population showed to be the expansion origin. The result of the analysis of molecular variance (AMOVA) also showed that the percentage of variation among populations (56.65%) was greater than that within a population (43.35%). The FST value was 0.566 5, and the genetic divergence among populations was significant. Mantel test results also indicated that the level of geneflow was positively correlated with geographic distances (R2= 0.721 1). The result showed a good correlation between genotype and geographic distribution of Morinda officinalis, and ITS gene sequencing could be useful molecular method for the genuineness and phylogeography of Morinda officinalis.

  2. Variation through the cell cycle in the dose-response of DNA neutral filter elution in X-irradiated synchronous CHO-cells

    International Nuclear Information System (INIS)

    Dose-response curves for DNA neutral (pH 9.6) filter elution were obtained with synchronized CHO cells exposed to X-rays at various phases of cell cycle. The dose response was similar in synchronized and plateau-phase G1 cells, as well as in cells arrested at the G1/S border using aphidicolin; it flattened as cells progressed into S phase and reached a minimum in the middle of this phase. An increase in DNA elution dose response, to values only slightly lower than those obtained with G1 cells, was observed as cells entered G2 phase. Significant alterations in the sedimentation properties of the DNA during S phase were also observed in Ehrlich ascites tumor cells using the neutral sucrose gradient centrifugation technique. A significant proportion of the DNA from S cells irradiated with 10 Gy sedimented at speeds (350S-700S) well above the maximum sedimentation speed expected for free sedimenting DNA molecules (ssub(max) = 350S), indicating the formation of a DNA complex. DNA from G1, G1/S, or G2 + M cells sedimented as expected for free sedimenting molecules. (author)

  3. High frequency of the IVS2-2A>G DNA sequence variation in SLC26A5, encoding the cochlear motor protein prestin, precludes its involvement in hereditary hearing loss

    Directory of Open Access Journals (Sweden)

    Pereira Fred A

    2005-08-01

    Full Text Available Abstract Background Cochlear outer hair cells change their length in response to variations in membrane potential. This capability, called electromotility, is believed to enable the sensitivity and frequency selectivity of the mammalian cochlea. Prestin is a transmembrane protein required for electromotility. Homozygous prestin knockout mice are profoundly hearing impaired. In humans, a single nucleotide change in SLC26A5, encoding prestin, has been reported in association with hearing loss. This DNA sequence variation, IVS2-2A>G, occurs in the exon 3 splice acceptor site and is expected to abolish splicing of exon 3. Methods To further explore the relationship between hearing loss and the IVS2-2A>G transition, and assess allele frequency, genomic DNA from hearing impaired and control subjects was analyzed by DNA sequencing. SLC26A5 genomic DNA sequences from human, chimp, rat, mouse, zebrafish and fruit fly were aligned and compared for evolutionary conservation of the exon 3 splice acceptor site. Alternative splice acceptor sites within intron 2 of human SLC26A5 were sought using a splice site prediction program from the Berkeley Drosophila Genome Project. Results The IVS2-2A>G variant was found in a heterozygous state in 4 of 74 hearing impaired subjects of Hispanic, Caucasian or uncertain ethnicity and 4 of 150 Hispanic or Caucasian controls (p = 0.45. The IVS2-2A>G variant was not found in 106 subjects of Asian or African American descent. No homozygous subjects were identified (n = 330. Sequence alignment of SLC26A5 orthologs demonstrated that the A nucleotide at position IVS2-2 is invariant among several eukaryotic species. Sequence analysis also revealed five potential alternative splice acceptor sites in intron 2 of human SLC26A5. Conclusion These data suggest that the IVS2-2A>G variant may not occur more frequently in hearing impaired subjects than in controls. The identification of five potential alternative splice acceptor sites in

  4. Population structure and gene flow of the Atlantic walrus ( Odobenus rosmarus rosmarus ) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation

    DEFF Research Database (Denmark)

    Andersen, L.W.; Born, E.W.; Gjertz, I.;

    1998-01-01

    The population structure of the Atlantic walrus, Odobenus rosmarus rosmarus, was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH-dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from nort...

  5. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

    DEFF Research Database (Denmark)

    Li, Shengting; Besenbacher, Søren; Li, Yingrui;

    2014-01-01

    In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise...

  6. Use of pyrosequencing and DNA barcodes to monitor variations in Firmicutes and Bacteroidetes communities in the gut microbiota of obese humans

    Directory of Open Access Journals (Sweden)

    Raoult Didier

    2008-12-01

    Full Text Available Abstract Background Recent studies of 16S rRNA genes in the mammalian gut microbiota distinguished a higher Firmicutes/Bacteroidetes ratio in obese individuals compared to lean individuals. This ratio was estimated using a clonal Sanger sequencing approach which is time-consuming and requires laborious data analysis. In contrast, new high-throughput pyrosequencing technology offers an inexpensive alternative to clonal Sanger sequencing and would significantly advance our understanding of obesity via the development of a clinical diagnostic method. Here we present a cost-effective method that combines 16S rRNA pyrosequencing and DNA barcodes of the Firmicutes and Bacteroidetes 16S rRNA genes to determine the Firmicutes/Bacteroidetes ratio in the gut microbiota of obese humans. Results The main result was the identification of DNA barcodes targeting the Firmicutes and Bacteroidetes phyla. These barcodes were validated using previously published 16S rRNA gut microbiota clone libraries. In addition, an accurate F/B ratio was found when the DNA barcodes were applied to short pyrosequencing reads of published gut metagenomes. Finally, the barcodes were utilized to define the F/B ratio of 16S rRNA pyrosequencing data generated from brain abscess pus and cystic fibrosis sputum. Conclusion Using DNA barcodes of Bacteroidetes and Firmicutes 16S rRNA genes combined with pyrosequencing is a cost-effective method for monitoring relevant changes in the relative abundance of Firmicutes and Bacteroidetes bacterial communities in microbial ecosystems.

  7. A physiologically based in silico model for trans-2-hexenal detoxicifcation and DNA adduct formation in human including interindividual variation indicates efficient detoxification and a negligible genotoxicity risk

    NARCIS (Netherlands)

    Kiwamoto, R.; Spenkelink, A.; Rietjens, I.M.C.M.; Punt, A.

    2013-01-01

    A number of a,ß-unsaturated aldehydes are present in food both as natural constituents and as flavouring agents. Their reaction with DNA due to their electrophilic a,ß-unsaturated aldehyde moiety may result in genotoxicity as observed in some in vitro models, thereby raising a safety concern. A ques

  8. Lineage-specific variations of congruent evolution among DNA sequences from three genomes, and relaxed selective constraints on rbcL in Cryptomonas (Cryptophyceae

    Directory of Open Access Journals (Sweden)

    Tran Hoang-Dung

    2005-10-01

    Full Text Available Abstract Background Plastid-bearing cryptophytes like Cryptomonas contain four genomes in a cell, the nucleus, the nucleomorph, the plastid genome and the mitochondrial genome. Comparative phylogenetic analyses encompassing DNA sequences from three different genomes were performed on nineteen photosynthetic and four colorless Cryptomonas strains. Twenty-three rbcL genes and fourteen nuclear SSU rDNA sequences were newly sequenced to examine the impact of photosynthesis loss on codon usage in the rbcL genes, and to compare the rbcL gene phylogeny in terms of tree topology and evolutionary rates with phylogenies inferred from nuclear ribosomal DNA (concatenated SSU rDNA, ITS2 and partial LSU rDNA, and nucleomorph SSU rDNA. Results Largely congruent branching patterns and accelerated evolutionary rates were found in nucleomorph SSU rDNA and rbcL genes in a clade that consisted of photosynthetic and colorless species suggesting a coevolution of the two genomes. The extremely accelerated rates in the rbcL phylogeny correlated with a shift from selection to mutation drift in codon usage of two-fold degenerate NNY codons comprising the amino acids asparagine, aspartate, histidine, phenylalanine, and tyrosine. Cysteine was the sole exception. The shift in codon usage seemed to follow a gradient from early diverging photosynthetic to late diverging photosynthetic or heterotrophic taxa along the branches. In the early branching taxa, codon preferences were changed in one to two amino acids, whereas in the late diverging taxa, including the colorless strains, between four and five amino acids showed changes in codon usage. Conclusion Nucleomorph and plastid gene phylogenies indicate that loss of photosynthesis in the colorless Cryptomonas strains examined in this study possibly was the result of accelerated evolutionary rates that started already in photosynthetic ancestors. Shifts in codon usage are usually considered to be caused by changes in functional

  9. Identification of variations of gene expression of visceral adipose and renal tissue in type 2 diabetic rats using cDNA representational difference analysis

    Institute of Scientific and Technical Information of China (English)

    杨架林; 李果; 张芳林; 刘优萍; 张迪; 周文中; 许光武; 杨义生; 罗敏

    2003-01-01

    Objectives To identify differences in gene expression in renal and visceral adipose tissue in type 2 diabetic rats using cDNA representational difference analysis (RDA) and to explore the molecular pathogenesis of type 2 diabetes and its chronic vascular complications.Methods A rat model of type 2 diabetes was generated by administration of a high fat and calorie diet combined with a low dose of streptozocin (STZ) injected into the tail vein. The difference bands were generated by cDNA representational difference analysis (cDNA RDA). The final difference products were ligated into the pUC-18 vector and sequenced. A bioformatics analysis was performed on the obtained expressed sequence tags (ESTs), and then the expression levels of known and novel genes were verified by semi-quantitative reverse transcription-PCR (RT-PCR). At the same time, full-length cDNA of a novel gene was cloned in silico.Results The type 2 diabetic rats in this experiment experienced hyperglycemia, lipidemia, lower insulin sensitivity and normal body weight. We obtained 9 novel ESTs and 2 novel genes from renal tissue of rats and 6 novel ESTs and 1 known gene, the rat lipoprotein lipase (LPL) gene from their visceral adipose tissue. The 2 novel genes (RS91 and RS2) from the renal tissue were both very similar to serine (or cysteine) proteinase inhibitor, clade F and eukaryotic translation initiation factor 3 and subunit 5 (EIF-3 epsilon). The expression of both novel genes and the LPL gene were upregulated in renal and visceral adipose tissue of type 2 diabetic and fat-enriched rats. Full-length cDNA of the novel gene RS91 was cloned in silico.Conclusions① The rat model of type 2 diabetes generated in this study was ideal because the disease in the animals closely mimicked type 2 diabetic patients ② cDNA RDA is a flexible, inexpensive, more accurate, sensitive and highly effective technique for identifying differences in gene expression ③ Six novel ESTs and 1 known gene were obtained

  10. Identification of a New Variable Sequence in the P1 Cytadhesin Gene of Mycoplasma pneumoniae: Evidence for the Generation of Antigenic Variation by DNA Recombination between Repetitive Sequences

    OpenAIRE

    Kenri, Tsuyoshi; Taniguchi, Rie; Sasaki, Yuko; Okazaki, Norio; Narita, Mitsuo; Izumikawa, Kinichi; Umetsu, Masao; Sasaki, Tsuguo

    1999-01-01

    A Mycoplasma pneumoniae cytadhesin P1 gene with novel nucleotide sequence variation has been identified. Four clinical strains of M. pneumoniae were found to carry this type of P1 gene. This new P1 gene is similar to the known group II P1 genes but possesses novel sequence variation of approximately 300 bp in the RepMP2/3 region. The position of the new variable region is distant from the previously reported variable regions known to differ between group I and II P1 genes. Two sequences close...

  11. Variations of HBV-DNA quantification and concentration of α-L-fucosidase and alpha fetal protein%HBV-DNA、AFU和AFP水平与肝损害的相关性

    Institute of Scientific and Technical Information of China (English)

    欧超伟; 陈绍鹏; 雷耀珍; 郝彦强

    2011-01-01

    目的 探讨HBV-DNA定量与α-L-岩藻糖苷酶(AFU)和甲胎蛋白(AFP)浓度变化的关系.方法 对373例慢性乙型肝炎患者血清进行HBV-DNA定量、AFU与AFP浓度检测,根据HBV-DNA水平分为3组:HBV-DNA 1×10copies/ml以下为阴性组;HBV-DNA 1×10~1×10copies/ml为低病毒量组;HBV-DNA 1×10~1×10copies/ml为高病毒量组进行分析.结果不同病毒量组的AFU、AFP浓度变化显示HBV-DNA低病毒量组和高病毒量组与正常对照组比较的差异则有统计学意义(P<0.05).AFU与AFP的阳性比例随病毒复制量的增加而升高.结论 对乙型肝炎病毒感染者,应定期进行血清HBV-DNA定量检测,评估病毒的复制状况,并同时检测AFU和AFP浓度,尽早发现肝组织的损害程度及演变过程,达到早期治疗的目的.%Objective To investigate the relationship between HBV-DNA quantification and concentration variation of α-L-fucosidase(AFU) and alpha fetal protein(AFP). Methods The levels of AFU,AFP and HBV-DNA in the serum of 373 chronic hepatitis B patients were determined. The 373 chronic hepatitis B patients were divided into 3 groups based the levels of HBV-DNA,that is the negative group(HBV-DNA <1×103 copies/ml(the low viral load group(HBV-DNA 1 ×104 ~1 ×105copies/ml); high viral load group (HBV-DNA 1×106~1×108copies/ml). Results The levels of AFU and AFP in low and high viral load groups were significantly different as compared with that of the norrmal control group (P<0.05).The positive rates of AFU and AFP increases along with the increase of virus replication. Conclusion HBV-DNA in the HBV carriers should be determined at regular intervals,the replication of HBV-DNA be assessed and the levels of AFU and AFP be simultaneously detected to diagnose the ealy liver lesions for early treatment.

  12. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  13. 人类线粒体DNA变异的检测方法和思路%Methods and Thoughts on Detecting Nucleotide Variations in Human Mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    姚永刚; 孔庆鹏; 张亚平

    2001-01-01

    基于线粒体DNA(mtDNA)的研究对于人群源流迁移、线粒体相关疾病病因的探讨和法医鉴定等具有重要意义,就检测人线粒体突变的一些常用方法,如RFLP、SSO和控制区测序等作一小结和归纳,并重点介绍目前mtDNA突变的筛选方法和思路。另外,还总结了近年来对人mtDNA方面的研究结果,对世界人群中主要单倍型类群(haplogroup)特征变异位点和相应的酶切检测引物作了归纳。

  14. Mitochondrial DNA control region sequence variation suggests an independent origin of an {open_quotes}Asian-specific{close_quotes} 9-bp deletion in Africans

    Energy Technology Data Exchange (ETDEWEB)

    Soodyall, H.; Redd, A.; Vigilant [Pennsylvania State Univ., Univeristy Park, PA (United States)] [and others

    1994-09-01

    The intergenic noncoding region between the cytochrome oxidase II and lysyl tRNA genes of human mitochondrial DNA (mtDNA) is associated with two tandemly arranged copies of a 9-bp sequence. A deletion of one of these repeats has been found at varying frequencies in populations of Asian descent, and is commonly referred to as an {open_quotes}Asian-specific{close_quotes} marker. We report here that the 9-bp deletion is also found at a frequency of 10.2% (66/649) in some indigenous African populations, with frequencies of 28.6% (20/70) in Pygmies, 26.6% (12/45) in Malawians and 15.4% (31/199) in southeastern Bantu-speaking populations. The deletion was not found in 123 Khoisan individuals nor in 209 western Bantu-speaking individuals, with the exception of 3 individuals from one group that was admixed with Pygmies. Sequence analysis of the two hypervariable segments of the mtDNA control region reveals that the types associated with the African 9-bp deletion are different from those found in Asian-derived populations with the deletion. Phylogenetic analysis separates the {open_quotes}African{close_quotes} and {open_quotes}Asian{close_quotes} 9-bp deletion types into two different clusters which are statistically supported. Mismatch distributions based on the number of differences between pairs of mtDNA types are consistent with this separation. These findings strongly support the view that the 9-bp deletion originated independently in Africa and in Asia.

  15. Host-Associated Population Variations of Bemisia tabaci (Genn.) (Hemiptera:Sternorrhyncha: Aleyrodidae) Characterized with Random DNA Markers

    OpenAIRE

    Helmi, A.

    2011-01-01

    Whitefly, Bemisia tabaci (Genn.) is an important sucking plant sap pest of field, horticultural and ornamental plants causing feeding injuries besides spreading plant diseases by acting as a vector of Gemini-viruses. The polyphagous nature of the pest makes it as a highly complex species. The influence of six host plants belonging to three different plant families utilized by the species on the population differences at molecular level was attempted using Random Amplified Polymorphic DNA (RAP...

  16. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

    OpenAIRE

    Wood, HM; Belvedere,O; Conway, C; Daly, C; Chalkley, R; Bickerdike, M; McKinley, C; Egan, P; Ross, L; Hayward, B; Morgan, J.; Davidson, L; MacLennan, K; Ong, TK; Papagiannopoulos, K.

    2010-01-01

    The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm th...

  17. Analysis and validation of genome-specific DNA variations in 5' flanking conserved sequences of wheat low-molecular-weight glutenin subunit genes

    Institute of Scientific and Technical Information of China (English)

    LONG; Hai; WEI; Yuming

    2006-01-01

    The thirty-three 5' flanking conserved sequences of the known low-molecular-weight subunit (LMW-GS) genes have been divided into eight clusters, which was in agreement with the classification based on the deduced N-terminal protein sequences. The DNA polymorphism between the eight clusters was obtained by sequence alignment, and a total of 34 polymorphic positions were observed in the approximately 200 bp regions, among which 18 polymorphic positions were candidate SNPs. Seven cluster-specific primer sets were designed for seven out of eight clusters containing cluster-specific bases, with which the genomic DNA of the ditelosomic lines of group 1 chromosomes of a wheat variety 'Chinese Spring' was employed to carry out chromosome assignment. The subsequent cloning and DNA sequencing of PCR fragments validated the sequences specificity of the 5' flanking conserved sequences between LMW-GS gene groups in different genomes. These results suggested that the coding and 5' flanking regions of LMW-GS genes are likely to have evolved in a concerted fashion. The seven primer sets developed in this study could be used to isolate the complete ORFs of seven groups of LMW-GS genes, respectively, and therefore possess great value for further research in the contributions of a single LMW-GS gene to wheat quality in the complex genetic background and the efficient selections of quality-related components in breeding programs.

  18. Control control control: a reassessment and comparison of GenBank and chromatogram mtDNA sequence variation in Baltic grey seals (Halichoerus grypus.

    Directory of Open Access Journals (Sweden)

    Katharina Fietz

    Full Text Available Genetic data can provide a powerful tool for those interested in the biology, management and conservation of wildlife, but also lead to erroneous conclusions if appropriate controls are not taken at all steps of the analytical process. This particularly applies to data deposited in public repositories such as GenBank, whose utility relies heavily on the assumption of high data quality. Here we report on an in-depth reassessment and comparison of GenBank and chromatogram mtDNA sequence data generated in a previous study of Baltic grey seals. By re-editing the original chromatogram data we found that approximately 40% of the grey seal mtDNA haplotype sequences posted in GenBank contained errors. The re-analysis of the edited chromatogram data yielded overall similar results and conclusions as the original study. However, a significantly different outcome was observed when using the uncorrected dataset based on the GenBank haplotypes. We therefore suggest disregarding the existing GenBank data and instead using the correct haplotypes reported here. Our study serves as an illustrative example reiterating the importance of quality control through every step of a research project, from data generation to interpretation and submission to an online repository. Errors conducted in any step may lead to biased results and conclusions, and could impact management decisions.

  19. Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic

    Directory of Open Access Journals (Sweden)

    Maria Rosimere Xavier Amaral

    2015-08-01

    Full Text Available The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA. Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97 within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.

  20. Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic.

    Science.gov (United States)

    Amaral, Maria Rosimere Xavier; Albrecht, Marc; McKinley, Alan Shane; de Carvalho, Adriana Márcia Ferreira; de Sousa Junior, Severino Cavalcante; Diniz, Fabio Mendonça

    2015-08-19

    The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA). Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97) within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.

  1. A case study on the genetic origin of the high oleic acid trait through FAD2-1 DNA sequence variation in safflower (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Sara eRapson

    2015-09-01

    Full Text Available The safflower (Carthamus tinctorius L. is considered a strongly domesticated species with a long history of cultivation. The hybridization of safflower with its wild relatives has played an important role in the evolution of cultivars and is of particular interest with regards to their production of high quality edible oils. Original safflower varieties were all rich in linoleic acid, while varieties rich in oleic acid have risen to prominence in recent decades. The high oleic acid trait is controlled by a partially recessive allele ol at a single locus OL. The ol allele was found to be a defective microsomal oleate desaturase FAD2-1. Here we present DNA sequence data and DNA Southern blot analysis suggesting that there has been an ancient hybridization and introgression of the FAD2-1 gene into C. tinctorius from its wild relative C. palaestinus. It is from this gene that FAD2-1Δ was derived more recently. Identification and characterization of the genetic origin and diversity of FAD2-1 could aid safflower breeders in reducing population size and generations required for the development of new high oleic acid varieties by using perfect molecular marker-assisted selection.

  2. Clonal variation of DNA repair in a human glioma cell line This study was supported by the Cancer Research Campaign and the Bob Champion Cancer Trust

    International Nuclear Information System (INIS)

    Clonal heterogeneity in response to ionizing radiation was found for a human glioma cell line, IN859. The authors have investigated the most sensitive clone, the most resistant clone and the parent line for differences in DNA repair fidelity using the method of plasmid reconstitution. Significant differences in repair fidelity were found between the two clones, and between the sensitive clone and the parent line. The resistant clone and the parent lines showed the greater repair fidelity. A comparison of two different restriction enzymes, which cleave the plasmid with blunt or cohesive-ended double-strand breaks, did not reveal differences in repair fidelity. Equal numbers of plasmids were integrated in each cell line, but the sensitive clone showed a higher frequency of misrepair of cleaved plasmid. Misrepair was characterized by partial or complete loss of sequence at the site of plasmid cleavage. It is concluded that the radiosensitive clone exhibits increased misrepair. (author). 15 refs.; 5 figs.; 2 tabs

  3. Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa.

