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Sample records for abcc8 dna variations

  1. A novel mutation of ABCC8 gene in a patient with diazoxide-unresponsive congenital hyperinsulinism

    PubMed Central

    Park, Ji Sook; Lee, Hong-Jun

    2016-01-01

    Congenital hyperinsulinism (CHI) is a rare condition that can cause irreversible brain damage during the neonatal period owing to the associated hypoglycemia. Hypoglycemia in CHI occurs secondary to the dysregulation of insulin secretion. CHI has been established as a genetic disorder of islet-cell hyperplasia, associated with a mutation of the ABCC8 or KCNJ11 genes, which encode the sulfonylurea receptor 1 and the inward rectifying potassium channel (Kir6.2) subunit of the ATP-sensitive potassium channel, respectively. We report the case of a female newborn infant who presented with repetitive seizures and episodes of apnea after birth, because of hypoglycemia. Investigations revealed hypoglycemia with hyperinsulinemia, but no ketone bodies, and a low level of free fatty acids. High dose glucose infusion, enteral feeding, and medications could not maintain the patient's serum glucose level. Genetic testing revealed a new variation of ABCC8 mutation. Therefore, we report this case of CHI caused by a novel mutation of ABCC8 in a half-Korean newborn infant with diazoxide-unresponsive hyperinsulinemic hypoglycemia. PMID:28018462

  2. Neonatal diabetes mellitus due to a novel ABCC8 gene mutation mimicking an organic acidemia.

    PubMed

    Thakkar, Akanksha N; Muranjan, Mamta N; Karande, Sunil; Shah, Nalini S

    2014-07-01

    Neonatal diabetes mellitus and organic acidemias, may present with similar features like hyperglycemia, ketoacidosis and failure to thrive. A four-mo-old girl presented with diabetic ketoacidosis following a febrile respiratory illness during which high anion gap metabolic acidosis and hyperglycemia were detected. She also had hyperammonemia, which led to diagnostic uncertainty. Euglycemia was achieved with insulin injections. Genotyping revealed a homozygous novel mutation of the ABCC8 gene coding for the SUR1 subunit of the pancreatic beta cell potassium channel. Subsequently, the child was successfully transitioned to oral glibenclamide therapy. Developmental delay was noted on follow-up which raised the possibility of intermediate DEND syndrome. A possible cause for hyperammonemia in neonatal diabetes mellitus has been postulated in the discussion.

  3. Variations in brain DNA

    PubMed Central

    Avila, Jesús; Gómez-Ramos, Alberto; Soriano, Eduardo

    2014-01-01

    It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain. PMID:25505410

  4. Replication of KCNJ11 (p.E23K) and ABCC8 (p.S1369A) Association in Russian Diabetes Mellitus 2 Type Cohort and Meta-Analysis

    PubMed Central

    Sokolova, Ekaterina Alekseevna; Bondar, Irina Arkadievna; Shabelnikova, Olesya Yurievna; Pyankova, Olga Vladimirovna; Filipenko, Maxim Leonidovich

    2015-01-01

    The genes ABCC8 and KCNJ11 have received intense focus in type 2 diabetes mellitus (T2DM) research over the past two decades. It has been hypothesized that the p.E23K (KCNJ11) mutation in the 11p15.1 region may play an important role in the development of T2DM. In 2009, Hamming et al. found that the p.1369A (ABCC8) variant may be a causal factor in the disease; therefore, in this study we performed a meta-analysis to evaluate the association between these single nucleotide polymorphisms (SNPs), including our original data on the Siberian population (1384 T2DM and 414 controls). We found rs5219 and rs757110 were not associated with T2DM in this population, and that there was linkage disequilibrium in Siberians (D’=0.766, r2= 0.5633). In addition, the haplotype rs757110[T]-rs5219[C] (p.23K/p.S1369) was associated with T2DM (OR = 1.52, 95% CI: 1.04-2.24). We included 44 original studies published by June 2014 in a meta-analysis of the p.E23K association with T2DM. The total OR was 1.14 (95% CI: 1.11-1.17) for p.E23K for a total sample size of 137,298. For p.S1369A, a meta-analysis was conducted on a total of 10 studies with a total sample size of 14,136 and pooled OR of 1.14 [95% CI (1.08-1.19); p = 2 x 10-6]. Our calculations identified causal genetic variation within the ABCC8/KCNJ11 region for T2DM with an OR of approximately 1.15 in Caucasians and Asians. Moreover, the OR value was not dependent on the frequency of p.E23K or p.S1369A in the populations. PMID:25955821

  5. Congenital Hyperinsulinism–Associated ABCC8 Mutations That Cause Defective Trafficking of ATP-Sensitive K+ Channels

    PubMed Central

    Yan, Fei-Fei; Lin, Yu-Wen; MacMullen, Courtney; Ganguly, Arupa; Stanley, Charles A.; Shyng, Show-Ling

    2008-01-01

    Congenital hyperinsulinism (CHI) is a disease characterized by persistent insulin secretion despite severe hypoglycemia. Mutations in the pancreatic ATP-sensitive K+ (KATP) channel proteins sulfonylurea receptor 1 (SUR1) and Kir6.2, encoded by ABCC8 and KCNJ11, respectively, is the most common cause of the disease. Many mutations in SUR1 render the channel unable to traffic to the cell surface, thereby reducing channel function. Previous studies have shown that for some SUR1 trafficking mutants, the defects could be corrected by treating cells with sulfonylureas or diazoxide. The purpose of this study is to identify additional mutations that cause channel biogenesis/trafficking defects and those that are amenable to rescue by pharmacological chaperones. Fifteen previously uncharacterized CHI-associated missense SUR1 mutations were examined for their biogenesis/trafficking defects and responses to pharmacological chaperones, using a combination of immunological and functional assays. Twelve of the 15 mutations analyzed cause reduction in cell surface expression of KATP channels by >50%. Sulfonylureas rescued a subset of the trafficking mutants. By contrast, diazoxide failed to rescue any of the mutants. Strikingly, the mutations rescued by sulfonylureas are all located in the first transmembrane domain of SUR1, designated as TMD0. All TMD0 mutants rescued to the cell surface by the sulfonylurea tolbutamide could be subsequently activated by metabolic inhibition on tolbutamide removal. Our study identifies a group of CHI-causing SUR1 mutations for which the resulting KATP channel trafficking and expression defects may be corrected pharmacologically to restore channel function. PMID:17575084

  6. Successful sulfonylurea treatment of a neonate with neonatal diabetes mellitus due to a novel missense mutation, p.P1199L, in the ABCC8 gene.

    PubMed

    Oztekin, O; Durmaz, E; Kalay, S; Flanagan, S E; Ellard, S; Bircan, I

    2012-08-01

    Neonatal/infancy-onset diabetes mellitus is a monogenic form of diabetes with onset within 6 months of age. Two distinct types of neonatal diabetes mellitus have been recognized: permanent and transient. Mutations within the K(+)ATP channel and insulin genes are found in most patients with permanent diabetes mellitus. There have been several reports of the successful transition from insulin to sulfonylurea agents in patients with permanent diabetes mellitus caused by mutations in the KCNJ11 gene. We report on a term female neonate with a novel missense mutation, p.P1199L, in the ABCC8 gene that encodes the sulfonylurea receptor 1 whose treatment was successfully converted from insulin to sulfonylurea.

  7. Noncoding chloroplast DNA variation in Mexican pines.

    PubMed

    Perez de la Rosa, J; Harris, S A; Farjon, A

    1995-11-01

    Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA in order to study restriction site variation in 12 Mexican pine species. Two length mutations were identified that are of diagnostic value for two subgenera or sections of the genus. Phylogenetic analysis of the restriction site and length variation showed patterns of variation largely consistent with previous arrangements of these pines, except for the position of Pinus nelsonii, indicating that Pinus section Parraya Mayr, as circumscribed by Little and Critchfield (1969) and later authors, is not a monophyletic group.

  8. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  9. Retroviral DNA Transposition: Themes and Variations

    PubMed Central

    Skalka, Anna Marie

    2015-01-01

    SUMMARY Retroviruses and LTR retrotransposons are transposable elements that encapsidate the RNAs that are intermediates in the transposition of DNA copies of their genomes (proviruses), from one cell (or one locus) to another. Mechanistic similarities in DNA transposase enzymes and retroviral/retrotransposon integrases underscore the close evolutionary relationship among these elements. The retroviruses are very ancient infectious agents, presumed to have evolved from Ty3/Gypsy LTR retrotransposons (1), and DNA copies of their sequences can be found embedded in the genomes of most, if not all, members of the tree of life. All retroviruses share a specific gene arrangement and similar replication strategies. However, given their ancestries and occupation of diverse evolutionary niches, it should not be surprising that unique sequences have been acquired in some retroviral genomes and that the details of the mechanism by which their transposition is accomplished can vary. While every step in the retrovirus lifecycle is, in some sense, relevant to transposition, this Chapter focuses mainly on the early phase of retroviral replication, during which viral DNA is synthesized and integrated into its host genome. Some of the initial studies that set the stage for current understanding are highlighted, as well as more recent findings obtained through use of an ever-expanding technological toolbox including genomics, proteomics, and siRNA screening. Persistence in the area of structural biology has provided new insight into conserved mechanisms as well as variations in detail among retroviruses, which can also be instructive. PMID:25844274

  10. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  11. Mitochondrial DNA variation in human radiation and disease.

    PubMed

    Wallace, Douglas C

    2015-09-24

    Environmental adaptation, predisposition to common diseases, and, potentially, speciation may all be linked through the adaptive potential of mitochondrial DNA (mtDNA) alterations of bioenergetics. This Perspective synthesizes evidence that human mtDNA variants may be adaptive or deleterious depending on environmental context and proposes that the accrual of mtDNA variation could contribute to animal speciation via adaptation to marginal environments.

  12. Geographic variation of human mitochondrial DNA from Papua New Guinea

    SciTech Connect

    Stoneking, M.; Wilson, A.C. ); Jorde, L.B. ); Bhatia, K. )

    1990-03-01

    High resolution mitochondrial DNA (mtDNA) restriction maps, consisting of an average of 370 sites per mtDNA map, were constructed for 119 people from 25 localities in Papua, New Guinea (PNG). Comparison of these PNG restriction maps to published maps from Australian, Caucasian, Asian and African mtDNAs reveals that PNG has the lowest amount of mtDNA variation, and that PNG mtDNA lineages originated from Southeast Asia. The statistical significance of geographic structuring of populations with respect to mtDNA was assessed by comparing observed G{sub ST} values to a distribution of G{sub ST} values generated by random resampling of the data. These analyses show that there is significant structuring of mtDNA variation among worldwide populations, between highland and coastal PNG populations, and even between two highland PNG populations located approximately 200 km apart. However, coastal PNG populations are essentially panmictic, despite being spread over several hundred kilometers. The high resolution technique for examining mtDNA variation, coupled with extensive geographic sampling within a single defined area, leads to an enhanced understanding of the influence of geography on mtDNA variation in human populations.

  13. Variation in nuclear DNA concentrations during urination.

    PubMed

    Johnson, Donald J; Calderaro, Alexa C; Roberts, Katherine A

    2007-01-01

    This study examined the cellular origin and concentration of nuclear DNA in human urine. Ten subjects provided two entire, first-morning voids: one as a single specimen and one as a consecutive series of samples. The serial samples were centrifuged, organically extracted, and quantified by slot-blot analysis. Total DNA concentrations ranged from 0.02 to 21.3 ng/mL for the males and 25.0 to 96.9 ng/mL for the females. The female samples were found to contain numerous vaginal epithelial cells. DNA was detected in all of the serial samples of nine subjects; however, the DNA concentrations varied considerably. With six subjects, the DNA concentration of the first serial sample was at least three times greater than that of the entire void. DNA was only detected in the first 21% of the void from one male subject. The results of this study have implications for the collection of urine samples.

  14. Mitochondrial DNA copy number variation across human cancers

    PubMed Central

    Reznik, Ed; Miller, Martin L; Şenbabaoğlu, Yasin; Riaz, Nadeem; Sarungbam, Judy; Tickoo, Satish K; Al-Ahmadie, Hikmat A; Lee, William; Seshan, Venkatraman E; Hakimi, A Ari; Sander, Chris

    2016-01-01

    Mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), are observed throughout cancers. Here, we survey mtDNA copy number variation across 22 tumor types profiled by The Cancer Genome Atlas project. We observe a tendency for some cancers, especially of the bladder, breast, and kidney, to be depleted of mtDNA, relative to matched normal tissue. Analysis of genetic context reveals an association between incidence of several somatic alterations, including IDH1 mutations in gliomas, and mtDNA content. In some but not all cancer types, mtDNA content is correlated with the expression of respiratory genes, and anti-correlated to the expression of immune response and cell-cycle genes. In tandem with immunohistochemical evidence, we find that some tumors may compensate for mtDNA depletion to sustain levels of respiratory proteins. Our results highlight the extent of mtDNA copy number variation in tumors and point to related therapeutic opportunities. DOI: http://dx.doi.org/10.7554/eLife.10769.001 PMID:26901439

  15. DNA Template Dependent Accuracy Variation of Nucleotide Selection in Transcription

    PubMed Central

    Mellenius, Harriet; Ehrenberg, Måns

    2015-01-01

    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. PMID:25799551

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

    PubMed

    Mellenius, Harriet; Ehrenberg, Måns

    2015-01-01

    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.

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

    PubMed Central

    Li, Shizhao; Zhu, Yufei; Zhi, Lihui; Han, Xiaoying; Shen, Jing; Liu, Yanli; Yao, Junhu; Yang, Xiaojun

    2016-01-01

    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 hypomethylation

  18. Interindividual variation with respect to DNA repair in human cells

    SciTech Connect

    Leonard, R.C.; Leonard, J.C.; Bender, M.A.; Wieland, J.; Setlow, R.B.

    1989-01-01

    Ecogenetics is the study of genetically determined differences among individuals in their susceptibility to the actions of physical, chemical, and biological agents in the environment. An individual's most basic level of response to these environmental agents may be the ability to repair physical and chemical damage to DNA. We have been engaged in a survey of DNA-repair measurements in a healthy working population in order to determine the extent of the population variability in these endpoints and to assess the value of these screening protocols in identifying individuals who are at the extremes of the distribution. In addition, we are measuring intraindividual variation over time, as well as the correlations between measurements of different repair systems. The endpoints that we have chosen to use are cytogenetic responses (SCE's and micronucleus formation) and DNA excision repair (unscheduled DNA synthesis and removal of O{sup 6} guanine methylation) in human peripheral lymphocytes exposed to 254 nm ultraviolet light, x-rays, the bifunctional alkylating agent mitomycin C, or the monofunctional alkylating agent N-methyl-N-nitro-nitrosoguanidine (MNNG). These four test mutagens produce spectra of DNA lesions eliciting different types of DNA repair. 3 refs., 1 tab.

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

    PubMed

    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.

  20. DNA-protein recognition and sequence-dependent variations of DNA conformational properties

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2015-03-01

    Parameters of B-DNA, the major form of the double helix, depend on its sequence. This dependence can contribute to the recognition of specific DNA sequences by proteins. Here we try to analyze this contribution quantitatively. In the first approach to this goal we used experimental data on the sequence dependence of DNA bending rigidity and its helical repeat. The solution data on these parameters of B-DNA were derived from the experiments on cyclization of short DNA fragments with specially designed sequences. The data allowed calculating the sequence variations of DNA bending energy, as well as the variations of the energy of torsional deformation of the double helix associated with a protein binding. The results show that DNA conformational parameters can have very limited influence on the sequence specificity of protein binding. In the second approach we analyzed the experimental data on the binding affinity of the nucleosome core with DNA fragments of different sequences. The conclusions derived in these two approaches are in a good agreement with one another.

  1. The study of human Y chromosome variation through ancient DNA.

    PubMed

    Kivisild, Toomas

    2017-03-04

    High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

  2. Nuclear DNA content variation and evolution in liverworts.

    PubMed

    Bainard, Jillian D; Forrest, Laura L; Goffinet, Bernard; Newmaster, Steven G

    2013-09-01

    Across embryophytes there is a significant range in DNA content, both in regards to genome size (total DNA in an unreduced chromosome complement) and degree of endoreduplication (when DNA replication not followed by division resulting in various ploidy levels within the same individual). However, there is little information available on DNA content evolution in liverworts, the likely sister group to all other living plants. This study seeks to detect a phylogenetic structure in the variation in genome size and degree of endopolyploidy within liverworts. Furthermore, we test the hypothesis that shifts in breeding systems and genome size are correlated, as polyploidy is suggested to be a possible mechanism for the evolution of monoecy in liverworts and could therefore be associated with larger genome sizes. Genome size was determined for 67 liverwort species from 33 families using flow cytometry. Estimates for 48 species and 16 families are new to science. A phylogeny was reconstructed using the plastid gene rbcL. Over all taxa analyzed, there was a considerable range in genome size estimates with 1C-values from 0.27 pg (Jungermannia rubra) to 20.46 pg (Phyllothallia fuegiana). Large genome sizes were also found in the Haplomitriopsida. None of the liverwort species showed evidence of endopolyploidy. Although some taxa may be polyploids, a correlation between shifts in genome size and breeding system is lacking. Importantly, genome size variation in liverworts exhibits strong phylogenetic signal (Pagel's λ=0.99955).

  3. Intra‐ and Interspecific Variation in DNA Content in Cistus (Cistaceae)

    PubMed Central

    ELLUL, PHILIPPE; BOSCAIU, MONICA; VICENTE, OSCAR; MORENO, VICENTE; ROSSELLÓ, JOSEP A.

    2002-01-01

    Flow cytometry, using propidium iodide and 4′,6‐diamidano‐2-phenylindole staining, was used to estimate the nuclear DNA content (2C) and the proportion of A–T base pairs in 16 species of the Mediterranean genus Cistus. Genome sizes were shown to be constant within species, since no significant intraspecific variation in 2C DNA content was detected. At the genus level, up to about 1·5‐fold differences in absolute DNA amounts were observed, ranging from 3·92 pg in C. crispus to 5·88 pg in C. monspeliensis. The (AT) : (GC) ratio was close to 1, and was similar for all species examined, ranging from 47·87 % A–T content in C. clusii, to 50·67 % in C. populifolius. Pink‐flowered species (subgenus Cistus) had lower DNA amounts than white‐flowered species (subgenera Leucocistus and Halimioides). However, the distribution of DNA amounts in Cistus appeared to be continuous and did not permit a clear separation of infra‐generic ranks in the genus. PMID:12234146

  4. Chromatin fiber polymorphism triggered by variations of DNA linker lengths.

    PubMed

    Collepardo-Guevara, Rosana; Schlick, Tamar

    2014-06-03

    Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin's diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.

  5. Nonneutral mitochondrial DNA variation in humans and chimpanzees

    SciTech Connect

    Nachman, M.W.; Aquadro, C.F.; Brown, W.M.

    1996-03-01

    We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases. 59 refs., 2 figs., 8 tabs.

  6. Analysis of sequence variation in Gnathostoma spinigerum mitochondrial DNA by single-strand conformation polymorphism analysis and DNA sequence.

    PubMed

    Ngarmamonpirat, Charinthon; Waikagul, Jitra; Petmitr, Songsak; Dekumyoy, Paron; Rojekittikhun, Wichit; Anantapruti, Malinee T

    2005-03-01

    Morphological variations were observed in the advance third stage larvae of Gnathostoma spinigerum collected from swamp eel (Fluta alba), the second intermediate host. Larvae with typical and three atypical types were chosen for partial cytochrome c oxidase subunit I (COI) gene sequence analysis. A 450 bp polymerase chain reaction product of the COI gene was amplified from mitochondrial DNA. The variations were analyzed by single-strand conformation polymorphism and DNA sequencing. The nucleotide variations of the COI gene in the four types of larvae indicated the presence of an intra-specific variation of mitochondrial DNA in the G. spinigerum population.

  7. Microsatellite DNA variation in Bornean orangutans (Pongo pygmaeus).

    PubMed

    Warren, K S; Nijmian, I J; Lenstra, J A; Swan, R A; Heriyanto; den Boer, M

    2000-04-01

    Orangutans (Pongo pygmaeus) on the islands of Borneo and Sumatra are considered two separate subspecies. However, the genetic relationships between isolated populations on Borneo are not clear. This study determined the extent of variation within the Bornean subspecies of orangutan, using microsatellite DNA analysis. Blood samples were collected from 96 individuals of known origin from East, West and Central Kalimantan. Human microsatellite primer pairs located at human map position D2S141, D4S431, D 11S925, D16S420 and D17S791 were suitable for use in primates. D4S431 appeared monomorphic for all orangutans. In three cases (D2S141 East and West and D16S420 West), a highly significant excess of homozygous allele frequencies was detected, but with other primer pairs no significant difference in allele frequencies occurred. We conclude that the divergence between the different populations on Borneo is less than the variation within the populations. There was also evidence that inbreeding occurred within the populations.

  8. Mitochondrial DNA variations associated with recurrent pregnancy loss among Indian women.

    PubMed

    Vanniarajan, Ayyasamy; Govindaraj, Periyasamy; Carlus, S Justin; Aruna, Meka; Aruna, P; Kumar, Ajay; Jayakar, Richard Issac; Lionel, Anath C; Gupta, Sandeep; Rao, Lakshmi; Gupta, Nalini J; Chakravarthy, Baidyanath; Deenadayal, Mamatha; Selvaraj, Kamala; Andal, Sadaranga; Reddy, B Mohan; Singh, Lalji; Thangaraj, Kumarasamy

    2011-05-01

    Several genetic factors have been found to be associated with recurrent pregnancy loss (RPL). However, not many attempts have been made to associate the mitochondrial DNA (mtDNA) variations with RPL. Therefore, we have analyzed the complete mtDNA of 100 women with RPL and 12 aborted fetal tissues. Our analysis revealed a total of 681 variations, most of which were in NADH Dehydrogenase (ND) genes that encode mitochondrial enzyme Complex I. Presence of T4216C variation (ND1 gene) in 9% of the RPL women and several pathogenic, and novel mutations suggest the role of mtDNA variations in RPL.

  9. Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae.

    PubMed

    Kim, Y D; Jansen, R K

    1998-12-01

    Comparative restriction site mapping of the chloroplast genome was performed to examine phylogenetic relationships among 27 species representing 16 genera of the Berberidaceae and two outgroups. Chloroplast genomes of the species included in this study showed no major structural rearrangements (i.e., they are collinear to tobacco cpDNA) except for the extension of the inverted repeat in species of Berberis and Mahonia. Excluding several regions that exhibited severe length variation, a total of 501 phylogenetically informative sites was mapped for ten restriction enzymes. The strict consensus tree of 14 equally parsimonious trees indicated that some berberidaceous genera (Berberis, Mahonia, Diphylleia) are not monophyletic. To explore phylogenetic utility of different parsimony methods phylogenetic trees were generated using Wagner, Dollo, and weighted parsimony for a reduced data set that included 18 species. One of the most significant results was the recognition of the four chromosomal groups, which were strongly supported regardless of the parsimony method used. The most notable difference among the trees produced by the three parsimony methods was the relationships among the four chromosomal groups. The cpDNA trees also strongly supported a close relationship of several generic pairs (e.g., Berberis-Mahonia, Epimedium-Vancouveria, etc.). Maximum likelihood values were computed for the four different tree topologies of the chromosomal groups, two Wagner, one Dollo, and one weighted topology. The results indicate that the weighted tree has the highest likelihood value. The lowest likelihood value was obtained for the Dollo tree, which had the highest bootstrap and decay values. Separate analyses using only the Inverted Repeat (IR) region resulted in a tree that is identical to the weighted tree. Poor resolution and/or support for the relationships among the four chromosomal lineages of the Berberidaceae indicate that they may have radiated from an ancestral

  10. Microsatellite DNA and mitochondrial DNA variation in remnant and translocated sea otter (Enhydra lutris) populations

    USGS Publications Warehouse

    Larson, Shawn E.; Jameson, Ronald J.; Bodkin, James L.; Staedler, Michelle; Bentzen, Paul

    2002-01-01

    All existing sea otter (Enhydra lutris) populations have suffered at least 1, and in some cases 2, population bottlenecks. The 1st occurred during the 18th and 19th centuries as a result of commercial hunting that eliminated sea otters from much their native range and reduced surviving populations to small remnants. The 2nd bottleneck occurred when small numbers of otters were reintroduced, via translocation, to areas where the species had been eliminated. We examined genetic variation at 7 microsatellite loci and the mitochondrial DNA (mtDNA) control region in 3 remnant populations, Amchitka Island (Aleutian Islands, Alaska), central coastal California, and Prince William Sound (Alaska), and in 2 reintroduced populations, southeast Alaska and Washington, that were founded with transplants from Amchitka, and in the case of southeast Alaska, individuals from Prince William Sound as well. We found no evidence of reduced genetic diversity in translocated populations. Average expected microsatellite heterozygosities (HE) were similar in all populations (range, 0.40–0.47), and mtDNA haplotype diversities were higher in reintroduced populations (0.51 for both Washington and southeast Alaska) than in remnant populations (X̄ = 0.35; range, 0.18–0.45). The levels of genetic diversity we observed within sea otter populations were relatively low when compared with other mammals and are thought to be the result of fur trade exploitation.

  11. The fractal based analysis of human face and DNA variations during aging.

    PubMed

    Namazi, Hamidreza; Akrami, Amin; Hussaini, Jamal; Silva, Osmar N; Wong, Albert; Kulish, Vladimir V

    2017-01-16

    Human DNA is the main unit that shapes human characteristics and features such as behavior. Thus, it is expected that changes in DNA (DNA mutation) influence human characteristics and features. Face is one of the human features which is unique and also dependent on his gen. In this paper, for the first time we analyze the variations of human DNA and face simultaneously. We do this job by analyzing the fractal dimension of DNA walk and face during human aging. The results of this study show the human DNA and face get more complex by aging. These complexities are mapped on fractal exponents of DNA walk and human face. The method discussed in this paper can be further developed in order to investigate the direct influence of DNA mutation on the face variations during aging, and accordingly making a model between human face fractality and the complexity of DNA walk.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation

    PubMed Central

    Wang, J; Abbott, R J; Peng, Y L; Du, F K; Liu, J-Q

    2011-01-01

    It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China. PMID:21448232

  14. Human mitochondrial DNA variation and the origin of Basques.

    PubMed

    Bertranpetit, J; Sala, J; Calafell, F; Underhill, P A; Moral, P; Comas, D

    1995-01-01

    The hypervariable segment I of the control region of the mtDNA (positions 16024-16383) was PCR-amplified from mouth scrape and hairs and sequenced in 45 unrelated individuals of pure matrilineal Basque descent. Twenty-seven different sequences were found, of which 21 are unique to the Basques. The allelic partition observed, together with resampling experiments, suggested that much more variation remained to be discovered. The mean pairwise difference in number of nucleotides between individuals was 3-15, a very low value. Moreover, the number of steps for the most parsimonious tree is very low compared to the number of different sequences. Both findings suggest that the Basque population was founded by a few lineages that diverged in a short time span. The number of nucleotide differences between individuals was shown not to be influenced by the distance between their birthplaces, thus validating the sampling strategy used a posteriori. The pairwise difference distribution agreed well with the three-parameter model proposed by Rogers & Harpending (1992). The parameter estimates found for the Basques implied that a demographic expansion (or perhaps two, given the bimodal shape of the distribution) took place sometime between 14500 and 42000 BP which is in agreement with archaeological data. Our sample was compared to other populations for which D-loop sequences were available through the Nei & Miller (1990) distance. In a neighbour-joining tree, all the Caucasoid samples, including the Basques, appeared tightly clustered, whereas African samples were the most distant to the Caucasoids and also the most heterogeneous. Although classical markers, such as blood groups and protein polymorphisms, clearly separate the Basques (and the Sardinians) from other European populations, this distinctiveness was not found using D-loop sequences.

  15. The 1001 Arabidopsis DNA Methylomes: An Important Resource for Studying Natural Genetic, Epigenetic, and Phenotypic Variation.

    PubMed

    Lang, Zhaobo; Xie, Shaojun; Zhu, Jian-Kang

    2016-11-01

    Intraspecific phenotypic diversity is controlled by natural genetic and epigenetic variation. Kawakatsu et al. recently sequenced the DNA methylomes of a global collection of over 1000 Arabidopsis accessions, and have thereby provided a comprehensive resource for studying natural genetic and epigenetic variation as well as the association of such variation with phenotypic diversity.

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

    PubMed Central

    2011-01-01

    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. PMID:21569271

  17. DNA and RNA ligases: structural variations and shared mechanisms.

    PubMed

    Pascal, John M

    2008-02-01

    DNA and RNA ligases join 3' OH and 5' PO4 ends in polynucleotide substrates using a three-step reaction mechanism that involves covalent modification of both the ligase enzyme and the polynucleotide substrate with AMP. In the past three years, several polynucleotide ligases have been crystallized in complex with nucleic acid, providing the introductory views of ligase enzymes engaging their substrates. Crystal structures for two ATP-dependent DNA ligases, an NAD+-dependent DNA ligase, and an ATP-dependent RNA ligase demonstrate how ligases utilize the AMP group and their multi-domain architectures to manipulate nucleic acid structure and catalyze the end-joining reaction. Together with unliganded crystal structures of DNA and RNA ligases, a more comprehensive and dynamic understanding of the multi-step ligation reaction mechanism has emerged.

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

    PubMed

    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.

  19. Extensive ribosomal DNA genic variation in the columnar cactus Lophocereus.

    PubMed

    Hartmann, S; Nason, J D; Bhattacharya, D

    2001-08-01

    Sequence analysis of the hypervariable internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) is commonly used to gain insights into plant and animal population structure and phylogeny. We characterized ITS1, ITS2, and the 5.8S coding region of 18 senita (Lophocereus) individuals from 12 different populations in Baja as well as from closely related cactus species. Analyses of multiple clones demonstrated extensive paralogy in the senita rDNA gene family. We identified at least two putatively non-recombining rDNA operons in senita as well as multiple paralogous sequences within each operon. Usage of PCR, reverse transcriptase (RT)-PCR, Southern blot, primary sequence analyses of the 18S rDNA gene, and secondary structure analyses of the 5.8S rRNA showed that one of the operons encodes rDNA pseudogenes in a low copy-number (Truncated), whereas the second operon encodes an expressed rRNA (Functional). Surprisingly, we found extensive paralogy not only in the ITS regions but also in the 5.8S coding regions in senita both within and between operons. Phylogenetic analyses suggest that the second rDNA operon originated prior to the divergence of Lophocereus. A significant (p < 0.05) divergence-rate acceleration was found in the Lophocereus 5.8S rDNA coding region in the Functional operon in comparison to Pereskiopsis porteri (Cactaceae) and Portulaca molokiniensis (Portulacaceae) with Silene dioica and Spinacia oleracea as the outgroups.

  20. Survey of variation in human transcription factors reveals prevalent DNA binding changes

    PubMed Central

    Barrera, Luis A.; Rogers, Julia M.; Gisselbrecht, Stephen S.; Rossin, Elizabeth J.; Woodard, Jaie; Mariani, Luca; Kock, Kian Hong; Inukai, Sachi; Siggers, Trevor; Shokri, Leila; Gordân, Raluca; Sahni, Nidhi; Cotsapas, Chris; Hao, Tong; Yi, Song; Kellis, Manolis; Daly, Mark J.; Vidal, Marc; Hill, David E.; Bulyk, Martha L.

    2016-01-01

    Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA-binding activity and used universal protein binding microarrays to assay sequence-specific DNA-binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA-binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA-binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA-binding activities, which may contribute to phenotypic variation. PMID:27013732

  1. DNA Content Variation and Its Significance in the Evolution of the Genus Micrasterias (Desmidiales, Streptophyta)

    PubMed Central

    Poulíèková, Aloisie; Mazalová, Petra; Vašut, Radim J.; Šarhanová, Petra; Neustupa, Jiøí; Škaloud, Pavel

    2014-01-01

    It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae. PMID:24465986

  2. Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

    PubMed Central

    Gibbons, John G.; Branco, Alan T.; Godinho, Susana A.; Yu, Shoukai; Lemos, Bernardo

    2015-01-01

    Tandemly repeated ribosomal DNA (rDNA) arrays are among the most evolutionary dynamic loci of eukaryotic genomes. The loci code for essential cellular components, yet exhibit extensive copy number (CN) variation within and between species. CN might be partly determined by the requirement of dosage balance between the 5S and 45S rDNA arrays. The arrays are nonhomologous, physically unlinked in mammals, and encode functionally interdependent RNA components of the ribosome. Here we show that the 5S and 45S rDNA arrays exhibit concerted CN variation (cCNV). Despite 5S and 45S rDNA elements residing on different chromosomes and lacking sequence similarity, cCNV between these loci is strong, evolutionarily conserved in humans and mice, and manifested across individual genotypes in natural populations and pedigrees. Finally, we observe that bisphenol A induces rapid and parallel modulation of 5S and 45S rDNA CN. Our observations reveal a novel mode of genome variation, indicate that natural selection contributed to the evolution and conservation of cCNV, and support the hypothesis that 5S CN is partly determined by the requirement of dosage balance with the 45S rDNA array. We suggest that human disease variation might be traced to disrupted rDNA dosage balance in the genome. PMID:25583482

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

    PubMed

    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).

  4. Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines.

    PubMed

    Li, Qing; Eichten, Steven R; Hermanson, Peter J; Springer, Nathan M

    2014-03-01

    DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-inherited DMRs provide an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at these DMRs during the generations of the NIL population development. DNA methylation level was associated with local genotypes in nearly all of the >30,000 potential cases of inheritance. The majority of the DMRs were not associated with small RNAs. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits locally (cis) inherited patterns, is highly stable, and does not require active programming by small RNAs for maintenance. DNA methylation may contribute to heritable epigenetic information in many eukaryotic genomes. In this study, we have documented the inheritance patterns and trans-generational stability for nearly 1000 DNA methylation variants in a segregating maize population. At most loci studied, the DNA methylation differences are locally inherited and are not influenced by the other allele or other genomic regions. The inheritance of DNA methylation levels across generations is quite robust with almost no examples of unstable inheritance, suggesting that DNA methylation differences can be quite stably inherited, even in segregating populations.

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

    PubMed

    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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25487335

  7. Mitochondrial DNA variations in Madras motor neuron disease

    PubMed Central

    Govindaraj, Periyasamy; Nalini, Atchayaram; Krishna, Nithin; Sharath, Anugula; Khan, Nahid Akhtar; Tamang, Rakesh; Devi, M. Gourie; Brown, Robert H.; Thangaraj, Kumarasamy

    2013-01-01

    Although the Madras Motor Neuron Disease (MMND) was found three decades ago, its genetic basis has not been elucidated, so far. The symptom at onset was impaired hearing, upper limb weakness and atrophy. Since some clinical features of MMND overlap with mitochondrial disorders, we analyzed the complete mitochondrial genome of 45 MMND patients and found 396 variations, including 13 disease-associated, 2 mt-tRNA and 33 non-synonymous (16 MT-ND, 10 MT-CO, 3 MT-CYB and 4 MT-ATPase). A rare variant (m.8302A>G) in mt-tRNALeu was found in three patients. We predict that these variation(s) may influence the disease pathogenesis along with some unknown factor(s). PMID:23419391

  8. Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA.

    PubMed

    Tomaru, N; Takahashi, M; Tsumura, Y; Takahashi, M; Ohba, K

    1998-05-01

    Mitochondrial (mt) DNA variation in Japanese beech, Fagus crenata (Fagaceae), was studied in 17 populations distributed throughout the species' range. Total genomic DNA of samples from single trees representing each of 12 populations were digested with 18 restriction enzymes and hybridized with three probes containing coxI, coxIII, and atpA gene sequences. Thirty-four of the 54 enzyme/probe combinations showed polymorphisms and all the individuals were subsequently analyzed with six combinations of three probes and two enzymes. Restriction fragment length polymorphisms were evident around all three genes, allowing the identification of eight distinct haplotypes. Haplotype diversity within the populations was found to be very low (HS = 0.031), but population differentiation to be much higher (GST = 0.963). The mtDNA variation was strikingly different from allozyme variation (HS = 0.209; GST = 0.039). Gene flow for maternally inherited mtDNA should be restricted to seed dispersal while nuclear gene flow occurs by both seed and pollen dispersal. Therefore, the difference in the variation between mtDNA and allozymes may be largely a result of the much higher rate of gene flow associated with pollen dispersal than with seed dispersal. The mtDNA variation displayed strong geographic structure, which may reflect the species' distribution in the last glacial maximum and subsequent colonization, and probably also reflects intraspecific phylogeography of the species.

  9. A localized transition in the size variation of circular DNA in nanoslits

    NASA Astrophysics Data System (ADS)

    Strychalski, Elizabeth A.; Stavis, Samuel M.; Geist, Jon

    2013-03-01

    We observe a localized transition in the size variation of circular DNA between strong and moderate regimes of nanofluidic slitlike confinement. We applied a rigorous statistical analysis to our recent experimental measurements of DNA size for linear and circular topologies in nanoslits with depths around ~2p, where p is the DNA persistence length [E. A. Strychalski, J. Geist, M. Gaitan, L. E. Locascio, S. M. Stavis. Macromolecules, 45, 1602-1611 (2012)]. Our empirical approach revealed a localized transition between confinement regimes for circular DNA at a nanoslit depth of ~3p but detected no such transition for linear DNA with a similar contour length. These results provide the first indication of the localized influence of polymer topology on size variation across changing nanoslit depths. Improved understanding of differences in polymer behavior due to topology in this controversial system is of fundamental importance in polymer science and will inform new nanofluidic methods for biopolymer analysis.

  10. MICROSATELLITE DNA VARIATION IN TWO FATHEAD MINNOW (PIMEPHALES PROMELAS) STOCKS

    EPA Science Inventory

    Adverse effects on more than 2000 species of fish in the U.S. and Canada are estimated by sensitvity results of fathead minnow (Pimephales promelas) acute toxicity tests. Whether survival and susceptibility to toxicants are influenced by genetic variation is still under question...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. Mitochondrial DNA sequence variation in human evolution and disease.

    PubMed Central

    Wallace, D C

    1994-01-01

    Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations. Images PMID:8090716

  13. Mitochondrial DNA and Y-chromosome variation in the caucasus.

    PubMed

    Nasidze, I; Ling, E Y S; Quinque, D; Dupanloup, I; Cordaux, R; Rychkov, S; Naumova, O; Zhukova, O; Sarraf-Zadegan, N; Naderi, G A; Asgary, S; Sardas, S; Farhud, D D; Sarkisian, T; Asadov, C; Kerimov, A; Stoneking, M

    2004-05-01

    We have analyzed mtDNA HVI sequences and Y chromosome haplogroups based on 11 binary markers in 371 individuals, from 11 populations in the Caucasus and the neighbouring countries of Turkey and Iran. Y chromosome haplogroup diversity in the Caucasus was almost as high as in Central Asia and the Near East, and significantly higher than in Europe. More than 27% of the variance in Y-haplogroups can be attributed to differences between populations, whereas mtDNA showed much lower heterogeneity between populations (less then 5%), suggesting a strong influence of patrilocal social structure. Several groups from the highland region of the Caucasus exhibited low diversity and high differentiation for either or both genetic systems, reflecting enhanced genetic drift in these small, isolated populations. Overall, the Caucasus groups showed greater similarity with West Asian than with European groups for both genetic systems, although this similarity was much more pronounced for the Y chromosome than for mtDNA, suggesting that male-mediated migrations from West Asia have influenced the genetic structure of Caucasus populations.

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

    PubMed

    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.

  15. Human body epigenome maps reveal noncanonical DNA methylation variation.

    PubMed

    Schultz, Matthew D; He, Yupeng; Whitaker, John W; Hariharan, Manoj; Mukamel, Eran A; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R; Urich, Mark A; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J; Wang, Wei; Ecker, Joseph R

    2015-07-09

    Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual's cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals' phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.

  16. Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

    PubMed Central

    Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.

    2015-01-01

    Summary Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual’s cells, with epigenetic mechanisms that could play tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns1,2. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals’ phased genome3, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in multiple genomic contexts varies substantially among human tissues. PMID:26030523

  17. Mitochondrial DNA variations in ova and blastocyst: implications in assisted reproduction.

    PubMed

    Shamsi, Monis Bilal; Govindaraj, Periyasamy; Chawla, Latika; Malhotra, Neena; Singh, Neeta; Mittal, Suneeta; Talwar, Pankaj; Thangaraj, Kumarasamy; Dada, Rima

    2013-03-01

    Mitochondrial DNA (mtDNA) of oocyte is critical for its function, embryo quality and development. Analysis of complete mtDNA of 49 oocytes and 18 blastocysts from 67 females opting for IVF revealed 437 nucleotide variations. 40.29% samples had either disease associated or non-synonymous novel or pathogenic mutation in evolutionarily conserved regions. Samples with disease associated mtDNA mutations had low fertilization rate and poor embryo quality, however no difference in implantation or clinical pregnancy rate was observed. Screening mtDNA from oocyte/blastocyst is a simple, clinically reliable method for diagnostic evaluation of female infertility and may reduce risk of mtDNA disease transmission.

  18. Inter- and intraspecific mitochondrial DNA variation in North American bears (Ursus)

    USGS Publications Warehouse

    Cronin, M.A.; Amstrup, S.; Garner, G.; Vyse, Ernest R.

    1991-01-01

    We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondrial DNA sequence divergence in brown bears and polar bears is lower than in black bears. The two morphological forms of U. arctos, grizzly and coastal brown bears, are not in distinct mtDNA lineages. Interspecific comparisons indicate that brown bears and polar bears share similar mitochondrial DNA (0.023 base substitutions per nucleotide) which is quite divergent (0.078 base substitutions per nucleotide) from that of black bears. High mitochondrial DNA divergence within black bears and paraphyletic relationships of brown and polar bear mitochondrial DNA indicate that intraspecific variation across species' ranges should be considered in phylogenetic analyses of mitochondrial DNA.

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

    PubMed

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

    2012-11-01

    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 of DNA SBs/alkaline labile sites in MNBCs were not reduced by applying the standard assay protocol as compared with the laboratory's own protocol. There was large inter-laboratory variation in FPG-sensitive sites by the laboratory-specific protocol and the variation was reduced when the samples were analysed by the standard protocol. The SBs and FPG-sensitive sites were measured in the same experiment, indicating that the large spread in the latter lesions was the main reason for the reduced inter-laboratory variation. However, it remains worrying that half of the participating laboratories obtained poor results using the standard procedure. This study indicates that future comet assay validation trials should take steps to evaluate the implementation of standard procedures in participating laboratories.

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

    SciTech Connect

    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 this system will work on the

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

    PubMed

    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.

  2. Sequential Model Selection based Segmentation to Detect DNA Copy Number Variation

    PubMed Central

    Hu, Jianhua; Zhang, Liwen; Wang, Huixia Judy

    2016-01-01

    Summary Array-based CGH experiments are designed to detect genomic aberrations or regions of DNA copy-number variation that are associated with an outcome, typically a state of disease. Most of the existing statistical methods target on detecting DNA copy number variations in a single sample or array. We focus on the detection of group effect variation, through simultaneous study of multiple samples from multiple groups. Rather than using direct segmentation or smoothing techniques, as commonly seen in existing detection methods, we develop a sequential model selection procedure that is guided by a modified Bayesian information criterion. This approach improves detection accuracy by accumulatively utilizing information across contiguous clones, and has computational advantage over the existing popular detection methods. Our empirical investigation suggests that the performance of the proposed method is superior to that of the existing detection methods, in particular, in detecting small segments or separating neighboring segments with differential degrees of copy-number variation. PMID:26954760

  3. Mitochondrial DNA sequence variation in Iranian native dogs.

    PubMed

    Amiri Ghanatsaman, Zeinab; Adeola, Adeniyi C; Asadi Fozi, Masood; Ma, Ya-Ping; Peng, Min-Sheng; Wang, Guo-Dong; Esmailizadeh, Ali; Zhang, Ya-Ping

    2017-03-17

    The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise FST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.

  4. Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes

    PubMed Central

    Evans, Joseph; McCormick, Ryan F.; Morishige, Daryl; Olson, Sara N.; Weers, Brock; Hilley, Josie; Klein, Patricia; Rooney, William; Mullet, John

    2013-01-01

    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 19th 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. PMID:24265758

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

    PubMed

    Evans, Joseph; McCormick, Ryan F; Morishige, Daryl; Olson, Sara N; Weers, Brock; Hilley, Josie; Klein, Patricia; Rooney, William; Mullet, John

    2013-01-01

    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.

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

    PubMed

    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.

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

    PubMed Central

    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

  8. Microsatellite DNA and mitochondrial DNA variation in polar bears (Ursus maritimus) from the Beaufort and Chukchi seas, Alaska

    USGS Publications Warehouse

    Cronin, M.A.; Amstrup, Steven C.; Scribner, K.T.

    2006-01-01

    Radiotelemetry data have shown that polar bears (Ursus maritimus Phipps, 1774) occur in separate subpopulations in the Chukchi Sea and the southern Beaufort Sea. However, segregation is not absolute, and there is overlap of ranges of animals in each subpopulation. We used genetic variation at eight microsatellite DNA loci and mitochondrial DNA (mtDNA) to further assess the degree of spatial structure of polar bears from the Chukchi and southern Beaufort seas. Microsatellite allele frequencies and mtDNA haplotype frequencies of bears from the southern Beaufort and Chukchi seas did not differ significantly. Lack of differentiation at both maternally inherited mtDNA and bi-parentally inherited microsatellite loci suggests that gene flow between the two areas is mediated by both sexes. The genetic data indicate that polar bears in the southern Beaufort and Chukchi seas compose one interbreeding population. However, there is considerable fidelity to ranges in each area, particularly by adult females. The combined genetic and movement data suggest that polar bears could be managed as Beaufort Sea and Chukchi Sea subpopulations of a combined southern Beaufort Sea and Chukchi Sea population. ?? 2006 NRC.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  11. Ag K-edge EXAFS analysis of DNA-templated fluorescent silver nanoclusters: insight into the structural origins of emission tuning by DNA sequence variations.

    PubMed

    Neidig, Michael L; Sharma, Jaswinder; Yeh, Hsin-Chih; Martinez, Jennifer S; Conradson, Steven D; Shreve, Andrew P

    2011-08-10

    DNA-templated silver nanoclusters are promising biological fluorescence probes due to their useful fluorescence properties, including tunability of emission wavelength through DNA template sequence variations. Ag K-edge EXAFS analysis of DNA-templated silver nanoclusters has been used to obtain insight into silver nanocluster bonding, size, and structural correlations to fluorescence. The results indicate the presence of small silver nanoclusters (<30 silver atoms) containing Ag-Ag bonds and Ag-N/O ligations to DNA. The DNA sequence used leads to differences in silver-DNA ligation as well as silver nanocluster size. The results support a model in which cooperative effects of both Ag-DNA ligation and variations in cluster size lead to the tuning of the fluorescence emission of DNA-templated silver nanoclusters.

  12. Mitochondrial DNA sequence variation among populations and host races of Lambdina fiscellaria (Gn.) (Lepidoptera: Geometridae).

    PubMed

    Sperling, F A; Raske, A G; Otvos, I S

    1999-02-01

    The hemlock looper, Lambdina fiscellaria (Gn.), is a recurring major forest pest that is widely distributed in North America. Three subspecies (L. f. fiscellaria, L. f. lugubrosa (Hulst) and L. f. somniaria (Hulst)) have been recognized based on larval host or adult pheromone differences, but no consistent morphological differences have been reported. To clarify their taxonomic status, we surveyed mitochondrial DNA (mtDNA) sequence and restriction site variation in two protein coding genes, cytochrome oxidase I and II (COI and COII), in populations across the range of L. fiscellaria. In addition to variation in COI and COII, we found an intergenic spacer region of 20-23 bp located between the tRNA tyrosine gene and the start of COI. Of the 141 specimens of L. fiscellaria assayed, 137 were grouped into two distinct mtDNA lineages, one of which was disproportionately associated with eastern populations and one with western populations. However, single specimens and two populations in eastern Canada had mtDNA resembling that of western populations. Three divergent and rare haplotypes had basal affinities to the two common lineages. The two major lineages of L. fiscellaria were diverged by approximately 2% from each other, as well as from the mtDNA of two outgroup species, L. athasaria (Walker) and L. pellucidaria(G. & R.). The two outgroup species had essentially the same mtDNA and may be conspecific. We interpret the pattern of mtDNA variation within L. fiscellaria as indicating genetic polymorphism within a single species without clear subspecific divisions, rather than evidence of multiple cryptic species.

  13. Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates.

    PubMed

    Gonseth, Semira; de Smith, Adam J; Roy, Ritu; Zhou, Mi; Lee, Seung-Tae; Shao, Xiaorong; Ohja, Juhi; Wrensch, Margaret R; Walsh, Kyle M; Metayer, Catherine; Wiemels, Joseph L

    2016-09-01

    Epigenome-wide DNA methylation association studies have identified highly replicable genomic loci sensitive to maternal smoking during gestation. The role of inter-individual genetic variation in influencing DNA methylation, leading to the possibility of confounding or bias of such associations, has not been assessed. We investigated whether the DNA methylation levels at the top 10 CpG sites previously associated with exposure to maternal smoking during gestation were associated with individual genetic variation at the genome-wide level. Genome-wide association tests between DNA methylation at the top 10 candidate CpG and genome-wide SNPs were performed in 736 case and control participants of the California Childhood Leukemia Study. Three of the strongest maternal-smoking sensitive CpG sites in newborns were significantly associated with SNPs located proximal to each gene: cg18146737 in the GFI1 gene with rs141819830 (P = 8.2×10(-44)), cg05575921 in the AHRR gene with rs148405299 (P = 5.3×10(-10)), and cg12803068 in the MYO1G gene with rs61087368 (P = 1.3×10(-18)). For the GFI1 CpG cg18146737, the underlying genetic variation at rs141819830 confounded the association between maternal smoking and DNA methylation in our data (the regression coefficient changed from -0.02 [P = 0.139] to -0.03 [P = 0.015] after including the genotype). Our results suggest that further studies using DNA methylation at cg18146737, cg05575921, or cg12803068 that aim to assess exposure to maternal smoking during gestation should include genotype at the corresponding SNP. New methods are required for adequate and routine inclusion of genotypic influence on DNA methylation in epigenome-wide association studies to control for potential confounding.

  14. mtDNA Variation among Greenland Eskimos: The Edge of theBeringian Expansion

    PubMed Central

    Saillard, Juliette; Forster, Peter; Lynnerup, Niels; Bandelt, Hans-Jürgen; Nørby, Søren

    2000-01-01

    The Eskimo-Aleut language phylum is distributed from coastal Siberia across Alaska and Canada to Greenland and is well distinguished from the neighboring Na Dene languages. Genetically, however, the distinction between Na Dene and Eskimo-Aleut speakers is less clear. In order to improve the genetic 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 the groups D2 and D3 found in Siberia and Alaska and are exclusively A2 but at the same time lack the A2 root type. The data are in agreement with the view that the present Greenland Eskimos essentially descend from Alaskan Neo-Eskimos. European mtDNA types are absent in our Eskimo sample. PMID:10924403

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

    SciTech Connect

    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

  16. Varietal Tracing of Virgin Olive Oils Based on Plastid DNA Variation Profiling

    PubMed Central

    Pérez-Jiménez, Marga; Besnard, Guillaume; Dorado, Gabriel; Hernandez, Pilar

    2013-01-01

    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. PMID:23950947

  17. Mitochondrial-DNA variation among subspecies and populations of sea otters (Enhydra lutris)

    USGS Publications Warehouse

    Cronin, M.A.; Bodkin, J.L.; Ballachey, B.E.; Estes, J.A.; Patton, J.C.

    1996-01-01

    We used restriction-enzyme analysis of polymerase-chain reaction-amplified, mitochondrial DNA (mtDNA) to assess genetic differentiation of subspecies and populations of sea otters throughout the range of the species. There were several haplotypes of mtDNA in each subspecies and geographically separate populations. MtDNA sequence divergence of haplotypes of sea otters was 0.0004-0.0041 base substitutions per nucleotide. E. l. nereis appears to have monophyletic mitochondrial DNA, while E. l. lutris and E. l. kenyoni do not. Different frequencies of haplotypes of mtDNA among populations reflect current restriction of gene flow and the unique histories of different populations. There are two or three haplotypes of mtDNA and diversity of haplotypes is 0.1376-0.5854 in each population of otters. This is consistent with theoretical work, which suggests that population bottlenecks of sea otters probably did not result in major losses of genetic variation for individual populations, or the species as a whole.

  18. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes.

    PubMed

    Teh, Ai Ling; Pan, Hong; Chen, Li; Ong, Mei-Lyn; Dogra, Shaillay; Wong, Johnny; MacIsaac, Julia L; Mah, Sarah M; McEwen, Lisa M; Saw, Seang-Mei; Godfrey, Keith M; Chong, Yap-Seng; Kwek, Kenneth; Kwoh, Chee-Keong; Soh, Shu-E; Chong, Mary F F; Barton, Sheila; Karnani, Neerja; Cheong, Clara Y; Buschdorf, Jan Paul; Stünkel, Walter; Kobor, Michael S; Meaney, Michael J; Gluckman, Peter D; Holbrook, Joanna D

    2014-07-01

    Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health over the lifecourse. Epigenetics, and in particular DNA methylation marks, have been postulated as a mechanism for the enduring effects of the prenatal environment. Accordingly, neonate methylomes contain molecular memory of the individual in utero experience. However, interindividual variation in methylation can also be a consequence of DNA sequence polymorphisms that result in methylation quantitative trait loci (methQTLs) and, potentially, the interaction between fixed genetic variation and environmental influences. We surveyed the genotypes and DNA methylomes of 237 neonates and found 1423 punctuate regions of the methylome that were highly variable across individuals, termed variably methylated regions (VMRs), against a backdrop of homogeneity. MethQTLs were readily detected in neonatal methylomes, and genotype alone best explained ∼25% of the VMRs. We found that the best explanation for 75% of VMRs was the interaction of genotype with different in utero environments, including maternal smoking, maternal depression, maternal BMI, infant birth weight, gestational age, and birth order. Our study sheds new light on the complex relationship between biological inheritance as represented by genotype and individual prenatal experience and suggests the importance of considering both fixed genetic variation and environmental factors in interpreting epigenetic variation.

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

    PubMed

    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.

  20. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

    PubMed Central

    Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.

    2016-01-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

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

    NASA Astrophysics Data System (ADS)

    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

  2. Genome-wide quantitative assessment of variation in DNA methylation patterns

    PubMed Central

    Xie, Hehuang; Wang, Min; de Andrade, Alexandre; de F. Bonaldo, Maria; Galat, Vasil; Arndt, Kelly; Rajaram, Veena; Goldman, Stewart; Tomita, Tadanori; Soares, Marcelo B.