    Science.gov (United States)

    Cherni, Lotfi; Loueslati, Besma Yaacoubi; Pereira, Luísa; Ennafaâ, Hajer; Amorim, António; El Gaaied, Amel Ben Ammar

    2005-02-01

    North African populations are considered genetically closer to Eurasians than to sub-Saharans. However, they display a considerably high mtDNA heterogeneity among them, namely in the frequencies of the U6, East African, and sub-Saharan haplogroups. In this study, we describe and compare the female gene pools of two neighboring Tunisian populations, Kesra (Berber) and Zriba (non-Berber), which have contrasting historical backgrounds. Both populations presented lower diversity values than those observed for other North African populations, and they were the only populations not showing significant negative Fu's F(S) values. Kesra displayed a much higher proportion of typical sub-Saharan haplotypes (49%, including 4.2% of M1 haplogroup) than Zriba (8%). With respect to U6 sequences, frequencies were low (2% in Kesra and 8% in Zriba), and all belonged to the subhaplogroup U6a. An analysis of these data in the context of North Africa reveals that the emerging picture is complex, because Zriba would match the profile of a Berber Moroccan population, whereas Kesra, which shows twice the frequency of sub-Saharan lineages normally observed in northern coastal populations, would match a western Saharan population except for the low U6 frequency. The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far.

  4. Of mice and the 'Age of Discovery': the complex history of colonization of the Azorean archipelago by the house mouse (Mus musculus) as revealed by mitochondrial DNA variation.

    Science.gov (United States)

    Gabriel, S I; Mathias, M L; Searle, J B

    2015-01-01

    Humans have introduced many species onto remote oceanic islands. The house mouse (Mus musculus) is a human commensal and has consequently been transported to oceanic islands around the globe as an accidental stowaway. The history of these introductions can tell us not only about the mice themselves but also about the people that transported them. Following a phylogeographic approach, we used mitochondrial D-loop sequence variation (within an 849- to 864-bp fragment) to study house mouse colonization of the Azores. A total of 239 sequences were obtained from all nine islands, and interpretation was helped by previously published Iberian sequences and 66 newly generated Spanish sequences. A Bayesian analysis revealed presence in the Azores of most of the D-loop clades previously described in the domesticus subspecies of the house mouse, suggesting a complex colonization history of the archipelago as a whole from multiple geographical origins, but much less heterogeneity (often single colonization?) within islands. The expected historical link with mainland Portugal was reflected in the pattern of D-loop variation of some of the islands but not all. A more unexpected association with a distant North European source area was also detected in three islands, possibly reflecting human contact with the Azores prior to the 15th century discovery by Portuguese mariners. Widening the scope to colonization of the Macaronesian islands as a whole, human linkages between the Azores, Madeira, the Canaries, Portugal and Spain were revealed through the sharing of mouse sequences between these areas. From these and other data, we suggest mouse studies may help resolve historical uncertainties relating to the 'Age of Discovery'.

  5. Phylogeography of an alpine plant (Bupleurum smithii, Apiaceae) endemic to the Qinghai-Tibetan Plateau and adjacent regions inferred from chloroplast DNA sequence variation

    Institute of Scientific and Technical Information of China (English)

    Cai ZHAO; Xiang-Guang MA; Qian-Long LIANG; Chang-Bao WANG; Xing-Jin HE

    2013-01-01

    To obtain a better understanding of how Quaternary climatic oscillations influenced range distributions and intraspecific split of alpine plants on the Qinghai-Tibetan Plateau (QTP) and in adjacent regions,we investigated the extant phylogeographical structure of Bupleurum smithii in this area based on 22 populations and 103 individuals spanning the entire distribution region of this species using chloroplast DNA sequences.Two major haplotype lineages were identified,and at least two corresponding glacial refugia maintaining in the northeastern and eastern edge of the QTP during the Last Glacial Maximum were revealed.Secondary contact between populations and efficient gene flow were also found between two major haplotype lineages.In addition,based on the geographic distribution of haplotypes,we found that populations on the platform derived from individuals that recolonized this area from refugia situated at the northeastem and eastern edges of the QTP,and that B.smithii recolonized from southern to northern China during inter-and post-glacial periods.

  6. Variation of TTC Repeat Pattern In The Dna of Mycobacterium Leprae Isolates Obtained from Archeological Bones and Leprosy Patients From East Nusa Tenggara

    Directory of Open Access Journals (Sweden)

    Dinar Adriaty

    2012-12-01

    Full Text Available The existence of leprosy or kusta or Morbus Hansen or Hansen’s disease has been known for years, including in Indonesia. Starting from the discovery of Mycobacterium leprae isolates from ancient bone (about 1.000 years B.C, the archaeological excavations results in East Nusa Tenggara, interesting questions arise about how the development of leprosy in eastern Indonesia is. Biology molecular study would become a powerful tool to investigate the presence of leprosy bacillary whether there are similarities between the genomes of M. leprae isolates in the primeval and the present. PCR examinations were performed on mandibular bone fragments from ancient human who lived 1000 years B.C. discovered in archaeological surveys on the island of Lembata and three leprosy patients from East Nusa Tenggara. The DNA extraction was performed using a kit from Qiagen products and its TTC repeating pattern was seen with the method of direct sequencing. It turned out that the TTC profile obtained from samples of archaeological was as many as 13 copies, while the repetition of TTC in three samples of leprosy patients were 15, 17 and 26 copies. The different number of TTC repetition shows the different isolates of M. leprae between in the ancient times and the present. Further studies are needed to verify the differences in the genome that occur, for example from the study of SNPs (single nucleotide polymorphisms.

  7. Interspecific variation in the repair of UV damaged DNA in the genus Xiphophorus as a factor in the decline of the Rio Grande Platyfish.

    Science.gov (United States)

    Mitchell, David; Paniker, Lakshmi; Lin, Kevin; Fernandez, André

    2015-01-01

    The fish genus Xiphophorus consists of 26 species distributed along the eastern slopes of mountain ranges extending from northern Mexico to Belize and Nicaragua. We analyzed light-dependent repair of UV-induced DNA damage in at least two species from each of the four monophyletic Xiphophorus groups. We found that the northern platyfish had significantly reduced photoenzymatic repair compared to the other three groups, including the northern swordtails, southern platyfish and southern swordtails. All of the species of the northern platyfish, including the Marbled (meyeri), Northern (gordoni) and Monterrey Platyfish (couchianus) are the northernmost species in the genus and are the only three species in the genus that are currently found on the IUCN Red List of Threatened Species. Satellite data from the past 30 years (1979-2008) correlate greater increases in shorter wavelength UVB with higher latitudes within the Xiphophorus range. We suggest that, combined with other consequences of human population growth, anthropogenic deozonation resulting in a disproportionate increase in UVB in temperate latitudes may be a contributing factor in the decline and extirpation of the northern platyfish.

  8. Indole acetic acid production by fluorescent Pseudomonas spp. from the rhizosphere of Plectranthus amboinicus (Lour.) Spreng. and their variation in extragenic repetitive DNA sequences.

    Science.gov (United States)

    Sethia, Bedhya; Mustafa, Mariam; Manohar, Sneha; Patil, Savita V; Jayamohan, Nellickal Subramanian; Kumudini, Belur Satyan

    2015-06-01

    Fluorescent Pseudomonas (FP) is a heterogenous group of growth promoting rhizobacteria that regulate plant growth by releasing secondary metabolic compounds viz., indole acetic acid (IAA), siderophores, ammonia and hydrogen cyanide. In the present study, IAA producing FPs from the rhizosphere of Plectranthus amboinicus were characterized morphologically, biochemically and at the molecular level. Molecular identification of the isolates were carried out using Pseudomonas specific primers. The effect of varying time (24, 48, 72 and 96 h), Trp concentrations (100, 200, 300, 400 and 500 μg x ml(-1)), temperature (10, 26, 37 and 50 ± 2 degrees C) and pH (6, 7 and 8) on IAA production by 10 best isolates were studied. Results showed higher IAA production at 72 h incubation, at 300 μg x ml(-1) Trp concentration, temperature 26 ± 2 degrees C and pH 7. TLC with acidified ethyl acetate extract showed that the IAA produced has a similar Rf value to that of the standard IAA. Results of TLC were confirmed by HPLC analysis. Genetic diversity of the isolates was also studied using 40 RAPD and 4 Rep primers. Genetic diversity parameters such as dominance, Shannon index and Simpson index were calculated. Out of 40 RAPD primers tested, 9 (2 OP-D series and 7 OP-E series) were shortlisted for further analysis. Studies using RAPD, ERIC, BOX, REP and GTG5 primers revealed that isolates exhibit significant diversity in repetitive DNA sequences irrespective of the rhizosphere. PMID:26155673

  9. Diversity within the genus Elymus (Poaceae: Triticeae) as investigated by the analysis of the nr5S rDNA variation in species with St and H haplomes.

    Science.gov (United States)

    Baum, B R; Edwards, T; Johnson, D A

    2015-02-01

    The genus Elymus ("Ryegrass") is a repository for a range of species with a variety of haplome contents; hence the pejorative name "dustbin" genus. We have analyzed 1,059 sequences from 128 accessions representing 24 species to investigate the relationships among the StH haplomes-containing species described by Yen and Yang (Genus Elymus Beijing 5:58-362, 2013). Sequences were assigned to "unit classes" of orthologous sequences and subjected to a suite of analyses including BLAST (Basic Local Alignment Search Tool) searches, phylogenetic analysis and population genetic analysis to estimate species diversity. Our results support the genome analyses in Yen and Yang (Genus Elymus Beijing 5:58-362, 2013), i.e., genomic constitution StStHH including variants restricted to Elymus. Population genetic analysis of the 5S nrDNA sequence data revealed that the within-species variance component is roughly ±89 %; thus, we were unable to identify molecular markers capable to separate the 24 species analyzed. Separate phylogenetic analyses of the two unit classes and of all the data exhibit a trend only of the species to cluster on the phylograms. Finally, the analysis provides evidence for the multiple origins of American and Eurasian species. PMID:25248636

  10. Influence of allelic Variations of hypoxia-related and DNA repair genes on patient outcome and toxicity in head and neck cancer treated with radiotherapy plus cetuximab.

    Science.gov (United States)

    Muñoz, Carmen; Caballero, Miguel; Hakim, Sofia; Verger, Eugenia; Grau, Juan Jose

    2016-08-01

    Although cetuximab plus radiotherapy is a standard treatment for patients with inoperable head and neck squamous cell carcinoma (HNSCC), its efficacy varies greatly among individuals. To identify predictive markers of efficacy, we examined the effects of single nucleotide polymorphisms (SNPs) in hypoxia-related and DNA repair genes on the clinical outcome and occurrence of skin toxicity. We analyzed 61 consecutive patients with HNSCC for the presence of specific SNPs (HIF-1α, HIF-2α, HIF-1β, VHL, FIH-1, XRCC1, and XRCC5). The results were then correlated with time to progression (TTP), overall survival (OS), and toxicity (epithelitis, mucositis, and folliculitis). The median TTP and OS were better in patients with severe vs mild mucositis (17 vs 7 months, p = 0.03; and 26 vs 12 months, p = 0.016, respectively) and folliculitis (10 vs 7 months, p = 0.01, and 26 vs 10 months, p < 0.001, respectively). Patients with the HIF-1α CT/TT genotype had better OS than those with the wild-type HIF-1α CC genotype (28 vs 13 months, p = 0.035). Patients with the XRCC5 GG/AA genotype had longer TTP than patients with the XRCC5 AG genotype (11 vs 7 months, p = 0.035). Severe skin toxicity and SNPs of HIF-1α and XRCC5 were associated with different outcomes among patients treated with radiotherapy plus cetuximab. PMID:26245169

  11. Mitochondrial DNA suggests a single maternal origin for the widespread triploid parthenogenetic pest species, Paratanytarsus grimmii, but microsatellite variation shows local endemism

    Institute of Scientific and Technical Information of China (English)

    Melissa Carew; Bryant Gagliardi; Ary A.Hoffmann

    2013-01-01

    Parthenogenesis is common among invasive pest species,with many parthenogenetic species also showing polyploidy.Parthenogenetic polyploid species often have multiple hybrid origins and the potential to rapidly spread over vast geographical areas.In this study,we examine patterns of mitochondrial and microsatellite variation in a widespread triploid parthenogenetic chironomid pest species,Paratanytarsus grimmii.Based on samples from five countries,including Australia,England,Germany,Japan,and Canada,we found extremely low mitochondrial diversity (< 0.14%),with most individuals sharing a common and widespread haplotype.In contrast,microsatellite diversity revealed 41 clonal variants,which were regionally endemic.These findings suggest a single invasive maternal lineage of P.grimmii is likely to have recently spread over a broad geographical range.High levels of genotypic endemism suggest P.grimmii populations have remained relatively isolated after an initial spread,with little ongoing migration.This,in part,can be attributed to rapid genetic differentiation via mutations of common clonal genotypes after P.grimmii spread,but multiple polyploidization and subsequent founder events are also likely to be contributing factors.

  12. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

    Science.gov (United States)

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

    2015-12-01

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. PMID:26608057

  13. 不育夫妇中男性精子DNA碎片指数变异的研究%Variation of sperm DNA fragmentation index in male partners from infertile couples

    Institute of Scientific and Technical Information of China (English)

    费前进; 金建远; 倪吴花; 黄学锋

    2013-01-01

    目的 探讨不育夫妇中男性精子DNA碎片指数(DNA fragmentation index,DFI)的变异程度.方法 2009年4月至2012年4月,将539对不育夫妇中的539例男性纳入本研究.根据世界卫生组织标准(1999年),应用精子染色质扩散(sperm chromatin dispersion,SCD)试验对每名男性进行至少1次的重复精液常规分析和DFI检测,计算DFI的变异系数(coefficient of variation,CV),对DFI的变异程度及其影响因素进行统计分析.结果 539例男性中,有473例、59例、6例和1例分别行1次、2次、3次和4次重复精液常规分析和DFI检测,共计613次重复检测,重复检测和首次检测的间隔时间为0.5~34个月,中位数3.0(1.0~11.0)个月.539份首次检测样本间的DFI变异系数(between-sample coefficient of variation,CVB)为71.2%.与首次检测间隔0.5~3个月、3~12个月和12~34个月的DFI与首次检测的DFI比较,差异均有统计学意义(P<0.01).以18%作为男性生育力的DFI阈值,539例男性中有142例(26.3%,95%CI:22.6%~30.0%)的首次和重复检测DFI值分别位于阈值两侧.539例男性自身DFI的变异系数(within-subject coefficient of variation,CVw)为0.0~110.5%,中位数为26.0%(12.6%~42.8%),精子总数、精子浓度、精子活动力和精子形态的CVw的中位数分别为41.9%(21.8%~72.6%)、31.9%(15.1%~62.5%)、29.4%(13.2%~55.4%)和46.0%(22.4%~87.1%),各精液常规参数的CVw分别与DFI的CVw比较,差异均有统计学意义(P<0.01).DFI的CVw与精子总数、精子浓度和DFI重复检测的间隔时间密切相关(P<0.05).结论 不育夫妇中的男性精子DFI是一个变异较大的参数,应对每例男性的DFI进行重复检测才能反映其精子DNA损伤的水平.%Objective To investigate variation of sperm DNA fragmentation index (DFI) in male partners of infertile couples.Methods A total of 539 males between April 2009 and April 2012 were analyzed.At least one repeated

  14. Male fertility versus sterility, cytotype, and DNA quantitative variation in seed production in diploid and tetraploid sea lavenders (Limonium sp., Plumbaginaceae) reveal diversity in reproduction modes.

    Science.gov (United States)

    Róis, Ana Sofia; Teixeira, Generosa; Sharbel, Timothy F; Fuchs, Jörg; Martins, Sérgio; Espírito-Santo, Dalila; Caperta, Ana D

    2012-12-01

    were present in each seed. Flow cytometric seed screens using such mature seeds showed quantitative variations in seeds ploidy level. It is concluded that male function seems to play an important role in the reproduction modes of Limonium diploids and tetraploids.

  15. Cleaving DNA with DNA

    Science.gov (United States)

    Carmi, Nir; Balkhi, Shameelah R.; Breaker, Ronald R.

    1998-03-01

    A DNA structure is described that can cleave single-stranded DNA oligonucleotides in the presence of ionic copper. This ``deoxyribozyme'' can self-cleave or can operate as a bimolecular complex that simultaneously makes use of duplex and triplex interactions to bind and cleave separate DNA substrates. Bimolecular deoxyribozyme-mediated strand scission proceeds with a kobs of 0.2 min-1, whereas the corresponding uncatalyzed reaction could not be detected. The duplex and triplex recognition domains can be altered, making possible the targeted cleavage of single-stranded DNAs with different nucleotide sequences. Several small synthetic DNAs were made to function as simple ``restriction enzymes'' for the site-specific cleavage of single-stranded DNA.

  16. [Genetic variation and phylogeography of the bank vole (Clethrionomys glareolus, Arvicolinae, Rodentia) in Russia with special reference to the introgression of the mtDNA of a closely related species, red-backed vole (C. rutilus)].

    Science.gov (United States)

    Abramson, N I; Rodchenkova, E N; Kostygov, A Iu

    2009-05-01

    Totally, 294 bank voles (Clethrionomys glareolus) and 18 red-backed voles (C. rutilus) from 62 sites of European Russia were studied. Incomplete sequences (967 bp) of the mitochondrial cytochrome b gene were determined for 93 C. glareolus individuals from 56 sites and 18 C. rutilus individuals from the same habitats. Analysis of the cytochrome b gene variation has demonstrated that practically the entire European part of Russia, Ural, and a considerable part of Western Europe are inhabited by bank voles of the same phylogroup, displaying an extremely low genetic differentiation. Our data suggest that C. glareolus very rapidly colonized over the presently occupied territory in the post-Pleistocene period from no more than two (central European and western European) refugia for ancestral populations with a small efficient size. PCR typing of the mitochondrial cytochrome b gene allowed us to assess the scale of mtDNA introgression from a closely related species, C. rutilus, and to outline the geographical zone of this introgression. Comparison with the red-backed vole haplotypes in the habitats shared by both species favors the hypothesis of an ancient hybridization event (mid-Holocene) and a subsequent introgression. These results suggest that the hybridization took place in the southern and middle Pre-Ural region. PMID:19534420

  17. DNA Probes Show Genetic Variation in Cyanobacterial Symbionts of the Azolla Fern and a Closer Relationship to Free-Living Nostoc Strains than to Free-Living Anabaena Strains

    OpenAIRE

    Plazinski, Jacek; Zheng, Qi; Taylor, Rona; Croft, Lynn; Rolfe, Barry G.; Gunning, Brian E. S.

    1990-01-01

    Twenty-two isolates of Anabaena azollae derived from seven Azolla species from various geographic and ecological sources were characterized by DNA-DNA hybridization. Cloned DNA fragments derived from the genomic sequences of three different A. azollae isolates were used to detect restriction fragment length polymorphism among all symbiotic anabaenas. DNA clones were radiolabeled and hybridized against southern blot transfers of genomic DNAs of different isolates of A. azollae digested with re...

  18. Common DNA sequence variation and psychiatric disease

    OpenAIRE

    Ripke, S

    2014-01-01

    In a genome-wide association study (GWAS), a large number of SNPs are genotyped in a large number of cases (with disease) and controls (without disease) using commercially available high-throughput genotyping platforms. In a GWAS, the genotype data collected in cases and unaffected, population-matched controls are compared. Other than identifying individuals with the disease, there is no requirement for prior biological knowledge of the trait under investigation. This analysis approach has di...

  19. Genetisk variation og langt liv

    DEFF Research Database (Denmark)

    Sørensen, Mette

    2013-01-01

    andre ikke gør. I dette ph.d.-projekt undersøgte vi sammenhængen mellem levetid og variation i tre biologiske skadesprocesser. De tre er: antioxidanter, væksthormon/insulin-signalering og DNA-reparation. Vi fandt nye genvariationer, hvoraf nogle har positiv indflydelse på chancen for at blive meget...

  20. FROG - Fingerprinting Genomic Variation Ontology.

    Directory of Open Access Journals (Sweden)

    E Abinaya

    Full Text Available Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies. FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  1. FROG - Fingerprinting Genomic Variation Ontology.