    2011-01-01

    Genomic DNA methylation contributes substantively to transcriptional regulations that underlie mammalian development and cellular differentiation. Much effort has been made to decipher the molecular mechanisms governing the establishment and maintenance of DNA methylation patterns. However, little is known about genome-wide variation of DNA methylation patterns. In this study, we introduced the concept of methylation entropy, a measure of the randomness of DNA methylation patterns in a cell population, and exploited it to assess the variability in DNA methylation patterns of Alu repeats and promoters. A few interesting observations were made: (i) within a cell population, methylation entropy varies among genomic loci; (ii) among cell populations, the methylation entropies of most genomic loci remain constant; (iii) compared to normal tissue controls, some tumors exhibit greater methylation entropies; (iv) Alu elements with high methylation entropy are associated with high GC content but depletion of CpG dinucleotides and (v) Alu elements in the intronic regions or far from CpG islands are associated with low methylation entropy. We further identified 12 putative allelic-specific methylated genomic loci, including four Alu elements and eight promoters. Lastly, using subcloned normal fibroblast cells, we demonstrated the highly variable methylation patterns are resulted from low fidelity of DNA methylation inheritance. PMID:21278160

  3. Nonmonotonous variation of DNA angular separation during asymmetric pulsed field electrophoresis.

    PubMed

    Nazemifard, Neda; Bhattacharjee, Subir; Masliyah, Jacob H; Harrison, D Jed

    2013-09-01

    Asymmetric pulsed field electrophoresis within crystalline arrays is used to generate angular separation of DNA molecules. Four regimes of the frequency response are observed, a low frequency rise in angular separation, a plateau, a subsequent decline, and a second plateau at higher frequencies. It is shown that the frequency response for different sized DNA is governed by the relation between pulse time and the reorientation time of DNA molecules. The decline in angular separation at higher frequencies has not previously been analyzed. Real-time videos of single DNA molecules migrating under high frequency-pulsed electric field show the molecules no longer follow the head to tail switching, ratchet mechanism seen at lower frequencies. Once the pulse period is shorter than the reorientation time, the migration mechanism changes significantly. The molecule reptates along the average direction of the two electric fields, which reduces the angular separation. A freely jointed chain model of DNA is developed where the porous structure is represented with a hexagonal array of obstacles. The model qualitatively predicts the variation of DNA angular separation with respect to frequency.

  4. mtDNA variation in caste populations of Andhra Pradesh, India.

    PubMed

    Bamshad, M; Fraley, A E; Crawford, M H; Cann, R L; Busi, B R; Naidu, J M; Jorde, L B

    1996-02-01

    Various anthropological analyses have documented extensive regional variation among populations on the subcontinent of India using morphological, protein, blood group, and nuclear DNA polymorphisms. These patterns are the product of complex population structure (genetic drift, gene flow) and a population history noted for numerous branching events. As a result, the interpretation of relationships among caste populations of South India and between Indians and continental populations remains controversial. The Hindu caste system is a general model of genetic differentiation among endogamous populations stratified by social forces (e.g., religion and occupation). The mitochondrial DNA (mtDNA) molecule has unique properties that facilitate the exploration of population structure. We analyzed 36 Hindu men born in Andhra Pradesh who were unrelated matrilineally through at least 3 generations and who represent 4 caste populations: Brahmin (9), Yadava (10), Kapu (7), and Relli (10). Individuals from Africa (36), Asia (36), and Europe (36) were sampled for comparison. A 200-base-pair segment of hypervariable segment 2 (HVS2) of the mtDNA control region was sequenced in all individuals. In the Indian castes 25 distinct haplotypes are identified. Aside from the Cambridge reference sequence, only two haplotypes are shared between caste populations. Middle castes form a highly supported cluster in a neighbor-joining network. Mean nucleotide diversity within each caste is 0.015, 0.012, 0.011, and 0.012 for the Brahmin, Yadava, Kapu, and Relli, respectively. mtDNA variation is highly structured between castes (GST = 0.17; p < 0.002). The effects of social structure on mtDNA variation are much greater than those on variation measured by traditional markers. Explanations for this discordance include (1) the higher resolving power of mtDNA, (2) sex-dependent gene flow, (3) differences in male and female effective population sizes, and (4) elements of the kinship structure. Thirty

  5. Tandem repeats and length variation in the mitochondrial DNA control region of Epirrita autumnata (Lepidoptera: Geometridae).

    PubMed

    Snäll, N; Huoponen, K; Savontaus, M L; Ruohomäki, K

    2002-10-01

    The organization of the mitochondrial DNA (mtDNA) control region (CR) of the autumnal moth, Epirrita autumnata, is described. The E. autumnata CR presents a distinct type of lepidopteran CR with domains of non-repetitive and repetitive sequences. The CRs show considerable length variation owing to a variable number of short approximately 29-bp sequence blocks that are repeated between 6 and 14 times in tandem. The organization of such a tandem array is unique among the insect CRs examined so far. Furthermore, the E. autumnata CR, which may reach 1075 bp in length, is considerably longer than previously reported lepidopteran CRs, which reach 311-499 bp in length. Like other lepidopteran CRs, the E. autumnata CR contains two long homopolymer runs that may be involved in mtDNA replication and (or) transcription.

  6. Nuclear DNA Content Variation and Species Relationships in the Genus Lupinus (Fabaceae)

    PubMed Central

    NAGANOWSKA, BARBARA; WOLKO, BOGDAN; ŚLIWIŃSKA, ELWIRA; KACZMAREK, ZYGMUNT

    2003-01-01

    The 2C nuclear DNA content has been estimated by flow cytometry in 18 species and botanical forms of the genus Lupinus (family Fabaceae), using propidium iodide as a fluorescent dye. They represented distinct infrageneric taxonomic groups and differed in somatic chromosome numbers. Estimated 2C DNA values ranged from 0·97 pg in L. princei to 2·44 pg in L. luteus, which gives a more than 2·5-fold variation. Statistical analysis of the data obtained resulted in a grouping that supports the generally accepted taxonomic classification of the Old World lupins. The rough-seeded L. princei turned out to be an interesting exception, getting closer to smooth-seeded species. Results of DNA content analyses are discussed with regards to the phylogenetic relationships among the Old World lupins and some aspects of the evolution of the genus. PMID:12853281

  7. Ribosomal DNA and Stellate gene copy number variation on the Y chromosome of Drosophila melanogaster.

    PubMed

    Lyckegaard, E M; Clark, A G

    1989-03-01

    Multigene families on the Y chromosome face an unusual array of evolutionary forces. Both ribosomal DNA and Stellate, the two families examined here, have multiple copies of similar sequences on the X and Y chromosomes. Although the rate of sequence divergence on the Y chromosome depends on rates of mutation, gene conversion and exchange with the X chromosome, as well as purifying selection, the regulation of gene copy number may also depend on other pleiotropic functions, such as maintenance of chromosome pairing. Gene copy numbers were estimated for a series of 34 Y chromosome replacement lines using densitometric measurements of slot blots of genomic DNA from adult Drosophila melanogaster. Scans of autoradiographs of the same blots probed with the cloned alcohol dehydrogenase gene, a single copy gene, served as internal standards. Copy numbers span a 6-fold range for ribosomal DNA and a 3-fold range for Stellate DNA. Despite this magnitude of variation, there was no association between copy number and segregation variation of the sex chromosomes.

  8. Population subdivision in Europe's great bustard inferred from mitochondrial and nuclear DNA sequence variation.

    PubMed

    Pitra, C; Lieckfeldt, D; Alonso, J C

    2000-08-01

    A continent-wide survey of sequence variation in mitochondrial (mt) and nuclear (n) DNA of the endangered great bustard (Otis tarda) was conducted to assess the extent of phylogeographic structure in a morphologically monotypic bird. DNA sequence variation in a combined 809 bp segment of the mtDNA genome from 66 individuals from the last six breeding regions showed relatively low levels of intraspecific sequence diversity (n = 0.32%) but significant differences in the regional distribution of 11 haplotypes (phiST = 0.49). Despite their exceptional potential for dispersal, a complete and long-term historical separation between the populations from the Iberian Peninsula (Spain) and mainland Europe (Hungary, Slovakia, Germany, and Russia) was demonstrated. Divergence between populations based on a 3-bp insertion-deletion polymorphism within the intron region of the nuclear CHD-Z gene was geographically concordant with the primary subdivision identified within the mtDNA sequences. Inferred aspects of phylogeography were used to formulate conservation recommendations for this endangered species.

  9. Nuclear DNA content in Miscanthus sp. and the geographical variation pattern in Miscanthus lutarioriparius

    PubMed Central

    Sheng, Jiajing; Hu, Xiaohu; Zeng, Xiaofei; Li, Ye; Zhou, Fasong; Hu, Zhongli; Jin, Surong; Diao, Ying

    2016-01-01

    The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions. PMID:27698438

  10. Mitochondrial DNA Variation and the Evolution of Robertsonian Chromosomal Races of House Mice, Mus Domesticus

    PubMed Central

    Nachman, M. W.; Boyer, S. N.; Searle, J. B.; Aquadro, C. F.

    1994-01-01

    The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time. PMID:8005418

  11. Nuclear DNA content in Miscanthus sp. and the geographical variation pattern in Miscanthus lutarioriparius

    NASA Astrophysics Data System (ADS)

    Sheng, Jiajing; Hu, Xiaohu; Zeng, Xiaofei; Li, Ye; Zhou, Fasong; Hu, Zhongli; Jin, Surong; Diao, Ying

    2016-10-01

    The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions.

  12. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

    PubMed Central

    Baker, C S; Perry, A; Bannister, J L; Weinrich, M T; Abernethy, R B; Calambokidis, J; Lien, J; Lambertsen, R H; Ramírez, J U; Vasquez, O

    1993-01-01

    Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting. PMID:8367488

  13. Mitochondrial DNA variation in the hybridizing fire-bellied toads, Bombina bombina and B. variegata.

    PubMed

    Szymura, J M; Uzzell, T; Spolsky, C

    2000-07-01

    Using five restriction enzymes, geographical variation of mitochondrial DNA (mtDNA) in Bombina bombina and B. variegata was studied in samples from 20 locations. Each restriction enzyme produced a species-specific fragment pattern. B. bombina haplotypes A and B were closely related to each other. In contrast, haplotypes A and B of B. variegata formed two distinct lineages. A very distinctive haplotype (C) was found in the Carpathian Mountains, whereas two other haplotypes, D and E (differing by a single AvaI site), were present in western Europe and the Balkans, respectively. Populations polymorphic for haplotypes D and E occurred in the central Balkans where the haplotypes could replace each other clinally. mtDNA sequence divergence between B. bombina and B. variegata was estimated as 6.0-8.1% and 4.7-5.2% between type C and types D/E of B. variegata. The latter divergence is contrary to allozyme and morphological data that place the western and Carpathian B. v. variegata together (Nei's D = 0.07) and separate them from the Balkan subspecies B. v. scabra (Nei's D = 0.18). Broad interspecific correlation among morphology, allozymes and mtDNA types in European fire-bellied toads argues that, despite continuous hybridization (interrupted perhaps during Pleistocene glacial maxima), little or no mtDNA introgression between the species has occurred outside the narrow hybrid zones that separate these parapatric species.

  14. Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly.

    PubMed

    Tranah, Gregory J; Lam, Ernest T; Katzman, Shana M; Nalls, Michael A; Zhao, Yiqiang; Evans, Daniel S; Yokoyama, Jennifer S; Pawlikowska, Ludmila; Kwok, Pui-Yan; Mooney, Sean; Kritchevsky, Stephen; Goodpaster, Bret H; Newman, Anne B; Harris, Tamara B; Manini, Todd M; Cummings, Steven R

    2012-09-01

    The decline in activity energy expenditure underlies a range of age-associated pathological conditions, neuromuscular and neurological impairments, disability, and mortality. The majority (90%) of the energy needs of the human body are met by mitochondrial oxidative phosphorylation (OXPHOS). OXPHOS is dependent on the coordinated expression and interaction of genes encoded in the nuclear and mitochondrial genomes. We examined the role of mitochondrial genomic variation in free-living activity energy expenditure (AEE) and physical activity levels (PAL) by sequencing the entire (~16.5 kilobases) mtDNA from 138 Health, Aging, and Body Composition Study participants. Among the common mtDNA variants, the hypervariable region 2 m.185G>A variant was significantly associated with AEE (p=0.001) and PAL (p=0.0005) after adjustment for multiple comparisons. Several unique nonsynonymous variants were identified in the extremes of AEE with some occurring at highly conserved sites predicted to affect protein structure and function. Of interest is the p.T194M, CytB substitution in the lower extreme of AEE occurring at a residue in the Qi site of complex III. Among participants with low activity levels, the burden of singleton variants was 30% higher across the entire mtDNA and OXPHOS complex I when compared to those having moderate to high activity levels. A significant pooled variant association across the hypervariable 2 region was observed for AEE and PAL. These results suggest that mtDNA variation is associated with free-living AEE in older persons and may generate new hypotheses by which specific mtDNA complexes, genes, and variants may contribute to the maintenance of activity levels in late life.

  15. Mitochondrial DNA variation in Mauritania and Mali and their genetic relationship to other Western Africa populations.

    PubMed

    González, A M; Cabrera, V M; Larruga, J M; Tounkara, A; Noumsi, G; Thomas, B N; Moulds, J M

    2006-09-01

    Mitochondrial DNA (mtDNA) variation was analyzed in Mauritania and Mali, and compared to other West African samples covering the considerable geographic, ethnic and linguistic diversity of this region. The Mauritanian mtDNA profile shows that 55% of their lineages have a west Eurasian provenance, with the U6 cluster (17%) being the best represented. Only 6% of the sub-Saharan sequences belong to the L3A haplogroup a frequency similar to other Berber speaking groups but significantly different to the Arabic speaking North Africans. The historic Arab slave trade may be the main cause of this difference. Only one HV west Eurasian lineage has been detected in Mali but 40% of the sub-Saharan sequences belong to cluster L3A. The presence of L0a representatives demonstrates gene flow from eastern regions. Although both groups speak related dialects of the Mande branch, significant genetic differences exist between the Bambara and Malinke groups. The West African genetic variation is well structured by geography and language, but more detailed ethnolinguistic clustering suggest that geography is the main factor responsible for this differentiation.

  16. Spatial distribution of mitochondrial and microsatellite DNA variation in Daubenton's bat within Scotland.

    PubMed

    Ngamprasertwong, Thongchai; Mackie, Iain J; Racey, Paul A; Piertney, Stuart B

    2008-07-01

    Daubenton's bat (Myotis daubentonii) is a known reservoir for European bat lyssavirus type 2 (EBLV-2). An appreciation of the potential for epidemiological spread and disease risk requires an understanding of the dispersal of the primary host, and any large-scale geographical barriers that may impede gene flow. The spatial pattern of microsatellite and mitochondrial DNA variation was examined to infer patterns of dispersal of bats among 35 populations across Scotland. DNA sequence variation at the mitochondrial control region and ND1 genes revealed two distinct phylogeographical clades, with generally nonoverlapping geographical distributions except for a small number of populations where both matrilines were found in sympatry. Such discontinuity suggests that Scotland was recolonized twice following the retreat of the Pleistocene ice sheet with little subsequent matrilineal introgression. However, eight microsatellite loci showed low levels of genetic divergence among populations, even between populations from the two distinct mitochondrial DNA clades. An overall, macrogeographical genetic isolation-by-distance pattern was observed, with high levels of gene flow among local populations. Apparently contrasting patterns of mitochondrial and microsatellite divergence at different scales could be explained by sex-specific differences in gene flow at large scales.

  17. Large scale DNA sequencing: new challenges emerge--the 2007 Human Genome Variation Society scientific meeting.

    PubMed

    Oetting, William S

    2008-05-01

    The annual scientific meeting of the Human Genome Variation Society (HGVS) was held on 23 October 2007, in San Diego, CA. The major theme of this meeting was "New DNA Sequencing Technologies & Human Genome Variation." A series of speakers provided information on several new technologies that produce DNA sequence data on a scale far beyond what was possible even a few years ago. These new technologies produce up to gigabases of nucleotides on a single run. Already, two individuals have had their entire genome sequenced, resulting in the identification of many novel DNA variants. Several new questions now need to be answered. What impact do these novel variants have on the phenotypes? How are we to associate private variants in a single individual with disease, especially when current association studies require genotyping thousands of individuals? Further work will be required to create methodologies to analyze these variants to determine if they are potentially disease-producing or are phenotypically silent. For the technology to be useful in a medical setting it will be crucial to answer to these questions.

  18. Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster.

    PubMed

    Wei, Kevin H-C; Grenier, Jennifer K; Barbash, Daniel A; Clark, Andrew G

    2014-12-30

    Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence.

  19. Variations in duplex DNA conformation detected by the binding of monoclonal autoimmune antibodies.

    PubMed Central

    Braun, R P; Lee, J S

    1986-01-01

    Four monoclonal antibodies (Jel 229, 239, 241, 242) which bound to duplex DNA were prepared from two autoimmune female NZB/NZW mice. Their binding to various nucleic acids was investigated by a competitive solid phase radioimmune assay which allows the estimation of relative binding constants. None of the antibodies showed any consistent variation of binding constant with base composition and thus they must recognize features of the DNA backbone. Jel 241 binds across the major groove but the interaction with poly(pyrimidine) X poly(purine) DNAs was barely detectable. This antibody appears to recognize the "alternating-B" conformation which is promoted by methylation of pyrimidines in alternating sequences. The other three antibodies bind in the minor groove. In particular, for Jel 229 the preferred antigen was poly(dG) X poly(dC) with only weak binding to poly(dA) X poly(dT). This suggests a requirement for a wide minor groove. Thus autoimmune antibodies provide examples of "analogue" recognition and can be used to detect structural variations in the grooves of duplex DNA. PMID:3725591

  20. Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER.

    PubMed

    Holzinger, Emily R; Hulgan, Todd; Ellis, Ronald J; Samuels, David C; Ritchie, Marylyn D; Haas, David W; Kallianpur, Asha R; Bloss, Cinnamon S; Clifford, David B; Collier, Ann C; Gelman, Benjamin B; Marra, Christina M; McArthur, Justin C; McCutchan, J Allen; Morgello, Susan; Simpson, David M; Franklin, Donald R; Rosario, Debralee; Selph, Doug; Letendre, Scott; Grant, Igor

    2012-12-01

    HIV-associated sensory neuropathy remains an important complication of combination antiretroviral therapy and HIV infection. Mitochondrial DNA haplogroups and single nucleotide polymorphisms (SNPs) have previously been associated with symptomatic neuropathy in clinical trial participants. We examined associations between mitochondrial DNA variation and HIV-associated sensory neuropathy in CNS HIV Antiretroviral Therapy Effects Research (CHARTER). CHARTER is a USA-based longitudinal observational study of HIV-infected adults who underwent a structured interview and standardized examination. HIV-associated sensory neuropathy was determined by trained examiners as ≥1 sign (diminished vibratory and sharp-dull discrimination or ankle reflexes) bilaterally. Mitochondrial DNA sequencing was performed and haplogroups were assigned by published algorithms. Multivariable logistic regression of associations between mitochondrial DNA SNPs, haplogroups, and HIV-associated sensory neuropathy were performed. In analyses of associations of each mitochondrial DNA SNP with HIV-associated sensory neuropathy, the two most significant SNPs were at positions A12810G [odds ratio (95 % confidence interval) = 0.27 (0.11-0.65); p = 0.004] and T489C [odds ratio (95 % confidence interval) = 0.41 (0.21-0.80); p = 0.009]. These synonymous changes are known to define African haplogroup L1c and European haplogroup J, respectively. Both haplogroups were associated with decreased prevalence of HIV-associated sensory neuropathy compared with all other haplogroups [odds ratio (95 % confidence interval) = 0.29 (0.12-0.71); p = 0.007 and odds ratio (95 % confidence interval) = 0.42 (0.18-1.0); p = 0.05, respectively]. In conclusion, in this cohort of mostly combination antiretroviral therapy-treated subjects, two common mitochondrial DNA SNPs and their corresponding haplogroups were associated with a markedly decreased prevalence of HIV-associated sensory neuropathy.

  1. Low mitochondrial DNA variation among American alligators and a novel non-coding region in crocodilians.

    PubMed

    Glenn, Travis C; Staton, Joseph L; Vu, Alex T; Davis, Lisa M; Bremer, Jaime R Alvarado; Rhodes, Walter E; Brisbin, I Lehr; Sawyer, Roger H

    2002-12-15

    We analyzed 1317-1823 base pairs (bp) of mitochondrial DNA sequence beginning in the 5' end of cytochrome b (cyt b) and ending in the central domain of the control region for 25 American alligators (Alligator mississippiensis) and compared these to a homologous sequence from a Chinese alligator (A. sinensis). Both species share a non-coding spacer between cyt b and tRNA(Thr). Chinese alligator cyt b differs from that of the American alligator by 17.5% at the nucleotide level and 13.8% for inferred amino acids, which is consistent with their presumed ancient divergence. Only two cyt b haplotypes were detected among the 25 American alligators (693-1199 bp surveyed), with one haplotype shared among 24 individuals. One alligator from Mississippi differed from all other alligators by a single silent substitution. The control region contained only slightly more variation among the 25 American alligators, with two variable positions (624 bp surveyed), yielding three haplotypes with 22, two, and one individuals in each of these groups. Previous genetic studies examining allozymes and the proportion of variable microsatellite DNA loci also found low levels of genetic diversity in American alligators. However, in contrast with allozymes, microsatellites, and morphology, the mtDNA data shows no evidence of differentiation among populations from the extremes of the species range. These results suggest that American alligators underwent a severe population bottleneck in the late Pleistocene, resulting in nearly homogenous mtDNA among all American alligators today.

  2. Systematic localization of common disease-associated variation in regulatory DNA.

    PubMed

    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; Johnson, Audra K; Canfield, Theresa K; Giste, Erika; Diegel, Morgan; Bates, Daniel; Hansen, R Scott; Neph, Shane; Sabo, Peter J; Heimfeld, Shelly; Raubitschek, Antony; Ziegler, Steven; Cotsapas, Chris; Sotoodehnia, Nona; Glass, Ian; Sunyaev, Shamil R; Kaul, Rajinder; Stamatoyannopoulos, John A

    2012-09-07

    Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs). Eighty-eight percent of such DHSs are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes. We identified distant gene targets for hundreds of variant-containing DHSs that may explain phenotype associations. Disease-associated variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks. We also demonstrated tissue-selective enrichment of more weakly disease-associated variants within DHSs and the de novo identification of pathogenic cell types for Crohn's disease, multiple sclerosis, and an electrocardiogram trait, without prior knowledge of physiological mechanisms. Our results suggest pervasive involvement of regulatory DNA variation in common human disease and provide pathogenic insights into diverse disorders.

  3. Intragenomic rDNA ITS2 Variation in the Neotropical Anopheles (Nyssorhynchus) albitarsis Complex (Diptera: Culicidae)

    DTIC Science & Technology

    2006-12-07

    However, in Allopb,/er, there are examples of rONA intragenomic variation (\\X’ilkerson et al. 2004; Fairley et al. 2005), but its prevalence and...Anopheles species (Onyabe and Conn 1999; Wilkerson et al. 2004; Fairley et aI. 200S) and in other mos- quitoes in subfamily Culicinae (Black et a!. 1989...DNA 1TS2 sequences. J :-.led Entomo!’ 33:109-116. Dover GA. 1982. Molecular dri"e: a cnhesive mode of species evolution. Nature. 299:111-117. Fairley

  4. Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes.

    PubMed Central

    Melton, T; Clifford, S; Martinson, J; Batzer, M; Stoneking, M

    1998-01-01

    Previous studies of mtDNA variation in indigenous Taiwanese populations have suggested that they held an ancestral position in the spread of mtDNAs throughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995), but the question of an absolute proto-Austronesian homeland remains. To search for Asian roots for indigenous Taiwanese populations, 28 mtDNAs representative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwan) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Alu insertion loci were analyzed, to determine if the pattern of mtDNA variation is concordant with nuclear DNA variation. Tribal groups shared considerable mtDNA sequence identity (P>.90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs with a 9-bp deletion have considerable mainland-Asian diversity and have spread to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any other populations, but these shared types were widely dispersed geographically throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overall, the results suggest that the Taiwanese have temporally deep roots, probably in central or south China, and have been isolated from other Asian populations in recent history. PMID:9837834

  5. Phase variable DNA repeats in Neisseria gonorrhoeae influence transcription, translation, and protein sequence variation

    PubMed Central

    Zelewska, Marta A.; Pulijala, Madhuri; Spencer-Smith, Russell; Mahmood, Hiba-Tun-Noor A.; Norman, Billie; Churchward, Colin P.; Calder, Alan

    2016-01-01

    There are many types of repeated DNA sequences in the genomes of the species of the genus Neisseria, from homopolymeric tracts to tandem repeats of hundreds of bases. Some of these have roles in the phase-variable expression of genes. When a repeat mediates phase variation, reversible switching between tract lengths occurs, which in the species of the genus Neisseria most often causes the gene to switch between on and off states through frame shifting of the open reading frame. Changes in repeat tract lengths may also influence the strength of transcription from a promoter. For phenotypes that can be readily observed, such as expression of the surface-expressed Opa proteins or pili, verification that repeats are mediating phase variation is relatively straightforward. For other genes, particularly those where the function has not been identified, gathering evidence of repeat tract changes can be more difficult. Here we present analysis of the repetitive sequences that could mediate phase variation in the Neisseria gonorrhoeae strain NCCP11945 genome sequence and compare these results with other gonococcal genome sequences. Evidence is presented for an updated phase-variable gene repertoire in this species, including a class of phase variation that causes amino acid changes at the C-terminus of the protein, not previously described in N. gonorrhoeae. PMID:28348872

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

    PubMed

    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

  7. Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.)

    PubMed Central

    Schellenbaum, Paul; Mohler, Volker; Wenzel, Gerhard; Walter, Bernard

    2008-01-01

    Background In traditional vine areas, the production should present a typicity that partly depends on the grapevine variety. Therefore, vine improvement is considered difficult because of the limited choice in the natural variability of the cultivars within the limits of their characteristics. A possibility to circumvent this problem is the use of somatic variability. In vitro somatic embryogenesis and organogenesis can lead to genotypic and phenotypic variations, described as somaclonal variation, that could be useful for the selection of improved grapevine genotypes. Results In order to study tissue culture-induced variation of grapevine, we have analysed 78 somaclones obtained from somatic embryos of two distinct cultivars using molecular marker techniques. SSRs were only useful to verify the conservation of the microsatellite genotype between the somaclones and the respective mother clones. AFLP polymorphism between mother clones and somaclones was 1.3–2.8 times higher to that found between clones. However, a majority of the somaclones (45/78) exhibited only few changes. Seven and five somaclones of 'Chardonnay 96' and 'Syrah 174', respectively, which covered at least all polymorphic loci found in AFLP analysis were used for MSAP study. All of the 120 polymorphic fragments were found only in the somaclones. The percentage of full methylation at CCGG recognition sites was slightly higher in somaclones due to more polymorphic bands generated after cleavage by EcoRI/HpaII. Different digestion patterns revealed different methylation status, especially different levels of de-methylation, that are the consequence of the in vitro culture. Conclusion MSAP highlights DNA methylation variation in somaclones compared to mother clones and, therefore, is a powerful tool for genotypic characterisation of somatic embryo-derived grapevines. The detection of the same polymorphic bands in numerous somaclones of different cultivars suggests the possibility of hot spots of DNA

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

    USGS Publications Warehouse

    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.

  9. Excessive genomic DNA copy number variation in the Li–Fraumeni cancer predisposition syndrome

    PubMed Central

    Shlien, Adam; Tabori, Uri; Marshall, Christian R.; Pienkowska, Malgorzata; Feuk, Lars; Novokmet, Ana; Nanda, Sonia; Druker, Harriet; Scherer, Stephen W.; Malkin, David

    2008-01-01

    DNA copy number variations (CNVs) are a significant and ubiquitous source of inherited human genetic variation. However, the importance of CNVs to cancer susceptibility and tumor progression has not yet been explored. Li–Fraumeni syndrome (LFS) is an autosomal dominantly inherited disorder characterized by a strikingly increased risk of early-onset breast cancer, sarcomas, brain tumors and other neoplasms in individuals harboring germline TP53 mutations. Known genetic determinants of LFS do not fully explain the variable clinical phenotype in affected family members. As part of a wider study of CNVs and cancer, we conducted a genome-wide profile of germline CNVs in LFS families. Here, by examining DNA from a large healthy population and an LFS cohort using high-density oligonucleotide arrays, we show that the number of CNVs per genome is well conserved in the healthy population, but strikingly enriched in these cancer-prone individuals. We found a highly significant increase in CNVs among carriers of germline TP53 mutations with a familial cancer history. Furthermore, we identified a remarkable number of genomic regions in which known cancer-related genes coincide with CNVs, in both LFS families and healthy individuals. Germline CNVs may provide a foundation that enables the more dramatic chromosomal changes characteristic of TP53-related tumors to be established. Our results suggest that screening families predisposed to cancer for CNVs may identify individuals with an abnormally high number of these events. PMID:18685109

  10. Detection of Variation in Long-Term Micropropagated Mature Pistachio via DNA-Based Molecular Markers.

    PubMed

    Akdemir, Hülya; Suzerer, Veysel; Tilkat, Engin; Onay, Ahmet; Çiftçi, Yelda Ozden

    2016-12-01

    Determination of genetic stability of in vitro-grown plantlets is needed for safe and large-scale production of mature trees. In this study, genetic variation of long-term micropropagated mature pistachio developed through direct shoot bud regeneration using apical buds (protocol A) and in vitro-derived leaves (protocol B) was assessed via DNA-based molecular markers. Randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) were employed, and the obtained PIC values from RAPD (0.226), ISSR (0.220), and AFLP (0.241) showed that micropropagation of pistachio for different periods of time resulted in "reasonable polymorphism" among donor plant and its 18 clones. Mantel's test showed a consistence polymorphism level between marker systems based on similarity matrices. In conclusion, this is the first study on occurrence of genetic variability in long-term micropropagated mature pistachio plantlets. The obtained results clearly indicated that different marker approaches used in this study are reliable for assessing tissue culture-induced variations in long-term cultured pistachio plantlets.

  11. MtDNA T4216C variation in multiple sclerosis: a systematic review and meta-analysis.

    PubMed

    Andalib, Sasan; Emamhadi, Mohammadreza; Yousefzadeh-Chabok, Shahrokh; Salari, Arsalan; Sigaroudi, Abdolhosein Emami; Vafaee, Manouchehr Seyedi

    2016-12-01

    MtDNA T4216C variation has frequently been investigated in Multiple Sclerosis (MS) patients; nonetheless, controversy has existed about the evidence of association of this variation with susceptibility to MS. The present systematic review and meta-analysis converge the results of the preceding publications, pertaining to association of mtDNA T4216C variation with susceptibility to MS, into a common conclusion. A computerized literature search in English was carried out to retrieve relevant publications from which required data were extracted. Using a fixed effect model, pooled odds ratio (OR), 95 % confidence interval (95 % CI), and P value were calculated for association of mtDNA T4216C variation with susceptibility to MS. The pooled results showed that there was a significant association between mtDNA T4216C variation and MS (OR = 1.38, 95 % CI = 1.13-1.67, P = 0.001). The present systematic review and meta-analysis suggest that mtDNA T4216C variation is a contributory factor in susceptibility to MS.

  12. Intragenomic and interspecific 5S rDNA sequence variation in five Asian pines.

    PubMed

    Liu, Zhan-Lin; Zhang, Daming; Wang, Xiao-Quan; Ma, Xiao-Fei; Wang, Xiao-Ru

    2003-01-01

    Patterns of intragenomic and interspecific variation of 5S rDNA in Pinus (Pinaceae) were studied by cloning and sequencing multiple 5S rDNA repeats from individual trees. Five pines, from both subgenera, Pinus and Strobus, were selected. The 5S rDNA repeat in pines has a conserved 120-base pair (bp) transcribed region and an intergenic spacer region of variable length (382-608 bp). The evolutionary rate in the spacer region is three- to sevenfold higher than in the genic region. We found substantial sequence divergence between the two subgenera. Intragenomic sequence heterogeneity was high for all species, and more than 86% of the clones within each individual were unique. The 5S gene tree revealed that different 5S repeats within individuals are polyphyletic, indicating that their ancestral divergence preceded the speciation events. The degrees of interspecific and intragenomic divergence among diploxylon pines are similar. The observed sequence patterns suggest that concerted evolution has been acting after the diversification of the two subgenera but very weak after the speciation of the four diploxylon pines. Sequence patterns in P. densata are consistent with hybrid origin. It had higher intragenomic diversity and maintained polymorphic copies of the parental types in addition to new and recombinant types unique to the hybrid.

  13. Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2

    PubMed Central

    Batovska, Jana; Cogan, Noel O. I.; Lynch, Stacey E.; Blacket, Mark J.

    2016-01-01

    Internal Transcribed Spacer 2 (ITS2) is a popular DNA barcoding marker; however, in some animal species it is hypervariable and therefore difficult to sequence with traditional methods. With next-generation sequencing (NGS) it is possible to sequence all gene variants despite the presence of single nucleotide polymorphisms (SNPs), insertions/deletions (indels), homopolymeric regions, and microsatellites. Our aim was to compare the performance of Sanger sequencing and NGS amplicon sequencing in characterizing ITS2 in 26 mosquito species represented by 88 samples. The suitability of ITS2 as a DNA barcoding marker for mosquitoes, and its allelic diversity in individuals and species, was also assessed. Compared to Sanger sequencing, NGS was able to characterize the ITS2 region to a greater extent, with resolution within and between individuals and species that was previously not possible. A total of 382 unique sequences (alleles) were generated from the 88 mosquito specimens, demonstrating the diversity present that has been overlooked by traditional sequencing methods. Multiple indels and microsatellites were present in the ITS2 alleles, which were often specific to species or genera, causing variation in sequence length. As a barcoding marker, ITS2 was able to separate all of the species, apart from members of the Culex pipiens complex, providing the same resolution as the commonly used Cytochrome Oxidase I (COI). The ability to cost-effectively sequence hypervariable markers makes NGS an invaluable tool with many applications in the DNA barcoding field, and provides insights into the limitations of previous studies and techniques. PMID:27799340

  14. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations.

    PubMed Central

    Redd, A J; Stoneking, M

    1999-01-01

    We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul. PMID:10441589

  15. Biological origins of long-range correlations and compositional variations in DNA.

    PubMed Central

    Larhammar, D; Chatzidimitriou-Dreismann, C A

    1993-01-01

    The occurrence of certain long-range correlations between nucleotides in DNA sequences of living organisms has recently been reported. The biological origin of these correlations was unknown. The correlations were proposed to be concerned with fractal structure and differences between intron-containing and intron-less sequences. We and others have reported that no consistent difference exists between intron-containing and intron-less sequences. In agreement with this, we demonstrate here that the long-range correlations are trivially equivalent to the varying ratio R between pyrimidines and purines (or any other nucleotide combinations) in different regions of a DNA sequence. Moreover, we show that this variation of R has simple biological explanations: Differences in base composition occur along most DNA sequences and are associated with (i) simple repeats (ii) differences in codon composition (due to the amino acid composition in the encoded protein), (iii) change of the direction of transcription (and thus also translation), and (iv) differences between protein- and rRNA-encoding segments. Seven biological examples are given. PMID:8255772

  16. DNA Sequence Analysis of SLC26A5, Encoding Prestin, in a Patient-Control Cohort: Identification of Fourteen Novel DNA Sequence Variations

    PubMed Central

    Minor, Jacob S.; Tang, Hsiao-Yuan; Pereira, Fred A.; Alford, Raye Lynn

    2009-01-01

    Background Prestin, encoded by the gene SLC26A5, is a transmembrane protein of the cochlear outer hair cell (OHC). Prestin is required for the somatic electromotile activity of OHCs, which is absent in OHCs and causes severe hearing impairment in mice lacking prestin. In humans, the role of sequence variations in SLC26A5 in hearing loss is less clear. Although prestin is expected to be required for functional human OHCs, the clinical significance of reported putative mutant alleles in humans is uncertain. Methodology/Principal Findings To explore the hypothesis that SLC26A5 may act as a modifier gene, affecting the severity of hearing loss caused by an independent etiology, a patient-control cohort was screened for DNA sequence variations in SLC26A5 using sequencing and allele specific methods. Patients in this study carried known pathogenic or controversial sequence variations in GJB2, encoding Connexin 26, or confirmed or suspected sequence variations in SLC26A5; controls included four ethnic populations. Twenty-three different DNA sequence variations in SLC26A5, 14 of which are novel, were observed: 4 novel sequence variations were found exclusively among patients; 7 novel sequence variations were found exclusively among controls; and, 12 sequence variations, 3 of which are novel, were found in both patients and controls. Twenty-one of the 23 DNA sequence variations were located in non-coding regions of SLC26A5. Two coding sequence variations, both novel, were observed only in patients and predict a silent change, p.S434S, and an amino acid substitution, p.I663V. In silico analysis of the p.I663V amino acid variation suggested this variant might be benign. Using Fisher's exact test, no statistically significant difference was observed between patients and controls in the frequency of the identified DNA sequence variations. Haplotype analysis using HaploView 4.0 software revealed the same predominant haplotype in patients and controls and derived haplotype blocks

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

    PubMed

    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

  18. Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway

    PubMed Central

    Di Fruscio, Giuseppina; Schulz, Angela; De Cegli, Rossella; Savarese, Marco; Mutarelli, Margherita; Parenti, Giancarlo; Banfi, Sandro; Braulke, Thomas; Nigro, Vincenzo; Ballabio, Andrea

    2015-01-01

    The autophagy-lysosomal pathway (ALP) regulates cell homeostasis and plays a crucial role in human diseases, such as lysosomal storage disorders (LSDs) and common neurodegenerative diseases. Therefore, the identification of DNA sequence variations in genes involved in this pathway and their association with human diseases would have a significant impact on health. To this aim, we developed Lysoplex, a targeted next-generation sequencing (NGS) approach, which allowed us to obtain a uniform and accurate coding sequence coverage of a comprehensive set of 891 genes involved in lysosomal, endocytic, and autophagic pathways. Lysoplex was successfully validated on 14 different types of LSDs and then used to analyze 48 mutation-unknown patients with a clinical phenotype of neuronal ceroid lipofuscinosis (NCL), a genetically heterogeneous subtype of LSD. Lysoplex allowed us to identify pathogenic mutations in 67% of patients, most of whom had been unsuccessfully analyzed by several sequencing approaches. In addition, in 3 patients, we found potential disease-causing variants in novel NCL candidate genes. We then compared the variant detection power of Lysoplex with data derived from public whole exome sequencing (WES) efforts. On average, a 50% higher number of validated amino acid changes and truncating variations per gene were identified. Overall, we identified 61 truncating sequence variations and 488 missense variations with a high probability to cause loss of function in a total of 316 genes. Interestingly, some loss-of-function variations of genes involved in the ALP pathway were found in homozygosity in the normal population, suggesting that their role is not essential. Thus, Lysoplex provided a comprehensive catalog of sequence variants in ALP genes and allows the assessment of their relevance in cell biology as well as their contribution to human disease. PMID:26075876

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

    PubMed

    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.

  20. Intraindividual and interspecies variation in the 5S rDNA of coregonid fish.

    PubMed

    Sajdak, S L; Reed, K M; Phillips, R B

    1998-06-01

    This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate DNA sequence for comparisons of closely related taxa.

  1. Intraspecific Variation in Ribosomal DNA in Populations of the Potato Cyst Nematode Globodera pallida

    PubMed Central

    Blok, V. C.; Malloch, G.; Harrower, B.; Phillips, M. S.; Vrain, T. C.

    1998-01-01

    The relationships among a number of populations of Globodera pallida from Britian, the Netherlands, Germany, Switzerland, and South America were examined using PCR amplification of the ribosomal cistron between the 18S and 28S genes that include the two intergenic spacer regions (ITS1 and ITS2) and the 5.8S gene. Amplifications produced a similar-sized product of 1150 bp from all populations. Digestion of the amplified fragment with a number of restriction enzymes showed differences among the populations. The restriction enzyme RsaI distinguished the most populations. The RFLP patterns revealed by this enzyme were complex and could have arisen from heterogeneity between individuals within populations and from differences between the repeats of an individual. Sequence analysis from six of the populations, together with RFLP analysis of PCR products, shows that there is intraspecific variation in the rDNA of G. pallida. PMID:19274220

  2. DNA sequence-dependent variation in nucleosome structure, stability, and dynamics detected by a FRET-based analysis.

    PubMed

    Kelbauskas, L; Woodbury, N; Lohr, D

    2009-02-01

    Förster resonance energy transfer (FRET) techniques provide powerful and sensitive methods for the study of conformational features in biomolecules. Here, we review FRET-based studies of nucleosomes, focusing particularly on our work comparing the widely used nucleosome standard, 5S rDNA, and 2 promoter-derived regulatory element-containing nucleosomes, mouse mammary tumor virus (MMTV)-B and GAL10. Using several FRET approaches, we detected significant DNA sequence-dependent structure, stability, and dynamics differences among the three. In particular, 5S nucleosomes and 5S H2A/H2B-depleted nucleosomal particles have enhanced stability and diminished DNA dynamics, compared with MMTV-B and GAL10 nucleosomes and particles. H2A/H2B-depleted nucleosomes are of interest because they are produced by the activities of many transcription-associated complexes. Significant location-dependent (intranucleosomal) stability and dynamics variations were also observed. These also vary among nucleosome types. Nucleosomes restrict regulatory factor access to DNA, thereby impeding genetic processes. Eukaryotic cells possess mechanisms to alter nucleosome structure, to generate DNA access, but alterations often must be targeted to specific nucleosomes on critical regulatory DNA elements. By endowing specific nucleosomes with intrinsically higher DNA accessibility and (or) enhanced facility for conformational transitions, DNA sequence-dependent nucleosome dynamics and stability variations have the potential to facilitate nucleosome recognition and, thus, aid in the crucial targeting process. This and other nucleosome structure and function conclusions from FRET analyses are discussed.

  3. DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys).

    PubMed

    Matson, C W; Baker, R J

    2001-08-01

    The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.

  4. Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility

    PubMed Central

    Fahmideh, Maral Adel; Lavebratt, Catharina; Schüz, Joachim; Röösli, Martin; Tynes, Tore; Grotzer, Michael A.; Johansen, Christoffer; Kuehni, Claudia E; Lannering, Birgitta; Prochazka, Michaela; Schmidt, Lisbeth S; Feychting, Maria

    2016-01-01

    Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk. The study is based on the largest series of PBT cases to date. Saliva DNA from 245 cases and 489 controls, aged 7–19 years at diagnosis/reference date, was genotyped for 68 SNPs. Data were analyzed using unconditional logistic regression. The results showed EGFRrs730437 and EGFRrs11506105 may decrease susceptibility to PBTs, whereas ERCC1rs3212986 may increase risk of these tumors. Moreover, stratified analyses indicated CHAF1Ars243341, CHAF1Ars2992, and XRCC1rs25487 were associated with a decreased risk of astrocytoma subtype. Furthermore, an increased risk of non-astrocytoma subtype associated with EGFRrs9642393, EME1rs12450550, ATMrs170548, and GLTSCRrs1035938 as well as a decreased risk of this subtype associated with XRCC4rs7721416 and XRCC4rs2662242 were detected. This study indicates SNPs in EGFR, ERCC1, CHAF1A, XRCC1, EME1, ATM, GLTSCR1, and XRCC4 may be associated with the risk of PBTs. Therefore, cell cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways. PMID:27613841

  5. Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae.

    PubMed

    Magni, C R; Ducousso, A; Caron, H; Petit, R J; Kremer, A

    2005-02-01

    Quercus rubra is one of the most important timber and ornamental tree species from eastern North America. It is a widespread species growing under variable ecological conditions. Chloroplast DNA variation was studied by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) in 290 individuals from 66 populations sampled throughout the natural range. A total of 12 haplotypes were detected, with one found in 75% of the trees. Population differentiation is relatively low (G(ST) = 0.46), even when similarities between haplotypes are taken into account (N(ST) = 0.50), pointing to a weak phylogeographical structure. Furthermore, no spatial structure of genetic diversity could be detected. The genetic differentiation increased northwards, reflecting the postglacial history of Q. rubra. The unusual aspect of this study was the low level of chloroplast DNA genetic differentiation in Q. rubra compared to that typically observed in other oak species. Palynological evidence indicates that during the last glacial maximum, Q. rubra had one major distribution range with populations located relatively far to the north, resulting in only modest movement northwards when climate improved, whereas European white oaks were largely restricted to the southern European peninsulas and experienced extensive movements during the postglacial period. The contrasted geographical features and levels of tree species richness of both continents might further explain why congeneric species sharing similar life history traits have genetic structures that are so different.

  6. Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

    PubMed Central

    James, Stephen A.; O'Kelly, Michael J.T.; Carter, David M.; Davey, Robert P.; van Oudenaarden, Alexander; Roberts, Ian N.

    2009-01-01

    Ribosomal DNA (rDNA) plays a key role in ribosome biogenesis, encoding genes for the structural RNA components of this important cellular organelle. These genes are vital for efficient functioning of the cellular protein synthesis machinery and as such are highly conserved and normally present in high copy numbers. In the baker's yeast Saccharomyces cerevisiae, there are more than 100 rDNA repeats located at a single locus on chromosome XII. Stability and sequence homogeneity of the rDNA array is essential for function, and this is achieved primarily by the mechanism of gene conversion. Detecting variation within these arrays is extremely problematic due to their large size and repetitive structure. In an attempt to address this, we have analyzed over 35 Mbp of rDNA sequence obtained from whole-genome shotgun sequencing (WGSS) of 34 strains of S. cerevisiae. Contrary to expectation, we find significant rDNA sequence variation exists within individual genomes. Many of the detected polymorphisms are not fully resolved. For this type of sequence variation, we introduce the term partial single nucleotide polymorphism, or pSNP. Comparative analysis of the complete data set reveals that different S. cerevisiae genomes possess different patterns of rDNA polymorphism, with much of the variation located within the rapidly evolving nontranscribed intergenic spacer (IGS) region. Furthermore, we find that strains known to have either structured or mosaic/hybrid genomes can be distinguished from one another based on rDNA pSNP number, indicating that pSNP dynamics may provide a reliable new measure of genome origin and stability. PMID:19141593

  7. Intraspecific sequence variation of chloroplast DNA among the component species of deciduous broad-leaved forests in Japan.

    PubMed

    Iwasaki, Takaya; Aoki, Kyoko; Seo, Akihiro; Murakami, Noriaki

    2006-09-01

    To select appropriate plant materials for a phylogeography of deciduous broad-leaved forests in Japan, we surveyed intraspecific chloroplast DNA variation in 34 species found in these forests. A relatively large number of intraspecific cpDNA variations were detected in ten species: Carpinus japonica (nucleotide diversity pi=0.00083), C. laxiflora (pi=0.00221), Magnolia obovata (pi=0.00134), Lindera triloba (pi=0.00255), L. obtusiloba (pi=0.00289), Pourthiaea villosa var. leavis (pi=0.00263), Acer japonicum (pi=0.00170), A. micranthum (pi=0.00237), Euonymus oxyphyllus (pi=0.00322) and Styrax obassia (pi=0.00100).

  8. Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device

    PubMed Central

    Dube, Simant; Qin, Jian; Ramakrishnan, Ramesh

    2008-01-01

    Copy Number Variations (CNVs) of regions of the human genome have been associated with multiple diseases. We present an algorithm which is mathematically sound and computationally efficient to accurately analyze CNV in a DNA sample utilizing a nanofluidic device, known as the digital array. This numerical algorithm is utilized to compute copy number variation and the associated statistical confidence interval and is based on results from probability theory and statistics. We also provide formulas which can be used as close approximations. PMID:18682853

  9. Genetic variation of the East Balkan Swine (Sus scrofa) in Bulgaria, revealed by mitochondrial DNA and Y chromosomal DNA.

    PubMed

    Hirata, D; Doichev, V D; Raichev, E G; Palova, N A; Nakev, J L; Yordanov, Y M; Kaneko, Y; Masuda, R

    2015-04-01

    East Balkan Swine (EBS) Sus scrofa is the only aboriginal domesticated pig breed in Bulgaria and is distributed on the western coast of the Black Sea in Bulgaria. To reveal the breed's genetic characteristics, we analysed mitochondrial DNA (mtDNA) and Y chromosomal DNA sequences of EBS in Bulgaria. Nucleotide diversity (πn ) of the mtDNA control region, including two newly found haplotypes, in 54 EBS was higher (0.014 ± 0.007) compared with that of European (0.005 ± 0.003) and Asian (0.006 ± 0.003) domestic pigs and wild boar. The median-joining network based on the mtDNA control region showed that the EBS and wild boar in Bulgaria comprised mainly two major mtDNA clades, European clade E1 (61.3%) and Asian clade A (38.7%). The coexistence of two mtDNA clades in EBS in Bulgaria may be the relict of historical pig translocation. Among the Bulgarian EBS colonies, the geographical differences in distribution of two mtDNA clades (E1 and A) could be attributed to the source pig populations and/or historical crossbreeding with imported pigs. In addition, analysis of the Y chromosomal DNA sequences for the EBS revealed that all of the EBS had haplotype HY1, which is dominant in European domestic pigs.

  10. The impact of genetic variation and cigarette smoke on DNA methylation in current and former smokers from the COPDGene study.

    PubMed

    Qiu, Weiliang; Wan, Emily; Morrow, Jarrett; Cho, Michael H; Crapo, James D; Silverman, Edwin K; DeMeo, Dawn L

    2015-01-01

    DNA methylation can be affected by systemic exposures, such as cigarette smoking and genetic sequence variation; however, the relative impact of each on the epigenome is unknown. We aimed to assess if cigarette smoking and genetic variation are associated with overlapping or distinct sets of DNA methylation marks and pathways. We selected 85 Caucasian current and former smokers with genome-wide single nucleotide polymorphism (SNP) genotyping available from the COPDGene study. Genome-wide methylation was obtained on DNA from whole blood using the Illumina HumanMethylation27 platform. To determine the impact of local sequence variation on DNA methylation (mQTL), we examined the association between methylation and SNPs within 50 kb of each CpG site. To examine the impact of cigarette smoking on DNA methylation, we examined the differences in methylation by current cigarette smoking status. We detected 770 CpG sites annotated to 708 genes associated at an FDR < 0.05 in the cis-mQTL analysis and 1,287 CpG sites annotated to 1,242 genes, which were nominally associated in the smoking-CpG association analysis (P(unadjusted) < 0.05). Forty-three CpG sites annotated to 40 genes were associated with both SNP variation and current smoking; this overlap was not greater than that expected by chance. Our results suggest that cigarette smoking and genetic variants impact distinct sets of DNA methylation marks, the further elucidation of which may partially explain the variable susceptibility to the health effects of cigarette smoking. Ascertaining how genetic variation and systemic exposures differentially impact the human epigenome has relevance for both biomarker identification and therapeutic target development for smoking-related diseases.

  11. Associations between sequence variations in the mitochondrial DNA D-loop region and outcome of hepatocellular carcinoma

    PubMed Central

    LI, SHILAI; WAN, PEIQI; PENG, TAO; XIAO, KAIYIN; SU, MING; SHANG, LIMING; XU, BANGHAO; SU, ZHIXIONG; YE, XINPING; PENG, NING; QIN, QUANLIN; LI, LEQUN

    2016-01-01

    The association between mitochondrial DNA (mtDNA) polymorphisms or mutations and the prognoses of cancer have been investigated previously, but the results have been ambiguous. In the present study, the associations between sequence variations in the mtDNA D-loop region and the outcomes of patients with hepatocellular carcinoma (HCC) were analysed. A total of 140 patients with HCC (123 males and 17 females), who were hospitalised to undergo radical resection, were studied. Polymerase chain reaction and direct sequencing were performed to detect the sequence variations in the mtDNA D-loop region. Multivariate and univariate analyses were conducted to determine important factors in the prognosis of HCC. A total of 150 point sequence variations were observed in the 140 cases (13 point mutations, 8 insertions, 20 deletions and 116 polymorphisms). The variation rate was 13.4% (150/1, 122). mtDNA nucleotide 150 (C/T) was an independent factor in the logistic regression for early/late recurrence of HCC. Patients with 150T appeared to have later recurrences. In a Cox proportional hazards regression model, hepatitis B virus DNA, Child-Pugh class, differentiation degree, tumour-node-metastasis (TNM) stage, nucleotide 16263 (T/C) and nucleotide 315 (N/insertion C) were independent factors for tumour-free survival time. Patients with the 16263T allele had a greater tumour-free survival time than patients with the 16263C allele. Similarly, patients with 315 insertion C had a superior tumour-free survival time when compared with patients with 315 N (normal). In the Cox proportional hazards regression model, recurrence type (early/late), Child-Pugh class, TNM stage and adjuvant treatment after tumour recurrence (none or one/more than one treatment) were independent factors for overall survival. None of the mtDNA variations served as independent factors. Patients with late recurrence, Child-Pugh class A, and low TNM stages and/or those who received more than one adjuvant treatment

  12. Day and night variations in the repair of ionizing-radiation-induced DNA damage in mouse splenocytes.

    PubMed

    Palombo, Philipp; Moreno-Villanueva, Maria; Mangerich, Aswin

    2015-04-01

    In mammals, biological rhythms synchronize physiological and behavioral processes to the 24-h light-dark (LD) cycle. At the molecular level, self-sustaining processes, such as oscillations of transcription-translation feedback loops, control the circadian clock, which in turn regulates a wide variety of cellular processes, including gene expression and cell cycle progression. Furthermore, previous studies reported circadian oscillations in the repair capacity of DNA lesions specifically repaired by nucleotide excision repair (NER). However, it is so far only poorly understood if DNA repair pathways other than NER are under circadian control, in particular base excision and DNA strand break repair. In the present study, we analyzed potential day and night variations in the repair of DNA lesions induced by ionizing radiation (i.e., mainly oxidative damage and DNA strand breaks) in living mouse splenocytes using a modified protocol of the automated FADU assay. Our results reveal that splenocytes isolated from mice during the light phase (ZT06) displayed higher DNA repair activity than those of the dark phase (ZT18). As analyzed by highly sensitive and accurate qPCR arrays, these alterations were accompanied by significant differences in expression profiles of genes involved in the circadian clock and DNA repair. Notably, the majority of the DNA repair genes were expressed at higher levels during the light phase (ZT06). This included genes of all major DNA repair pathways with the strongest differences observed for genes of base excision and DNA double strand break repair. In conclusion, here we provide novel evidence that mouse splenocytes exhibit significant differences in the repair of IR-induced DNA damage during the LD cycle, both on a functional and on a gene expression level. It will be interesting to test if these findings could be exploited for therapeutic purposes, e.g. time-of-the-day-specific application of DNA-damaging treatments used against blood

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

    PubMed

    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.

  14. Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA.