    Science.gov (United States)

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  2. Salt Tolerance of Rice Variation Germplasm with Transformed Common Wild Rice (Oryza rufipogon) DNA%导入普通野生稻DNA的水稻变异种质的耐盐性鉴定

    Institute of Scientific and Technical Information of China (English)

    吕学莲; 白海波; 李树华; 蔡正云; 高晓原

    2012-01-01

    The research aimed to study salt tolerance of rice variation germplasm with transformed common wild rice DNA, and screen out the materials with high salt tolerance, so as to provide germplasm for salt-tolerant rice breeding. Ten rice variation germplasms of 'Ningjing 23' were used to study germination and seedling growth. The results showed that, when treated with 170 mmol/L NaCl, the germination level and germination rate of materials D42, D5-54, D5-27, D-10, D102, DJ18 and D68 were high, and its relative salt harm rate were low. With the solution containing 120 mmol/L NaCl, the salt tolerance of D5-27, DJ18, D5-54 and D-10 were strong, and the ratio of salt treatment and non-salt treatment of ground and underground, fresh and dry weights were high. The increased soluble sugar content of materials D5-27, DJ18, D5-54 and D-10 were higher than its receptor. Materials D42, D5-54, D5-27, D-10, D102, DJ18 and D68 had high salt tolerance in germinating stage, and materials D5-27, DJ18, D5-54 and D-10 had high salt tolerance in seedling stage.%旨在研究导入普通野生稻DNA的水稻后代的耐盐性,从中筛选出耐盐性较强的材料,为水稻耐盐育种提供种质资源.以普通野生稻DNA导入到宁夏栽培水稻‘宁粳23号’中获得的10份变异后代为材料,研究各材料在盐胁迫下的发芽特性和幼苗生长情况.结果表明在170 mmol/L NaCl处理下,材料D42、D5-54、D5-27、D-10、D102、DJ18和D68的发芽势和发芽率均较高,相对盐害率较低,在盐浓度为120 mmol/L时,材料D5-27、DJ18、D5-54和D-10的耐盐性为强,地上和地下鲜、干重的盐处理与非盐处理的比值较高,材料D5-27、DJ18、D5-54和D-10的可溶性糖积累量高于其受体.材料D42、D5-54、D5-27、D-10、D102、DJ18和D68的芽期耐盐性较强,材料D5-27、DJ18、D5-54和D-10属于苗期较耐盐的材料.

  3. Variational principles

    CERN Document Server

    Moiseiwitsch, B L

    2004-01-01

    This graduate-level text's primary objective is to demonstrate the expression of the equations of the various branches of mathematical physics in the succinct and elegant form of variational principles (and thereby illuminate their interrelationship). Its related intentions are to show how variational principles may be employed to determine the discrete eigenvalues for stationary state problems and to illustrate how to find the values of quantities (such as the phase shifts) that arise in the theory of scattering. Chapter-by-chapter treatment consists of analytical dynamics; optics, wave mecha

  4. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  5. Heritable epigenetic variation among maize inbreds.

    Directory of Open Access Journals (Sweden)

    Steve R Eichten

    2011-11-01

    Full Text Available Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays, an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs. Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic

  6. Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States

    Energy Technology Data Exchange (ETDEWEB)

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A.; Tomkinson, Alan E.; Ellenberger, Tom (Scripps); (Maryland-MED); (WU-MED); (LBNL)

    2010-09-13

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a 'jackknife model' in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.

  7. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.

    Science.gov (United States)

    Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal; Tainer, John A; Tomkinson, Alan E; Ellenberger, Tom

    2010-07-27

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a "jackknife model" in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers. PMID:20518483

  8. Programmable Quantitative DNA Nanothermometers.

    Science.gov (United States)

    Gareau, David; Desrosiers, Arnaud; Vallée-Bélisle, Alexis

    2016-07-13

    Developing molecules, switches, probes or nanomaterials that are able to respond to specific temperature changes should prove of utility for several applications in nanotechnology. Here, we describe bioinspired strategies to design DNA thermoswitches with programmable linear response ranges that can provide either a precise ultrasensitive response over a desired, small temperature interval (±0.05 °C) or an extended linear response over a wide temperature range (e.g., from 25 to 90 °C). Using structural modifications or inexpensive DNA stabilizers, we show that we can tune the transition midpoints of DNA thermometers from 30 to 85 °C. Using multimeric switch architectures, we are able to create ultrasensitive thermometers that display large quantitative fluorescence gains within small temperature variation (e.g., > 700% over 10 °C). Using a combination of thermoswitches of different stabilities or a mix of stabilizers of various strengths, we can create extended thermometers that respond linearly up to 50 °C in temperature range. Here, we demonstrate the reversibility, robustness, and efficiency of these programmable DNA thermometers by monitoring temperature change inside individual wells during polymerase chain reactions. We discuss the potential applications of these programmable DNA thermoswitches in various nanotechnology fields including cell imaging, nanofluidics, nanomedecine, nanoelectronics, nanomaterial, and synthetic biology. PMID:27058370

  9. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent d...

  10. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.;

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  11. [DNA computing].

    Science.gov (United States)

    Błasiak, Janusz; Krasiński, Tadeusz; Popławski, Tomasz; Sakowski, Sebastian

    2011-01-01

    Biocomputers can be an alternative for traditional "silicon-based" computers, which continuous development may be limited due to further miniaturization (imposed by the Heisenberg Uncertainty Principle) and increasing the amount of information between the central processing unit and the main memory (von Neuman bottleneck). The idea of DNA computing came true for the first time in 1994, when Adleman solved the Hamiltonian Path Problem using short DNA oligomers and DNA ligase. In the early 2000s a series of biocomputer models was presented with a seminal work of Shapiro and his colleguas who presented molecular 2 state finite automaton, in which the restriction enzyme, FokI, constituted hardware and short DNA oligomers were software as well as input/output signals. DNA molecules provided also energy for this machine. DNA computing can be exploited in many applications, from study on the gene expression pattern to diagnosis and therapy of cancer. The idea of DNA computing is still in progress in research both in vitro and in vivo and at least promising results of these research allow to have a hope for a breakthrough in the computer science. PMID:21735816

  12. DNA probes

    International Nuclear Information System (INIS)

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  13. Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants.

    Science.gov (United States)

    Alvarado, Sebastian; Rajakumar, Rajendhran; Abouheif, Ehab; Szyf, Moshe

    2015-01-01

    Complex quantitative traits, like size and behaviour, are a pervasive feature of natural populations. Quantitative trait variation is the product of both genetic and environmental factors, yet little is known about the mechanisms through which their interaction generates this variation. Epigenetic processes, such as DNA methylation, can mediate gene-by-environment interactions during development to generate discrete phenotypic variation. We therefore investigated the developmental role of DNA methylation in generating continuous size variation of workers in an ant colony, a key trait associated with division of labour. Here we show that, in the carpenter ant Camponotus floridanus, global (genome-wide) DNA methylation indirectly regulates quantitative methylation of the conserved cell-signalling gene Epidermal growth factor receptor to generate continuous size variation of workers. DNA methylation can therefore generate quantitative variation in a complex trait by quantitatively regulating the transcription of a gene. This mechanism, alongside genetic variation, may determine the phenotypic possibilities of loci for generating quantitative trait variation in natural populations. PMID:25758336

  14. Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants.

    Science.gov (United States)

    Alvarado, Sebastian; Rajakumar, Rajendhran; Abouheif, Ehab; Szyf, Moshe

    2015-03-11

    Complex quantitative traits, like size and behaviour, are a pervasive feature of natural populations. Quantitative trait variation is the product of both genetic and environmental factors, yet little is known about the mechanisms through which their interaction generates this variation. Epigenetic processes, such as DNA methylation, can mediate gene-by-environment interactions during development to generate discrete phenotypic variation. We therefore investigated the developmental role of DNA methylation in generating continuous size variation of workers in an ant colony, a key trait associated with division of labour. Here we show that, in the carpenter ant Camponotus floridanus, global (genome-wide) DNA methylation indirectly regulates quantitative methylation of the conserved cell-signalling gene Epidermal growth factor receptor to generate continuous size variation of workers. DNA methylation can therefore generate quantitative variation in a complex trait by quantitatively regulating the transcription of a gene. This mechanism, alongside genetic variation, may determine the phenotypic possibilities of loci for generating quantitative trait variation in natural populations.

  15. Chloroplast DNA trnQ-rps16 variation and genetic structure of nine wild Chinese cherry (Cerasus pseudocerasus Lindl.) populations%9个野生中国樱桃群体叶绿体 DNA trnQ-rps16序列变异及其遗传结构分析

    Institute of Scientific and Technical Information of China (English)

    陈涛; 王小蓉; 罗华; 王春涛; 张家志; 罗明敏

    2012-01-01

    Chinese cherry (Cerasus pseudocerasus Lindl.) is one of the most economically domestic fruit trees in China. The rich variation of wild Chinese cherry is the most important breeding resource for existing cultivars. In order to reveal the levels and distribution of genetic variation within wild Chinese cherry of Sichuan Province, China, where is rich in wild Chinese cherry, the sequence variation of chloroplast DNA trnQ-rps16 intergenic spacer was analyzed in 145 individuals of all nine existing populations (seven from Sichuan, two from Shanxi and Guizhou provinces) of China. The results showed that trnQ-rps16 sequence were aligned with 13 polymorphic sites (1.87%), including 3 substitutions and 10 indels in 145 individuals, which revealed a low level of genetic diversity (h= 0.562,Π= 0.00184). Compared to other regions (h= 0.733, Π= 0.00243), a rather lower genetic diversity (h= 0.544,π= 0.00203) was found in the populations from Sichuan, and a large scale of genetic diversity among the seven populations was detected (h= 0-0.708; π= 0-0.00298), ranging from EM (h=0.000, Π=0.000) to TL (h=0.708, Π=0.00298). The low genetic diversity of populations may be strongly affected by founder effect and bottleneck effect because of the marginal nature, recent reduction, and consequent genetic drift of these populations. In addition, a fairly low genetic differentiation (FST= 0.21573) was found among the studied populations. This suggest that gene flow seems to originate from pronounced seed dispersal abilities of the species and it may play a significant role in shaping such a genetic structure. The long generation cycle of the species may also contribute to this structure. Based on these findings, a conservational plan for sampling or preserving fewer populations but more individuals from each population for the species was proposes.%中国樱桃(Cerasus pseudocerasus Lindl.)是我国古老的具有较高经济价值的栽培果树之一,个别性状突 出的野生

  16. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  17. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  18. Fleet DNA (Presentation)

    Energy Technology Data Exchange (ETDEWEB)

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  19. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  20. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

    LIU; Tao; LIN; Lin; ZHAO; Hong; JIANG; Long

    2005-01-01

    This review summarizes recent advances in DNA sensor. Major areas of DNA sensor covered in this review include immobilization methods of DNA, general techniques of DNA detection and application of nanoparticles in DNA sensor.

  1. Sequence length variation of internal genic space of 16S rDNA-23S rDNA in biohydrogen-bacterium%产氢菌的16S -23S rDNA间隔区的长度变异性分析

    Institute of Scientific and Technical Information of China (English)

    李永峰; 郑国香; 张文启; 李建政; 胡立杰

    2005-01-01

    生物制氢细菌Rennanqilyf3的16S rRNA gene (rDNA)-23S rDNA间隔区碱基序列被测定.利用PCR扩增间隔区DNA,间隔区碱基序列存在长度多态现象.用这一长度多态现象进行产氢发酵细菌的辨认和识别.产氢发酵细菌Rennanqilyf3的16S rRNA gene (rDNA)-23S rDNA间隔区的PCR产品从1 270 到398 bp,共有5个序列.碱基数目分别为1 270、398、638、437 和 436 bp.%A method based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions was developed for the identification of species for fermentative biohydrogen-producing bacterium. The sizes of the PCR products varied from 1 270 to 398 bp. Strain of Rennanqilyf3 were characterized as having products of 1 270,398,638, 437 and 436bp.

  2. DNA-repair gene variants are associated with glioblastoma survival

    DEFF Research Database (Denmark)

    Wibom, Carl; Sjöström, Sara; Henriksson, Roger;

    2012-01-01

    Abstract Patient outcome from glioma may be influenced by germline variation. Considering the importance of DNA repair in cancer biology as well as in response to treatment, we studied the relationship between 1458 SNPs, which captured the majority of the common genetic variation in 136 DNA repai...

  3. Genetic variation between susceptible and non-susceptible snails to Schistosoma infection using random amplified polymorphic DNA analysis (RAPDs Variação genética entre moluscos susceptíveis e não susceptíveis à infecção pelo Schistosoma através da análise do DNA polimórfico amplificado aleatóriamente (RAPDs

    Directory of Open Access Journals (Sweden)

    Abdel-Hamid Zaki ABDEL-HAMID

    1999-09-01

    Full Text Available Susceptibility of snails to infection by certain trematodes and their suitability as hosts for continued development has been a bewildering problem in host-parasite relationships. The present work emphasizes our interest in snail genetics to determine what genes or gene products are specifically responsible for susceptibility of snails to infection. High molecular weight DNA was extracted from both susceptible and non-susceptible snails within the same species Biomphalaria tenagophila. RAPD was undertaken to distinguish between the two types of snails. Random primers (10 mers were used to amplify the extracted DNA by the polymerase chain reaction (PCR followed by polyacrylamide gel electrophoresis (PAGE and silver staining. The results suggest that RAPD represents an efficient means of genome comparison, since many molecular markers were detected as genetic variations between susceptible and non-susceptible snails.A susceptibilidade de moluscos à infecção por certos trematódeos e a sua capacidade como hospedeiro para o contínuo desenvolvimento é o problema mais deslumbrante nas relações parasita hospedeiro. O presente trabalho, focaliza nosso interesse na genética dos moluscos para determinar quais genes ou produtos gênicos são especificamente responsáveis pela susceptibilidade do molusco à infecção. DNA de alto peso molecular, foi extraído de ambos moluscos susceptíveis e não susceptíveis da espécie Biomphalaria tenagophila. Iniciadores aleatórios com 10 pares de bases foram usados na amplificação aleatória (RAPD de ambos os DNAs e análise por eletroforese em gel de poliacrilamida e coloração com prata. Os resultados mostram que a amplificação aleatória do DNA representa um eficiente caminho para a comparação dos genomas desde que marcadores moleculares foram detectados como variantes genéticos entre os moluscos susceptíveis e não susceptíveis.

  4. DNA vaccines

    Science.gov (United States)

    Gregersen, Jens-Peter

    2001-12-01

    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  5. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman

    2003-01-01

    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  6. 四种群东方田鼠线粒体DNA D-loop多态性研究%Study on Sequence Variation of Mitochondrial D-loop Gene and Polymorphism among four populations of Reed Vole (Microtus fortis)

    Institute of Scientific and Technical Information of China (English)

    谢建云; 冯洁; 柏熊; 胡建华; 高诚

    2008-01-01

    目的 探讨我国不同地区东方田鼠线粒体DNA D-loop多态性.方法 对四个种群东方田鼠线粒体DNA(mt DNA)D-loop片段进行测序,并对测序结果用Clustal W软件进行比对,通过MEGA Version3.1软件构建基于平均遗传距离的NJ(neighbor-joining,邻接法)分子系统进化树,用Dnasp4.0分析所有序列的多态位点、核苷酸多样性、单倍型数目、单倍型多样性以及进行Tajima's中性显著性检验.结果 四个种群34个东方田鼠个体的mtDNA D-loop区全序列共发现19个单倍型,单倍型比例为55.88%,单倍型多样性和核苷酸多样性分别为0.934±0.024和0.04334±0.00285.以台湾田鼠(Microtus kikuchii)线粒体全序列(GenBank登录号AF348082)为对照,共检测到核苷酸变异位点172个,约占核苷酸总教的18.66%.由分子系统进化树可发现所有34只东方田鼠分为两大类,小体型黑龙江东方田鼠为一类,其他三个种群东方田鼠为另外一类,在这一类别中,又有两个分支,其中所有宁夏种群鼠及3只大体型黑龙江种群鼠为一个分支,所有洞庭湖种群鼠和其他5只大体型黑龙江种群鼠为另一个分支.结论 我国东方田鼠在mt DNA D-loop片段存在种内遗传多态性,种群内和种群间都存在一定的遗传变异,并且黑龙江小体型种群东方田鼠表现出与其他三种群东方田鼠更大的差异水平.

  7. Analysis of chromatin integrity and DNA damage of buffalo spermatozoa.

    Science.gov (United States)

    Mahmoud, K Gh M; El-Sokary, A A E; Abdel-Ghaffar, A E; Abou El-Roos, M E A; Ahmed, Y F

    2015-01-01

    This study was conducted to determine chromatin integrity and DNA damage by DNA electrophoresis and comet assays of buffalo fresh and frozen semen. Semen samples were collected from four buffalo bulls and evaluated after freezing for semen motility, viability, sperm abnormalities, chromatin integrity and DNA damage. A significant variation was found in semen parameters after thawing. Highly significant differences (Partificial insemination. PMID:27175169

  8. DNA nanotechnology

    OpenAIRE

    Seeman, Nadrian C.

    2003-01-01

    Since Watson and Crick’s determination of its structure nearly 50 years ago, DNA has come to fill our lives in many areas, from genetic counseling to forensics, from genomics to gene therapy. These, and other ways in which DNA affects human activities, are related to its function as genetic material, not just our genetic material, but the genetic material of all living organisms. Here, we will ignore DNA’s biological role; rather, we will discuss how the properties that make it so successful ...

  9. Modeling inhomogeneous DNA replication kinetics.

    Directory of Open Access Journals (Sweden)

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  10. Rationally designed coiled-coil DNA looping peptides control DNA topology.

    Science.gov (United States)

    Gowetski, Daniel B; Kodis, Erin J; Kahn, Jason D

    2013-09-01

    Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein-DNA nanostructures.

  11. Genetic Variation of Host Populations of Liriomyza sativae Blanchard

    Institute of Scientific and Technical Information of China (English)

    WANG Li-ping; DU Yu-zhou; HE Ya-ting; ZHENG Fu-shan; LU Zi-qiang

    2008-01-01

    In this study, partial sequences of the mitochondrial cytochrome oxidase subunit Ⅰ (mtDNA-COI) gene and the ribosomal internal transcribed spacer 1 (rDNA-ITS1) gene, isolated from five artificial populations of Liriomyza sativae (Diptera:Agromyzidae), were sequenced and compared, to analyze their genetic variation. Analysis of the mtDNA-CO1 gene showed that a low genetic variation was detected among the five populations and only five variable sites were found in the nucleotide sequences. Most of the observed variations that occurred within the populations were because of nucleotide transitions, whereas, the interpopulation variation was because of the differences in haplotype frequencies occurring among the host populations. Analysis of the rDNA-ITS1 gene revealed a small diversity in the five host populations. The trend of genetic differentiation in the host populations was consistent with the preference of L. sativae to the plant hosts.

  12. Individual epigenetic variation: When, why, and so what?

    Science.gov (United States)

    Epigenetics provides a potential explanation for how environmental factors modify the risk for common diseases among individuals. Interindividual variation in DNA methylation and epigenetic regulation has been reported at specific genomic regions including transposable elements, genomically imprinte...

  13. Analysis diagnosis and clinical study of simple mitochondria DNA variations in type 2 diabetes mellitus%单纯线粒体DNA变异的2型糖尿病的检验诊断和临床研究

    Institute of Scientific and Technical Information of China (English)

    郦卫星; 吕建新

    2007-01-01

    目的 分析线粒体DNA(mitochondria DNA,mtDNA)变异与2型糖尿病(T2DM)及其并发症的关系,探讨mtDNA检测对于T2DM的诊断价值.方法 采用PCR产物直接测序法对浙江籍汉族人群中无血缘关系的315例T2DM患者及158名正常对照个体的mtDNA片段(nt3153~nt3551)进行分析,同时对每例患者作常规生化检测.结果 T2DM患者组和健康对照组与标准序列比对存在着大量的基因变异位点,具有中国汉族人的多态性.把患者检测到的变异位点结合临床资料分析发现T3183A、A3243G、T3290C、T3338C、T3398C、G3421A、C3435T等基因变异与糖尿病家族史或并发症有密切联系.比较有家族史和无家族史的有基因变异的T2DM患者,有家族史组发病年龄较无家族史组明显提前[(47.7±11.1)岁与(55.1±13.8)岁,t=2.489,P<0.05],有家族史组的体重指数(BMI)显著低于无家族史组[(20.59±5.16)kg/m2与(23.82±2.32)kg/m2,t=3.234,P<0.01],差异有统计学意义;而两组的甘油三酯(TG)[(1.32±0.60)mmol/L与(1.33±0.68)mmol/L,t=0.071,P>0.05]、总胆固醇(TC)[(4.07±1.23)mmol/L与(4.13±0.72)mmol/L,t=0.277,P>0.05]、空腹血糖(FBG)[(9.27±2.52)mmol/L与(9.49±3.36)mmol/L,t=0.308,P>0.05]等差异无统计学意义.结论 中国汉族人mtDNA存在多态性,T2DM患者mtDNA中存在着大量的变异位点,尽管mtDNA变异位点与糖尿病特征、家族史或并发症有一定关系,但目前尚不能作为诊断T2DM的独立指标.

  14. Standardization of anti-DNA antibody assays.

    Science.gov (United States)

    Pisetsky, David S

    2013-07-01

    Antibodies to DNA (anti-DNA) are the serological hallmark of systemic lupus erythematosus and represent important biomarkers for clinical and research purposes. These antibodies are part of a family of antibodies to nucleosomes and bind to conserved sites widely present on DNA. While the value of anti-DNA as a biomarker is well established, the assay for these antibodies has involved a variety of DNA sources and systems to detect DNA-anti-DNA interactions. The influence of these variations on antibody detection has complicated assay standardization. As an antigen, DNA has unique features since it is a highly charged polymer that has structural heterogeneity. This heterogeneity can affect antigenicity which can vary on the basis of DNA origin, size, conformation and mobility. In addition, as a polymer, DNA can promote patterns of antibody binding based on monogamous or bivalent interaction which require an extended polynucleotide structure. Understanding the nature of DNA as an antigen can facilitate interpretation of serological tests and underpin efforts at better standardization.

  15. TA1 oncofetal rat liver cDNA and putative amino acid permease: temporal correlation with c-myc during acute CCl4 liver injury and variation of RNA levels in response to amino acids in hepatocyte cultures.

    Science.gov (United States)

    Shultz, V D; Campbell, W; Karr, S; Hixson, D C; Thompson, N L

    1999-01-01

    TA1 is a rat liver oncofetal cDNA and a member of an emerging family of evolutionarily conserved molecules with homology to amino acid transporters and permeases. The aim of these studies was to characterize the regulation and role of TA1 in acute rat liver injury by examining its relation to regeneration and metabolic stress. Following a single dose of CCl4, TA1 message was expressed 3-48 h. The major 3.3-kb TA1 transcript correlated temporally with c-myc expression. A novel 2.9-kb TA1 transcript was expressed more variably 24-48 h. TA1 protein was restricted to hepatocytes in G0 and G1 phases of the cell cycle. Relative to CCl4, a much smaller increase in TA1 was noted after partial hepatectomy and TA1 preceded the peak of c-myc expression. In vitro TA1 was not induced in hepatocytes by EGF or the acute-phase cytokines IL-6 and TNF-alpha, but was found to be modulated in response to amino acid availability. TA1 expression increased in media without arginine and glutamine and was repressed by total amino acid levels 5-fold over basal MEM. Together, these results contrast with the constitutive expression observed in transformed cells and suggest an adaptive role for TA1 during liver injury.

  16. PCR-based random amplified polymorphic DNA technique used for the genetic variations of pathogenic strains of Paragonimus westermani%卫氏并殖吸虫致病品系PCR-RAPD分子标记的初步研究

    Institute of Scientific and Technical Information of China (English)

    钱宝珍; 沈琦

    2006-01-01

    目的探讨卫氏并殖吸虫致病品系PCR-RAPD分子标记.方法应用随机扩增多态DNA(PCR-RAPD)技术,对浙江宁海小汀、宁海西溪、遂昌、临安等地卫氏并殖吸虫囊蚴进行遗传变异研究.结果通过8条寡核苷酸随机引物扩增,B17-1600bp为浙江宁海小汀肺吸虫种群特异性DNA片段,A9-680bp为浙江宁海西溪,遂昌、临安三地肺吸虫种群共有特异性DNA片段.结论结果提示B17-1600bp,A9-680bp可作为卫氏并殖吸虫不同致病品系的分子标记.

  17. DNA-modified Electrodes Fabricated using Copper-Free Click Chemistry for Enhanced Protein Detection

    OpenAIRE

    Furst, Ariel L.; Hill, Michael G.; Barton, Jacqueline K.

    2013-01-01

    A method of DNA monolayer formation has been developed using copper-free click chemistry that yields enhanced surface homogeneity and enables variation in the amount of DNA assembled; extremely low-density DNA monolayers, with as little as 5% of the monolayer being DNA, have been formed. These DNA-modified electrodes (DMEs) were characterized visually, with AFM, and electrochemically, and were found to facilitate DNA-mediated reduction of a distally bound redox probe. These low-density monola...

  18. First evidence of DNA methylation in insect Tribolium castaneum: environmental regulation of DNA methylation within heterochromatin.

    Science.gov (United States)

    Feliciello, Isidoro; Parazajder, Josip; Akrap, Ivana; Ugarković, Durđica

    2013-05-01

    DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.

  19. Study on Somaclonal Variation of Spring Wheat

    Institute of Scientific and Technical Information of China (English)

    JIANG Shu-mei; HU Shang-lian; LI Wen-xiong

    2004-01-01

    Somaclonal variation of calli and regenerated plants of spring wheat ware detected by using technique RAPD in the study. Calli at different culture stages and regenerated plants derived from young spikes and immature embryos were used as materials. Molecular variation could be reflected from electrophoresis patternof RAPD fragments at different culture stage in calli, and in regenerated plants derived from different explants, even no phenotype variations were found. Somaclonal variation in calli and in regenerated plants appeared regularly: A higher frequency of variation in hybrids F2 was detected than that of the cultivar that is stable genetically. High variation frequency of RAPD fragments appeared in calli when cultured 75 days. The identical variations of RAPD fragments were observed in calli and in the regenerated plants induced from different genotype or explants. The variation frequency detected is higher in regenerated plants than that of in calli. RAPD could be applied easily and simply to determine variation in level of DNA at each stage cultured in vitro.

  20. DNA Microarrays

    Science.gov (United States)

    Nguyen, C.; Gidrol, X.

    Genomics has revolutionised biological and biomedical research. This revolution was predictable on the basis of its two driving forces: the ever increasing availability of genome sequences and the development of new technology able to exploit them. Up until now, technical limitations meant that molecular biology could only analyse one or two parameters per experiment, providing relatively little information compared with the great complexity of the systems under investigation. This gene by gene approach is inadequate to understand biological systems containing several thousand genes. It is essential to have an overall view of the DNA, RNA, and relevant proteins. A simple inventory of the genome is not sufficient to understand the functions of the genes, or indeed the way that cells and organisms work. For this purpose, functional studies based on whole genomes are needed. Among these new large-scale methods of molecular analysis, DNA microarrays provide a way of studying the genome and the transcriptome. The idea of integrating a large amount of data derived from a support with very small area has led biologists to call these chips, borrowing the term from the microelectronics industry. At the beginning of the 1990s, the development of DNA chips on nylon membranes [1, 2], then on glass [3] and silicon [4] supports, made it possible for the first time to carry out simultaneous measurements of the equilibrium concentration of all the messenger RNA (mRNA) or transcribed RNA in a cell. These microarrays offer a wide range of applications, in both fundamental and clinical research, providing a method for genome-wide characterisation of changes occurring within a cell or tissue, as for example in polymorphism studies, detection of mutations, and quantitative assays of gene copies. With regard to the transcriptome, it provides a way of characterising differentially expressed genes, profiling given biological states, and identifying regulatory channels.

  1. Protocol for extraction of genomic DNA from swine solid tissues

    Directory of Open Access Journals (Sweden)

    Fernando Henrique Biase

    2002-01-01

    Full Text Available Molecular diagnostics are performed by using DNA from different body tissues. However, it is necessary to obtain genomic DNA of good quality. Due to the impossibility of collecting blood from slaughtered animals, DNA extraction from solid tissues is necessary. The objective of this study was to describe a protocol of DNA extraction from swine skin, adipose, brain, liver, kidney and muscle tissues. We obtained high molecular weight DNA of good quality, shown by agarose gel and amplification of two DNA fragments, 605bp and 891pb, by PCR. Spectrophotometric analysis of DNA concentration showed variation among the DNA from different tissues, with the liver and adipose tissues presenting the greatest and the smallest concentration, respectively. The described protocol has proven to be advantageous due to its simplicity, quickness, affordable reagents and absence of phenol, resulting in a high molecular weight DNA of good quality from several tissues.

  2. Forensic DNA methylation profiling from evidence material for investigative leads.

    Science.gov (United States)

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-07-01

    DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369]. PMID:27099236

  3. Forensic DNA methylation profiling from evidence material for investigative leads.

    Science.gov (United States)

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-07-01

    DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369].

  4. Studies of DNA-carbon nanotube interactions

    Science.gov (United States)

    Hughes, Mary Elizabeth

    2008-10-01

    Recently a new biomaterial consisting of a DNA-wrapped single-walled carbon nanotube, and known as a DNA/SWNT, has been discovered. The possible applications of this hybrid are varied and range from genomic sequencing to nanoscale electronics to molecular delivery. The realization of these potential applications requires more knowledge about the microscopic properties of this material. In this thesis, I present studies of: the orientation of nucleobases on the nanotube sidewall; the sequence and length dependence of the DNA-nanotube interaction; and solution conditions to manipulate the DNA/SWNT hybrid. The measurement of the UV optical absorbance of DNA/SWNT and the nucleotide absorbance from DNA/SWNT provide the first experimental confirmation that DNA binds to nanotubes through pi-stacking. Because the hypochromic absorbance typical of pi-stacked structures are expected to occur primarily for DNA dipole transitions that lie along the axis of the optically anisotropic SWNTs, the absorbance changes following binding of DNA to the nanotubes reveals the preferred orientation assumed by each of the four bound nucleotides with respect to the nanotube's long axis. The first observations of pronounced sequence- and length-dependent variations in the binding between ssDNA and SWNTs in aqueous solution are presented. These observations rely on the discovery that there exists a range of DNA lengths able to hybridize with SWNTs that can nevertheless be dissociated at temperatures below the boiling point of water. Quantitative results comparing the isochronal dissociation temperatures and binding energies of DNA/SWNT composed of differing DNA sequences and lengths are given. These results indicate variability and complexity in the binding mechanism responsible for the stability of the hybrid system that transcends simple models based on the sum of independent base-nanotube interactions. Binding energies between a DNA base and nanotube (0.05 to 0.09 eV per base) are similar

  5. Child Development and Structural Variation in the Human Genome

    Science.gov (United States)

    Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

    2013-01-01

    Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

  6. Optimal Placement of Origins for DNA Replication

    OpenAIRE

    Karschau, Jens; Blow, J. Julian; de Moura, Alessandro P. S.

    2012-01-01

    DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyse these stochastic properties of DNA and derive the positions of origins corresponding to the minimum replication time. We show that under some conditions the minimization of replication time leads to ...

  7. Calculus of variations

    CERN Document Server

    Elsgolc, L E; Stark, M

    1961-01-01

    Calculus of Variations aims to provide an understanding of the basic notions and standard methods of the calculus of variations, including the direct methods of solution of the variational problems. The wide variety of applications of variational methods to different fields of mechanics and technology has made it essential for engineers to learn the fundamentals of the calculus of variations. The book begins with a discussion of the method of variation in problems with fixed boundaries. Subsequent chapters cover variational problems with movable boundaries and some other problems; sufficiency

  8. MPLIFICATION AND VARIATION ANALYSIS OF JIAOZHOU BAY PELAGIC COPEPOD 18S RIBOSOMAL RNA GENE (18S rDNA)%胶州湾浮游桡足类18S核糖体RNA基因(18S rDNA)扩增及序列变异初步研究

    Institute of Scientific and Technical Information of China (English)

    门荣新; 杨官品; 刘永健; 管晓菁

    2005-01-01

    采用PCR扩增、文库构建、限制性片段长度多态性分析、序列分析和系统学分析等方法,初步研究了夏季胶州湾上层海水浮游桡足类核糖体小亚基RNA基因(18S rDNA)约1.5kb片段的序列变异.从浮游生物混合DNA中选择性扩增桡足类18S rDNA,建立桡足类18S rDNA变异类型文库,并从文库中随机挑选的30个克隆进行分析.结果表明,Vsp I限制性内切酶能将这些克隆分成频率分别为0.17、0.23和0.6的3种操作分类单元(OTUs),遗传多样性指数达到0.95.3条OTU代表克隆序列与甲壳纲桡足亚纲核苷酸差异数在75.4-97.8之间,而与其他亚纲的差异都高于100.3条OTU代表克隆序列均属于桡足亚纲,其中,AY437861和AY437862属于哲水蚤目.3条OTU代表克隆序列可分为2个高变异区和3个相对保守区,其GC%分别为47.37%、48.16%和48.57%.研究结果表明,混合DNA提取方法简单,设计的引物可选择性地扩增浮游桡足类18S rDNA,根据18S rDNA序列序列变异描述浮游桡足类多样性是可行的.研究结果也为在浮游桡足类分类中引入18S rDNA序列奠定了基础.

  9. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    Energy Technology Data Exchange (ETDEWEB)

    X Qiu; D Rau; V Parsegian; L Fang; C Knobler; W Gelbart

    2011-12-31

    Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.

  10. 线粒体D-loop序列变异与东方鲀属鱼类系统发育%PHYLOGENETIC RELATIONSHIPS OF THE GENUS TAKIFUGU (TETRAODONTIFORMES, TETRAODONTIDAE) TESTED BY mtDNA D-LOOP REGION SEQUENCE VARIATIONS

    Institute of Scientific and Technical Information of China (English)

    张玉波; 甘小妮; 何舜平

    2009-01-01

    The pufferfishes of the genus Takifugu are East Asian fish, mainly distribute along the coastal region in western part of the Sea of Japan and the East China. This genus is attached more and more importance to researchers, for Takifugu rubripes, which is one species in it, has been a new model fish in the post-genomic era. The details of the phylogenetic relationships within the genus remain unresolved. In the present paper, mitochondrial D-loop sequences of 11 species of the genus Takifugu were determined and analyzed to test the present phylogenetic hypotheses. The sequence saturation analysis was inferred from the shape of the trend line, which indicated that the sequence was unsaturated and could be used in the following phylogenetic analysis. After alignment, the sequence compositions and variations were analyzed by using MEGA 3 software. There were 841 sites, among which 395 sites were variable, and 267 were informative. There was significant difference in base compositional bias between the ingroup and the outgroup species. The uncorrected p-distance matrix obtained from the analysis of the alignment of all D-loop sequences showed that the relationships among the different species were closely. Neighbor-joining, Maximum Parsimony, Maximum Likelihood and Bayesian methods were employed for phylogenetics analysis, respectively. Due to the SH test about the phylogeny hypothesis, we chose the Bayesian tree as our best tree in this paper. The Bayesian tree has described a more clearly phylogeny and the analysis also has pointed out the basal species in the genus. The results indicate that the genus form a monophyletic groups, with the sister group consisted by T. oblongus and T. alboplumbeus is the basal group of the genus. Our results also show some confusion about the taxonomy in the genus, according to the data and combined analysis with the morphological characters, we suppose some species are in fact synonymous in this genus, which suggest that the taxonomy

  11. 亚洲玉米螟不同地理种群基于COⅠ基因序列初步分析%Variation of mtDNA COⅠ sequences in different geographic populations of the Asian corn borer, Ostrinia furnacalis

    Institute of Scientific and Technical Information of China (English)

    黄丽莉; 阙海勇; 陈超; 匡先钜; 薛芳森

    2012-01-01

    The mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COⅠ ) of 6 gen-populations of Ostrinia furnacalis ( Guenee) was sequenced. The identity and variation of the resultant sequences and their phylogenic relationships were established by Mega 5. The results show that there are some differences in COⅠ sequences among different geo-populations of 0. furnacalis and that the average evolutionary divergence between populations is 0. 012. Molecular phylogeny showed that the Sanyan, Guangzhou and Nanchang populations formed one branch, and the Taian, Haerbin and Langfang populations formed separate branches. The results of evolutionary divergence and molecular phylogeny suggest that the separation of different geo-populations of 0. furnacalis is, at least to some extent, relative to geographic distance.%本研究通过对我国亚洲玉米螟Ostrinia furnacalis (Guenée)6个地理种群的线粒体DNA COⅠ基因进行测序,运用分子进化遗传分析软件MEGA5对序列进行对比和同源性分析,并建立系统发育关系.结果表明,COⅠ基因在6个地理种群中进化具有—定的差异,平均遗传距离为0.013;进化树显示,亚洲玉米螟的三亚种群、广州种群与南昌种群聚为一支,然后与泰安种群聚为一支,再与哈尔滨种群聚为一支;而廊坊种群另聚成一支.遗传分歧度与系统发育进化关系均表明不同地理种群的遗传分化与地理距离之间具有一定的相关性.

  12. Variation in MAPT is not a contributing factor to the incomplete penetrance in LHON.

    Science.gov (United States)

    Hudson, Gavin; Yu-Wai-Man, Patrick; Griffiths, Philip G; Horvath, Rita; Carelli, Valerio; Zeviani, Massimo; Chinnery, Patrick F

    2011-07-01

    Leber's hereditary optic neuropathy (LHON) is a common cause of inherited blindness, primarily due to one of three mitochondrial DNA (mtDNA) mutations. LHON, which has an unexplained variable penetrance and pathology, is characterised by disruption of the mitochondrial respiratory chain ultimately resulting in degeneration of the retinal ganglion cells. Phosphorylation of the tau protein is known to cause neurodegeneration and variation in MAPT has been associated with a range of neurodegenerative disorders. Given the relationship between MAPT variation and altered mitochondrial respiratory chain function, we hypothesised that MAPT variation could contribute to the risk of blindness in LHON mtDNA mutation carriers. We studied MAPT variation in a large, well characterised LHON cohort, but were unable to find an association between MAPT genetic variation and visual failure in LHON mtDNA mutation carriers. Our findings suggest that genetic variation in MAPT is unlikely to make a major contribution to the risk of blindness among LHON mutation carriers.

  13. Keeping mtDNA in shape between generations.

    Directory of Open Access Journals (Sweden)

    James B Stewart

    2014-10-01

    Full Text Available Since the unexpected discovery that mitochondria contain their own distinct DNA molecules, studies of the mitochondrial DNA (mtDNA have yielded many surprises. In animals, transmission of the mtDNA genome is explicitly non-Mendelian, with a very high number of genome copies being inherited from the mother after a drastic bottleneck. Recent work has begun to uncover the molecular details of this unusual mode of transmission. Many surprising variations in animal mitochondrial biology are known; however, a series of recent studies have identified a core of evolutionarily conserved mechanisms relating to mtDNA inheritance, e.g., mtDNA bottlenecks during germ cell development, selection against specific mtDNA mutation types during maternal transmission, and targeted destruction of sperm mitochondria. In this review, we outline recent literature on the transmission of mtDNA in animals and highlight the implications for human health and ageing.

  14. Comparative Analysis of Eubacterial DNA Polymerase Ⅲ Alpha Subunits

    Institute of Scientific and Technical Information of China (English)

    Xiao-Qian Zhao; Jian-Fei Hu; Jun Yu

    2006-01-01

    DNA polymerase Ⅲ is one of the five eubacterial DNA polymerases that is responsible for the replication of DNA duplex. Among the ten subunits of the DNA polymerase Ⅲ core enzyme, the alpha subunit catalyzes the reaction for polymerizing both DNA strands. In this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequencebased phylogenetic and structural analyses. We found that all eubacterial genomes have one or more alpha subunits, which form either homodimers or heterodimers.Phylogenetic and domain structural analyses as well as copy number variations of the alpha subunit in each bacterium indicate the classification of alpha subunit into four basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essence in genome composition analysis. We also consolidated the naming convention to avoid further confusion in gene annotations.

  15. Sperm DNA oxidative damage and DNA adducts.

    Science.gov (United States)

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-12-01

    The objective of this study was to investigate DNA damage and adducts in sperm from coke oven workers who have been exposed to polycyclic aromatic hydrocarbons. A longitudinal study was conducted with repeated measurements during spermatogenesis. Coke-oven workers (n=112) from a coke-oven plant served the PAH-exposed group, while administrators and security personnel (n=67) served the control. Routine semen parameters (concentration, motility, vitality, and morphology) were analyzed simultaneously; the assessment of sperm DNA integrity endpoints included DNA fragmentation, bulky DNA adducts, and 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGuo). The degree of sperm DNA fragmentation was measured using the terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL) assay and sperm chromatin structure assay (SCSA). The PAH-exposed group had a significant increase in bulky DNA adducts and 8-oxo-dGuo compared to the control subjects (Ps=0.002 and 0.045, respectively). Coke oven workers' percentages of DNA fragmentation and denaturation from the PAH-exposed group were not significantly different from those of the control subjects (Ps=0.232 and 0.245, respectively). Routine semen parameters and DNA integrity endpoints were not correlated. Concentrations of 8-oxo-dGuo were positively correlated with percentages of DNA fragmentation measured by both TUNEL and SCSA (Ps=0.045 and 0.034, respectively). However, the concentrations of 8-oxo-dGuo and percentages of DNA fragmentation did not correlate with concentrations of bulky DNA adducts. In summary, coke oven workers with chronic exposure to PAHs experienced decreased sperm DNA integrity. Oxidative stress could contribute to the degree of DNA fragmentation. Bulky DNA adducts may be independent of the formation of DNA fragmentation and oxidative adducts in sperm. Monitoring sperm DNA integrity is recommended as a part of the process of assessing the impact of occupational and environmental toxins on sperm

  16. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  17. Mitochondrial DNA variants in obesity.

    Directory of Open Access Journals (Sweden)

    Nadja Knoll

    Full Text Available Heritability estimates for body mass index (BMI variation are high. For mothers and their offspring higher BMI correlations have been described than for fathers. Variation(s in the exclusively maternally inherited mitochondrial DNA (mtDNA might contribute to this parental effect. Thirty-two to 40 mtDNA single nucleotide polymorphisms (SNPs were available from genome-wide association study SNP arrays (Affymetrix 6.0. For discovery, we analyzed association in a case-control (CC sample of 1,158 extremely obese children and adolescents and 435 lean adult controls. For independent confirmation, 7,014 population-based adults were analyzed as CC sample of n = 1,697 obese cases (BMI ≥ 30 kg/m2 and n = 2,373 normal weight and lean controls (BMI<25 kg/m2. SNPs were analyzed as single SNPs and haplogroups determined by HaploGrep. Fisher's two-sided exact test was used for association testing. Moreover, the D-loop was re-sequenced (Sanger in 192 extremely obese children and adolescents and 192 lean adult controls. Association testing of detected variants was performed using Fisher's two-sided exact test. For discovery, nominal association with obesity was found for the frequent allele G of m.8994G/A (rs28358887, p = 0.002 located in ATP6. Haplogroup W was nominally overrepresented in the controls (p = 0.039. These findings could not be confirmed independently. For two of the 252 identified D-loop variants nominal association was detected (m.16292C/T, p = 0.007, m.16189T/C, p = 0.048. Only eight controls carried the m.16292T allele, five of whom belonged to haplogroup W that was initially enriched among these controls. m.16189T/C might create an uninterrupted poly-C tract located near a regulatory element involved in replication of mtDNA. Though follow-up of some D-loop variants still is conceivable, our hypothesis of a contribution of variation in the exclusively maternally inherited mtDNA to the observed larger correlations for BMI between mothers and

  18. Mitochondrial DNA sequences in single hairs from a southern African population.

    OpenAIRE

    Vigilant, L.; Pennington, R; Harpending, H; Kocher, T.D.; Wilson, A C

    1989-01-01

    Hypervariable parts of mitochondrial DNA (mtDNA) were amplified enzymatically and sequenced directly by using genomic DNA from single plucked human hairs. This method has been applied to study mtDNA sequence variation among 15 members of the !Kung population. A genealogical tree relating these aboriginal, Khoisan-speaking southern Africans to 68 other humans and to one chimpanzee has the deepest branches occurring amongst the !Kung, a result consistent with an African origin of human mtDNA. F...