    PubMed

    Wang, Hong-Wei; Ge, Song

    2006-11-01

    Cathaya argyrophylla is an endangered conifer restricted to subtropical mountains of China. To study phylogeographical pattern and demographic history of C. argyrophylla, species-wide genetic variation was investigated using sequences of maternally inherited mtDNA and biparentally inherited nuclear DNA. Of 15 populations sampled from all four distinct regions, only three mitotypes were detected at two loci, without single region having a mixed composition (G(ST) = 1). Average nucleotide diversity (theta(ws) = 0.0024; pi(s) = 0.0029) across eight nuclear loci is significantly lower than those found for other conifers (theta(ws) = 0.003 approximately 0.015; pi(s) = 0.002 approximately 0.012) based on estimates of multiple loci. Because of its highest diversity among the eight nuclear loci and evolving neutrally, one locus (2009) was further used for phylogeographical studies and eight haplotypes resulting from 12 polymorphic sites were obtained from 98 individuals. All the four distinct regions had at least four haplotypes, with the Dalou region (DL) having the highest diversity and the Bamian region (BM) the lowest, paralleling the result of the eight nuclear loci. An AMOVA revealed significant proportion of diversity attributable to differences among regions (13.4%) and among populations within regions (8.9%). F(ST) analysis also indicated significantly high differentiation among populations (F(ST) = 0.22) and between regions (F(ST) = 0.12-0.38). Non-overlapping distribution of mitotypes and high genetic differentiation among the distinct geographical groups suggest the existence of at least four separate glacial refugia. Based on network and mismatch distribution analyses, we do not find evidence of long distance dispersal and population expansion in C. argyrophylla. Ex situ conservation and artificial crossing are recommended for the management of this endangered species.

  15. Variation.

    ERIC Educational Resources Information Center

    Hamilton City Board of Education (Ontario).

    Suggestions for studying the topic of variation of individuals and objects (balls) to help develop elementary school students' measurement, comparison, classification, evaluation, and data collection and recording skills are made. General suggestions of variables that can be investigated are made for the study of human variation. Twelve specific…

  16. Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas.

    PubMed

    Tapio, Miika; Marzanov, Nurbiy; Ozerov, Mikhail; Cinkulov, Mirjana; Gonzarenko, Galina; Kiselyova, Tatyana; Murawski, Maciej; Viinalass, Haldja; Kantanen, Juha

    2006-09-01

    Three distinct mitochondrial maternal lineages (haplotype Groups A, B, and C) have been found in the domestic sheep. Group B has been observed primarily in European domestic sheep. The European mouflon carries this haplotype group. This could suggest that European mouflon was independently domesticated in Europe, although archaeological evidence supports sheep domestication in the central part of the Fertile Crescent. To investigate this question, we sequenced a highly variable segment of mitochondrial DNA (mtDNA) in 406 unrelated animals from 48 breeds or local varieties. They originated from a wide area spanning northern Europe and the Balkans to the Altay Mountains in south Siberia. The sample included a representative cross-section of sheep breeds from areas close to the postulated Near Eastern domestication center and breeds from more distant northern areas. Four (A, B, C, and D) highly diverged sheep lineages were observed in Caucasus, 3 (A, B and C) in Central Asia, and 2 (A and B) in the eastern fringe of Europe, which included the area north and west of the Black Sea and the Ural Mountains. Only one example of Group D was detected. The other haplotype groups demonstrated signs of population expansion. Sequence variation within the lineages implied Group A to have expanded first. This group was the most frequent type only in Caucasian and Central Asian breeds. Expansion of Group C appeared most recently. The expansion of Group B involving Caucasian sheep took place at nearly the same time as the expansion of Group A. Group B expansion for the eastern European area started approximately 3,000 years after the earliest inferred expansion. An independent European domestication of sheep is unlikely. The distribution of Group A variation as well as other results are compatible with the Near East being the domestication site. Groups C and D may have been introgressed later into a domestic stock, but larger samples are needed to infer their geographical origin. The

  17. Glacial survival of the Norwegian lemming (Lemmus lemmus) in Scandinavia: inference from mitochondrial DNA variation.

    PubMed

    Fedorov, V B; Stenseth, N C

    2001-04-22

    In order to evaluate the biogeographical hypothesis that the Norwegian lemming (Lemmus lemmus) survived the last glacial period in some Scandinavian refugia, we examined variation in the nucleotide sequence of the mitochondrial control region (402 base pairs (bp)) and the cytochrome b (cyt b) region (633 bp) in Norwegian and Siberian (Lemmus sibiricus) lemmings. The phylogenetic distinction and cyt b divergence estimate of 1.8% between the Norwegian and Siberian lemmings suggest that their separation pre-dated the last glaciation and imply that the Norwegian lemming is probably a relic of the Pleistocene populations from Western Europe. The star-like control region phylogeny and low mitochondrial DNA diversity in the Norwegian lemming indicate a reduction in its historical effective size followed by population expansion. The average estimate of post-bottleneck time (19-21 kyr) is close to the last glacial maximum (18-22 kyr BP). Taking these findings and the fossil records into consideration, it seems likely that, after colonization of Scandinavia in the Late Pleistocene, the Norwegian lemming suffered a reduction in its population effective size and survived the last glacial maximum in some local Scandinavian refugia, as suggested by early biogeographical work.

  18. Molecular Variation in Chloroplast DNA Regions in Ancestral Species of Wheat

    PubMed Central

    Miyashita, N. T.; Mori, N.; Tsunewaki, K.

    1994-01-01

    Restriction map variation in two 5-6-kb chloroplast DNA regions of five diploid Aegilops species in the section Sitopsis and two wild tetraploid wheats, Triticum dicoccoides and Triticum araraticum, was investigated with a battery of four-cutter restriction enzymes. A single accession each of Triticum durum, Triticum timopheevi and Triticum aestivum was included as a reference. More than 250 restriction sites were scored, of which only seven sites were found polymorphic in Aegilops speltoides. No restriction site polymorphisms were detected in all of the other diploid and tetraploid species. In addition, six insertion/deletion polymorphisms were detected, but they were mostly unique or species-specific. Estimated nucleotide diversity was 0.0006 for A. speltoides, and 0.0000 for all the other investigated species. In A. speltoides, none of Tajima's D values was significant, indicating no clear deviation from the neutrality of molecular polymorphisms. Significant non-random association was detected for three combinations out of 10 possible pairs between polymorphic restriction sites in A. speltoides. Phylogenetic relationship among all the plastotypes (plastid genotype) suggested the diphyletic origin of T. dicoccoides and T. araraticum. A plastotype of one A. speltoides accession was identical to the major type of T. araraticum (T. timopheevi inclusively). Three of the plastotypes found in the Sitopsis species are very similar, but not identical, to that of T. dicoccoides, T. durum and T. aestivum. PMID:7916310

  19. Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia

    PubMed Central

    Sanna, Daria; Pala, Maria; Cossu, Piero; Dedola, Gian Luca; Melis, Sonia; Fresu, Giovanni; Morelli, Laura; Obinu, Domenica; Tonolo, Giancarlo; Secchi, Giannina; Triunfo, Riccardo; Lorenz, Joseph G.; Scheinfeldt, Laura; Torroni, Antonio; Robledo, Renato; Francalacci, Paolo

    2011-01-01

    We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits. PMID:21734814

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

    PubMed Central

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

    2004-01-01

    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

  1. Variation of entropic elasticity of DNA-Psoralen complex under UV light

    NASA Astrophysics Data System (ADS)

    Rocha, M. S.; Mesquita, O. N.

    2005-08-01

    We measure the entropic elasticity of a single λ-DNA molecule and of a single DNA-Psoralen complex by doing stretching experiments with an optical tweezers. Psoralen is a photosensitive drug used in the treatment of many skin diseases, by impeding DNA replication. Psolaren intercalates the DNA and can form crosslinks with pyrimidine basis in opposite strands of DNA, when illuminated with UVA light. As crosslinks form the persistence length of the complex increases, indicating an increase in rigidity of the complex. We study the kinetics of DNA-Psoralen crosslink formation via changes in entropic elasticity of the complex.

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

    PubMed

    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.

  3. Transgenerational Variations in DNA Methylation Induced by Drought Stress in Two Rice Varieties with Distinguished Difference to Drought Resistance

    PubMed Central

    Li, Mingshou; Lou, Qiaojun; Xia, Hui; Wang, Pei; Li, Tiemei; Liu, Hongyan; Luo, Lijun

    2013-01-01

    Adverse environmental conditions have large impacts on plant growth and crop production. One of the crucial mechanisms that plants use in variable and stressful natural environments is gene expression modulation through epigenetic modification. In this study, two rice varieties with different drought resistance levels were cultivated under drought stress from tilling stage to seed filling stage for six successive generations. The variations in DNA methylation of the original generation (G0) and the sixth generation (G6) of these two varieties in normal condition (CK) and under drought stress (DT) at seedling stage were assessed by using Methylation Sensitive Amplification Polymorphism (MSAP) method. The results revealed that drought stress had a cumulative effect on the DNA methylation pattern of both varieties, but these two varieties had different responses to drought stress in DNA methylation. The DNA methylation levels of II-32B (sensitive) and Huhan-3 (resistant) were around 39% and 32%, respectively. Genome-wide DNA methylation variations among generations or treatments accounted for around 13.1% of total MSAP loci in II-32B, but was only approximately 1.3% in Huhan-3. In II-32B, 27.6% of total differentially methylated loci (DML) were directly induced by drought stress and 3.2% of total DML stably transmitted their changed DNA methylation status to the next generation. In Huhan-3, the numbers were 48.8% and 29.8%, respectively. Therefore, entrainment had greater effect on Huhan-3 than on II-32B. Sequence analysis revealed that the DML were widely distributed on all 12 rice chromosomes and that it mainly occurred on the gene’s promoter and exon region. Some genes with DML respond to environmental stresses. The inheritance of epigenetic variations induced by drought stress may provide a new way to develop drought resistant rice varieties. PMID:24244664

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

    SciTech Connect

    Sung, Rou-Jia; Zhang, Michael; Qi, Yan; Verdine, Gregory L.

    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.

  5. Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences

    PubMed Central

    Olsen, Morten Tange; Pampoulie, Christophe; Daníelsdóttir, Anna K; Lidh, Emmelie; Bérubé, Martine; Víkingsson, Gísli A; Palsbøll, Per J

    2014-01-01

    The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci. PMID:24963377

  6. Reproductive Fitness and Random Amplified Polymorphic DNA Variation among Isolates of Pratylenchus vulnus

    PubMed Central

    Pinochet, P.; Cenis, J. L.; Fernández, C.; Doucet, M.; Maruli, J.

    1994-01-01

    The reproductive fitness of seven isolates of Pratylenchus vulnus from different geographical areas and hosts was assessed in monoxenic cultures (carrot), and greenhouse cultures (plum, sour orange, and quince). The genetic makeup of the different isolates was compared by Random Amplified Polymorphic DNA (RAPD-PCR). The apple (PvAP-S) and apricot (PvAT-F) isolates reproduced less in monoxenic cultures than the rose (PvRO-S) and walnut (PvWA-A and PvWA-U) isolates. On plum, the rose isolate (PvRO-S) reproduced better than the apple (PvAP-S) and walnut isolate from the United States (PvWA-U). On sour orange, the apple (PvAP-S), unknown origin (PvU-UK), and walnut isolate from Argentina (PvWA-A) multiplied well, whereas the walnut isolate from the United States (PvWA-U), apricot (PvAT-F), and rose (PvRO-S) did not. On quince, the apple (PvAP-S) and walnut (PvWA-U) isolates showed a higher reproduction than the one from unknown origin (PvU-UK). RAPD-PCR patterns among the seven P. vulnus isolates were similar, although high intraspecific varibility was detected. Very few bands of P. neglectus were shared by any population of P. vulnus. A high degree of similarity was found among the patterns corresponding to the rose (PvRO-S), apple (PvAP-S), walnut from the United States (PvWA-U), and unknown origin (PvUK-U) isolates. The apricot isolate (PvAT-F) was the most dissimilar among the seven isolates. No correlation could be established between the genetic variation of P. vulnus detected by RAPD-PCR and reproductive fitness. Results demonstrate high genetic varibility between geographically separated populations of P. vulnus. PMID:19279892

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

    PubMed

    Okello, J B A; Nyakaana, S; Masembe, C; Siegismund, H R; Arctander, P

    2005-09-01

    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. A relatively low overall nucleotide diversity was observed (pi = 1.9%), as compared to other large mammals so far studied from the same region. Within populations, nucleotide diversity varied from 1.52% in Zambia to 1.92% in Queen Elizabeth and Masai Mara. Overall, low but significant genetic differentiation was observed in the total data set (F(ST) = 0.138; P = 0.001), and at the population level, patterns of differentiation support previously suggested hippopotamus subspecies designations (F(CT) = 0.103; P = 0.015). Evidence that the common hippopotamus recently expanded were revealed by: (i) lack of clear geographical structure among haplotypes, (ii) mismatch distributions of pairwise differences (r = 0.0053; P = 0.012) and site-frequency spectra, (iii) Fu's neutrality statistics (F(S) = -155.409; P < 0.00001) and (iv) Fu and Li's statistical tests (D* = -3.191; P < 0.01, F* = -2.668; P = 0.01). Mismatch distributions, site-frequency spectra and neutrality statistics performed at subspecies level also supported expansion of Hippopotamus amphibius across Africa. We interpret observed common hippopotamus population history in terms of Pleistocene drainage overflow and suggest recognising the three subspecies that were sampled in this study as separate management units in future conservation planning.

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

    PubMed Central

    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 with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15

  9. Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

    PubMed

    Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

    2015-07-01

    We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661.

  10. Seasonal variation in environmental DNA in relation to population size and environmental factors

    PubMed Central

    Buxton, Andrew S.; Groombridge, Jim J.; Zakaria, Nurulhuda B.; Griffiths, Richard A.

    2017-01-01

    Analysing DNA that organisms release into the environment (environmental DNA, or eDNA) has enormous potential for assessing rare and cryptic species. At present the method is only reliably used to assess the presence-absence of species in natural environments, as seasonal influences on eDNA in relation to presence, abundance, life stages and seasonal behaviours are poorly understood. A naturally colonised, replicated pond system was used to show how seasonal changes in eDNA were influenced by abundance of adults and larvae of great crested newts (Triturus cristatus). Peaks in eDNA were observed in early June when adult breeding was coming to an end, and between mid-July and mid-August corresponding to a peak in newt larval abundance. Changes in adult body condition associated with reproduction also influenced eDNA concentrations, as did temperature (but not rainfall or UV). eDNA concentration fell rapidly as larvae metamorphosed and left the ponds. eDNA concentration may therefore reflect relative abundance in different ponds, although environmental factors can affect the concentrations observed. Nevertheless, eDNA surveys may still represent an improvement over unadjusted counts which are widely used in population assessments but have unreliable relationships with population size. PMID:28393885

  11. Mitochondrial DNA variation in chinook salmon and chum salmon detected by restriction enzyme analysis of polymerase chain reaction products

    USGS Publications Warehouse

    Cronin, M.; Spearman, R.; Wilmot, R.; Patton, J.; Bickman, J.

    1993-01-01

    We analyze intraspecific mitochondrial DNA variation in chinook salmon from drainages in the Yukon River, the Kenai River, and Oregon and California rivers; and chum salmon from the Yukon River and vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified seperately using the polymerase chain reaction and then digested with at least 19 restrictions enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base subsitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (8) occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rviers and four occured in the Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock seperation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.

  12. MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations

    PubMed Central

    K, Shamnamole; Jalali, Saakshi; Scaria, Vinod; Bhardwaj, Anshu

    2013-01-01

    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. PMID:23585830

  13. Variation in nuclear DNA content in Malus species and cultivated apples.

    PubMed

    Tatum, Tatiana C; Stepanovic, Svetlana; Biradar, D P; Rayburn, A Lane; Korban, Schuyler S

    2005-10-01

    The nuclear DNA content for a group of 40 Malus species and hybrids has been estimated using flow cytometry. Estimates of nuclear DNA content for this germplasm collection range from 1.45 pg for Malus fusca (diploid) to 2.57 pg for Malus ioensis (triploid). Among diploids, the nuclear (2C) DNA ranges from 1.45 pg for M. fusca to 1.68 pg for Malus transitoria. Among triploids, the nuclear (3C) DNA content ranges from 2.37 pg / 3C for Malus sikkimensis to 2.57 pg / 3C for M. ioensis. Given the complexity of the apple genome and its suggested allopolyploid origin, the results obtained in this study confirm earlier reports that polyploids can easily withstand the loss of a certain amount of DNA, and that there is a slight tendency towards diminished haploid nuclear DNA content with increased polyploidy.

  14. Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation.

    PubMed

    Verhulst, Eveline C; Mateman, A Christa; Zwier, Mathijs V; Caro, Samuel P; Verhoeven, Koen J F; van Oers, Kees

    2016-04-01

    Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here, we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the dopamine receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and nonhuman animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency.

  15. Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns

    PubMed Central

    Kornyshev, A. A.; Lee, D. J.; Wynveen, A.; Leikin, S.

    2011-01-01

    The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function. PMID:21593127

  16. Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns.

    PubMed

    Kornyshev, A A; Lee, D J; Wynveen, A; Leikin, S

    2011-09-01

    The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical X-ray diffraction patterns of DNA contain information about the flexibility, interactions and sequence-related variations encoded within the helical structure. To extract this information, we have developed a new diffraction theory that accounts for these effects. We show how double helix non-ideality and fluctuations broaden the diffraction peaks. Meridional intensity profiles of the peaks at the first three helical layer lines reveal information about structural adaptation and intermolecular interactions. The meridional width of the fifth layer line peaks is inversely proportional to the helical coherence length that characterizes sequence-related and thermal variations in the double helix structure. Analysis of measured fiber diffraction patterns based on this theory yields important parameters that control DNA structure, packing and function.

  17. Chloroplast and Mitochondrial DNA Variation in HORDEUM VULGARE and HORDEUM SPONTANEUM

    PubMed Central

    Holwerda, Barry C.; Jana, Sakti; Crosby, William L.

    1986-01-01

    A survey of restriction fragment polymorphism in Hordeum vulgare and Hordeum spontaneum was made using 17 and 16 hexanucleotide restriction endonucleases on chloroplast (cp) and mitochondrial (mt) DNA, respectively. The plant accessions originated from various places throughout the Fertile Cresent and Mediterranean. The types of changes in cpDNA consisted of nucleotide substitutions and insertions and deletions on the order of 100 base pairs. In contrast, mtDNA has most likely undergone larger insertions and deletions of up to 20 kilobase pairs in addition to rearrangements. Grouping of mtDNA fragment data showed that in some cases geographical affinities existed between the two species, whereas in others there were no clear affinities. Nucleotide diversity estimates derived from the restriction fragment data were used in a number of comparisons of variability. Comparisons of overall mtDNA variability (nucleotide diversity = 9.68 x 10-4) with cpDNA variability (nucleotide diversity = 6.38 x 10-4 ) indicated that the former are somewhat more variable. Furthermore, there was no indication that the wild H. spontaneum (cpDNA diversity = 5.57 x 10-4; mtDNA diversity = 6.04 x 10 -4) was more variable than the land races of H. vulgare (cpDNA diversity = 5.88 x 10-4; mtDNA diversity = 9.79 x 10-4). In fact, on the basis of mtDNA diversity, H. vulgare was the more variable species. Comparison of organelle nucleotide diversity estimates with an estimate of nuclear nucleotide diversity derived from existing isozyme data provided evidence that both organelle genomes are evolving at a slower rate than the nuclear genome. PMID:17246361

  18. Exploring the Impacts of Ordinary Laboratory Alterations During Forensic DNA Processing on Peak Height Variation, Thresholds, and Probability of Dropout.

    PubMed

    Rowan, Kayleigh E; Wellner, Genevieve A; Grgicak, Catherine M

    2016-01-01

    Impacts of validation design on DNA signal were explored, and the level of variation introduced by injection, capillary changes, amplification, and kit lot was surveyed by examining a set of replicate samples ranging in mass from 0.25 to 0.008 ng. The variations in peak height, heterozygous balance, dropout probabilities, and baseline noise were compared using common statistical techniques. Data indicate that amplification is the source of the majority of the variation observed in the peak heights, followed by capillary lots. The use of different amplification kit lots did not introduce variability into the peak heights, heterozygous balance, dropout, or baseline. Thus, if data from case samples run over a significant time period are not available during validation, the validation must be designed to, at a minimum, include the amplification of multiple samples of varying quantity, with known genotype, amplified and run over an extended period of time using multiple pipettes and capillaries.

  19. Mitochondrial DNA variation in bull trout (Salvelinus confluentus) from northwestern North America: implications for zoogeography and conservation.

    PubMed

    Taylor, E B; Pollard, S; Louie, D

    1999-07-01

    Bull trout, Salvelinus confluentus (Salmonidae), are distributed in northwestern North America from Nevada to Yukon Territory, largely in interior drainages. The species is of conservation concern owing to declines in abundance, particularly in southern portions of its range. To investigate phylogenetic structure within bull trout that might form the basis for the delineation of major conservation units, we conducted a mitochondrial DNA (mtDNA) survey in bull trout from throughout its range. Restriction fragment length polymorphism (RFLP) analysis of four segments of the mtDNA genome with 11 restriction enzymes resolved 21 composite haplotypes that differed by an average of 0.5% in sequence. One group of haplotypes predominated in 'coastal' areas (west of the coastal mountain ranges) while another predominated in 'interior' regions (east of the coastal mountains). The two putative lineages differed by 0.8% in sequence and were also resolved by sequencing a portion of the ND1 gene in a representative of each RFLP haplotype. Significant variation existed within individual sample sites (12% of total variation) and among sites within major geographical regions (33%), but most variation (55%) was associated with differences between coastal and interior regions. We concluded that: (i) bull trout are subdivided into coastal and interior lineages; (ii) this subdivision reflects recent historical isolation in two refugia south of the Cordilleran ice sheet during the Pleistocene: the Chehalis and Columbia refugia; and (iii) most of the molecular variation resides at the interpopulation and inter-region levels. Conservation efforts, therefore, should focus on maintaining as many populations as possible across as many geographical regions as possible within both coastal and interior lineages.

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

    PubMed

    Salas, A; Rasmussen, E M; Lareu, M V; Morling, N; Carracedo, A

    2001-12-27

    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, analysis of mtDNA sequencing implies a great lab effort when a high number of samples must be analyzed. The present work introduces a novel and reliable method for the screening of mtDNA variation in the first and second hypervariables (HV1 and HV2) regions which we have denominated fluorescent single strand conformation polymorphism (SSCP) of overlapping fragments (FSSCP-OF). FSSCP-OF is based on the basic theory of SSCP analysis and combines two complementary strategies: the use of PCR amplified overlapping fragments and fluorescent detection technology. The overlap region contains a high percentage (50%) of the d-loop mtDNA variation and for this reason, the probability to detect a polymorphic position by SSCP analysis is clearly increased in comparison to conventional SSCP methods due to the fact that the same polymorphic position is usually placed in a different "relative" position in the two overlapped fragments. The use of multicolor fluorescent technology allows also the multiplex amplification of overlapping fragment and its subsequent analysis in an automatic sequencer. We have analyzed 50 samples of unrelated individuals through the FSSCP-OF technique and we have found that using this methodology the probability to distinguish two samples with different sequences is close to 100%. FSSCP-OF has other important advantages with respect to previous screening methods, such as the automation and standardization of the protocols, which is of special interest for the forensic routine.

  1. Variation in germ line mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission

    PubMed Central

    Freyer, Christoph; Cree, Lynsey M.; Mourier, Arnaud; Stewart, James B.; Koolmeister, Camilla; Milenkovic, Dusanka; Wai, Timothy; Floros, Vasileios I.; Hagström, Erik; Chatzidaki, Emmanouella E.; Wiesner, Rudolph J.; Samuels, David C; Larsson, Nils-Göran; Chinnery, Patrick F.

    2012-01-01

    A genetic bottleneck explains the marked changes in mitochondrial DNA (mtDNA) heteroplasmy observed during the transmission of pathogenic mutations, but the precise timing remains controversial, and it is not clear whether selection plays a role. These issues are critically important for the genetic counseling of prospective mothers, and developing treatments aimed at disease prevention. By studying mice transmitting a heteroplasmic single base-pair deletion in the mitochondrial tRNAMet gene, we show that mammalian mtDNA heteroplasmy levels are principally determined prenatally within the developing female germ line. Although we saw no evidence of mtDNA selection prenatally, skewed heteroplasmy levels were observed in the offspring of the next generation, consistent with purifying selection. High percentage levels of the tRNAMet mutation were linked to a compensatory increase in overall mitochondrial RNAs, ameliorating the biochemical phenotype, and explaining why fecundity is not compromised. PMID:23042113

  2. Variations of Human DNA Polymerase Genes as Biomarkers of Prostate Cancer Progression

    DTIC Science & Technology

    2011-07-01

    analysis was done by single - strand conformation polymorphism , a technique that can miss muta- tions [Pearce et al., 2008]. We recently sequenced the complete...7) mice exhibit increased single - stranded DNA breaks, chromosomal aberrations, and mutagenicity compared to normal animals [Cabelof et al., 2003...a single -nucleotide gapped DNA template (the natural pol b substrate), and that this interaction is essential for pol b conformational activation

  3. Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice

    PubMed Central

    Zhao, Qiongyi; Li, Xiang; Jupp, Bianca; Chesworth, Rose; Lawrence, Andrew J.; Bredy, Timothy

    2016-01-01

    Continued vulnerability to relapse during abstinence is characteristic of cocaine addiction and suggests that drug-induced neuroadaptations persist during abstinence. However, the precise cellular and molecular attributes of these adaptations remain equivocal. One possibility is that cocaine self-administration leads to enduring changes in DNA methylation. To address this possibility, we isolated neurons from medial prefrontal cortex and performed high throughput DNA sequencing to examine changes in DNA methylation following cocaine self-administration. Twenty-nine genomic regions became persistently differentially methylated during cocaine self-administration, and an additional 28 regions became selectively differentially methylated during abstinence. Altered DNA methylation was associated with isoform-specific changes in the expression of co-localizing genes. These results provide the first neuron-specific, genome-wide profile of changes in DNA methylation induced by cocaine self-administration and protracted abstinence. Moreover, our findings suggest that altered DNA methylation facilitates long-term behavioral adaptation in a manner that extends beyond the perpetuation of altered transcriptional states. PMID:27213137

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

    PubMed Central

    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. Possible causes of morphological variation in an endemic Moroccan groundsel (Senecio leucanthemifolius var. casablancae): evidence from chloroplast DNA and random amplified polymorphic DNA markers.

    PubMed

    Coleman, Max; Abbott, Richard J

    2003-02-01

    Genetic variation was assessed in Senecio leucanthemifolius var. casablancae (Compositae), a Moroccan Atlantic coast endemic, in order to examine possible causes of atypical leaf morphology in three populations south of the known range. Evidence for introgression from S. glaucus ssp. coronopifolius and/or divergence was investigated with molecular markers. Both random amplified polymorphic DNA (RAPD) and chloroplast (cp) DNA restriction fragment length polymorphism (RFLP) differentiated the species well. Some evidence that hybridization may have occurred between the two species was provided by cpDNA markers. However, biparentally inherited RAPD markers failed to provide any support for the hypothesis that intermediate leaf morphologies in atypical populations arose through hybridization. Consequently, they are most likely to have arisen via divergence caused by drift and/or selection. Genetic distances among populations of S. leucanthemifolius were significant in all but one case. Isolation by distance was indicated by a significant positive correlation between genetic and geographical distances (r = 0.68, P = 0.01, Mantel test). These results suggest that long-distance achene dispersal is rare, despite the presence of a well-developed pappus. The observed loss of pappus at achene maturity may explain this unexpected result. Due to the morphological distinction of var. casablancae from other varieties of S. leucanthemifolius, we suggest elevation to species rank and treatment of the atypical material at infraspecific rank.

  6. DNA Damage Follows Repair Factor Depletion and Portends Genome Variation in Cancer Cells after Pore Migration.

    PubMed

    Irianto, Jerome; Xia, Yuntao; Pfeifer, Charlotte R; Athirasala, Avathamsa; Ji, Jiazheng; Alvey, Cory; Tewari, Manu; Bennett, Rachel R; Harding, Shane M; Liu, Andrea J; Greenberg, Roger A; Discher, Dennis E

    2017-01-23

    Migration through micron-size constrictions has been seen to rupture the nucleus, release nuclear-localized GFP, and cause localized accumulations of ectopic 53BP1-a DNA repair protein. Here, constricted migration of two human cancer cell types and primary mesenchymal stem cells (MSCs) increases DNA breaks throughout the nucleoplasm as assessed by endogenous damage markers and by electrophoretic "comet" measurements. Migration also causes multiple DNA repair proteins to segregate away from DNA, with cytoplasmic mis-localization sustained for many hours as is relevant to delayed repair. Partial knockdown of repair factors that also regulate chromosome copy numbers is seen to increase DNA breaks in U2OS osteosarcoma cells without affecting migration and with nucleoplasmic patterns of damage similar to constricted migration. Such depletion also causes aberrant levels of DNA. Migration-induced nuclear damage is nonetheless reversible for wild-type and sub-cloned U2OS cells, except for lasting genomic differences between stable clones as revealed by DNA arrays and sequencing. Gains and losses of hundreds of megabases in many chromosomes are typical of the changes and heterogeneity in bone cancer. Phenotypic differences that arise from constricted migration of U2OS clones are further illustrated by a clone with a highly elongated and stable MSC-like shape that depends on microtubule assembly downstream of the transcription factor GATA4. Such changes are consistent with reversion to a more stem-like state upstream of cancerous osteoblastic cells. Migration-induced genomic instability can thus associate with heritable changes.

  7. Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas

    PubMed Central

    Li, Jun; Huang, Qian; Sun, Mengxiang; Zhang, Tianyao; Li, Hao; Chen, Biyun; Xu, Kun; Gao, Guizhen; Li, Feng; Yan, Guixin; Qiao, Jiangwei; Cai, Yongping; Wu, Xiaoming

    2016-01-01

    Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs. T0 DRGs, which suggested that 32 °C might be a more intense external stimulus than 18 °C resulting in more changes in the DNA methylation status of cultured microspores. Additionally, 32 °C treatment for 6 h led to increased CHG differential methylations of transposons (DMTs), which were mainly constituted by overlaps between the hypomethylated differentially methylated regions (hypo-DMRs) and transposon elements (TEs). Further analysis demonstrated that the DRGs and their paralogs exhibited differential methylated/demethylated patterns. To summarize, the present study is the first methylome analysis of cultured microspores in response to STHS and may provide valuable information on the roles of DNA methylation in heat response. PMID:27917903

  8. The hidden history of the snowshoe hare, Lepus americanus: extensive mitochondrial DNA introgression inferred from multilocus genetic variation.

    PubMed

    Melo-Ferreira, José; Seixas, Fernando A; Cheng, Ellen; Mills, L Scott; Alves, Paulo C

    2014-09-01

    Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In North America, hares (Lepus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in North America - the snowshoe hare (Lepus americanus), the white-tailed jackrabbit (L. townsendii) and the black-tailed jackrabbit (L. californicus) - by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mtDNA) locus (6240 bp; 94 specimens). A multilocus-multispecies coalescent-based phylogeny suggests that L. americanus diverged ~2.7 Ma and that L. californicus and L. townsendii split more recently (~1.2 Ma). Within L. americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other North American species. While the isolation-with-migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mtDNA divergence revealed historical mtDNA introgression from L. californicus into the Pacific Northwest populations of L. americanus. This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.

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

    PubMed

    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.

  10. Nuclear DNA content variation in life history phases of the Bonnemasoniaceae (Rhodophyta).

    PubMed

    Salvador Soler, Noemi; Gómez Garreta, Amelia; Ribera Siguan, Ma Antonia; Kapraun, Donald F

    2014-01-01

    Nuclear DNA content in gametophytes and sporophytes or the prostrate phases of the following species of Bonnemaisoniaceae (Asparagopsis armata, Asparagopsis taxiformis, Bonnemaisonia asparagoides, Bonnemaisonia clavata and Bonnemaisonia hamifera) were estimated by image analysis and static microspectrophotometry using the DNA-localizing fluorochrome DAPI (4', 6-diamidino-2-phenylindole, dilactate) and the chicken erythrocytes standard. These estimates expand on the Kew database of DNA nuclear content. DNA content values for 1C nuclei in the gametophytes (spermatia and vegetative cells) range from 0.5 pg to 0.8 pg, and for 2C nuclei in the sporophytes or the prostrate phases range from 1.15-1.7 pg. Although only the 2C and 4C values were observed in the sporophyte or the prostrate phase, in the vegetative cells of the gametophyte the values oscillated from 1C to 4C, showing the possible start of endopolyploidy. The results confirm the alternation of nuclear phases in these Bonnemaisoniaceae species, in those that have tetrasporogenesis, as well as those that have somatic meiosis. The availability of a consensus phylogenetic tree for Bonnemaisoniaceae has opened the way to determine evolutionary trends in DNA contents. Both the estimated genome sizes and the published chromosome numbers for Bonnemaisoniaceae suggest a narrow range of values consistent with the conservation of an ancestral genome.

  11. ITS2-rDNA Sequence Variation of Phlebotomus sergenti s.l. (Dip: Psychodidae) Populations in Iran

    PubMed Central

    Moin-Vaziri, Vahideh; Oshaghi, Mohammad Ali; Yaghoobi-Ershadi, Mohammad Reza; Derakhshandeh-Peykar, Pupak; Abaei, Mohammad Reza; Mohtarami, Fatemeh; Zahraei-Ramezani, Ali Reza; Nadim, Aboulhassan

    2016-01-01

    Background: Phlebotomus sergenti s.l. is considered the most likely vector of Leishmania tropica in Iran. Although two morphotypes- P. sergenti sergenti (A) and P. sergenti similis (B)-have been formally described, further morphological and a molecular analysis of mitochondrial cytochrome oxidase I (mtDNA-COI) gene revealed inconsistencies and suggests that the variation between the morphotypes is intraspecific and the morphotypes might be identical species. Methods: We examined the sequence of the ITS2-rDNA of Iranian specimens of P. sergenti s.l., comprising P. cf sergenti, P. cf similis, and intermediate morphotypes, together with available data in Genbank. Results: Sequence analysis showed 5.2% variation among P. sergenti s.l. morphotypes. Almost half of the variation was due to the number of an AT microsatellite repeats in the center of the spacer. Nine haplotypes were found in the species constructing three main lineages corresponding to the origin of the colonies located in southwest (SW), northeast (NE), and northwest-center-southeast (NCS). Lineages NCS and NE included both typical P. cf sergenti and P. cf similis and intermediate morphotypes. Conclusion: Phylogenetic sequence analysis revealed that, except for one Iranian sample, which was close to the European samples, other Iranian haplotypes were associated with the northeastern Mediterranean populations including Turkey, Cyprus, Syria, and Pakistan. Similar to the sequences of mtDNA COI gene, ITS2 sequences could not resolve P. sergenti from P. similis and did not support the possible existence of sibling species or subspecies within P. sergenti s.l.. PMID:28032098

  12. Associations between genetic variation in one-carbon metabolism and LINE-1 DNA methylation in histologically normal breast tissues.

    PubMed

    Llanos, Adana A M; Marian, Catalin; Brasky, Theodore M; Dumitrescu, Ramona G; Liu, Zhenhua; Mason, Joel B; Makambi, Kepher H; Spear, Scott L; Kallakury, Bhaskar V S; Freudenheim, Jo L; Shields, Peter G

    2015-01-01

    Genome-wide DNA hypomethylation is an early event in the carcinogenic process. Percent methylation of long interspersed nucleotide element-1 (LINE-1) is a biomarker of genome-wide methylation and is a potential biomarker for breast cancer. Understanding factors associated with percent LINE-1 DNA methylation in histologically normal tissues could provide insight into early stages of carcinogenesis. In a cross-sectional study of 121 healthy women with no prior history of cancer who underwent reduction mammoplasty, we examined associations between plasma and breast folate, genetic variation in one-carbon metabolism, and percent LINE-1 methylation using multivariable regression models (adjusting for race, oral contraceptive use, and alcohol use). Results are expressed as the ratio of LINE-1 methylation relative to that of the referent group, with the corresponding 95% confidence intervals (CI). We found no significant associations between plasma or breast folate and percent LINE-1 methylation. Variation in MTHFR, MTR, and MTRR were significantly associated with percent LINE-1 methylation. Variant allele carriers of MTHFR A1289C had 4% lower LINE-1 methylation (Ratio 0.96, 95% CI 0.93-0.98), while variant allele carriers of MTR A2756G (Ratio 1.03, 95% CI 1.01-1.06) and MTRR A66G (Ratio 1.03, 95% CI 1.01-1.06) had 3% higher LINE-1 methylation, compared to those carrying the more common genotypes of these SNPs. DNA methylation of LINE-1 elements in histologically normal breast tissues is influenced by polymorphisms in genes in the one-carbon metabolism pathway. Future studies are needed to investigate the sociodemographic, environmental and additional genetic determinants of DNA methylation in breast tissues and the impact on breast cancer susceptibility.

  13. Associations between genetic variation in one-carbon metabolism and LINE-1 DNA methylation in histologically normal breast tissues

    PubMed Central

    Llanos, Adana A M; Marian, Catalin; Brasky, Theodore M; Dumitrescu, Ramona G; Liu, Zhenhua; Mason, Joel B; Makambi, Kepher H; Spear, Scott L; Kallakury, Bhaskar V S; Freudenheim, Jo L; Shields, Peter G

    2015-01-01

    Genome-wide DNA hypomethylation is an early event in the carcinogenic process. Percent methylation of long interspersed nucleotide element-1 (LINE-1) is a biomarker of genome-wide methylation and is a potential biomarker for breast cancer. Understanding factors associated with percent LINE-1 DNA methylation in histologically normal tissues could provide insight into early stages of carcinogenesis. In a cross-sectional study of 121 healthy women with no prior history of cancer who underwent reduction mammoplasty, we examined associations between plasma and breast folate, genetic variation in one-carbon metabolism, and percent LINE-1 methylation using multivariable regression models (adjusting for race, oral contraceptive use, and alcohol use). Results are expressed as the ratio of LINE-1 methylation relative to that of the referent group, with the corresponding 95% confidence intervals (CI). We found no significant associations between plasma or breast folate and percent LINE-1 methylation. Variation in MTHFR, MTR, and MTRR were significantly associated with percent LINE-1 methylation. Variant allele carriers of MTHFR A1289C had 4% lower LINE-1 methylation (Ratio 0.96, 95% CI 0.93–0.98), while variant allele carriers of MTR A2756G (Ratio 1.03, 95% CI 1.01–1.06) and MTRR A66G (Ratio 1.03, 95% CI 1.01–1.06) had 3% higher LINE-1 methylation, compared to those carrying the more common genotypes of these SNPs. DNA methylation of LINE-1 elements in histologically normal breast tissues is influenced by polymorphisms in genes in the one-carbon metabolism pathway. Future studies are needed to investigate the sociodemographic, environmental and additional genetic determinants of DNA methylation in breast tissues and the impact on breast cancer susceptibility. PMID:26090795

  14. Extensive Pyrosequencing Reveals Frequent Intra-Genomic Variations of Internal Transcribed Spacer Regions of Nuclear Ribosomal DNA

    PubMed Central

    Li, Dezhu; Sun, Yongzhen; Niu, Yunyun; Chen, Zhiduan; Luo, Hongmei; Pang, Xiaohui; Sun, Zhiying; Liu, Chang; Lv, Aiping; Deng, Youping; Larson-Rabin, Zachary; Wilkinson, Mike; Chen, Shilin

    2012-01-01

    Background Internal transcribed spacer of nuclear ribosomal DNA (nrDNA) is already one of the most popular phylogenetic and DNA barcoding markers. However, the existence of its multiple copies has complicated such usage and a detailed characterization of intra-genomic variations is critical to address such concerns. Methodology/Principal Findings In this study, we used sequence-tagged pyrosequencing and genome-wide analyses to characterize intra-genomic variations of internal transcribed spacer 2 (ITS2) regions from 178 plant species. We discovered that mutation of ITS2 is frequent, with a mean of 35 variants per species. And on average, three of the most abundant variants make up 91% of all ITS2 copies. Moreover, we found different congeneric species share identical variants in 13 genera. Interestingly, different species across different genera also share identical variants. In particular, one minor variant of ITS2 in Eleutherococcus giraldii was found identical to the ITS2 major variant of Panax ginseng, both from Araliaceae family. In addition, DNA barcoding gap analysis showed that the intra-genomic distances were markedly smaller than those of the intra-specific or inter-specific variants. When each of 5543 variants were examined for its species discrimination efficiency, a 97% success rate was obtained at the species level. Conclusions Identification of identical ITS2 variants across intra-generic or inter-generic species revealed complex species evolutionary history, possibly, horizontal gene transfer and ancestral hybridization. Although intra-genomic multiple variants are frequently found within each genome, the usage of the major variants alone is sufficient for phylogeny construction and species determination in most cases. Furthermore, the inclusion of minor variants further improves the resolution of species identification. PMID:22952830

  15. Evolutionary history of asexual hybrid loaches (Cobitis: Teleostei) inferred from phylogenetic analysis of mitochondrial DNA variation.

    PubMed

    Janko, K; Kotlík, P; Ráb, P

    2003-11-01

    Reconstruction of the evolutionary history of asexual lineages undermines their suitability as models for the studies of evolutionary consequences of sexual reproduction. Using molecular tools we addressed the origin, age and maternal ancestry of diploid and triploid asexual lineages arisen through the hybridization between spiny loaches Cobitis elongatoides, C. taenia and C. tanaitica. Reconstructions of the phylogenetic relationships among mitochondrial DNA (mtDNA) haplotypes, revealed by sequence analyses, suggest that both hybrid complexes (C. elongatoides-taenia and C. elongatoides-tanaitica) contained several asexual lineages of independent origin. Cobitis elongatoides was the exclusive maternal ancestor of all the C. elongatoides-tanaitica hybrids, whereas within the C. elongatoides-taenia complex, hybridization was reciprocal. In both complexes the low haplotype divergences were consistent with a recent origin of asexual lineages. Combined mtDNA and allozyme data suggest that the triploids arose through the incorporation of a haploid sperm genome into unreduced ova produced by diploid hybrids.

  16. Genetic variation in wild and hatchery population of Catla catla (Hamilton, 1822) analyzed through mtDNA cytochrome b region.

    PubMed

    Behera, Bijay Kumar; Kunal, Swaraj Priyaranjan; Baisvar, Vishwamitra Singh; Meena, Dharmendra Kumar; Panda, Debarata; Pakrashi, Sudip; Paria, Prasenjit; Das, Pronob; Debnath, Dipesh; Parida, Pranaya Kumar; Das, Basanta Kumar; Jena, Joykrushna

    2017-01-10

    Catla (Catla catla) is a one of the most harvested Indian major carps and is widely cultured fish species in Indian subcontinent. In the present study, genetic variability between hatchery and wild stocks of Catla was surveyed using sequence data of mitochondrial DNA of partial 307 bp of cytochrome b region. A total of 174 Catla individuals were examined from three different river basins and hatcheries. Significant genetic heterogeneity was observed for the sequence data (FST = 0.308, p ≤ 0.001). However, analysis of molecular variance (AMOVA) resulted in insignificant genetic differentiation among the samples of three rivers and culture zones (FCT = -0.10, p = 0.44). The result suggested a significant genetic variation within different riverine system, low genetic differentiation among samples from river basins and a lack of genetic variation in hatchery populations.

  17. AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication.

    PubMed

    Blanca, José M; Prohens, Jaime; Anderson, Gregory J; Zuriaga, Elena; Cañizares, Joaquín; Nuez, Fernando

    2007-07-01

    The pepino (Solanum muricatum) is a vegetatively propagated, domesticated native of the Andes, where it grows with wild relatives. We used AFLPs and a 1-kb sequence of the 3-methylcrotonyl-CoA carboxylase gene to study variation of 27 accessions of S. muricatum and 35 collections of 10 species of wild relatives (Solanum section Basarthrum). A total of 298 AFLP fragments and 29 DNA sequence haplotypes were detected. Cluster and principal coordinate analyses and other genetic parameters estimated from both types of markers, show that S. muricatum is closely related to the species from one of the series (Caripensia) of section Basarthrum and that >90% of the variation of the cultigen is also represented in that series. Pepino is highly diverse, either because it is not monophyletic or it has been subjected to regular introgression with wild species, or both. Although a continuous distribution of the genetic variation occurred within the cultivated species, three genetic clusters were recognized. Cluster 1 is mostly centered in Ecuador, cluster 2 in Ecuador and Peru, and cluster 3 in Colombia and Ecuador. Cluster 3 also includes all modern cultivars studied. These results and other evidence suggest that northern Ecuador/southern Colombia is the main center of pepino diversity and the center of origin. The high genetic variation of this cultigen indicates that domestication does not always produce a genetic bottleneck.

  18. Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans.

    PubMed

    Wendt, Frank R; King, Jonathan L; Novroski, Nicole M M; Churchill, Jennifer D; Ng, Jillian; Oldt, Robert F; McCulloh, Kelly L; Weise, Jessica A; Smith, David Glenn; Kanthaswamy, Sreetharan; Budowle, Bruce

    2017-02-27

    Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11×10(-26) and 2.79×10(-29), respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49×10(-63). Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

  19. mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

    PubMed Central

    Easton, R. D.; Merriwether, D. A.; Crews, D. E.; Ferrell, R. E.

    1996-01-01

    Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types. PMID:8659527

  20. mtDNA variation in the Yanomami: evidence for additional New World founding lineages.

    PubMed

    Easton, R D; Merriwether, D A; Crews, D E; Ferrell, R E

    1996-07-01

    Native Americans have been classified into four founding haplogroups with as many as seven founding lineages based on mtDNA RFLPs and DNA sequence data. mtDNA analysis was completed for 83 Yanomami from eight villages in the Surucucu and Catrimani Plateau regions of Roraima in northwestern Brazil. Samples were typed for 15 polymorphic mtDNA sites (14 RFLP sites and 1 deletion site), and a subset was sequenced for both hypervariable regions of the mitochondrial D-loop. Substantial mitochondrial diversity was detected among the Yanomami, five of seven accepted founding haplotypes and three others were observed. Of the 83 samples, 4 (4.8%) were lineage B1, 1 (1.2%) was lineage B2, 31 (37.4%) were lineage C1, 29 (34.9%) were lineage C2, 2 (2.4%) were lineage D1, 6 (7.2%) were lineage D2, 7 (8.4%) were a haplotype we designated "X6," and 3 (3.6%) were a haplotype we designated "X7." Sequence analysis found 43 haplotypes in 50 samples. B2, X6, and X7 are previously unrecognized mitochondrial founding lineage types of Native Americans. The widespread distribution of these haplotypes in the New World and Asia provides support for declaring these lineages to be New World founding types.

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

    USGS Publications Warehouse

    Shields, Gerald F.; Adams, Deborah; Garner, Gerald W.; 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.

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

    PubMed

    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

  3. Phylogeography of East Asian Lespedeza buergeri (Fabaceae) based on chloroplast and nuclear ribosomal DNA sequence variations.

    PubMed

    Jin, Dong-Pil; Lee, Jung-Hyun; Xu, Bo; Choi, Byoung-Hee

    2016-09-01

    The dynamic changes in land configuration during the Quaternary that were accompanied by climatic oscillations have significantly influenced the current distribution and genetic structure of warm-temperate forests in East Asia. Although recent surveys have been conducted, the historical migration of forest species via land bridges and, especially, the origins of Korean populations remains conjectural. Here, we reveal the genetic structure of Lespedeza buergeri, a warm-temperate shrub that is disjunctively distributed around the East China Sea (ECS) at China, Korea, and Japan. Two non-coding regions (rpl32-trnL, psbA-trnH) of chloroplast DNA (cpDNA) and the internal transcribed spacer of nuclear ribosomal DNA (nrITS) were analyzed for 188 individuals from 16 populations, which covered almost all of its distribution. The nrITS data demonstrated a genetic structure that followed geographic boundaries. This examination utilized AMOVA, comparisons of genetic differentiation based on haplotype frequency/genetic mutations among haplotypes, and Mantel tests. However, the cpDNA data showed contrasting genetic pattern, implying that this difference was due to a slower mutation rate in cpDNA than in nrITS. These results indicated frequent migration by this species via an ECS land bridge during the early Pleistocene that then tapered gradually toward the late Pleistocene. A genetic isolation between western and eastern Japan coincided with broad consensus that was suggested by the presence of other warm-temperate plants in that country. For Korean populations, high genetic diversity indicated the existence of refugia during the Last Glacial Maximum on the Korean Peninsula. However, their closeness with western Japanese populations at the level of haplotype clade implied that gene flow from western Japanese refugia was possible until post-glacial processing occurred through the Korea/Tsushima Strait land bridge.

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

    PubMed Central

    Gossner, Martin M.; Struwe, Jan-Frederic; Sturm, Sarah; Max, Simeon; McCutcheon, Michelle; Weisser, Wolfgang W.; Zytynska, Sharon E.

    2016-01-01

    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 genetic analysis

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

    PubMed

    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.

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

    PubMed Central

    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

  7. Characterization and Sequence Variation in the rDNA Region of Six Nematode Species of the Genus Longidorus (Nematoda)

    PubMed Central

    De Luca, F.; Reyes, A.; Grunder, J.; Kunz, P.; Agostinelli, A.; De Giorgi, C.; Lamberti, F.

    2004-01-01

    Total DNA was isolated from individual nematodes of the species Longidorus helveticus, L. macrosoma, L. arthensis, L. profundorum, L. elongatus, and L. raskii collected in Switzerland. The ITS region and D1-D2 expansion segments of the 26S rDNA were amplified and cloned. The sequences obtained were aligned in order to investigate sequence diversity and to infer the phylogenetic relationships among the six Longidorus species. D1-D2 sequences were more conserved than the ITS sequences that varied widely in primary structure and length, and no consensus was observed. Phylogenetic analyses using the neighbor-joining, maximum parsimony and maximum likelihood methods were performed with three different sequence data sets: ITS1-ITS2, 5.8S-D1-D2, and combining ITS1-ITS2+5.8S-D1-D2 sequences. All multiple alignments yielded similar basic trees supporting the existence of the six species established using morphological characters. These sequence data also provided evidence that the different regions of the rDNA are characterized by different evolution rates and by different factors associated with the generation of extreme size variation. PMID:19262800

  8. Sequence Variation in Amplification Target Genes and Standards Influences Interlaboratory Comparison of BK Virus DNA Load Measurement

    PubMed Central

    Solis, Morgane; Meddeb, Mariam; Sueur, Charlotte; Domingo-Calap, Pilar; Soulier, Eric; Chabaud, Angeline; Perrin, Peggy; Moulin, Bruno; Bahram, Seiamak; Stoll-Keller, Françoise; Caillard, Sophie; Barth, Heidi

    2015-01-01

    International guidelines define a BK virus (BKV) load of ≥4 log10 copies/ml as presumptive of BKV-associated nephropathy (BKVN) and a cutoff for therapeutic intervention. To investigate whether BKV DNA loads (BKVL) are comparable between laboratories, 2 panels of 15 and 8 clinical specimens (urine, whole blood, and plasma) harboring different BKV genotypes were distributed to 20 and 27 French hospital centers in 2013 and 2014, respectively. Although 68% of the reported results fell within the acceptable range of the expected result ±0.5 log10, the interlaboratory variation ranged from 1.32 to 5.55 log10. Polymorphisms specific to BKV genotypes II and IV, namely, the number and position of mutations in amplification target genes and/or deletion in standards, arose as major sources of interlaboratory disagreements. The diversity of DNA purification methods also contributed to the interlaboratory variability, in particular for urine samples. Our data strongly suggest that (i) commercial external quality controls for BKVL assessment should include all major BKV genotypes to allow a correct evaluation of BKV assays, and (ii) the BKV sequence of commercial standards should be provided to users to verify the absence of mismatches with the primers and probes of their BKV assays. Finally, the optimization of primer and probe design and standardization of DNA extraction methods may substantially decrease interlaboratory variability and allow interinstitutional studies to define a universal cutoff for presumptive BKVN and, ultimately, ensure adequate patient care. PMID:26468499

  9. Interindividual variation in DNA methylation at a putative POMC metastable epiallele is associated with obesity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The estimated heritability of human BMI is close to 75%, but identified genetic variants explain only a small fraction of interindividual body-weight variation. Inherited epigenetic variants identified in mouse models named "metastable epialleles" could in principle explain this "missing heritabilit...

  10. DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription.

    PubMed

    Marilley, M; Radebaugh, C A; Geiss, G K; Laybourn, P J; Paule, M R

    2002-08-01

    Eukaryotic ribosomal RNA promoters exhibit an unusual conservation of non-canonical DNA structure (curvature, twist angle and duplex stability) despite a lack of primary sequence conservation. This raises the possibility that rRNA transcription factors might utilize structural anomalies in their sequence recognition process. We have analyzed in detail the interaction of the polymerase I transcription factor TIF-IB from Acanthmoeba castellanii with the CORE promoter. TIF-IB interacts primarily with the minor groove of the promoter. By correlating the effects on transcription and on DNA structure of promoter point mutations, we show that the TIF-IB interaction is strongly inhibited by increases in minor groove width. This suggests that a particular DNA structure is required for interaction with the transcription factor. In addition, TIF-IB induces a small bend in the promoter upon binding. Modeling of this bend reveals that it requires an additional narrowing of the minor groove, which would favor binding to mutants with narrower grooves. We also discuss how this narrowing would induce a small destabilization of the helix upstream of the transcription start site. Telestability predicts this would result in destabilization of the sequence that melts during initiation, suggesting that TIF-IB may have a role in stimulating melting.

  11. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.

    PubMed

    Bowling, A T; Del Valle, A; Bowling, M

    2000-02-01

    Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry.

  12. PCR/SSCP detects reliably and efficiently DNA sequence variations in large scale screening projects.

    PubMed

    Miterski, B; Krüger, R; Wintermeyer, P; Epplen, J T

    2000-06-01

    A simple and fast method with high reliability is necessary for the identification of mutations, polymorphisms and sequence variants (MPSV) within many genes and many samples, e.g. for clarifying the genetic background of individuals with multifactorial diseases. Here we review our experience with the polymerase chain reaction/single-strand conformation polymorphism (PCR/SSCP) analysis to identify MPSV in a number of genes thought to be involved in the pathogenesis of multifactorial neurological disorders, including autoimmune diseases like multiple sclerosis (MS) and neurodegenerative disorders like Parkinson s disease (PD). The method is based on the property of the DNA that the electrophoretic mobility of single stranded nucleic acids depends not only on their size but also on their sequence. The target sequences were amplified, digested into fragments ranging from 50-240 base pairs (bp), heat-denatured and analysed on native polyacrylamide (PAA) gels of different composition. The analysis of a great number of different PCR products demonstrates that the detection rate of MPSV depends on the fragment lengths, the temperature during electrophoresis and the composition of the gel. In general, the detection of MPSV is neither influenced by their location within the DNA fragment nor by the type of substitution, i.e., transitions or transversions. The standard PCR/SSCP system described here provides high reliability and detection rates. It allows the efficient analysis of a large number of DNA samples and many different genes.

  13. Nuclear markers, mitochondrial DNA and male secondary sexual traits variation in a newt hybrid zone (Triturus vulgaris x T. montandoni).