  19. MitoVariome: a variome database of human mitochondrial DNA

    OpenAIRE

    Lee, Yong Seok; Kim, Woo-Yeon; Ji, Mihyun; Kim, Ji Han; Bhak, Jong

    2009-01-01

    Background Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forensics, degenerative diseases, cancers, and aging process. Typically, human mitochondrial DNA has various features such as HVSI, HVSII, single-nucleotide polymorphism (SNP), restriction enzyme sites, and short tandem repeat (STR). Results We present a variome database (MitoVariom...

  20. Wolbachia and DNA Barcoding Insects: Patterns, Potential, and Problems

    OpenAIRE

    M. Alex Smith; Claudia Bertrand; Kate Crosby; Eveleigh, Eldon S.; Jose Fernandez-Triana; Fisher, Brian L.; Jason Gibbs; Mehrdad Hajibabaei; Winnie Hallwachs; Katharine Hind; Jan Hrcek; Da-Wei Huang; Milan Janda; Janzen, Daniel H.; Yanwei Li

    2012-01-01

    Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Us...

  1. Human beta-defensin gene copy number variation and consequences in disease and evolution

    OpenAIRE

    Pala, Raquel Rodrigues

    2012-01-01

    Research on human genetic variation has shown that the human genome is not a fixed, invariant framework, but that there can be extensive structural variation. This variation includes copy number variation (CNV), which can lead to changes in DNA dosage contributing significantly to variation between individual human genomes and heritable traits. Human beta-defensins are small, secreted antimicrobial peptides encoded by DEFB genes located in a cluster of at least seven genes on 8p23.1. These...

  2. Osmylated DNA, a novel concept for sequencing DNA using nanopores

    Science.gov (United States)

    Kanavarioti, Anastassia

    2015-03-01

    Saenger sequencing has led the advances in molecular biology, while faster and cheaper next generation technologies are urgently needed. A newer approach exploits nanopores, natural or solid-state, set in an electrical field, and obtains base sequence information from current variations due to the passage of a ssDNA molecule through the pore. A hurdle in this approach is the fact that the four bases are chemically comparable to each other which leads to small differences in current obstruction. ‘Base calling’ becomes even more challenging because most nanopores sense a short sequence and not individual bases. Perhaps sequencing DNA via nanopores would be more manageable, if only the bases were two, and chemically very different from each other; a sequence of 1s and 0s comes to mind. Osmylated DNA comes close to such a sequence of 1s and 0s. Osmylation is the addition of osmium tetroxide bipyridine across the C5-C6 double bond of the pyrimidines. Osmylation adds almost 400% mass to the reactive base, creates a sterically and electronically notably different molecule, labeled 1, compared to the unreactive purines, labeled 0. If osmylated DNA were successfully sequenced, the result would be a sequence of osmylated pyrimidines (1), and purines (0), and not of the actual nucleobases. To solve this problem we studied the osmylation reaction with short oligos and with M13mp18, a long ssDNA, developed a UV-vis assay to measure extent of osmylation, and designed two protocols. Protocol A uses mild conditions and yields osmylated thymidines (1), while leaving the other three bases (0) practically intact. Protocol B uses harsher conditions and effectively osmylates both pyrimidines, but not the purines. Applying these two protocols also to the complementary of the target polynucleotide yields a total of four osmylated strands that collectively could define the actual base sequence of the target DNA.

  3. Osmylated DNA, a novel concept for sequencing DNA using nanopores

    International Nuclear Information System (INIS)

    Saenger sequencing has led the advances in molecular biology, while faster and cheaper next generation technologies are urgently needed. A newer approach exploits nanopores, natural or solid-state, set in an electrical field, and obtains base sequence information from current variations due to the passage of a ssDNA molecule through the pore. A hurdle in this approach is the fact that the four bases are chemically comparable to each other which leads to small differences in current obstruction. ‘Base calling’ becomes even more challenging because most nanopores sense a short sequence and not individual bases. Perhaps sequencing DNA via nanopores would be more manageable, if only the bases were two, and chemically very different from each other; a sequence of 1s and 0s comes to mind. Osmylated DNA comes close to such a sequence of 1s and 0s. Osmylation is the addition of osmium tetroxide bipyridine across the C5–C6 double bond of the pyrimidines. Osmylation adds almost 400% mass to the reactive base, creates a sterically and electronically notably different molecule, labeled 1, compared to the unreactive purines, labeled 0. If osmylated DNA were successfully sequenced, the result would be a sequence of osmylated pyrimidines (1), and purines (0), and not of the actual nucleobases. To solve this problem we studied the osmylation reaction with short oligos and with M13mp18, a long ssDNA, developed a UV–vis assay to measure extent of osmylation, and designed two protocols. Protocol A uses mild conditions and yields osmylated thymidines (1), while leaving the other three bases (0) practically intact. Protocol B uses harsher conditions and effectively osmylates both pyrimidines, but not the purines. Applying these two protocols also to the complementary of the target polynucleotide yields a total of four osmylated strands that collectively could define the actual base sequence of the target DNA. (paper)

  4. DNA encoding a DNA repair protein

    Science.gov (United States)

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  5. Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    Yun Fei BAI; Qin Yu GE; Tong Xiang LI; Jin Ke WANG; Quan Jun LIU; Zu Hong LU

    2005-01-01

    The double-stranded DNA (dsDNA) probe contains two different protein binding sites.One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme.The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.

  6. Studying Variation in Tunes

    NARCIS (Netherlands)

    Janssen, B.; van Kranenburg, P.

    2014-01-01

    Variation in music can be caused by different phenomena: conscious, creative manipulation of musical ideas; but also unconscious variation during music recall. It is the latter phenomenon that we wish to study: variation which occurs in oral transmission, in which a melody is taught without the help

  7. SNP and gene networks construction and analysis from classification of copy number variations data

    OpenAIRE

    Liu, Yang; Lee, Yiu Fai; Ng, Michael K.

    2011-01-01

    Background Detection of genomic DNA copy number variations (CNVs) can provide a complete and more comprehensive view of human disease. It is interesting to identify and represent relevant CNVs from a genome-wide data due to high data volume and the complexity of interactions. Results In this paper, we incorporate the DNA copy number variation data derived from SNP arrays into a computational shrunken model and formalize the detection of copy number variations as a case-control classification ...

  8. Identifying Genetic Variation for Alcohol Dependence

    OpenAIRE

    Agrawal, Arpana; Bierut, Laura J.

    2012-01-01

    Researchers are using various strategies to identify the genes that may be associated with alcoholism. The initial efforts primarily relied on candidate gene and linkage studies; more recently, however, modern advances in genotyping have resulted in widespread use of genome-wide association studies for alcohol dependence. The key findings of the earlier studies were that variations (i.e., polymorphisms) in the DNA sequences of the genes encoding alcohol dehydrogenase 1B (i.e., the ADH1B gene)...

  9. Method for improved extraction of DNA from Nocardia asteroides.

    OpenAIRE

    Loeffelholz, M. J.; Scholl, D R

    1989-01-01

    In a variation of standard DNA extraction methods, Nocardia asteroides was repeatedly exposed to sodium dodecyl sulfate at 60 degrees C for 30 min; each extraction was followed by centrifugation, removal of the nucleic acid-rich supernatant, and suspension of the cell pellet in fresh sodium dodecyl sulfate. The pooled supernatants contained a substantially higher amount of DNA than the first supernatant alone. The possible implications of this procedure on the development of DNA probes are di...

  10. A positron annihilation study of hydrated DNA

    DEFF Research Database (Denmark)

    Warman, J. M.; Eldrup, Morten Mostgaard

    1986-01-01

    Positron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to -180.degree. C) for samples containing 10 and 50% wt of water. The ortho-positronium mean lifetime and its intensity show distinct variations with the degree...

  11. DNA gyrase can cleave short DNA fragments in the presence of quinolone drugs.

    OpenAIRE

    Cove, M E; Tingey, A P; Maxwell, A

    1997-01-01

    We have analysed the DNA cleavage reaction of DNA gyrase using oligonucleotides annealed to a single-stranded M13 derivative containing a preferred gyrase cleavage site. We find that gyrase can cleave duplexes down to approximately 20 bp in size in the presence of the quinolone drugs ciprofloxacin and oxolinic acid. Ciprofloxacin shows a variation in its site specificity with an apparent preference for G bases adjacent to the cleavage sites, whereas oxolinic acid stimulates cleavage predomina...

  12. DNA loops and semicatenated DNA junctions

    Directory of Open Access Journals (Sweden)

    Strauss François

    2000-07-01

    Full Text Available Abstract Background Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA · poly(TG DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA · poly(TG can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA · poly(TG but had not yet been characterized. Results Formation of Form X was found to occur upon reassociation of the strands of a DNA fragment containing a tract of poly(CA · poly(TG, in a process strongly stimulated by the nuclear proteins HMG1 and HMG2. By inserting Form X into DNA minicircles, we show that the DNA strands do not run fully side by side but instead form a DNA knot. When present in a closed DNA molecule, Form X becomes resistant to heating to 100°C and to alkaline pH. Conclusions Our data strongly support a model of Form X consisting in a DNA loop at the base of which the two DNA duplexes cross, with one of the strands of one duplex passing between the strands of the other duplex, and reciprocally, to form a semicatenated DNA junction also called a DNA hemicatenane.

  13. Phylogeographical Variation of Chloroplast DNA in Cork Oak (Quercus suber)

    OpenAIRE

    Lumaret, Roselyne; TRYPHON-DIONNET, MATHIEU; MICHAUD, HENRI; SANUY, AURÉLIE; IPOTESI, EMILIE; Born, Céline; MIR, CÉLINE

    2005-01-01

    • Background and Aims In the last decades, the geographical location of the centre of origin of Quercus suber (cork oak), a strictly western Mediterranean oak species, has been the subject of controversy.

  14. Melanesian mtDNA complexity.

    Directory of Open Access Journals (Sweden)

    Jonathan S Friedlaender

    Full Text Available Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA sequences from hypervariable regions 1 and 2 (HVR1 and HVR2 from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups. Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP, and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal Austronesian influence in this region remains unresolved.

  15. DNA extraction by zinc.

    OpenAIRE

    Kejnovský, E; Kypr, J

    1997-01-01

    A fast, very simple and efficient method of DNA extraction is described which takes advantage of DNA sedimentation induced by millimolar concentrations of ZnCl2. The zinc-induced sedimentation is furthermore strongly promoted by submillimolar phosphate anion concentrations. Within 90% of DNA irrespective of whether a plasmid DNA or short oligonucleotides are the extracted material. The method works with plasmid DNA and oligonucleotide concentrations as low as 100 ng/ml and 10 microg/ml, respe...

  16. Molecular Darwinism: the contingency of spontaneous genetic variation.

    Science.gov (United States)

    Arber, Werner

    2011-01-01

    The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be assigned to three natural strategies to generate genetic variants: 1) local sequence changes, 2) intragenomic reshuffling of DNA segments, and 3) acquisition of a segment of foreign DNA. In these processes, specific gene products are involved in cooperation with different nongenetic elements. Some genetic variations occur fully at random along the DNA filaments, others rather with a statistical reproducibility, although at many possible sites. We have to be aware that evolution in natural ecosystems is of higher complexity than under most laboratory conditions, not at least in view of symbiotic associations and the occurrence of horizontal gene transfer. The encountered contingency of genetic variation can possibly best ensure a long-term persistence of life under steadily changing living conditions.

  17. Variation of fundamental constants

    CERN Document Server

    Flambaum, V V

    2006-01-01

    We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

  18. Asynchronous Variational Integrators

    OpenAIRE

    Lew, A.; Marsden, J. E.; Ortiz, M.; West, M

    2003-01-01

    We describe a new class of asynchronous variational integrators (AVI) for nonlinear elastodynamics. The AVIs are distinguished by the following attributes: (i) The algorithms permit the selection of independent time steps in each element, and the local time steps need not bear an integral relation to each other; (ii) the algorithms derive from a spacetime form of a discrete version of Hamilton’s variational principle. As a consequence of this variational structure, the algorith...

  19. Calculus of variations

    CERN Document Server

    Gelfand, I M

    2000-01-01

    Based on a series of lectures given by I. M. Gelfand at Moscow State University, this book actually goes considerably beyond the material presented in the lectures. The aim is to give a treatment of the elements of the calculus of variations in a form both easily understandable and sufficiently modern. Considerable attention is devoted to physical applications of variational methods, e.g., canonical equations, variational principles of mechanics, and conservation laws.The reader who merely wishes to become familiar with the most basic concepts and methods of the calculus of variations need on

  20. Recognition of DNA Termini by the C-Terminal Region of the Ku80 and the DNA-Dependent Protein Kinase Catalytic Subunit

    OpenAIRE

    Woods, Derek S.; Catherine R Sears; Turchi, John J.

    2015-01-01

    DNA double strand breaks (DSBs) can be generated by endogenous cellular processes or exogenous agents in mammalian cells. These breaks are highly variable with respect to DNA sequence and structure and all are recognized in some context by the DNA-dependent protein kinase (DNA-PK). DNA-PK is a critical component necessary for the recognition and repair of DSBs via non-homologous end joining (NHEJ). Previously studies have shown that DNA-PK responds differentially to variations in DSB structur...

  1. DNA polymerase δ and DNA repair: DNA repair synthesis in human fibroblasts requires DNA polymerase δ

    International Nuclear Information System (INIS)

    When UV-irradiated cultured diploid human fibroblasts were permeabilized with Brij-58 then separated from soluble material by centrifugation, conservative DNA repair synthesis could be restored by a soluble factor obtained from the supernate of similarly treated HeLa cells. Monoclonal antibody to KB cell DNA polymerase α, while binding to HeLa DNA polymerase α, did not bind to the HeLa DNA polymerase δ. Moreover, at micromolar concentrations N2-(p-n-butylphenyl)-2'-deoxyguanosine 5'-triphosphate (BuPdGT) and 2(p-n-butylanilino)-2'-deoxyadenosine 5'-triphosphate (BuAdATP) were potent inhibitors of DNA polymerase α, but did not inhibit the DNA polymerase δ. Neither purified DNA polymerase α nor β could promote repair DNA synthesis in the permeabilized cells. Furthermore, if monoclonal antibodies to DNA polymerase α BuPdGTP, or BuAdATP was added to the reconstituted system, there was no significant inhibition

  2. Functionalizing Designer DNA Crystals

    Science.gov (United States)

    Chandrasekaran, Arun Richard

    nucleotides is usually pH dependent (pH < 6) four different TFOs were examined: TFO-1 was unmodified while TFOs 2-4 contained additional stabilizing analogues capable of extending triplex formation to pH 7. In addition, each of the TFOs contained a Cy5 dye at the 5'-end of the oligonucleotide to aid in characterization of TFO binding - crystals were obtained with all four variations of TFOs. Formation of DNA triplex in the motif was characterized by an electrophoretic mobility shift assay (EMSA), UV melting studies and FRET. Crystals containing TFO-1 (unmodified) and TFO-2 (with 2'-amino ethoxy modification) were isolated and flash-frozen in liquid nitrogen for X-ray data collection at beam line NSLS-X25. X-ray data was also collected for crystals of the 3-turn triangle without any TFO bound to it. Difference maps were done between the crystals with TFO against the one without to identify any additional electron density corresponding to the third strand in the triplex binding region. The data from the crystal containing TFO-2 was used to further analyze if the additional density can match the expected position of the TFO on the triangle motif. Since the additional density did not correspond to the entire binding region, 2Fo-Fc, 3Fo-2Fc and 4Fo-3Fc maps were done to check for missing pieces of the electron density. From the resulting 2Fo-Fc map, the asymmetric unit from the 3-turn triangle (31-bp duplex model based on previous structure 3UBI) was inserted into the density as a reference. However, the electron density corresponding to the TFO was still not continuous throughout the 13-nt triplex binding region and allowed only a partial fit of the TFO. The third nucleotide in positions 1, 3, 4, 6, 7 were fit into the density in the major groove of the underlying duplex with proper triplex configuration. The third chapter describes the triplex approach to position a functional group (the UV cross-linking agent psoralen) within a pre-formed DNA motif. Triplex formation and

  3. DNA fragmentation in apoptosis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cleavage of chromosomal DNA into oligonucleosomal size fragments is an integral part of apoptosis. Elegant biochemical work identified the DNA fragmentation factor (DFF) as a major apoptotic endonuclease for DNA fragmentation in vitro. Genetic studies in mice support the importance of DFF in DNA fragmentation and possibly in apoptosis in vivo. Recent work also suggests the existence of additional endonucleases for DNA degradation. Understanding the roles of individual endonucleases in apoptosis, and how they might coordinate to degrade DNA in different tissues during normal development and homeostasis, as well as in various diseased states, will be a major research focus in the near future.

  4. The Variational Fair Autoencoder

    NARCIS (Netherlands)

    C. Louizos; K. Swersky; Y. Li; M. Welling; R. Zemel

    2016-01-01

    We investigate the problem of learning representations that are invariant to certain nuisance or sensitive factors of variation in the data while retaining as much of the remaining information as possible. Our model is based on a variational autoencoding architecture with priors that encourage indep

  5. Variation of Fundamental Constants

    Science.gov (United States)

    Flambaum, V. V.

    2006-11-01

    Theories unifying gravity with other interactions suggest temporal and spatial variation of the fundamental ``constants'' in expanding Universe. The spatial variation can explain a fine tuning of the fundamental constants which allows humans (and any life) to appear. We appeared in the area of the Universe where the values of the fundamental constants are consistent with our existence. We present a review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra. Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

  6. [Uracil-DNA glycosylases].

    Science.gov (United States)

    Pytel, Dariusz; Słupianek, Artur; Ksiazek, Dominika; Skórski, Tomasz; Błasiak, Janusz

    2008-01-01

    Uracil is one of four nitrogen bases, most frequently found in normal RNA. Uracyl can be found also in DNA as a result of enzymatic or non-enzymatic deamination of cytosine as well as misincorporation of dUMP instead of dTMP during DNA replication. Uracil from DNA can be removed by DNA repair enzymes with apirymidine site as an intermediate. However, if uracil is not removed from DNA a pair C:G in parental DNA can be changed into a T:A pair in the daughter DNA molecule. Therefore, uracil in DNA may lead to a mutation. Uracil in DNA, similarly to thymine, forms energetically most favorable hydrogen bonds with adenine, therefore uracil does not change the coding properties of DNA. Uracil in DNA is recognized by uracil DNA glycosylase (UDGs), which initiates DNA base excision repair, leading to removing of uracil from DNA and replacing it by thymine or cytosine, when arose as a result of cytosine deamination. Eukaryotes have at least four nuclear UDGs: UNG2, SMUG1, TDG i MBD4, while UNG1 operates in the mitochondrium. UNG2 is involved in DNA repair associated with DNA replication and interacts with PCNA and RPA proteins. Uracil can also be an intermediate product in the process of antigen-dependent antibody diversification in B lymphocytes. Enzymatic deamination of viral DNA by host cells can be a defense mechanism against viral infection, including HIV-1. UNG2, MBD4 and TDG glycosylases may cooperate with mismatch repair proteins and TDG can be involved in nucleotide excision repair system.

  7. DNA damage and autophagy

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States); Panayiotidis, Mihalis I. [School of Community Health Sciences, University of Nevada, Reno, NV 89557 (United States); Franco, Rodrigo, E-mail: rfrancocruz2@unl.edu [Redox Biology Center and School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583 (United States)

    2011-06-03

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  8. Genetic Variation in Nacobbus aberrans: An Approach toward Taxonomic Resolution

    OpenAIRE

    Ibrahim, S. K.; Baldwin, J. G.; Roberts, P. A.; Hyman, B.C.

    1997-01-01

    Biochemical and molecular analyses of genetic variation were evaluated to address the taxonomic status of Nacobbus aberrans. Isolates from Mexico, Peru, and Argentina, cultured on tomato in the greenhouse, were analyzed with respect to isozyme and DNA marker variation. Although acid phosphatase and malate dehydrogenase revealed distinct profiles for each isolate, non-specific esterases revealed possible affinities between the Peruvian isolates and between the isolates from Mexico and Peru. Tw...

  9. Triplet repeat length bias and variation in the human transcriptome

    OpenAIRE

    Molla, Michael; Delcher, Arthur; Sunyaev, Shamil; Cantor, Charles; Kasif, Simon

    2009-01-01

    Length variation in short tandem repeats (STRs) is an important family of DNA polymorphisms with numerous applications in genetics, medicine, forensics, and evolutionary analysis. Several major diseases have been associated with length variation of trinucleotide (triplet) repeats including Huntington's disease, hereditary ataxias and spinobulbar muscular atrophy. Using the reference human genome, we have catalogued all triplet repeats in genic regions. This data revealed a bias in noncoding D...

  10. Massively Parallel Sequencing Approaches for Characterization of Structural Variation

    OpenAIRE

    Koboldt, Daniel C.; Larson, David E.; Chen, Ken; Ding, Li; Wilson, Richard K.

    2012-01-01

    The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to de...

  11. Mitochondrial DNA mutations in single human blood cells.

    Science.gov (United States)

    Yao, Yong-Gang; Kajigaya, Sachiko; Young, Neal S

    2015-09-01

    Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification. PMID:26149767

  12. DNA Open states and DNA hydratation

    International Nuclear Information System (INIS)

    It is a very well-known fact that an protonic exchange exists among natural DNA filaments and synthetic polynucleotides with the solvent (1--2). The existence of DNA open states, that is to say states for which the interior of the DNA molecule is exposed to the external environment, it has been demonstrated by means of proton-deuterium exchange (3). This work has carried out experiments measuring the dispersion of the traverse relaxation rate (4), as a pulsation rate function in a Carr-Purcell-Meiboom-Gill (CPMG) pulses sequence rate, to determine changes in the moist layer of the DNA molecule. The experiments were carried out under different experimental conditions in order to vary the probability that open states occurs, such as temperature or the exposure to electromagnetic fields. Some theoretical models were supposed to adjust the experimental results including those related to DNA non linear dynamic

  13. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  14. HPV DNA test

    Science.gov (United States)

    The HPV DNA test is used to check for high-risk HPV infection in women. HPV infection around the genitals is ... warts spread when you have sex. The HPV-DNA test is generally not recommended for detecting low- ...

  15. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  16. Gene Expression Analysis Using Agilent DNA Microarrays

    DEFF Research Database (Denmark)

    Stangegaard, Michael

    2009-01-01

    Hybridization of labeled cDNA to microarrays is an intuitively simple and a vastly underestimated process. If it is not performed, optimized, and standardized with the same attention to detail as e.g., RNA amplification, information may be overlooked or even lost. Careful balancing of the amount...... of labeled cDNA added to each slide reduces dye-bias and slide to slide variation. Efficient mixing of the hybridization solution throughout the hybridization reaction increases signals several fold. The amount of near perfect target-probe hybrids may be reduced by efficient stringency washes...

  17. Recombinant DNA in Medicine

    OpenAIRE

    Cederbaum, Stephen D.; Fareed, George C.; Lovett, Michael A.; Shapiro, Larry J.

    1984-01-01

    Studies in bacteria and bacterial viruses have led to methods to manipulate and recombine DNA in unique and reproducible ways and to amplify these recombined molecules millions of times. Once properly identified, the recombinant DNA molecules can be used in various ways useful in medicine and human biology. There are many applications for recombinant DNA technology. Cloned complementary DNA has been used to produce various human proteins in microorganisms. Insulin and growth hormone have been...

  18. DNA Damage Response

    OpenAIRE

    Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

    2011-01-01

    Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damag...

  19. DNA-Mediated Electrochemistry

    OpenAIRE

    Gorodetsky, Alon A.; Buzzeo, Marisa C.; Barton, Jacqueline K.

    2008-01-01

    The base pair stack of DNA has been demonstrated as a medium for long-range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here, we discuss the characteristi...

  20. Ensembl variation resources

    Directory of Open Access Journals (Sweden)

    Marin-Garcia Pablo

    2010-05-01

    Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

  1. Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [Univ. of Minnesota, Minneapolis, MN (United States)

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  2. Hysteresis in pressure-driven DNA denaturation.

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Lemus

    Full Text Available In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue.

  3. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  4. DNA damage response

    NARCIS (Netherlands)

    G. Giglia-Mari (Giuseppina); A. Zotter (Angelika); W. Vermeulen (Wim)

    2011-01-01

    textabstractStructural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network ofDNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance p

  5. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir;

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

  6. Quantum variational calculus

    CERN Document Server

    Malinowska, Agnieszka B

    2014-01-01

    This Brief puts together two subjects, quantum and variational calculi by considering variational problems involving Hahn quantum operators. The main advantage of its results is that they are able to deal with nondifferentiable (even discontinuous) functions, which are important in applications. Possible applications in economics are discussed. Economists model time as continuous or discrete. Although individual economic decisions are generally made at discrete time intervals, they may well be less than perfectly synchronized in ways discrete models postulate. On the other hand, the usual assumption that economic activity takes place continuously, is nothing else than a convenient abstraction that in many applications is far from reality. The Hahn quantum calculus helps to bridge the gap between the two families of models: continuous and discrete. Quantum Variational Calculus is self-contained and unified in presentation. It provides an opportunity for an introduction to the quantum calculus of variations fo...

  7. Variational Inequalities with Applications

    CERN Document Server

    Sofonea, Mircea

    2009-01-01

    Motivated by stimulating problems in contact mechanics, emphasizing antiplane frictional contact with linearly elastic and viscoelastic materials, this book focuses on the essentials with respect to the qualitative aspects of several classes of variational inequalities (VIs)

  8. Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting

    NARCIS (Netherlands)

    Vlijm, R.; Torre, J.; Dekker, C.

    2015-01-01

    The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, h

  9. Generalized quasi variational inequalities

    Energy Technology Data Exchange (ETDEWEB)

    Noor, M.A. [King Saud Univ., Riyadh (Saudi Arabia)

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  10. Variational time integrators

    OpenAIRE

    Lew, A.; Marsden, J. E.; Ortiz, M.; West, M

    2004-01-01

    The purpose of this paper is to review and further develop the subject of variational integration algorithms as it applies to mechanical systems of engineering interest. In particular, the conservation properties of both synchronous and asynchronous variational integrators (AVIs) are discussed in detail. We present selected numerical examples which demonstrate the excellent accuracy, conservation and convergence characteristics of AVIs. In these tests, AVIs are found to result in substantial ...

  11. Comparisons of direct extraction methods of microbial DNA from different paddy soils

    OpenAIRE

    Islam, Md. Rashedul; Sultana, Tahera; Melvin Joe, M.; Cho, Jang-Cheon; Sa, Tongmin

    2012-01-01

    Molecular analyses for the study of soil microbial communities often depend on the direct extraction of DNA from soils. The present work compares the effectiveness of three different methods of extracting microbial DNA from seven different paddy soils. Comparison among different DNA extraction methods against different paddy soil samples revealed a marked variation in DNA yields from 3.18–20.17 μg DNA/g of dry soil. However, irrespective of the soil samples and extraction methods the DNA frag...

  12. Risk assessment of DNA-reactive carcinogens in food

    International Nuclear Information System (INIS)

    Risk assessment of DNA-reactive carcinogens in food requires knowledge of the extent of DNA damage in the target organ which results from the competition between DNA adduct formation and repair. Estimates of DNA adduct levels can be made by direct measurement or indirectly as a consequence of their presence, for example, by tumor formation in animal models or exposed populations epidemiologically. Food-borne DNA-reactive carcinogens are present from a variety of sources. They are generally not intrinsically DNA-reactive but require bioactivation to DNA-reactive metabolites a process which may be modulated by the compound itself or the presence of other xenobiotics. A single DNA reactant may form several distinct DNA adducts each undergoing different rates of repair. Some DNA reactants may be photochemically activated or produce reactive oxygen species and thus indirect oxidative DNA damage. The levels of DNA adducts arising from exposures influenced by variations in the doses, the frequency with which an individual is exposed, and rates of DNA repair for specific adducts. Each adduct has a characteristic efficiency with which it induces mutations. Based on experience with the well-studied DNA-reactive food carcinogen aflatoxin B1 (AFB1), a limit of 20 ppb or ∼30 μg/day has been set and is considered a tolerable daily intake (TDI). Since AFB1 is considered a potent carcinogen, doses of 32P-postlabeling or the use of surrogates such as hemoglobin adducts, together with approaches to evaluate the results. A discussion of approaches to estimating possible threshold effects for DNA-reactive carcinogens is made

  13. A mechanism of gene amplification driven by small DNA fragments.

    Directory of Open Access Journals (Sweden)

    Kuntal Mukherjee

    Full Text Available DNA amplification is a molecular process that increases the copy number of a chromosomal tract and often causes elevated expression of the amplified gene(s. Although gene amplification is frequently observed in cancer and other degenerative disorders, the molecular mechanisms involved in the process of DNA copy number increase remain largely unknown. We hypothesized that small DNA fragments could be the trigger of DNA amplification events. Following our findings that small fragments of DNA in the form of DNA oligonucleotides can be highly recombinogenic, we have developed a system in the yeast Saccharomyces cerevisiae to capture events of chromosomal DNA amplification initiated by small DNA fragments. Here we demonstrate that small DNAs can amplify a chromosomal region, generating either tandem duplications or acentric extrachromosomal DNA circles. Small fragment-driven DNA amplification (SFDA occurs with a frequency that increases with the length of homology between the small DNAs and the target chromosomal regions. SFDA events are triggered even by small single-stranded molecules with as little as 20-nt homology with the genomic target. A double-strand break (DSB external to the chromosomal amplicon region stimulates the amplification event up to a factor of 20 and favors formation of extrachromosomal circles. SFDA is dependent on Rad52 and Rad59, partially dependent on Rad1, Rad10, and Pol32, and independent of Rad51, suggesting a single-strand annealing mechanism. Our results reveal a novel molecular model for gene amplification, in which small DNA fragments drive DNA amplification and define the boundaries of the amplicon region. As DNA fragments are frequently found both inside cells and in the extracellular environment, such as the serum of patients with cancer or other degenerative disorders, we propose that SFDA may be a common mechanism for DNA amplification in cancer cells, as well as a more general cause of DNA copy number variation

  14. Introgression of mitochondrial DNA among Myodes voles: consequences for energetics?

    Directory of Open Access Journals (Sweden)

    Boratyński Zbyszek

    2011-12-01

    Full Text Available Abstract Background Introgression of mitochondrial DNA (mtDNA is among the most frequently described cases of reticulate evolution. The tendency of mtDNA to cross interspecific barriers is somewhat counter-intuitive considering the key function of enzymes that it encodes in the oxidative-phosphorylation process, which could give rise to hybrid dysfunction. How mtDNA reticulation affects the evolution of metabolic functions is, however, uncertain. Here we investigated how morpho-physiological traits vary in natural populations of a common rodent (the bank vole, Myodes glareolus and whether this variation could be associated with mtDNA introgression. First, we confirmed that M. glareolus harbour mtDNA introgressed from M. rutilus by analyzing mtDNA (cytochrome b, 954 bp and nuclear DNA (four markers; 2333 bp in total sequence variation and reconstructing loci phylogenies among six natural populations in Finland. We then studied geographic variation in body size and basal metabolic rate (BMR among the populations of M. glareolus and tested its relationship with mtDNA type. Results Myodes glareolus and its arctic neighbour, M. rutilus, are reciprocally monophyletic at the analyzed nuclear DNA loci. In contrast, the two northernmost populations of M. glareolus have a fixed mitotype that is shared with M. rutilus, likely due to introgressive hybridization. The analyses of phenotypic traits revealed that the body mass and whole-body, but not mass corrected, BMR are significantly reduced in M. glareolus females from northern Finland that also have the introgressed mitotype. Restricting the analysis to the single population where the mitotypes coexist, the association of mtDNA type with whole-body BMR remained but those with mass corrected BMR and body mass did not. Mitochondrial sequence variation in the introgressed haplotypes is compatible with demographic growth of the populations, but may also be a result of positive selection. Conclusion Our

  15. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.

  16. Electronic Transport in DNA

    OpenAIRE

    Klotsa, Daphne; Römer, Rudolf A.; Turner, Matthew S.

    2005-01-01

    We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which electrons travel. Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA and lambda-DNA. We find that random and lambda-D...

  17. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske;

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  18. Estimates of DNA strand breakage in bottlenose dolphin (Tursiops truncatus leukocytes measured with the Comet and DNA diffusion assays

    Directory of Open Access Journals (Sweden)

    Adriana Díaz

    2009-01-01

    Full Text Available The analysis of DNA damage by mean of Comet or single cell gel electrophoresis (SCGE assay has been commonly used to assess genotoxic impact in aquatic animals being able to detect exposure to low concentrations of contaminants in a wide range of species. The aims of this work were 1 to evaluate the usefulness of the Comet to detect DNA strand breakage in dolphin leukocytes, 2 to use the DNA diffusion assay to determine the amount of DNA strand breakage associated with apoptosis or necrosis, and 3 to determine the proportion of DNA strand breakage that was unrelated to apoptosis and necrosis. Significant intra-individual variation was observed in all of the estimates of DNA damage. DNA strand breakage was overestimated because a considerable amount (~29% of the DNA damage was derived from apoptosis and necrosis. The remaining DNA damage in dolphin leukocytes was caused by factors unrelated to apoptosis and necrosis. These results indicate that the DNA diffusion assay is a complementary tool that can be used together with the Comet assay to assess DNA damage in bottlenose dolphins.

  19. Estimates of DNA strand breakage in bottlenose dolphin (Tursiops truncatus) leukocytes measured with the Comet and DNA diffusion assays.

    Science.gov (United States)

    Díaz, Adriana; Carro, Sandra; Santiago, Livia; Estévez, Juan; Guevara, Celia; Blanco, Miriam; Sánchez, Laima; Sánchez, Liena; López, Nirka; Cruz, Danilo; López, Ronar; Cuetara, Elizabeth B; Fuentes, Jorge Luis

    2009-04-01

    The analysis of DNA damage by mean of Comet or single cell gel electrophoresis (SCGE) assay has been commonly used to assess genotoxic impact in aquatic animals being able to detect exposure to low concentrations of contaminants in a wide range of species. The aims of this work were 1) to evaluate the usefulness of the Comet to detect DNA strand breakage in dolphin leukocytes, 2) to use the DNA diffusion assay to determine the amount of DNA strand breakage associated with apoptosis or necrosis, and 3) to determine the proportion of DNA strand breakage that was unrelated to apoptosis and necrosis. Significant intra-individual variation was observed in all of the estimates of DNA damage. DNA strand breakage was overestimated because a considerable amount (~29%) of the DNA damage was derived from apoptosis and necrosis. The remaining DNA damage in dolphin leukocytes was caused by factors unrelated to apoptosis and necrosis. These results indicate that the DNA diffusion assay is a complementary tool that can be used together with the Comet assay to assess DNA damage in bottlenose dolphins. PMID:21637693

  20. DNA-Metallodrugs Interactions Signaled by Electrochemical Biosensors: An Overview

    Directory of Open Access Journals (Sweden)

    Mauro Ravera

    2007-01-01

    Full Text Available The interaction of drugs with DNA is an important aspect in pharmacology. In recent years, many important technological advances have been made to develop new techniques to monitor biorecognition and biointeraction on solid devices. The interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. The propensity of a given compound to interact with DNA is measured as a function of the decrease of guanine oxidation signal on a DNA electrochemical biosensor. Covalent binding at N7 of guanine, electrostatic interactions, and intercalation are the events that this kind of biosensor can detect. In this context, the interaction between a panel of antitumoral Pt-, Ru-, and Ti-based metallodrugs with DNA immobilized on screen-printed electrodes has been studied. The DNA biosensors are used for semiquantitative evaluation of the analogous interaction occurring in the biological environment.

  1. Conformation dependent electronic transport in a DNA double-helix

    International Nuclear Information System (INIS)

    We present a tight-binding study of conformation dependent electronic transport properties of DNA double-helix including its helical symmetry. We have studied the changes in the localization properties of DNA as we alter the number of stacked bases within every pitch of the double-helix keeping fixed the total number of nitrogen bases within the DNA molecule. We take three DNA sequences, two of them are periodic and one is random and observe that in all the cases localization length increases as we increase the radius of DNA double-helix i.e., number of nucleobases within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and found that in presence of helical symmetry, depending on the interplay of conformal variation and disorder, DNA can be found in either metallic, semiconducting and insulating phases, as observed experimentally

  2. Chromatic variations suppress suprathreshold brightness variations.

    Science.gov (United States)

    Kingdom, Frederick A A; Bell, Jason; Gheorghiu, Elena; Malkoc, Gokhan

    2010-01-01

    Most objects in natural scenes are suprathreshold in both color (chromatic) and luminance contrast. How salient is each dimension? We have developed a novel method employing a stimulus similar to that used by B. C. Regan and J. D. Mollon (1997) who studied the relative saliencies of the two chromatic cardinal directions. Our stimuli consist of left- and right-oblique modulations of color and/or luminance defined within a lattice of circles. In the "separated" condition, the two modulations were presented separately as forced-choice pairs, and the task was to indicate which was more salient. In the "combined" condition, the two orthogonal-in-orientation modulations were added, and the task was to indicate the more salient orientation. The ratio of color to luminance contrast at the PSE was calculated for both conditions. Across color directions, 48% more luminance contrast relative to color contrast was required to achieve a PSE in the "combined" compared to the "separated" condition. A second experiment showed that the PSE difference was due to the luminance being masked by the color, rather than due to superior color grouping. We conclude that suprathreshold brightness variations are masked by suprathreshold color variations. PMID:20884478

  3. DNA氧化性损伤标志物8-羟基脱氧鸟苷在阿尔茨海默病和血管性痴呆患者血浆中的变化%Variation of plasma oxidative DNA damage marker 8-hydroxy-2'-deoxyguanosine in patients with Alzheimer's disease versus vascular dementia

    Institute of Scientific and Technical Information of China (English)

    朱红敏; 章军建; 杨英

    2013-01-01

    目的 观察阿尔茨海默病(AD)与血管性痴呆(VaD)患者血浆中DNA氧化损伤标志物8羟基脱氧鸟苷(8-OHdG)水平的变化,探讨DNA氧化损伤在AD和VaD发病中的作用. 方法 用酶联免疫吸附试验的方法测定35例AD患者和28例VaD患者以及与之年龄相匹配的23例健康者血浆中8-OHdG的水平,用简易智力量表(MMSE)评测AD和VaD患者的认知功能. 结果 AD组、VaD组、健康对照组患者血浆中8-OHdG浓度分别为(601.8±266.0)ng/L、(1748.0±665.6)ng/L和(352.0±94.5)ng/L,各组间血浆8OHdG水平差异有统计学意义(P<0.001).VaD组患者血浆中8-OHdG水平与对照组比较差异有统计学意义(P<0.05);而AD组患者血浆中8-OHdG水平与对照组比较差异无统计学意义(P>0.05);并且VaD组与AD组比较,8-OHdG水平变化的差异也有统计学意义(P<0.05).各组血浆8-OHdG水平与年龄均呈正相关,分别为:AD组(r=0.661,P<0.01)、VaD组(r=0.702,P<0.01)、正常对照组(r=0.719,P<0.01).而各组血浆8-OHdG水平与教育水平无明显相关性(均P>0.05).在AD组和VaD组患者中根据其危险因素(性别、吸烟、高血压、糖尿病、高血脂)进行分组,比较各组间血浆8-OHdG水平的差异,结果发现各组间比较差异均无统计学意义(均P>0.05).校正了性别、年龄、教育水平、吸烟、高血压、高血脂、糖尿病因素的影响后,采用多分类Logistic回归分析结果显示:血浆中高水平8-OHdG在VaD组中比AD组和正常对照组的可能性均高.VaD组血浆8-OHdG水平与MMSE分数呈显著负相关性(r=-0.592,P<0.01);AD组血浆8-OHdG水平与MMSE分数无相关性(r=-0.122,P>0.05). 结论 VaD患者存在明显的DNA氧化损伤,其血浆DNA氧化损伤程度显著高于AD患者与健康者;VaD患者的血浆DNA氧化损伤标志物8-OHdG与其认知功能损害程度密切相关.%Objective To observe the variation of plasma 8-hydroxy-2'-deoxyguanosine (8-OHdG),a biomarker of oxidative DNA

  4. DNA in Nanoscale Electronics

    Science.gov (United States)

    Slinker, Jason

    2012-10-01

    DNA, the quintessential molecule of life, possesses a number of attractive properties for use in nanoscale circuits. Charge transport (CT) through DNA itself is of both fundamental and practical interest. Fundamentally, DNA has a unique configuration of π-stacked bases in a well ordered, double helical structure. Given its unparalleled importance to life processes and its arrangement of conjugated subunits, DNA has been a compelling target of conductivity studies. In addition, further understanding of DNA CT will elucidate the biological implications of this process and advance its use in sensing technologies. We have investigated the fundamentals of DNA CT by measuring the electrochemistry of DNA monolayers under biologically-relevant conditions. We have uncovered both fundamental kinetic parameters to distinguish between competing models of operation as well as the practical implications of DNA CT for sensing. Furthermore, we are leveraging our studies of DNA conductivity for the manufacture of nanoscale circuits. We are investigating the electrical properties and self-assembly of DNA nanowires containing artificial base pair surrogates, which can be prepared through low cost and high throughput automated DNA synthesis. This unique and economically viable approach will establish a new paradigm for the scalable manufacture of nanoscale semiconductor devices.

  5. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  6. DNA damage and Repair Modify DNA methylation and Chromatin Domain of the Targeted Locus: Mechanism of allele methylation polymorphism.

    Science.gov (United States)

    Russo, Giusi; Landi, Rosaria; Pezone, Antonio; Morano, Annalisa; Zuchegna, Candida; Romano, Antonella; Muller, Mark T; Gottesman, Max E; Porcellini, Antonio; Avvedimento, Enrico V

    2016-01-01

    We characterize the changes in chromatin structure, DNA methylation and transcription during and after homologous DNA repair (HR). We find that HR modifies the DNA methylation pattern of the repaired segment. HR also alters local histone H3 methylation as well chromatin structure by inducing DNA-chromatin loops connecting the 5' and 3' ends of the repaired gene. During a two-week period after repair, transcription-associated demethylation promoted by Base Excision Repair enzymes further modifies methylation of the repaired DNA. Subsequently, the repaired genes display stable but diverse methylation profiles. These profiles govern the levels of expression in each clone. Our data argue that DNA methylation and chromatin remodelling induced by HR may be a source of permanent variation of gene expression in somatic cells. PMID:27629060

  7. A longitudinal study of epigenetic variation in twins

    Science.gov (United States)

    Caspi, Avshalom; Williams, Benjamin; Craig, Ian W; Houts, Renate; Ambler, Antony; Moffitt, Terrie E; Mill, Jonathan

    2010-01-01

    DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twinpairs and 45 DZ twin-pairs (total n = 182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research. PMID:20505345

  8. Transposable Elements: No More 'Junk DNA'

    OpenAIRE

    Kim, Yun-Ji; Lee, Jungnam; Han, Kyudong

    2012-01-01

    Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mec...