    PubMed

    Babik, W; Szymura, J M; Rafiński, J

    2003-07-01

    The smooth and the Montandon's newts (Triturus vulgaris and T. montandoni) are genetically similar sister species with highly divergent male secondary sexual traits involved in complex courtship behaviour. Their parapatric ranges overlap at moderate elevations in the Carpathian Mountains where they hybridize readily. Here we present a detailed study of genetic and morphological variation in populations from the area of sympatry. Analysis of variation at seven nuclear markers, mtDNA and male sexual secondary traits was complemented with an ecological survey of breeding sites characteristics. Extensive hybridization was revealed with back-cross individuals similar to either parental species predominating among hybrids. The hybrid zone exhibited a mosaic pattern: the genetic composition of the populations was correlated only weakly with their geographical position. No association with habitat type was found. Departures from Hardy-Weinberg proportions, significant linkage disequilibria and bimodal distribution of genotypes suggest strongly that assortative mating is an important factor shaping the genetic composition of hybrid populations. The pattern of cytonuclear disequilibria did not indicate much asymmetry in interspecific matings. Changes in the frequency of nuclear markers were highly concordant, whereas mtDNA showed much wider bidirectional introgression with 14% excess of T. montandoni haplotype. We argue that the mosaic structure of the newt hybrid zone results mainly from stochastic processes related to extinction and recolonization. Microgeographical differences in mtDNA introgression are explained by historical range shifts. Since morphologically intermediate males were underrepresented when compared to hybrid males identified by genetic markers, sexual selection acting against the morphological intermediates is implied. We discuss the implications of these findings in the context of reinforcement of prezygotic isolation in newts.

  14. Contrasting cpDNA variation in two Indonesian endemic lowland dipterocarp species and implications for their conservation.

    PubMed

    Rachmat, Henti Hendalastuti; Kamiya, Koichi; Harada, Ko

    2012-08-15

    Shorea javanica (Dipterocarpaceae) is an economically important dammar-producing tree, endemic to the tropical lowland forests of Sumatra and Java, Indonesia. However, its total population size is limited and this species is endangered. Shorea selanica is one of the very limited numbers of species in genus Shorea (Dipterocarpaceae) that grows in Wallacean. This species can be found only in the central part of the Moluccas, eastern Indonesia. Six populations (77 individuals in total) were sampled for S. javanica while three populations (27 individuals in total) were sampled for S. selanica. To determine genetic variation and population structure, three non-coding chloroplast DNA regions of trnL-trnF, psbC-trnS, trnS-trnfM and two non-coding chloroplast DNA regions of trnT-trnL, trnL-trnF were sequenced from S. javanica and S. selanica, respectively. There was no variation in the chloroplast DNA regions from S. javanica, except for one unique indel polymorphism. Nucleotide diversity within S. selanica populations ranged from 0 (Seram) to 0.00044 (Buru), with a pooled value of 0.00041. S. javanica was determined as having no population structure while high levels of genetic differentiation was found among populations of S. selanica (F(ST) = 0.702). Different pattern of population structure among the two species in this study suggested the need for distinct management and conservation strategies for each species. For S. javanica, connectivity within and among populations, including augmentation of population size across the species range, should be promoted. For S. selanica, an in situ conservation plan that defines core areas completely free from perturbation within each population is necessary.

  15. Mitochondrial DNA variation in rainbow trout (Oncorhynchus mykiss) across its native range: testing biogeographical hypotheses and their relevance to conservation.

    PubMed

    McCusker, M R; Parkinson, E; Taylor, E B

    2000-12-01

    North-western North America has been repeatedly glaciated over most of the past two million years, with the most recent glaciation occurring between 60 000 and 10 000 years ago. Intraspecific genetic variation in many species has been shaped by where they survived glaciation and what postglacial recolonization routes were used. In this study, molecular techniques were used to investigate biogeographical, taxonomic and conservation issues in rainbow trout, Oncorhynchus mykiss. Mitochondrial DNA (mtDNA) variation was assessed using a restriction fragment length polymorphism (RFLP) analysis, focusing mainly on the previously understudied northern extent of the species' range. Two phylogenetically distinct mitochondrial lineages were found that differed from each other by up to 1.8% in sequence. Although the geographical distributions of the two clades overlap extensively, diversity and distributional analyses strongly suggest that trout survived glaciation in both coastal and inland refugia followed by postglacial gene flow and secondary contact. Postglacial dispersal into British Columbia most likely occurred from the Queen Charlotte Islands and the Columbia River. Although trout most likely also survived glaciation along the coast of Washington, Oregon and California, as well as near the Bering Strait, evidence suggests that dispersal into British Columbia from these areas was limited. Sequence analysis of mitochondrial haplotypes revealed higher diversity in California than in the northern part of the species' range, indicating an ancient presence of the species in the south. Phylogeographic divergence probably predates adaptive variation in the species as suggested by evidence for parallel evolution of life history types across the range of O. mykiss.

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

    PubMed

    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.

  17. Genetic variation and exposure related risk estimation: will toxicology enter a new era? DNA repair and cancer as a paradigm.

    PubMed

    Mohrenweiser, Harvey W

    2004-01-01

    With the vast technological and informational resources increasingly available from investments in "genomics," toxicology and much of biological science, is faced with previously undreamed of opportunities and equally daunting challenges. The ability to generate the large quantities of data becoming routinely available could not be imagined a decade ago. The complexities of data analysis are increasingly the rate-limiting element in scientific advances. The expectations that these large scientific investments will reduce the incidence of human disease and improve health are very high. An emphasis on genetic variation and Toxicogenetics is expected to yield risk estimates for specific rather than average individuals and individuals with varied lifestyles and complex patterns of exposure. Examples from studies of polymorphic variation in DNA repair genes in the healthy population and cancer risk highlight the complexity and challenges of incorporating genetic variation into quantitative estimates of risk associated with environmentally relevant exposures. Similar issues exist in selecting the animal models most appropriate for predicting human risk from environmental exposures to toxic agents.

  18. Human amygdala volume is predicted by common DNA variation in the stathmin and serotonin transporter genes.

    PubMed

    Stjepanović, D; Lorenzetti, V; Yücel, M; Hawi, Z; Bellgrove, M A

    2013-07-16

    Despite the relevance of changes in amygdala volume to psychiatric illnesses and its heritability in both health and disease, the influence of common genetic variation on amygdala morphology remains largely unexplored. In the present study, we investigated the influence of a number of novel genetic variants on amygdala volume in 139 neurologically healthy individuals of European descent. Amygdala volume was significantly associated with allelic variation in the stathmin (STMN1) and serotonin transporter (SLC6A4) genes, which have been linked to healthy and disordered affective processing. These results were replicated across both manual and automated methods of amygdala parcellation, although manual tracing showed stronger effects, providing a cautionary note to studies relying on automated parcellation methods. Future studies will need to determine whether amygdala volume mediates the impact of stathmin and serotonin transporter gene variants on normal and dysfunctional emotion processing.

  19. Human amygdala volume is predicted by common DNA variation in the stathmin and serotonin transporter genes

    PubMed Central

    Stjepanović, D; Lorenzetti, V; Yücel, M; Hawi, Z; Bellgrove, M A

    2013-01-01

    Despite the relevance of changes in amygdala volume to psychiatric illnesses and its heritability in both health and disease, the influence of common genetic variation on amygdala morphology remains largely unexplored. In the present study, we investigated the influence of a number of novel genetic variants on amygdala volume in 139 neurologically healthy individuals of European descent. Amygdala volume was significantly associated with allelic variation in the stathmin (STMN1) and serotonin transporter (SLC6A4) genes, which have been linked to healthy and disordered affective processing. These results were replicated across both manual and automated methods of amygdala parcellation, although manual tracing showed stronger effects, providing a cautionary note to studies relying on automated parcellation methods. Future studies will need to determine whether amygdala volume mediates the impact of stathmin and serotonin transporter gene variants on normal and dysfunctional emotion processing. PMID:23860484

  20. Mitochondrial DNA Sequence Variation in North Atlantic Long-Finned Pilot Whales, Globicephala melas

    DTIC Science & Technology

    1994-06-01

    Strongylocentrotus purpuratus and S . droebachiensis. Evolution 44: 403-415. Rosel, P.E. (1992). Genetic population structure and systematic relationships of...reproduce and distribute copies of this thesis document in whole or in part Signale of Amho,i^ S ^*^ Joint Program in Oceanography, Massachusetts Institute...variation used in the studies described in this chapter include: 1) Genetic distance (d, p, S , or D) is a measure of the number of nucleotide

  1. Rare deficiency types of alpha 1-antitrypsin: electrophoretic variation and DNA haplotypes.

    PubMed Central

    Cox, D W; Billingsley, G D

    1989-01-01

    A deficiency of the plasma protease inhibitor alpha 1-antitrypsin (alpha 1AT), is usually associated with the deficiency allele PI*Z. However, other alleles can also produce a deficiency. Some of these rare deficiency alleles produce a low concentration (3%-15% of normal) of alpha 1AT and include Mmalton, Mduarte, Mheerlen, and Mprocida. Null, or nonproducing, alleles are associated with trace amounts (less than 1%) of plasma alpha 1AT. We have identified, using isoelectric focusing, the deficiency alleles in 222 patients (68 children and 154 adults) with alpha 1AT deficiency. In addition to PI*Z, we found low-producing alleles PI*Mmalton and PI*Mcobalt and four null (PI*QO) alleles. On the basis of a population frequency of .0122 for PI*Z, frequencies for other deficiency alleles are 1.1 x 10(-4) for PI*Mmalton, 2.5 x 10(-5) for PI*Mcobalt (which may be the same as that for PI*Mduarte, and 1.4 x 10(-4) for all null alleles combined. Using 12 polymorphic restriction sites with seven different restriction enzymes, we have obtained DNA haplotypes for each of the rare deficiency types. All of the rare deficiency alleles can be distinguished from PI*Z by their DNA haplotype, and most can be distinguished from each other. DNA haplotypes are useful to indicate the presence of new types of null alleles, to identify genetic compounds for rare deficiency alleles, and to identify the original normal allele from which each deficiency allele is derived. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:2786333

  2. Intraspecific Variation of Eysarcoris guttigerus (Hemiptera: Pentatomidae) in Japanese Southwest Population Based on Mitochondrial DNA.

    PubMed

    Yamaji, Takuya; Ishikawa, Tadashi; Nomura, Masashi

    2016-01-01

    The white-spotted globular bug Eysarcoris guttigerus (Thunberg) (Hemiptera: Pentatomidae) is widely distributed in East Asia and the Pacific region. In Japan, the species is found in grassy or composite weeds in the western area of the main islands and Ryukyu Islands of Japan. One notable characteristic of the Eysarcoris genus is the two white spots on the scutellum. This is not the case with the Ishigaki Island population, however, which sports red spots instead of white, suggesting that intraspecific variation exists in the species. Therefore, we investigated intraspecific variation in E. guttigerus using mitochondrial NADH dehydrogenase subunit 2 (ND2), cytochrome oxidase subunit 1 (CO1), cytochrome b (Cytb), tRNA-Serine (tRNA(ser)), NADH dehydrogenase subunit 1 (ND1), and 16S ribosomal RNA (16SrRNA) genes from 13 populations of Japan. The obtained maximum likelihood phylogenetic tree was divided into three groups--Group 1: Mainland, Group 2: Central Ryukyu Islands (Okinawa-Amamioshima Islands), and Group 3: South Ryukyu Islands (Ishigaki Island). The Ishigaki population was significantly separated from the other populations with consistent differences in spot color. The estimated period of divergence between the Ishigaki population and the other populations was consistent with the period of formation of the Kerama Gap in the Ryukyu arc. Thus, the process of formation of the Kerama Gap may have influenced the intraspecific variation of E. guttigerus.

  3. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

    PubMed Central

    Yuhki, N; O'Brien, S J

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations. Images PMID:1967831

  4. Intraspecific Variation of Eysarcoris guttigerus (Hemiptera: Pentatomidae) in Japanese Southwest Population Based on Mitochondrial DNA

    PubMed Central

    Yamaji, Takuya; Ishikawa, Tadashi; Nomura, Masashi

    2016-01-01

    The white-spotted globular bug Eysarcoris guttigerus (Thunberg) (Hemiptera: Pentatomidae) is widely distributed in East Asia and the Pacific region. In Japan, the species is found in grassy or composite weeds in the western area of the main islands and Ryukyu Islands of Japan. One notable characteristic of the Eysarcoris genus is the two white spots on the scutellum. This is not the case with the Ishigaki Island population, however, which sports red spots instead of white, suggesting that intraspecific variation exists in the species. Therefore, we investigated intraspecific variation in E. guttigerus using mitochondrial NADH dehydrogenase subunit 2 (ND2), cytochrome oxidase subunit 1 (CO1), cytochrome b (Cytb), tRNA-Serine (tRNAser), NADH dehydrogenase subunit 1 (ND1), and 16S ribosomal RNA (16SrRNA) genes from 13 populations of Japan. The obtained maximum likelihood phylogenetic tree was divided into three groups—Group 1: Mainland, Group 2: Central Ryukyu Islands (Okinawa-Amamioshima Islands), and Group 3: South Ryukyu Islands (Ishigaki Island). The Ishigaki population was significantly separated from the other populations with consistent differences in spot color. The estimated period of divergence between the Ishigaki population and the other populations was consistent with the period of formation of the Kerama Gap in the Ryukyu arc. Thus, the process of formation of the Kerama Gap may have influenced the intraspecific variation of E. guttigerus. PMID:26798143

  5. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history.

    PubMed

    Yuhki, N; O'Brien, S J

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. We present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  6. Lactase non-persistence is directed by DNA variation-dependent epigenetic aging

    PubMed Central

    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

    2016-01-01

    Inability to digest lactose due to lactase non-persistence is a common trait in adult mammals, with the exception of certain human populations that exhibit lactase persistence. It is not clear how the lactase gene can be dramatically downregulated with age in most individuals, but remains active in some. We performed a comprehensive epigenetic study of the human and mouse intestine using chromosome-wide DNA modification profiling and targeted bisulfite sequencing. Epigenetically-controlled regulatory elements were found to account for the differences in lactase mRNA levels between individuals, intestinal cell types and species. The importance of these regulatory elements in modulating lactase mRNA levels was confirmed by CRISPR-Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, as lactase persistence- and non-persistence-DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors facilitate a gradual accumulation of epigenetic changes with age to affect phenotypic outcome. PMID:27159559

  7. Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS)

    PubMed Central

    Radhakrishna, Uppala; Albayrak, Samet; Alpay-Savasan, Zeynep; Zeb, Amna; Turkoglu, Onur; Sobolewski, Paul; Bahado-Singh, Ray O.

    2016-01-01

    Congenital heart defect (CHD) is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS), with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated). Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS. PMID:27152866

  8. DNA.

    ERIC Educational Resources Information Center

    Felsenfeld, Gary

    1985-01-01

    Structural form, bonding scheme, and chromatin structure of and gene-modification experiments with deoxyribonucleic acid (DNA) are described. Indicates that DNA's double helix is variable and also flexible as it interacts with regulatory and other molecules to transfer hereditary messages. (DH)

  9. Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China.

    PubMed

    Li, F; Hu, T; Duan, N C; Li, W Y; Teng, Q; Li, H; Liu, W; Liu, Y; Cheng, T Y

    2016-01-01

    The present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5-72% for pcox1, 73.7-74.2% for pnad1 and 58-58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0-1.6% for pcox1, 0-1.9% for pnad1 and 0-1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1-12.5%, 13.3-17.7% and 8.5-18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

  10. Analysis of DNA sequence variation within marine species using Beta-coalescents

    PubMed Central

    Steinrücken, Matthias; Birkner, Matthias; Blath, Jochen

    2013-01-01

    We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially due to extreme reproductive behaviour, e.g. via Hedgecock’s “reproduction sweepstakes”. Besides the data analysis, in particular the inference of mutation rates and the estimation of the (real) time to the most recent common ancestor, we briefly address the question whether the genealogies might be adequately described by so-called Beta coalescents (as opposed to Kingman’s coalescent), allowing multiple mergers of genealogies. The choice of the underlying coalescent model for the genealogy has drastic implications for the estimation of the above quantities, in particular the real-time embedding of the genealogy. PMID:23376155

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

    PubMed

    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.

  12. A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa.

    PubMed

    Arredi, Barbara; Poloni, Estella S; Paracchini, Silvia; Zerjal, Tatiana; Fathallah, Dahmani M; Makrelouf, Mohamed; Pascali, Vincenzo L; Novelletto, Andrea; Tyler-Smith, Chris

    2004-08-01

    We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.

  13. [Genetic variation of Manchurian pheasant (Phasianus colchicus pallasi Rotshild, 1903) inferred from mitochondrial DNA control region sequences].

    PubMed

    Kozyrenko, M M; Fisenko, P V; Zhuravlev, Iu N

    2009-04-01

    Sequence variation of the mitochondrial DNA control region was studied in Manchurian pheasants (Phasianus colchicus pallasi Rotshild, 1903) representing three geographic populations from the southern part of the Russian Far East. Extremely low population genetic differentiation (F(ST) = 0.0003) pointed to a very high gene exchange between the populations. Combination of such characters as high haplotype diversity (0.884 to 0.913), low nucleotide diversity (0.0016 to 0.0022), low R2 values (0.1235 to 0.1337), certain patterns of pairwise-difference distributions, and the absence of phylogenetic structure suggested that the phylogenetic history of Ph. C. pallasi included passing through a bottleneck with further expansion in the postglacial period. According to the data obtained, it was suggested that differentiation between the mitochondrial lineages started approximately 100 000 years ago.

  14. Nuclear DNA Variation, Chromosome Numbers and Polyploidy in the Endemic and Indigenous Grass Flora of New Zealand

    PubMed Central

    MURRAY, B. G.; DE LANGE, P. J.; FERGUSON, A. R.

    2005-01-01

    • Background and Aims Little information is available on DNA C-values for the New Zealand flora. Nearly 85 % of the named species of the native vascular flora are endemic, including 157 species of Poaceae, the second most species-rich plant family in New Zealand. Few C-values have been published for New Zealand native grasses, and chromosome numbers have previously been reported for fewer than half of the species. The aim of this research was to determine C-values and chromosome numbers for most of the endemic and indigenous Poaceae from New Zealand. • Scope To analyse DNA C-values from 155 species and chromosome numbers from 55 species of the endemic and indigenous grass flora of New Zealand. • Key Results The new C-values increase significantly the number of such measurements for Poaceae worldwide. New chromosome numbers were determined from 55 species. Variation in C-value and percentage polyploidy were analysed in relation to plant distribution. No clear relationship could be demonstrated between these variables. • Conclusions A wide range of C-values was found in the New Zealand endemic and indigenous grasses. This variation can be related to the phylogenetic position of the genera, plants in the BOP (Bambusoideae, Oryzoideae, Pooideae) clade in general having higher C-values than those in the PACC (Panicoideae, Arundinoideae, Chloridoideae + Centothecoideae) clade. Within genera, polyploids typically have smaller genome sizes (C-value divided by ploidy level) than diploids and there is commonly a progressive decrease with increasing ploidy level. The high frequency of polyploidy in the New Zealand grasses was confirmed by our additional counts, with only approximately 10 % being diploid. No clear relationship between C-value, polyploidy and rarity was evident. PMID:16243852

  15. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation.

    PubMed

    Tishkoff, Sarah A; Gonder, Mary Katherine; Henn, Brenna M; Mortensen, Holly; Knight, Alec; Gignoux, Christopher; Fernandopulle, Neil; Lema, Godfrey; Nyambo, Thomas B; Ramakrishnan, Uma; Reed, Floyd A; Mountain, Joanna L

    2007-10-01

    Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the 2 populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another and are consistent with relatively deep linguistic divergence among the respective click languages.

  16. Application of DNA fingerprinting with digoxigenated oligonucleotide probe (CAC)5 to analysis of the genetic variation within Taenia taeniaeformis.

    PubMed

    Okamoto, M; Ueda, H; Hayashi, M; Oku, Y; Kurosawa, T; Kamiya, M

    1995-04-01

    DNA from T. taeniaeformis digested with the restriction endonuclease was hybridized with digoxigenated oligonucleotide probe (CAC)5. Metacestode and adult showed same clear multibanding patterns, which were characteristic of multilocus DNA fingerprinting. The fingerprinting patterns were quite different from those of the rodent hosts. Genetic variations in 4 laboratory-reared isolates of T. taeniaeformis, including 3 isolates which have been reported to be indistinguishable by infectivity, morphology and protein composition of metacestode, were investigated using this technique. Each of the 4 isolates exhibited isolate-specific fingerprinting patterns and were easily distinguished from one another, thus it was considered that (CAC)5 was a highly resolvable and informative probe for cestodes. However, it was also indicated that (CAC)5 was so sensitive that applying fingerprinting with (CAC)5 to taxonomical or phylogenetic analysis was limited where habitat of the host was restricted to the small area. In comparison to fingerprinting with 32P-labeled (CAC)5, fingerprinting with digoxigenated (CAC)5 represented more and sharper bands. It was considered that a digoxigenated probe was more useful for genetic analysis of cestodes.

  17. Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

    PubMed Central

    van Oven, Mannis; Brauer, Silke; Choi, Ying; Ensing, Joe; Schiefenhövel, Wulf; Stoneking, Mark; Kayser, Manfred

    2014-01-01

    The island region at the southeastern-most tip of New Guinea and its inhabitants known as Massim are well known for a unique traditional inter-island trading system, called Kula or Kula Ring. To characterize the Massim genetically, and to evaluate the influence of the Kula Ring on patterns of human genetic variation, we analyzed paternally inherited Y-chromosome (NRY) and maternally inherited mitochondrial (mt) DNA polymorphisms in >400 individuals from this region. We found that the nearly exclusively Austronesian-speaking Massim people harbor genetic ancestry components of both Asian (AS) and Near Oceanian (NO) origin, with a proportionally larger NO NRY component versus a larger AS mtDNA component. This is similar to previous observations in other Austronesian-speaking populations from Near and Remote Oceania and suggests sex-biased genetic admixture between Asians and Near Oceanians before the occupation of Remote Oceania, in line with the Slow Boat from Asia hypothesis on the expansion of Austronesians into the Pacific. Contrary to linguistic expectations, Rossel Islanders, the only Papuan speakers of the Massim, showed a lower amount of NO genetic ancestry than their Austronesian-speaking Massim neighbors. For the islands traditionally involved in the Kula Ring, a significant correlation between inter-island travelling distances and genetic distances was observed for mtDNA, but not for NRY, suggesting more male- than female-mediated gene flow. As traditionally only males take part in the Kula voyages, this finding may indicate a genetic signature of the Kula Ring, serving as another example of how cultural tradition has shaped human genetic diversity. PMID:24619143

  18. Mitochondrial DNA variation in space and time in the northeastern Pacific gastropod, Littorina keenae.

    PubMed

    Lee, Hyuk Je; Boulding, Elizabeth G

    2007-08-01

    The present population structure of a species reflects the influence of population history as well as contemporary processes. To examine the relative importance of these factors in shaping the current population structure of Littorina keenae, we sequenced 762 base pairs of the mitochondrial ND6 and cytochrome b genes in 584 snails from 13 sites along the northeastern Pacific coast. Haplotype network analysis revealed a 'star-like' genealogy indicative of a recent population expansion. Nested clade and mismatch analyses also supported the hypothesis of sudden population expansion following a population bottleneck during the Last Glacial Maximum. Analysis of molecular variance and pairwise Phi(ST) showed no significant spatial population differentiation from Mexico to Oregon - not even across the recognized biogeographic boundary at Point Conception. This is probably due to high contemporary gene flow during the free-swimming larval stage of this snail. Surprisingly, we found a highly significant temporal population differentiation between a San Pedro sample from 1996 and one from 2005, which gave an estimate of effective population size (N(e)) of only 135. Nearly statistically significant changes in the frequency of a particular haplotype in three other populations over 2-3 years further support Hedgecock's 'sweepstakes' hypothesis. When by chance nearly all of the progeny from an aggregation of highly fecund sisters that possess a rare haplotype successfully recruit to become the next generation, the rare haplotype can become temporarily common across the entire species' range. This modification of the sweepstakes hypothesis can explain why the temporal variation that we observed was much greater than the spatial variation.

  19. Sequence variation of Bemisia tabaci Chemosensory Protein 2 in cryptic species B and Q: New DNA markers for whitefly recognition.

    PubMed

    Liu, Guo-Xia; Ma, Hong-Mei; Xie, Hong-Yan; Xuan, Ning; Picimbon, Jean-François

    2016-01-15

    Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world.

  20. Random amplified polymorphic DNA variation among remnant big bluestem (Andropogon gerardii vitman) populations from Arkansas' grand prairie

    PubMed

    Gustafson; Gibson; Nickrent

    1999-10-01

    Random amplified polymorphic DNA (RAPD) analysis was used to characterize genetic diversity and genetic distinctiveness of Andropogon gerardii from remnant Arkansas prairies. Six oligonucleotide primers, which generated 37 RAPD bands, were used to analyse 30-32 plants from six Grand Prairie populations, Baker Prairie (Arkansas Ozarks), two Illinois prairies and two cultivars. Genetic diversity of the Arkansas remnants ranged from 82.7 to 99.3%, with 89% of the total genetic variation within and 11% among populations. The partitioning of genetic variation was consistent with that reported for other outcrossing perennial grasses, using the more conservative allozyme markers. Principal component analysis indicated a northern and southern association within Arkansas' Grand Prairie. Although there was no genetic structuring at the landscape level, the Illinois prairies and cultivars were different from all Arkansas prairies tested. There was significant within-population structuring in four of the seven Arkansas remnants, with a negative relationship between genetic similarity and geographical distance. The three nonstructured populations were from a linear railroad remnant, suggesting different population-level dynamics from nonlinear prairies. The results of this study indicated that small isolated remnant big bluestem populations were not genetically depauperate and that genetic relationships among populations could not be predicted solely on geographical proximity.

  1. Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray).

    PubMed

    Kooken, Jennifer; Fox, Karen; Fox, Alvin; Altomare, Diego; Creek, Kim; Wunschel, David; Pajares-Merino, Sara; Martínez-Ballesteros, Ilargi; Garaizar, Javier; Oyarzabal, Omar; Samadpour, Mansour

    2014-02-01

    This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.

  2. Phylogeny and chromosomal variations in East Asian Carex, Siderostictae group (Cyperaceae), based on DNA sequences and cytological data.

    PubMed

    Yano, Okihito; Ikeda, Hiroshi; Jin, Xiao-Feng; Hoshino, Takuji

    2014-01-01

    Carex (Cyperaceae) is one of the largest genera of the flowering plants, and comprises more than 2,000 species. In Carex, section Siderostictae with broader leaves distributed in East Asia is thought to be an ancestral group. We aimed to clarify the phylogenetic relationships and chromosomal variations within the section Siderostictae, and to examine the relationship of broad-leaved species of the sections Hemiscaposae and Surculosae from East Asia, inferred from DNA sequences and cytological data. Our results indicate that a monophyletic Siderostictae clade, including the sections Hemiscaposae, Siderostictae and Surculosae, as the earliest diverging group in the tribe Cariceae. Low chromosome numbers, 2n = 12 or 24, with large sizes were observed in these three sections. Our results suggest that the genus Carex might have originated or relictly restricted in the East Asia. Geographical distributions of diploid species are restricted in narrower areas, while those of tetraploid species are wider in East Asia. It is concluded that chromosomal variations in Siderostictae clade may have been caused by polyploidization and that tetraploid species may have been able to exploit their habitats by polyploidization.