  9. Modeling DNA beacons at the mesoscopic scale

    CERN Document Server

    Errami, Jalal; Theodorakopoulos, Nikos

    2007-01-01

    We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are...

  10. Development of novel electrical characterization methods and measurements of G4-DNA and DNA Derivatives

    CERN Document Server

    Livshits, Gideon I

    2015-01-01

    This dissertation presents an investigation into the electrical properties of two types of G4-DNA and several DNA-based molecules, targeting them as candidates for molecular wires and devices. Atomic force microscopy (AFM) and electrostatic force microscopy (EFM) comparison of co-deposited tetra- and intra-molecular G4-DNA reveals variations in morphology and different sensitivity to the applied electric field, suggesting that the folding orientation of the strands affects the molecular structure, i.e. either the tetrad unit or the tetrad-tetrad stacking or both, and therefore the charge mobility. Tetra-molecular G4-DNA is found to be twice as polarizable as intra-molecular G4-DNA, suggesting it has greater charge mobility. These promising results motivated direct electrical transport measurements on tetra-molecular G4-DNA using a special conductive AFM setup, profiling the conductance along the molecule. Reproducible currents of tens to over 100 pA were measured in many tetra-molecular G4-DNA molecules over ...

  11. Forensic DNA analysis.

    Science.gov (United States)

    McDonald, Jessica; Lehman, Donald C

    2012-01-01

    Before the routine use of DNA profiling, blood typing was an important forensic tool. However, blood typing was not very discriminating. For example, roughly 30% of the United States population has type A-positive blood. Therefore, if A-positive blood were found at a crime scene, it could have come from 30% of the population. DNA profiling has a much better ability for discrimination. Forensic laboratories no longer routinely determine blood type. If blood is found at a crime scene, DNA profiling is performed. From Jeffrey's discovery of DNA fingerprinting to the development of PCR of STRs to the formation of DNA databases, our knowledge of DNA and DNA profiling have expanded greatly. Also, the applications for which we use DNA profiling have increased. DNA profiling is not just used for criminal case work, but it has expanded to encompass paternity testing, disaster victim identification, monitoring bone marrow transplants, detecting fetal cells in a mother's blood, tracing human history, and a multitude of other areas. The future of DNA profiling looks expansive with the development of newer instrumentation and techniques. PMID:22693781

  12. Genetic variation and the de novo assembly of human genomes.

    Science.gov (United States)

    Chaisson, Mark J P; Wilson, Richard K; Eichler, Evan E

    2015-11-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. PMID:26442640

  13. Nucleosomes shape DNA polymorphism and divergence.

    Directory of Open Access Journals (Sweden)

    Sasha A Langley

    2014-07-01

    Full Text Available An estimated 80% of genomic DNA in eukaryotes is packaged as nucleosomes, which, together with the remaining interstitial linker regions, generate higher order chromatin structures [1]. Nucleosome sequences isolated from diverse organisms exhibit ∼10 bp periodic variations in AA, TT and GC dinucleotide frequencies. These sequence elements generate intrinsically curved DNA and help establish the histone-DNA interface. We investigated an important unanswered question concerning the interplay between chromatin organization and genome evolution: do the DNA sequence preferences inherent to the highly conserved histone core exert detectable natural selection on genomic divergence and polymorphism? To address this hypothesis, we isolated nucleosomal DNA sequences from Drosophila melanogaster embryos and examined the underlying genomic variation within and between species. We found that divergence along the D. melanogaster lineage is periodic across nucleosome regions with base changes following preferred nucleotides, providing new evidence for systematic evolutionary forces in the generation and maintenance of nucleosome-associated dinucleotide periodicities. Further, Single Nucleotide Polymorphism (SNP frequency spectra show striking periodicities across nucleosomal regions, paralleling divergence patterns. Preferred alleles occur at higher frequencies in natural populations, consistent with a central role for natural selection. These patterns are stronger for nucleosomes in introns than in intergenic regions, suggesting selection is stronger in transcribed regions where nucleosomes undergo more displacement, remodeling and functional modification. In addition, we observe a large-scale (∼180 bp periodic enrichment of AA/TT dinucleotides associated with nucleosome occupancy, while GC dinucleotide frequency peaks in linker regions. Divergence and polymorphism data also support a role for natural selection in the generation and maintenance of these

  14. Discrete Variational Optimal Control

    CERN Document Server

    Jimenez, Fernando; de Diego, David Martin

    2012-01-01

    This paper develops numerical methods for optimal control of mechanical systems in the Lagrangian setting. It extends the theory of discrete mechanics to enable the solutions of optimal control problems through the discretization of variational principles. The key point is to solve the optimal control problem as a variational integrator of a specially constructed higher-dimensional system. The developed framework applies to systems on tangent bundles, Lie groups, underactuated and nonholonomic systems with symmetries, and can approximate either smooth or discontinuous control inputs. The resulting methods inherit the preservation properties of variational integrators and result in numerically robust and easily implementable algorithms. Several theoretical and a practical examples, e.g. the control of an underwater vehicle, will illustrate the application of the proposed approach.

  15. Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses

    Directory of Open Access Journals (Sweden)

    Nawaz-ul-Rehman Muhammad

    2010-04-01

    Full Text Available Abstract Background Viruses of the genus Begomovirus (family Geminiviridae have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component. Results Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component. Conclusions The analysis has highlighted the greater genetic variation of DNA-B components, in

  16. DNA media storage

    Institute of Scientific and Technical Information of China (English)

    Christy M.Bogard; Eric C.Rouchka; Benjamin Arazi

    2008-01-01

    In 1994. University of Southern California computer scientist,Dr.Leonard Adleman solved the Hamiltonian path problem using DNA as a computational mechanism.He proved the principle that DNA computing could be used to solve computationally complex problems.Because of the limitations in discovery time,resource requirements,and sequence mismatches,DNA computing has not yet become a commonly accepted practice.However,advancements are continually being discovered that are evolving the field of DNA computing.Practical applications of DNA are not restricted to computation alone.This research presents a novel approach in which DNA could be used as a means of storing files.Through the use of multiple sequence alignment combined with intelligent heuristics,the most probabilistic file contents can be determined with minimal errors.

  17. DNA profiles from fingermarks.

    Science.gov (United States)

    Templeton, Jennifer E L; Linacre, Adrian

    2014-11-01

    Criminal investigations would be considerably improved if DNA profiles could be routinely generated from single fingermarks. Here we report a direct DNA profiling method that was able to generate interpretable profiles from 71% of 170 fingermarks. The data are based on fingermarks from all 5 digits of 34 individuals. DNA was obtained from the fingermarks using a swab moistened with Triton-X, and the fibers were added directly to one of two commercial DNA profiling kits. All profiles were obtained without increasing the number of amplification cycles; therefore, our method is ideally suited for adoption by the forensic science community. We indicate the use of the technique in a criminal case in which a DNA profile was generated from a fingermark on tape that was wrapped around a drug seizure. Our direct DNA profiling approach is rapid and able to generate profiles from touched items when current forensic practices have little chance of success. PMID:25391915

  18. Electrocatalysis in DNA Sensors.

    Science.gov (United States)

    Furst, Ariel; Hill, Michael G; Barton, Jacqueline K

    2014-12-14

    Electrocatalysis is often thought of solely in the inorganic realm, most often applied to energy conversion in fuel cells. However, the ever-growing field of bioelectrocatalysis has made great strides in advancing technology for both biofuel cells as well as biological detection platforms. Within the context of bioelectrocatalytic detection systems, DNA-based platforms are especially prevalent. One subset of these platforms, the one we have developed, takes advantage of the inherent charge transport properties of DNA. Electrocatalysis coupled with DNA-mediated charge transport has enabled specific and sensitive detection of lesions, mismatches and DNA-binding proteins. Even greater signal amplification from these platforms is now being achieved through the incorporation of a secondary electrode to the platform both for patterning DNA arrays and for detection. Here, we describe the evolution of this new DNA sensor technology. PMID:25435647

  19. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  20. Innovations. DNA detectives.

    OpenAIRE

    May, M

    1999-01-01

    To understand the many potential causes and resulting consequences of DNA damage, scientists first need methods to detect it. Canadian scientists X. Chris Le and Michael Weinfeld, with help from U.S. molecular biologist Steven Leadon, developed a selective, sensitive technique for measuring DNA damage. The scientists combined a thymine glycol antibody with thymine glycol to selectively tag a specific type of DNA damage. They then added a second antibody with fluorescing properties, and used l...

  1. Feature extraction and signal processing for nylon DNA microarrays

    OpenAIRE

    Bertucci F; Loï L; Bourgeois A.; Loriod B; Rougemont J; Lopez F; Hingamp P; Houlgatte R; Granjeaud S

    2004-01-01

    Abstract Background High-density DNA microarrays require automatic feature extraction methodologies and softwares. These can be a potential source of non-reproducibility of gene expression measurements. Variation in feature location or in signal integration methodology may be a significant contribution to the observed variance in gene expression levels. Results We explore sources of variability in feature extraction from DNA microarrays on Nylon membrane with radioactive detection. We introdu...

  2. Genomic and gene variation in Mycoplasma hominis strains

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Andersen, H; Birkelund, Svend;

    1987-01-01

    DNAs from 14 strains of Mycoplasma hominis isolated from various habitats, including strain PG21, were analyzed for genomic heterogeneity. DNA-DNA filter hybridization values were from 51 to 91%. Restriction endonuclease digestion patterns, analyzed by agarose gel electrophoresis, revealed no...... identity or cluster formation between strains. Variation within M. hominis rRNA genes was analyzed by Southern hybridization of EcoRI-cleaved DNA hybridized with a cloned fragment of the rRNA gene from the mycoplasma strain PG50. Five of the M. hominis strains showed identical hybridization patterns. These...... hybridization patterns were compared with those of 12 other mycoplasma species, which showed a much more complex band pattern. Cloned nonribosomal RNA gene fragments of M. hominis PG21 DNA were analyzed, and the fragments were used to demonstrate heterogeneity among the strains. A monoclonal antibody against...

  3. DNA Microarray Technique

    Directory of Open Access Journals (Sweden)

    Thakare SP

    2012-11-01

    Full Text Available DNA Microarray is the emerging technique in Biotechnology. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. It also includes screening and diagnostic applications. The DNA microarray hybridization applications include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs, and short tandem repeats (STRs. In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes.

  4. The Bacillus subtilis DnaD and DnaB Proteins Exhibit Different DNA Remodelling Activities

    OpenAIRE

    Zhang, Wenke; Carneiro, Maria J. V. M.; Turner, Ian J.; ALLEN, Stephanie; Roberts, Clive J.; Soultanas, Panos

    2005-01-01

    Primosomal protein cascades load the replicative helicase onto DNA. In Bacillus subtilis a putative primosomal cascade involving the DnaD-DnaB-DnaI proteins has been suggested to participate in both the DnaA and PriA-dependent loading of the replicative helicase DnaC onto the DNA. Recently we discovered that DnaD has a global remodelling DNA activity suggesting a more widespread role in bacterial nucleoid architecture. Here, we show that DnaB forms a “square-like” tetramer with a hole in the ...

  5. Seasonal Variation in Epidemiology

    Science.gov (United States)

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  6. Variational transition state theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  7. Sexual "Variation" without "Deviation"

    Science.gov (United States)

    Turnage, John R.; Logan, Daniel L.

    1975-01-01

    Non-heterosexual behavior continues to be labeled "deviant" or "maladaptive" by those propounding a learning formulation of sexual behavior. It is suggested that the term "variation" replace, in part, the term "deviation" when describing non-heterosexual behavior, especially homosexuality. (Author)

  8. Variation in decision making

    NARCIS (Netherlands)

    Dall, Sasha R. X.; Gosling, Samuel; Gordon D.A., Brown,; Dingemanse, Niels; Ido, Erev,; Martin, Kocher,; Laura, Schulz,; Todd, Peter M; Weissing, Franz; Wolf, Max; Hammerstein, Peter; Stevens, Jeffrey R.

    2012-01-01

    Variation in how organisms allocate their behavior over their lifetimes is key to determining Darwinian fitness., and thus the evolution of human and nonhuman decision making. This chapter explores how decision making varies across biologically and societally significant scales and what role such va

  9. Fluency Variation in Adolescents

    Science.gov (United States)

    De Andrade, Claudia Regina Furquim; Martins, Vanessa De Oliveira

    2007-01-01

    The Speech Fluency Profile of fluent adolescent speakers of Brazilian Portuguese, were examined with respect to gender and neurolinguistic variations. Speech samples of 130 male and female adolescents, aged between 12;0 and 17;11 years were gathered. They were analysed according to type of speech disruption; speech rate; and frequency of speech…

  10. The genus Basilichthys (Teleostei: Atherinopsidae revisited along its Chilean distribution range (21° to 40° S using variation in morphologyand mtDNA El género Basilichthys (Teleostei: Atherinopsidae analizado a lo largo de su distribución en Chile (21° a 40° S, utilizando rasgos morfológicos y variabilidad del ADN mitocondrial

    Directory of Open Access Journals (Sweden)

    DAVID VÉLIZ

    2012-03-01

    Full Text Available There is still doubt as to the number of species of the freshwater Chilean ichthyofauna, 64 % of which have conservation problems. One of the groups is that of the silversides of the genus Basilichthys. Three morphological species of this genus have been described in Chile with disjoint distributions: Basilichthys semotilus, B. microlepidotus and B. australis; the latter two overlap in distribution only in the Aconcagua River and are not easily distinguishable by morphological and meristic characters. In order to evaluate the efficacy of identification of these species by molecular techniques, we analyzed the sequence of 9 % of the mitochondrial DNA (Control Region and COI of individuals from the Loa River (21°41' S to the Valdivia River (39°50' S, adding meristic features for B. microlepidotus and B. australis in order to study population variation to clarify the taxonomy of the native species of the genus. The phylogenetic analysis showed that the individuals of Basilichthys semotilus form an haplogroup separated from the other species of the genus; however, B. australis and B. microlepidotus form a monophyletic group that shares the most common haplotypes. An analysis of meristic information showed no statistically significant differences in the number of lateral line scales or number of rays in the fins between B. microlepidotus and B. australis. These results do not support the current classification for the latter two species; there appears to be one group in the extreme north of the country (Basilichthys semotilus and a second group in central Chile which should be called B. microlepidotus. This information will be useful to review the conservation status of the Chilean fauna.Si bien aún existen dudas sobre el número de especies descritas en el país, se reconoce que el 64 % de la ictiofauna dulceacuícola chilena se encuentra en alguna categoría de peligro de conservación. Uno de los grupos categorizados como vulnerable y en

  11. Diurnal variations of Titan

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  12. Visible periodicity of strong nucleosome DNA sequences.

    Science.gov (United States)

    Salih, Bilal; Tripathi, Vijay; Trifonov, Edward N

    2015-01-01

    Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10-11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes--i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms--nucleosome positioning motifs--are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.

  13. Genetic analysis of environmental variation

    NARCIS (Netherlands)

    Hill, W.G.; Mulder, H.A.

    2010-01-01

    Environmental variation (VE) in a quantitative trait – variation in phenotype that cannot be explained by genetic variation or identifiable genetic differences – can be regarded as being under some degree of genetic control. Such variation may be either between repeated expressions of the same trait

  14. DNA polymorphism at the casein loci in sheep.

    Science.gov (United States)

    Di Gregorio, P; Rando, A; Pieragostini, E; Masina, P

    1991-01-01

    By using seven endonucleases and four bovine cDNA probes specific for alpha S1-, alpha S2-, beta-, and kappa-casein genes, nine restriction fragment length polymorphisms (RFLPs) have been found in the sheep orthologous DNA regions. In contrast to the low level of variation observed at the protein level, these DNA polymorphisms determine a high level of heterozygosity and, therefore, represent useful tools for genetic analyses since they can also be obtained without the need for gene expression. In fact, informative matings suggest that in sheep, as in cattle, the four loci are linked.

  15. Duck hepatitis B virus covalently closed circular DNA appears to survive hepatocyte mitosis in the growing liver

    Energy Technology Data Exchange (ETDEWEB)

    Reaiche-Miller, Georget Y.; Thorpe, Michael; Low, Huey Chi; Qiao, Qiao; Scougall, Catherine A. [School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005 (Australia); Mason, William S.; Litwin, Samuel [Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111 (United States); Jilbert, Allison R., E-mail: allison.jilbert@adelaide.edu.au [School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005 (Australia)

    2013-11-15

    Nucleos(t)ide analogues that inhibit hepatitis B virus (HBV) DNA replication are typically used as monotherapy for chronically infected patients. Treatment with a nucleos(t)ide analogue eliminates most HBV DNA replication intermediates and produces a gradual decline in levels of covalently closed circular DNA (cccDNA), the template for viral RNA synthesis. It remains uncertain if levels of cccDNA decline primarily through hepatocyte death, or if loss also occurs during hepatocyte mitosis. To determine if cccDNA survives mitosis, growing ducklings infected with duck hepatitis B virus (DHBV) were treated with the nucleoside analogue, Entecavir. Viremia was suppressed at least 10{sup 5}-fold, during a period when average liver mass increased 23-fold. Analysis of the data suggested that if cccDNA synthesis was completely inhibited, at least 49% of cccDNA survived hepatocyte mitosis. However, there was a large duck-to-duck variation in cccDNA levels, suggesting that low level cccDNA synthesis may contribute to this apparent survival through mitosis. - Highlights: • The hepatitis B virus nuclear template is covalently closed circular DNA (cccDNA). • cccDNA was studied during liver growth in duck hepatitis B virus infected ducks. • Virus DNA replication and new cccDNA synthesis were inhibited with Entecavir. • At least 49% of cccDNA appeared to survive hepatocyte mitosis. • Low level virus DNA synthesis may contribute to survival of cccDNA through mitosis.

  16. Duck hepatitis B virus covalently closed circular DNA appears to survive hepatocyte mitosis in the growing liver

    International Nuclear Information System (INIS)

    Nucleos(t)ide analogues that inhibit hepatitis B virus (HBV) DNA replication are typically used as monotherapy for chronically infected patients. Treatment with a nucleos(t)ide analogue eliminates most HBV DNA replication intermediates and produces a gradual decline in levels of covalently closed circular DNA (cccDNA), the template for viral RNA synthesis. It remains uncertain if levels of cccDNA decline primarily through hepatocyte death, or if loss also occurs during hepatocyte mitosis. To determine if cccDNA survives mitosis, growing ducklings infected with duck hepatitis B virus (DHBV) were treated with the nucleoside analogue, Entecavir. Viremia was suppressed at least 105-fold, during a period when average liver mass increased 23-fold. Analysis of the data suggested that if cccDNA synthesis was completely inhibited, at least 49% of cccDNA survived hepatocyte mitosis. However, there was a large duck-to-duck variation in cccDNA levels, suggesting that low level cccDNA synthesis may contribute to this apparent survival through mitosis. - Highlights: • The hepatitis B virus nuclear template is covalently closed circular DNA (cccDNA). • cccDNA was studied during liver growth in duck hepatitis B virus infected ducks. • Virus DNA replication and new cccDNA synthesis were inhibited with Entecavir. • At least 49% of cccDNA appeared to survive hepatocyte mitosis. • Low level virus DNA synthesis may contribute to survival of cccDNA through mitosis

  17. DNA-cell conjugates

    Energy Technology Data Exchange (ETDEWEB)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  18. Characterization of muntjac DNA

    International Nuclear Information System (INIS)

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

  19. Routine DNA testing

    Science.gov (United States)

    Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

  20. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  1. Recombinant DNA for Teachers.

    Science.gov (United States)

    Duvall, James G., III

    1992-01-01

    A science teacher describes his experience at a workshop to learn to teach the Cold Spring Harbor DNA Science Laboratory Protocols. These protocols lead students through processes for taking E. coli cells and transforming them into a new antibiotic resistant strain. The workshop featured discussions of the role of DNA recombinant technology in…

  2. Protein–DNA Interactions

    NARCIS (Netherlands)

    Kovacic, L.; Boelens, R.

    2012-01-01

    The recognition of specific DNA sequences by proteins and the coupling to signaling events are fundamental occurrences that lie at the root of many cellular processes. Many examples of tight control by protein–DNA interactions can be found in such dynamic processes as transcription, replication and

  3. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  4. Workshop on DNA repair.

    NARCIS (Netherlands)

    A.R. Lehmann (Alan); J.H.J. Hoeijmakers (Jan); A.A. van Zeeland (Albert); C.M.P. Backendorf (Claude); B.A. Bridges; A. Collins; R.P.D. Fuchs; G.P. Margison; R. Montesano; E. Moustacchi; A.T. Natarajan; M. Radman; A. Sarasin; E. Seeberg; C.A. Smith; M. Stefanini (Miria); L.H. Thompson; G.P. van der Schans; C.A. Weber (Christine); M.Z. Zdzienika

    1992-01-01

    textabstractA workshop on DNA repair with emphasis on eukaryotic systems was held, under the auspices of the EC Concerted Action on DNA Repair and Cancer, at Noordwijkerhout (The Netherlands) 14-19 April 1991. The local organization of the meeting was done under the auspices of the Medical Genetic C

  5. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao;

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  6. Molecular dynamics simulations demonstrate the regulation of DNA-DNA attraction by H4 histone tail acetylations and mutations.

    Science.gov (United States)

    Korolev, Nikolay; Yu, Hang; Lyubartsev, Alexander P; Nordenskiöld, Lars

    2014-10-01

    The positively charged N-terminal histone tails play a crucial role in chromatin compaction and are important modulators of DNA transcription, recombination, and repair. The detailed mechanism of the interaction of histone tails with DNA remains elusive. To model the unspecific interaction of histone tails with DNA, all-atom molecular dynamics (MD) simulations were carried out for systems of four DNA 22-mers in the presence of 20 or 16 short fragments of the H4 histone tail (variations of the 16-23 a. a. KRHRKVLR sequence, as well as the unmodified fragment a. a.13-20, GGAKRHRK). This setup with high DNA concentration, explicit presence of DNA-DNA contacts, presence of unstructured cationic peptides (histone tails) and K(+) mimics the conditions of eukaryotic chromatin. A detailed account of the DNA interactions with the histone tail fragments, K(+) and water is presented. Furthermore, DNA structure and dynamics and its interplay with the histone tail fragments binding are analysed. The charged side chains of the lysines and arginines play major roles in the tail-mediated DNA-DNA attraction by forming bridges and by coordinating to the phosphate groups and to the electronegative sites in the minor groove. Binding of all species to DNA is dynamic. The structure of the unmodified fully-charged H4 16-23 a.a. fragment KRHRKVLR is dominated by a stretched conformation. The H4 tail a. a. fragment GGAKRHRK as well as the H4 Lys16 acetylated fragment are highly flexible. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction and dynamics.

  7. Premeltons in DNA.

    Science.gov (United States)

    Sobell, Henry M

    2016-03-01

    Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A-DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A-transition), which differs from either A- or B-DNA. Called beta-DNA, this is both metastable and hyperflexible--and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A-DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5' and 3' ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions--all readily testable--as will be described in this review.

  8. Archaeal DNA replication.

    Science.gov (United States)

    Kelman, Lori M; Kelman, Zvi

    2014-01-01

    DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed. PMID:25421597

  9. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  10. Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics.

    Science.gov (United States)

    Josefsen, Mathilde H; Andersen, Sandra C; Christensen, Julia; Hoorfar, Jeffrey

    2015-07-01

    The efficiency of ten widely applied DNA extraction protocols was evaluated for suitability for diagnostic metagenomics. The protocols were selected based on a thorough literature study. Chicken fecal samples inoculated with about 1×10(3) and 1×10(6) CFU/g Campylobacter jejuni were used as a model. The evaluation was performed based on total DNA yield measured by fluorometry, and quality and quantity of C. jejuni DNA measured by real-time PCR. There was up to a 25-fold variance between the lowest (NucliSens miniMAG, BIOMÉRIEUX) and highest (PowerLyzer PowerSoil DNA Isolation Kit, MO BIO Laboratories) yielding protocols. The PowerLyzer PowerSoil DNA Isolation Kit performed significantly better than all other protocols tested. Selected protocols were modified, i.e., extended heating and homogenization, resulting in increased yields of total DNA. For QIAamp Fast DNA Stool Mini Kit (Qiagen) a 7-fold increase in total DNA was observed following the protocol for human DNA analysis and including a 5 min heating step at 70°C. For the PowerLyzer PowerSoil and the PowerFecal DNA Isolation Kit (MO BIO Laboratories) the total DNA fold increase was 1.6 to 1.8 when including an extra 10 min of bead-vortexing. There was no correlation between the yield of total DNA and the amount of PCR-amplifiable DNA from C. jejuni. The protocols resulting in the highest yield of total DNA did not show correspondingly increased levels of C. jejuni DNA as determined by PCR. In conclusion, substantial variation in the efficiency of the protocols to extract DNA was observed. The highest DNA yield was obtained with the PowerLyzer PowerSoil DNA Isolation Kit, whereas the FastDNA SPIN Kit for Feces (MP Biomedicals) resulted in the highest amount of PCR-amplifiable C. jejuni DNA. PMID:25937085

  11. Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics.

    Science.gov (United States)

    Josefsen, Mathilde H; Andersen, Sandra C; Christensen, Julia; Hoorfar, Jeffrey

    2015-07-01

    The efficiency of ten widely applied DNA extraction protocols was evaluated for suitability for diagnostic metagenomics. The protocols were selected based on a thorough literature study. Chicken fecal samples inoculated with about 1×10(3) and 1×10(6) CFU/g Campylobacter jejuni were used as a model. The evaluation was performed based on total DNA yield measured by fluorometry, and quality and quantity of C. jejuni DNA measured by real-time PCR. There was up to a 25-fold variance between the lowest (NucliSens miniMAG, BIOMÉRIEUX) and highest (PowerLyzer PowerSoil DNA Isolation Kit, MO BIO Laboratories) yielding protocols. The PowerLyzer PowerSoil DNA Isolation Kit performed significantly better than all other protocols tested. Selected protocols were modified, i.e., extended heating and homogenization, resulting in increased yields of total DNA. For QIAamp Fast DNA Stool Mini Kit (Qiagen) a 7-fold increase in total DNA was observed following the protocol for human DNA analysis and including a 5 min heating step at 70°C. For the PowerLyzer PowerSoil and the PowerFecal DNA Isolation Kit (MO BIO Laboratories) the total DNA fold increase was 1.6 to 1.8 when including an extra 10 min of bead-vortexing. There was no correlation between the yield of total DNA and the amount of PCR-amplifiable DNA from C. jejuni. The protocols resulting in the highest yield of total DNA did not show correspondingly increased levels of C. jejuni DNA as determined by PCR. In conclusion, substantial variation in the efficiency of the protocols to extract DNA was observed. The highest DNA yield was obtained with the PowerLyzer PowerSoil DNA Isolation Kit, whereas the FastDNA SPIN Kit for Feces (MP Biomedicals) resulted in the highest amount of PCR-amplifiable C. jejuni DNA.

  12. Census variation staffing.

    Science.gov (United States)

    Douglas, D A; Mayewski, J

    1996-02-01

    A Census Variation Staffing (CVS) model has been used successfully on all nursing units for 4 years. Historical data and nursing hours per patient day (NHPPD) are used to determine the staffing needs of each unit on a daily, shift-by-shift basis. CVS has been heralded as the single largest factor in the hospital's consistent profitability--averaging annual savings of $485,100. PMID:8632867

  13. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  14. Planar theory made variational

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, A.D.; Lande, A.; Smith, R.A.

    1985-04-08

    Within the framework of boson parquet-diagram summations in perturbation theory, we show analytically that several simple approximations lead inevitably to the radial distribution function g(r) which would be obtained with the Jastrow hypernetted-chain variational method. This is the first derivation of the Jastrow result from perturbation theory. Without mentioning pair correlation functions, we have a clear interpretation of g(r) and the structure function, S(k), in terms of diagram sums.

  15. Planar theory made variational

    International Nuclear Information System (INIS)

    Within the framework of boson parquet-diagram summations in perturbation theory, we show analytically that several simple approximations lead inevitably to the radial distribution function g(r) which would be obtained with the Jastrow hypernetted-chain variational method. This is the first derivation of the Jastrow result from perturbation theory. Without mentioning pair correlation functions, we have a clear interpretation of g(r) and the structure function, S(k), in terms of diagram sums

  16. DNA-repair measurements by use of the modified comet assay

    DEFF Research Database (Denmark)

    Godschalk, Roger W L; Ersson, Clara; Riso, Patrizia;

    2013-01-01

    The measurement of DNA-repair activity by extracts from cells or tissues by means of the single-cell gel electrophoresis (comet) assay has a high potential to become widely used in biomonitoring studies. We assessed the inter-laboratory variation in reported values of DNA-repair activity on...... line as having the highest level of DNA-repair activity. The two laboratories that reported discordant results (with another cell line having the highest level of DNA-repair activity) were those that reported to have little experience with the modified comet assay to assess DNA repair. The laboratories...

  17. Charge transport in l-DNA probed by conducting-AFM, and relationship with its structure

    OpenAIRE

    Heim, Thomas; Deresemes, Dominique; Vuillaume, Dominique

    2003-01-01

    We studied the electrical conductivity of DNA samples as function of the number of DNA molecules. We showed that the insulating gap (no current at low voltage) increases from ~1-2 V for bundles and large ropes to ~4-7 V for few DNA molecules. From the distance dependent variation of the current, a unique hopping distance of ~3 nm is calculated (polaron-hopping model) independently of the number of DNA in the sample. The highly resistive behavior of the single DNA is correlated with its flatte...

  18. The Variability of Cytoplasmic DNA Haplotypes of Norway Spruce in the Provenance Trials

    Directory of Open Access Journals (Sweden)

    V. E. Padutov

    2014-08-01

    Full Text Available A genetic analysis of mitochondrial (mtDNA and chloroplast (cpDNA genomes of 27 climatypes of Norway spruce was conducted in the provenance (Cherikov forestry district, Republic of Belarus. It was found that the analyzed climatypes presented boreal and carpathian mtDNA haplotypes. The first of them is found in all regions of growth climatypes (Priuralsky, Northwest, Central, Baltic, Byelorussian, Southwest, the second – only in Belarusian and Southwest regions. It is shown that polymorphism cpDNA significantly higher in comparison with the mtDNA. For a number of alleles of loci cpDNA the clinal variation was found in the frequency of their occurrence. It was revealed that some cpDNA haplotypes, as haplotypes mtDNA, of Norway spruce can be represented as in all regions of the investigated part of the range as on certain of its territories.

  19. Measurement of oxidative damage to DNA in nanomaterial exposed cells and animals

    DEFF Research Database (Denmark)

    Møller, Peter; Jensen, Ditte Marie; Christophersen, Daniel Vest;

    2015-01-01

    -reactivity with other molecules in cells. This review provides an overview of efforts to reliably detect oxidatively damaged DNA and a critical assessment of the published studies on DNA damage levels. Animal studies with high baseline levels of oxidatively damaged DNA are more likely to show positive associations...... of oxidatively damaged DNA in lung tissue. Oral exposure to nanosized carbon black, TiO2 , carbon nanotubes and ZnO is associated with elevated levels of oxidatively damaged DNA in tissues. These observations are supported by cell culture studies showing concentration-dependent associations between ENM exposure...... and oxidatively damaged DNA measured by the comet assay. Cell culture studies show relatively high variation in the ability of ENMs to oxidatively damage DNA; hence, it is currently impossible to group ENMs according to their DNA damaging potential. Environ. Mol. Mutagen., 2014. © 2014 Wiley Periodicals, Inc....

  20. Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation.

    Directory of Open Access Journals (Sweden)

    James P J Hall

    Full Text Available A main determinant of prolonged Trypanosoma brucei infection and transmission and success of the parasite is the interplay between host acquired immunity and antigenic variation of the parasite variant surface glycoprotein (VSG coat. About 0.1% of trypanosome divisions produce a switch to a different VSG through differential expression of an archive of hundreds of silent VSG genes and pseudogenes, but the patterns and extent of the trypanosome diversity phenotype, particularly in chronic infection, are unclear. We applied longitudinal VSG cDNA sequencing to estimate variant richness and test whether pseudogenes contribute to antigenic variation. We show that individual growth peaks can contain at least 15 distinct variants, are estimated computationally to comprise many more, and that antigenically distinct 'mosaic' VSGs arise from segmental gene conversion between donor VSG genes or pseudogenes. The potential for trypanosome antigenic variation is probably much greater than VSG archive size; mosaic VSGs are core to antigenic variation and chronic infection.

  1. Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

    Full Text Available Although the functional consequences of mitochondrial DNA (mtDNA genetic backgrounds (haplotypes, haplogroups have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers". We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74% and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%. The variant defining Caucasian haplogroup J (C295T increased the binding of TFAM (Electro Mobility Shift Assay and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1, a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mtDNA

  2. DNA vaccines against influenza.

    Science.gov (United States)

    Stachyra, Anna; Góra-Sochacka, Anna; Sirko, Agnieszka

    2014-01-01

    Genetic vaccine technology has been considerably developed within the last two decades. This cost effective and promising strategy can be applied for therapy of cancers and for curing allergy, chronic and infectious diseases, such as a seasonal and pandemic influenza. Despite numerous advantages, several limitations of this technology reduce its performance and can retard its commercial exploitation in humans and its veterinary applications. Inefficient delivery of the DNA vaccine into cells of immunized individuals results in low intracellular supply of suitable expression cassettes encoding an antigen, in its low expression level and, in turn, in reduced immune responses against the antigen. Improvement of DNA delivery into the host cells might significantly increase effectiveness of the DNA vaccine. A vast array of innovative methods and various experimental strategies have been applied in order to enhance the effectiveness of DNA vaccines. They include various strategies improving DNA delivery as well as expression and immunogenic potential of the proteins encoded by the DNA vaccines. Researchers focusing on DNA vaccines against influenza have applied many of these strategies. Recent examples of the most successful modern approaches are discussed in this review.

  3. DNA mini-barcodes.

    Science.gov (United States)

    Hajibabaei, Mehrdad; McKenna, Charly

    2012-01-01

    Conventional DNA barcoding uses an approximately 650 bp DNA barcode of the mitochondrial gene COI for species identification in animal groups. Similar size fragments from chloroplast genes have been proposed as barcode markers for plants. While PCR amplification and sequencing of a 650 bp fragment is consistent in freshly collected and well-preserved specimens, it is difficult to obtain a full-length barcode in older museum specimens and samples which have been preserved in formalin or similar DNA-unfriendly preservatives. A comparable issue may prevent effective DNA-based authentication and testing in processed biological materials, such as food products, pharmaceuticals, and nutraceuticals. In these cases, shorter DNA sequences-mini-barcodes-have been robustly recovered and shown to be effective in identifying majority of specimens to a species level. Furthermore, short DNA regions can be utilized via high-throughput sequencing platforms providing an inexpensive and comprehensive means of large-scale species identification. These properties of mini-barcodes, coupled with the availability of standardized and universal primers make mini-barcodes a feasible option for DNA barcode analysis in museum samples and applied diagnostic and environmental biodiversity analysis.

  4. HIV DNA Integration

    Science.gov (United States)

    Craigie, Robert; Bushman, Frederic D.

    2012-01-01

    Retroviruses are distinguished from other viruses by two characteristic steps in the viral replication cycle. The first is reverse transcription, which results in the production of a double-stranded DNA copy of the viral RNA genome, and the second is integration, which results in covalent attachment of the DNA copy to host cell DNA. The initial catalytic steps of the integration reaction are performed by the virus-encoded integrase (IN) protein. The chemistry of the IN-mediated DNA breaking and joining steps is well worked out, and structures of IN-DNA complexes have now clarified how the overall complex assembles. Methods developed during these studies were adapted for identification of IN inhibitors, which received FDA approval for use in patients in 2007. At the chromosomal level, HIV integration is strongly favored in active transcription units, which may promote efficient viral gene expression after integration. HIV IN binds to the cellular factor LEDGF/p75, which promotes efficient infection and tethers IN to favored target sites. The HIV integration machinery must also interact with many additional host factors during infection, including nuclear trafficking and pore proteins during nuclear entry, histones during initial target capture, and DNA repair proteins during completion of the DNA joining steps. Models for some of the molecular mechanisms involved have been proposed, but important details remain to be clarified. PMID:22762018

  5. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  6. What Controls DNA Looping?

    Directory of Open Access Journals (Sweden)

    Pamela J. Perez

    2014-08-01

    Full Text Available The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.

  7. Genetic variation in cultivated Rheum tanguticum populations

    Directory of Open Access Journals (Sweden)

    Yanping Hu

    2014-09-01

    Full Text Available To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied. Thirteen primers were used and a total of 320 DNA bands were scored. High levels of genetic diversity were detected in cultivated R. tanguticum (PPB = 82.19, H = 0.2498, H B = 0.3231, I = 0.3812 and could be explained by the outcrossing system, as well as long-lived and human-mediated seed exchanges. Analysis of molecular variance (AMOVA showed that more genetic variation was found within populations (76.1% than among them (23.9%. This was supported by the coefficient of gene differentiation (Gst = 0.2742 and Bayesian analysis (θB = 0.1963. The Mantel test revealed no significant correlation between genetic and geographic distances among populations (r = 0.1176, p = 0.3686. UPGMA showed that the five cultivated populations were separated into three clusters, which was in good accordance with the results provided by the Bayesian software STRUCTURE (K = 3. A short domestication history and no artificial selection may be an effective way of maintaining and conserving the gene pools of wild R. tanguticum.

  8. Species-specific lifespans: Can it be a lottery based on the mode of mitochondrial DNA replication?

    Science.gov (United States)

    Khaidakov, Magomed

    2016-04-01

    Accumulating evidence suggests that the aging process is, in part, driven by accumulation of large deletions in mitochondrial DNA (mtDNA). Here, I present a hypothesis that significant variations in lifespans can be explained by species-specific mtDNA sequence features that cause a shift in the mode of mtDNA replication and thus preclude the formation of large deletions. PMID:26930297

  9. Radiation-induced DNA damage and DNA repair

    International Nuclear Information System (INIS)

    Although DNA undergoes various types of damage from radiation, active oxygen, and the like, a living body has a plurality of DNA repair mechanisms responding to the types of DNA damage. On the other hand, there are a system that results in cell death if the repair is impossible and a mechanism to lead to concretization if further repair is not accurately made. This paper explains the following items as the basic researches on these types of DNA damage and the repair mechanisms: (1) biological effects of DNA damage, (2) effect of DNA damage on DNA synthesis, and (3) effects of DNA damage on cells. It also explains the effects of radiation on cells with a focus on specific mechanism for (1) DNA damage caused by direct action due to radiation and by indirect action due mainly to active oxygen, and (2) DNA repair mechanism that works on DNA double-strand break (DSB). (A.O.)

  10. DNA-PK assay

    Science.gov (United States)

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  11. Apoptosis and DNA Methylation

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Huan X.; Hackett, James A. [MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Nestor, Colm [MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Dunican, Donncha S.; Madej, Monika; Reddington, James P. [MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Pennings, Sari [Queen' s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ (United Kingdom); Harrison, David J. [Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Meehan, Richard R., E-mail: Richard.Meehan@hgu.mrc.ac.uk [MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU (United Kingdom); Breakthrough Research Unit, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU (United Kingdom)

    2011-04-01

    Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.

  12. Apoptosis and DNA Methylation

    Directory of Open Access Journals (Sweden)

    Richard R. Meehan

    2011-04-01

    Full Text Available Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.

  13. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Olsen, Maia E.; Bengtsson, Camilla Friis; Bertelsen, Mads Frost;

    2012-01-01

    feathers. As with nail and hair, we demonstrate that although DNA can, in general, be recovered from all parts of the feather, the quality of such DNA varies. As such, although one can expect a priori that genetic analyses are possible on the feather, for PCR based analyses, it is extremely difficult...... to predict the size of amplicon that can be used in such analyses. However, PCR-free genetic analyses that can exploit much smaller DNA fragments may promise to be a powerful tool for future exploitation....

  14. "Artifactual" arsenate DNA

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2012-01-01

    The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA(1) arose much skepticism, primarily due...... to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present...... evidence that the identification of arsenate DNA was artifactual....

  15. Analysis of DNA repair gene polymorphisms and survival in low-grade and anaplastic gliomas

    DEFF Research Database (Denmark)

    Berntsson, Shala Ghaderi; Wibom, Carl; Sjöström, Sara;

    2011-01-01

    The purpose of this study was to explore the variation in DNA repair genes in adults with WHO grade II and III gliomas and their relationship to patient survival. We analysed a total of 1,458 tagging single-nucleotide polymorphisms (SNPs) that were selected to cover DNA repair genes, in 81 grade ...

  16. Sequence analysis of the ribosomal DNA ITS2 region in two Trichogramma species (Hymenoptera: Trichogrammatidae

    Directory of Open Access Journals (Sweden)

    Ercan Sumer Fahriye

    2011-01-01

    Full Text Available Two egg parasitoid wasps, Trichogramma euproctidis (Girault and Trichogramma brassicae (Bezdenko (Hymenoptera: Trichogrammatidae were identified in the study. The taxonomy of these wasps is problematic because of their small size and lack of distinguishable morphological characters. The DNA sequence variation from the internal transcribed spacer 2 (ITS2 region of nuclear ribosomal DNA (rDNA was analyzed from these two Trichogramma species. This technique provides quick, simple and reliable molecular identification of Trichogramma species.

  17. Genome-scale DNA methylome and transcriptome profiling of human neutrophils

    OpenAIRE

    Chatterjee, Aniruddha; Stockwell, Peter A.; Rodger, Euan J.; Ian M Morison

    2016-01-01

    Methylation of DNA molecules is a key mechanism associated with human disease, altered gene expression and phenotype. Using reduced representation bisulphite sequencing (RRBS) technology we have analysed DNA methylation patterns in healthy individuals and identified genes showing significant inter-individual variation. Further, using whole genome transcriptome analysis (RNA-Seq) on the same individuals we showed a local and specific relationship of exon inclusion and variable DNA methylation ...

  18. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  19. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle;

    2013-01-01

    evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly......This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... the analysis of a stain, relevant from the point of view of a Court of Justice? This question relates to skeptical views previously voiced by commentators mainly in the judicial area, but is avoided by a large majority of forensic scientists. Notwithstanding, the pivotal role of this question has recently been...

  20. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.