  3. DNA Sequence and Expression Variation of Hop (Humulus lupulus) Valerophenone Synthase (VPS), a Key Gene in Bitter Acid Biosynthesis

    PubMed Central

    Castro, Consuelo B.; Whittock, Lucy D.; Whittock, Simon P.; Leggett, Grey; Koutoulis, Anthony

    2008-01-01

    Background The hop plant (Humulus lupulus) is a source of many secondary metabolites, with bitter acids essential in the beer brewing industry and others having potential applications for human health. This study investigated variation in DNA sequence and gene expression of valerophenone synthase (VPS), a key gene in the bitter acid biosynthesis pathway of hop. Methods Sequence variation was studied in 12 varieties, and expression was analysed in four of the 12 varieties in a series across the development of the hop cone. Results Nine single nucleotide polymorphisms (SNPs) were detected in VPS, seven of which were synonymous. The two non-synonymous polymorphisms did not appear to be related to typical bitter acid profiles of the varieties studied. However, real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis of VPS expression during hop cone development showed a clear link with the bitter acid content. The highest levels of VPS expression were observed in two triploid varieties, ‘Symphony’ and ‘Ember’, which typically have high bitter acid levels. Conclusions In all hop varieties studied, VPS expression was lowest in the leaves and an increase in expression was consistently observed during the early stages of cone development. PMID:18519445

  4. Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation.

    PubMed

    Pereira, L; Prata, M J; Amorim, A

    2000-11-01

    The analysis of the hypervariable regions I and II of mitochondrial DNA in Portugal showed that this Iberian population presents a higher level of diversity than some neighbouring populations. The classification of the different sequences into haplogroups revealed the presence of all the most important European haplogroups, including those that expanded through Europe in the Palaeolithic, and those whose expansion has occurred during the Neolithic. Additionally a rather distinct African influence was detected in this Portuguese survey, as signalled by the distributions of haplogroups U6 and L, present at higher frequencies than those usually reported in Iberian populations. The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country. This seems to point to different population movements as the main contributors for the two haplogroup introductions. We hypothesise that the recent Black African slave trade could have been the mediator of most of the L sequence inputs, while the population movement associated with the Muslim rule of Iberia has predominantly introduced U6 lineages.

  5. Genetic variations of Turkish bank vole, Myodes glareolus (Mammalia: Rodentia) inferred from mtDNA.

    PubMed

    Çolak, Reyhan; Olgun Karacan, Gül; Kandemir, Irfan; Çolak, Ercüment; Kankiliç, Teoman; Yigit, Nuri; Michaux, Johan

    2016-11-01

    The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations.

  6. Patterns of Mitochondrial DNA Variation in Indigenous Maize Races of Latin America

    PubMed Central

    Weissinger, A. K.; Timothy, D. H.; Levings, C. S.; Goodman, M. M.

    1983-01-01

    Mitochondrial DNAs (mtDNAs) were isolated from 93 diverse races of maize from Latin America. DNAs were examined by agarose gel electrophoresis of undigested DNA and by BamHI and EcoRI cleavage fragment analysis. Eighteen races contained plasmid-like mtDNAs. One race contained the S-1 and S-2 molecules associated with the S cytoplasmic male-sterile, and 17 were found to have the R-1 and R-2 plasmid-like DNAs. BamHI digestion of mtDNAs generated ten distinct electrophoretograms, and Eco RI digestion produced eight different fragment patterns. Races were assigned to one of 18 groups according to EcoRI and BamHI fragment patterns and whether or not they contained plasmid-like DNAs. Eight races produced restriction patterns similar to one of the characterized cytoplasmic male-steriles C, T, or S. Races from Meso-America and some from South America with Meso-American affinities were separated from other South American races. South American races were placed in three general classes of related groups. There was considerable agreement among the groupings here and those based on morphological and cytological affinities. PMID:17246141

  7. mtDNA variation in East Africa unravels the history of Afro-Asiatic groups.

    PubMed

    Boattini, Alessio; Castrì, Loredana; Sarno, Stefania; Useli, Antonella; Cioffi, Manuela; Sazzini, Marco; Garagnani, Paolo; De Fanti, Sara; Pettener, Davide; Luiselli, Donata

    2013-03-01

    East Africa (EA) has witnessed pivotal steps in the history of human evolution. Due to its high environmental and cultural variability, and to the long-term human presence there, the genetic structure of modern EA populations is one of the most complicated puzzles in human diversity worldwide. Similarly, the widespread Afro-Asiatic (AA) linguistic phylum reaches its highest levels of internal differentiation in EA. To disentangle this complex ethno-linguistic pattern, we studied mtDNA variability in 1,671 individuals (452 of which were newly typed) from 30 EA populations and compared our data with those from 40 populations (2970 individuals) from Central and Northern Africa and the Levant, affiliated to the AA phylum. The genetic structure of the studied populations--explored using spatial Principal Component Analysis and Model-based clustering--turned out to be composed of four clusters, each with different geographic distribution and/or linguistic affiliation, and signaling different population events in the history of the region. One cluster is widespread in Ethiopia, where it is associated with different AA-speaking populations, and shows shared ancestry with Semitic-speaking groups from Yemen and Egypt and AA-Chadic-speaking groups from Central Africa. Two clusters included populations from Southern Ethiopia, Kenya and Tanzania. Despite high and recent gene-flow (Bantu, Nilo-Saharan pastoralists), one of them is associated with a more ancient AA-Cushitic stratum. Most North-African and Levantine populations (AA-Berber, AA-Semitic) were grouped in a fourth and more differentiated cluster. We therefore conclude that EA genetic variability, although heavily influenced by migration processes, conserves traces of more ancient strata.

  8. [Mitochondrial DNA sequence variation, demographic history, and population structure of Amur sturgeon Acipenser schrenckii Brandt, 1869].

    PubMed

    Shedko, S V; Miroshnichenko, I L; Nemkova, G A; Koshelev, V N; Shedko, M B

    2015-02-01

    The variability of the mtDNA control region (D-loop) was examined in Amur sturgeon endemic to the Amur River. This species is also classified as critically endangered by the IUCN Red List of Threatened species. Sequencing of 796- to 812-bp fragments of the D-loop in 112 sturgeon collected in the Lower Amur revealed 73 different genotypes. The sample was characterized by a high level of haplotypic (0.976) and nucleotide (0.0194) diversity. The identified haplotypes split into two well-defined monophyletic groups, BG (n = 39) and SM (n = 34), differing (HKY distance) on average by 3.41% of nucleotide positions upon an average level of intragroup differences of 0.54 and 1.23%, respectively. Moreover, the haplotypes of the SM groups differed by the presence of a 13-14 bp deletion. Most ofthe samples (66 out of 112) carried BG haplotypes. Overall, the pattern of pairwise nucleotide differences and the results of neutrality tests, as well as the results of tests for compliance with the model of sudden demographic expansion or with the model of exponential growth pointed to a past significant increase in the number of Amur sturgeon, which was most clearly manifested in the analysis of data on the BG haplogroup. The constructed Bayesian skyline plots showed that this growth began about 18 to 16 thousand years ago. At present, the effective size of the strongly reduced (due to overharvesting) population of Amur sturgeon may be equal to or even lower than it was before the beginning of this growth during the Last Glacial Maximum. The presence in the mitochondrial gene pool ofAmur sturgeon of two haplogroups, their unequal evolutionary dynamics, and, judging by scanty data, their unequal representation in the Russian and Chinese parts of the Amur River basin point to the possible existence of at least two distinct populations of Amur sturgeon in the past.

  9. Temporal analysis of mtDNA variation reveals decreased genetic diversity in least terns

    USGS Publications Warehouse

    Draheim, Hope M.; Baird, Patricia; Haig, Susan M.

    2012-01-01

    The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics.

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

    PubMed

    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.

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

    PubMed

    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.

  12. DNA sequence variation in BpMADS2 gene in two populations of Betula pendula.

    PubMed

    Järvinen, Pia; Lemmetyinen, Juha; Savolainen, Outi; Sopanen, Tuomas

    2003-02-01

    The PISTILLATA (PI) homologue, BpMADS2, was isolated from silver birch (Betula pendula Roth) and used to study nucleotide polymorphism. Two regions (together about 2450 bp) comprising mainly untranslated sequences were sequenced from 10 individuals from each of two populations in Finland. The nucleotide polymorphism was low in the BpMADS2 locus, especially in the coding region. The synonymous site overall nucleotide diversity (pis) was 0.0043 and the nonsynonymous nucleotide diversity (pia) was only 0.000052. For the whole region, the pi values for the two populations were 0.0039 and 0.0045, and for the coding regions, the pi values were only 0 and 0.00066 (for the corresponding coding regions of Arabidopsis thaliana PI world-wide pi was 0.0021). Estimates of pi or theta did not differ significantly between the two populations, and the two populations were not diverged from each other. Two classes of BpMADS2 alleles were present in both populations, suggesting that this gene exhibits allelic dimorphism. In addition to the nucleotide site variation, two microsatellites were also associated within the haplotypes. This allelic dimorphism might be the result of postglacial re-colonization partly from northwestern, partly from southeastern/eastern refugia. The sequence comparison detected five recombination events in the regions studied. The large number of microsatellites in all of the three introns studied suggests that BpMADS2 is a hotspot for microsatellite formation.

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

    PubMed

    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.

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

    PubMed Central

    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

  15. GENETIC VARIATION IN RED RASPBERRIES (RUBUS IDAEUS L.; ROSACEAE) FROM SITES DIFFERING IN ORGANIC POLLUTANTS COMPARED WITH SYNTHETIC TANDEM REPEAT DNA PROBES

    EPA Science Inventory

    Two synthetic tandem repetitive DNA probes were used to compare genetic variation at variable-number-tandem-repeat (VNTR) loci among Rubus idaeus L. var. strigosus (Michx.) Maxim. (Rosaceae) individuals sampled at eight sites contaminated by pollutants (N = 39) and eight adjacent...

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

    PubMed Central

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

    2012-01-01

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

    PubMed

    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.

  18. 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

    USGS Publications Warehouse

    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.

  19. DNA

    ERIC Educational Resources Information Center

    Stent, Gunther S.

    1970-01-01

    This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)

  20. Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.

    PubMed

    Du, Xiangjun; Gertz, E Michael; Wojtowicz, Damian; Zhabinskaya, Dina; Levens, David; Benham, Craig J; Schäffer, Alejandro A; Przytycka, Teresa M

    2014-11-10

    While individual non-B DNA structures have been shown to impact gene expression, their broad regulatory role remains elusive. We utilized genomic variants and expression quantitative trait loci (eQTL) data to analyze genome-wide variation propensities of potential non-B DNA regions and their relation to gene expression. Independent of genomic location, these regions were enriched in nucleotide variants. Our results are consistent with previously observed mutagenic properties of these regions and counter a previous study concluding that G-quadruplex regions have a reduced frequency of variants. While such mutagenicity might undermine functionality of these elements, we identified in potential non-B DNA regions a signature of negative selection. Yet, we found a depletion of eQTL-associated variants in potential non-B DNA regions, opposite to what might be expected from their proposed regulatory role. However, we also observed that genes downstream of potential non-B DNA regions showed higher expression variation between individuals. This coupling between mutagenicity and tolerance for expression variability of downstream genes may be a result of evolutionary adaptation, which allows reconciling mutagenicity of non-B DNA structures with their location in functionally important regions and their potential regulatory role.

  1. Development of novel microsatellite DNA markers by cross-amplification and analysis of genetic variation in gerbils.

    PubMed

    Du, Xiaoyan; Chen, Zhenwen; Li, Wei; Tan, Yuanqing; Lu, Jing; Zhu, Xiangdong; Zhao, Taiyun; Dong, Gang; Zeng, Lin

    2010-01-01

    The objectives of this study are to establish microsatellite loci for the Mongolian gerbil based on mouse microsatellite DNA sequences and to investigate genetic variation in the laboratory gerbil (Capital Medical University, CMU) and 2 wild gerbil populations (from Yin Chuan city [YIN] and the Hohehot Municipality [HOH]). In total, 536 mouse microsatellite markers were chosen to identify polymorphic dinucleotide repeat loci in the gerbil by cross-amplification. Of these markers, 313 (58.39%) have been discretely amplified from the CMU laboratory gerbil and been sequenced. Of the 313 sequenced markers, 130 were confirmed as simple sequence repeat (SSR) loci in the gerbil. In total, 6 of those newly identified loci plus 6 identified in previous reports were used to estimate the genetic polymorphism for 30 laboratory gerbils and 54 wild gerbils (27 each of the HOH and YIN groups). A total of 29 alleles were observed in the 3 populations, and 11 of 12 loci (91.67%) are polymorphic markers. Nei's standard genetic distances of 0.0592 (CMU vs. HOH) and 0.1033 (CMU vs. YIN) were observed. The averages of observed versus expected heterozygosity are 0.5231/0.4008, 0.5051/0.3882, and 0.4825/0.3665 for the YIN, HOH, and CMU populations, respectively. These results show that cross-amplification using mouse microsatellite primers is an efficient way to identify gerbil SSR loci. By using these 12 selected markers, we have demonstrated that genetic variation level within the CMU population is higher than that has been reported previously and are comparable with the levels found in 2 wild populations.

  2. Phylogeography of Aedes (Stegomyia) aegypti (L.) and Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) based on mitochondrial DNA variations.

    PubMed

    Mousson, Laurence; Dauga, Catherine; Garrigues, Thomas; Schaffner, Francis; Vazeille, Marie; Failloux, Anna-Bella

    2005-08-01

    Aedes (Stegomyia) aegypti (l.) and Aedes (Stegomyia) albopictus (Skuse) are the most important vectors of the dengue and yellow-fever viruses. Both took advantage of trade developments to spread throughout the tropics from their native area: A. aegypti originated from Africa and a. albopictus from South-East Asia. We investigated the relationships between A. aegypti and A. albopictus mosquitoes based on three mitochondrial-DNA genes (cytochrome b, cytochrome oxidase I and NADH dehydrogenase subunit 5). Little genetic variation was observed for a. albopictus, probably owing to the recent spreading of the species via human activities. For A. aegypti, most populations from South America were found to be genetically similar to populations from South-East Asia (Thailand and Vietnam), except for one sample from Boa Vista (northern Amazonia), which was more closely related to samples from Africa (Guinea and Ivory Coast). This suggests that African populations of A. aegypti introduced during the slave trade have persisted in Boa Vista, resisting eradication campaigns.

  3. Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians.

    PubMed

    Dulik, Matthew C; Zhadanov, Sergey I; Osipova, Ludmila P; Askapuli, Ayken; Gau, Lydia; Gokcumen, Omer; Rubinstein, Samara; Schurr, Theodore G

    2012-02-10

    The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.

  4. Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians

    PubMed Central

    Dulik, Matthew C.; Zhadanov, Sergey I.; Osipova, Ludmila P.; Askapuli, Ayken; Gau, Lydia; Gokcumen, Omer; Rubinstein, Samara; Schurr, Theodore G.

    2012-01-01

    The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas. PMID:22281367

  5. mtDNA variation indicates Mongolia may have been the source for the founding population for the New World.

    PubMed Central

    Merriwether, D. A.; Hall, W. W.; Vahlne, A.; Ferrell, R. E.

    1996-01-01

    mtDNA RFLP variation was analyzed in 42 Mongolians from Ulan Bator. All four founding lineage types (A [4.76%], B [2.38%], C [11.9%], and D [19.04%]) identified by Torroni and colleagues were detected. Seven of the nine founding lineage types proposed by Bailliet and colleagues and Merriwether and Ferrell were detected (A2 [4.76%], B [2.38%], C1 [11.9%], D1 [7.14%], D2 [11.9%], X6 [16.7%], and X7 [9.5%]). Sixty-four percent of these 42 individuals had "Amerindian founding lineage" haplotypes. A survey of 24 restriction sites yielded 16 polymorphic sites and 21 different haplotypes. The presence of all four of the founding lineages identified by the Torroni group (and seven of Merriwether and Ferrell's nine founding lineages), combined with Mongolia's location with respect to the Bering Strait, indicates that Mongolia is a potential location for the origin of the founders of the New World. Since lineage B, which is widely distributed in the New World, is absent in Siberia, we conclude that Mongolia or a geographic location common to both contemporary Mongolians and American aboriginals is the more likely origin of the founders of the New World. PMID:8659526

  6. Phylogeography and regional endemism of a passively dispersing zooplankter: mitochondrial DNA variation in rotifer resting egg banks.

    PubMed

    Gómez, A; Carvalho, G R; Lunt, D H

    2000-11-07

    We investigated the phylogeography of the salt water rotifer Brachionus plicatilis, a cyclical parthenogen with passive dispersal mechanisms, using resting eggs recovered from saline lake sediments. Individual resting eggs were obtained from a large selection of lakes which were representative of five endorheic basins and the chain of coastal ponds in the Iberian Peninsula. The novel use of resting eggs allows the integration of seasonal and annual variations as well as the impact of stochastic effects such as drift and local extinction. A 653 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced from 98 eggs. Our results revealed a deep phylogeographical structure in this species, with a division into two main lineages with distinct geographical distributions, which probably diverged at the beginning of the Pleistocene period. Most of the mitochondrial DNA haplotypes were restricted to single lakes. Nested clade analysis supported Early Pleistocene fragmentation of populations, low gene flow and some long-distance colonization. These conclusions contrast strongly with previous ideas on rotifer biogeography and this pattern is consistent with a recolonization of the Iberian Peninsula from two glacial refugia. The results provide new insights into the processes responsible for the genetic diversification of passive dispersers, a life-history trait typical of zooplanktonic biotas.

  7. Large variation in mitochondrial DNA of sexual and parthenogenetic Dahlica triquetrella (Lepidoptera: Psychidae) shows multiple origins of parthenogenesis

    PubMed Central

    2013-01-01

    Background Obligate parthenogenesis is relatively rare in animals. Still, in some groups it is quite common and has evolved and persisted multiple times. These groups may provide important clues to help solve the ‘paradox of sex’. Several species in the Psychidae (Lepidoptera) have obligate parthenogenesis. Dahlica triquetrella is one of those species where multiple transitions to parthenogenesis are postulated based on intensive cytological and behavioural studies. This has led to the hypothesis that multiple transitions from sexuals to diploid parthenogens occurred during and after the last glacial period, followed by transitions from parthenogenetic diploids to parthenogenetic tetraploids. Our study is the first to test these hypotheses using a molecular phylogeny based on mtDNA from multiple sexual and parthenogenetic populations from a wide geographic range. Results Parthenogenetic (and sexual) D. triquetrella are not monophyletic, and considerable sequence variation is present suggesting multiple transitions to parthenogenesis. However, we could not establish ancestral sexual haplotypes from our dataset. Our data suggest that some parthenogenetic clades have evolved, indicating origins of parthenogenesis before the last glacial period. Conclusions Multiple transitions to parthenogenesis have taken place in Dahlica triquetrella, confirming previous hypotheses. The number of different parthenogenetic clades, haplotypes and their apparent evolutionary age, clearly show that parthenogenesis has been a very successful reproductive strategy in this species over a long period. PMID:23622052

  8. Organization and variation analysis of 5S rDNA in different ploidy-level hybrids of red crucian carp × topmouth culter.

    PubMed

    He, Weiguo; Qin, Qinbo; Liu, Shaojun; Li, Tangluo; Wang, Jing; Xiao, Jun; Xie, Lihua; Zhang, Chun; Liu, Yun

    2012-01-01

    Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.

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

    PubMed Central

    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.

    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 xenobiotic metabolism and 12 SNPs in 8 DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by 32P-postlabelling. Multivariable regression models were compared by Akaike’s information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 108 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<0.001). Compared with the environmental model, adding phase I SNPs and NER capacity provided the best fit, and could explain 17% more of the variation in adduct levels. NER capacity was affected by polymorphisms in the MTHFR and ERCC1 genes. Female non-smokers in this population had PAH-related DNA adduct levels 3-4 times higher than smokers and occupationally-exposed groups in previous studies, with large inter-individual variation which could best be explained by a combination of phase I genes and NER capacity. PMID:23175176

  10. The effects of mitochondrial DNA deletion and copy number variations on different exercise intensities in highly trained swimmers.

    PubMed

    Baykara, O; Sahin, S K; Akbas, F; Guven, M; Onaran, I

    2016-10-31

    It has been suggested that heavy exercise might increase oxidative stress, causing mitochondrial DNA (mtDNA) mutations as well as DNA mutations and changes in the mtDNA copy number in cells. mtDNA4977 deletion is one of the most common deletions seen on mitochondria. We hypothesize association between exercise induced oxidative stress and mtDNA damage in peripheral blood lymphocytes (PBLs) of highly trained swimmers. Therefore we studied the mtDNA4977 deletion level, mtDNA copy number and their relationship with cellular ATP and oxidative stress status in PBLs of swimmers. 8 highly trained and 8 normal trained swimmers and 8 non-athlete subjects were included in the study. The mtDNA4977 deletion and amount of mtDNA were measured using RT-PCR method whereas dichlorohydrofluoroscein (DCF) assay method was used to assess cellular oxidative stress and ATP levels were measured using bioluminescence method. Even though an increase in mtDNA4977 deletion was found in all study groups, the difference was not statistically significant (p=0.98). The mtDNA copy numbers were found to be surprisingly high in highly trained swimmers compared to normal trained swimmers and non-athlete subjects by 4.03 fold (p= 0.0002) and 5.58 fold (p=0.0003), respectively. No significant differences were found between groups by means of intracellular ATP levels (p=0.406) and oxidative stress (p=0.430).  No correlation was found between mtDNA copy number and intracellular ATP content of the PBLs (p=0.703). Our results suggest that heavy training does not have a specific effect on mtDNA4977 deletion but it may be affecting mitochondrial copy numbers which may act as a compensatory mechanism related to ATP levels in blood.

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

    PubMed Central

    Ding, Jun; Sidore, Carlo; Butler, Thomas J.; Wing, Mary Kate; Qian, Yong; Meirelles, Osorio; Busonero, Fabio; Tsoi, Lam C.; Maschio, Andrea; Angius, Andrea; Kang, Hyun Min; Nagaraja, Ramaiah; Cucca, Francesco; Abecasis, Gonçalo R.; Schlessinger, David

    2015-01-01

    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. PMID:26172475

  12. Sequence variation of the ribosomal DNA second internal transcribed spacer region in two spatially-distinct populations of Amblyomma americanum (L.) (Acari: Ixodidae).

    PubMed

    Reichard, M V; Kocan, A A; Van Den Bussche, R A; Barker, R W; Wyckoff, J H; Ewing, S A

    2005-04-01

    Sequence analysis of the ribosomal DNA second internal transcribed spacer (ITS 2) region in 2 spatially distinct populations of Amblyomma americanum (L.) revealed intraspecific variation. Nucleotide sequences from multiple DNA extractions and several polymerase chain reaction amplifications of eggs from mixed-parentage samples from both populations of ticks revealed that 12 of 1,145 (1.0%) sites varied. Three of the 12 sites of variation were distinct between the 2 A. americanum populations, which corresponded to a rate of 0.26%. Phylogenetic analysis based on ITS 2 sequences provided strong support (i.e., bootstrap value of 80%) that wild A. americanum clustered into a distinguishable group separate from those derived from colony ticks.

  13. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries

    PubMed Central

    An, Yang; Toyoda, Atsushi; Zhao, Chen; Fujiyama, Asao; Agata, Kiyokazu

    2015-01-01

    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. PMID:25646755

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

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

    Abstract 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. PMID:27007897

  16. Intraspecific variation and population structure of the German cockroach, Blattella germanica, revealed with RFLP analysis of the non-transcribed spacer region of ribosomal DNA.

    PubMed

    Mukha, D V; Kagramanova, A S; Lazebnaya, I V; Lazebnyi, O E; Vargo, E L; Schal, C

    2007-06-01

    Little information is available on genetic variation within and between populations of pest cockroaches. In this study, intraspecific HindIII polymorphism was investigated in the German cockroach, Blattella germanica (Linnaeus) (Dictyoptera, Blattaria: Blattellidae), using restriction fragment length polymorphisms (RFLP) of the non-transcribed spacer (NTS) region of ribosomal DNA (rDNA). Individual male insects were collected from infestations at three different pig farms. Each population was characterized by HindIII restriction fragment frequencies and haplotype (a particular X-chromosome pattern) frequencies. The inheritance of the X-chromosome HindIII rDNA patterns over 12 generations (3 years) follows Mendelian patterns, and the stability of this polymorphic marker indicates infrequent genetic recombination of variable sites. Although pairwise genetic distance measures were uncorrelated with geographical distance, the pattern of genetic differentiation of the three cockroach populations suggests that human-mediated transport of cockroaches is an important force in shaping the population genetic structure of cockroach infestations, at least at the regional scale of 10-100 km. Sequence variation in the ribosomal NTS is a useful marker, and RFLP of rDNA is a simple, robust and reproducible technique for differentiating recently diverged cockroach populations.

  17. Congruence of Microsatellite and Mitochondrial DNA Variation in Acrobat Ants (Crematogaster Subgenus Decacrema, Formicidae: Myrmicinae) Inhabiting Macaranga (Euphorbiaceae) Myrmecophytes

    PubMed Central

    Ueda, Shouhei; Nagano, Yusuke; Kataoka, Yowsuke; Komatsu, Takashi; Itioka, Takao; Shimizu-kaya, Usun; Inui, Yoko; Itino, Takao

    2015-01-01

    A previously reported mitochondrial DNA (mtDNA) phylogeny of Crematogaster (subgenus Decacrema) ants inhabiting Macaranga myrmecophytes indicated that the partners diversified synchronously and their specific association has been maintained for 20 million years. However, the mtDNA clades did not exactly match morphological species, probably owing to introgressive hybridization among younger species. In this study, we determined the congruence between nuclear simple sequence repeat (SSR, also called microsatellite) genotyping and mtDNA phylogeny to confirm the suitability of the mtDNA phylogeny for inferring the evolutionary history of Decacrema ants. Analyses of ant samples from Lambir Hills National park, northeastern Borneo, showed overall congruence between the SSR and mtDNA groupings, indicating that mtDNA markers are useful for delimiting species, at least at the local level. We also found overall high host-plant specificity of the SSR genotypes of Decacrema ants, consistent with the specificity based on the mtDNA phylogeny. Further, we detected cryptic genetic assemblages exhibiting high specificity toward particular plant species within a single mtDNA clade. This finding, which may be evidence for rapid ecological and genetic differentiation following a host shift, is a new insight into the previously suggested long-term codiversification of Decacrema ants and Macaranga plants. PMID:25692953

  18. Congruence of microsatellite and mitochondrial DNA variation in acrobat ants (Crematogaster subgenus Decacrema, Formicidae: Myrmicinae) inhabiting Macaranga (Euphorbiaceae) myrmecophytes.

    PubMed

    Ueda, Shouhei; Nagano, Yusuke; Kataoka, Yowsuke; Komatsu, Takashi; Itioka, Takao; Shimizu-Kaya, Usun; Inui, Yoko; Itino, Takao

    2015-01-01

    A previously reported mitochondrial DNA (mtDNA) phylogeny of Crematogaster (subgenus Decacrema) ants inhabiting Macaranga myrmecophytes indicated that the partners diversified synchronously and their specific association has been maintained for 20 million years. However, the mtDNA clades did not exactly match morphological species, probably owing to introgressive hybridization among younger species. In this study, we determined the congruence between nuclear simple sequence repeat (SSR, also called microsatellite) genotyping and mtDNA phylogeny to confirm the suitability of the mtDNA phylogeny for inferring the evolutionary history of Decacrema ants. Analyses of ant samples from Lambir Hills National park, northeastern Borneo, showed overall congruence between the SSR and mtDNA groupings, indicating that mtDNA markers are useful for delimiting species, at least at the local level. We also found overall high host-plant specificity of the SSR genotypes of Decacrema ants, consistent with the specificity based on the mtDNA phylogeny. Further, we detected cryptic genetic assemblages exhibiting high specificity toward particular plant species within a single mtDNA clade. This finding, which may be evidence for rapid ecological and genetic differentiation following a host shift, is a new insight into the previously suggested long-term codiversification of Decacrema ants and Macaranga plants.

  19. In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

    PubMed Central

    Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J.; Leitch, Ilia J.

    2015-01-01

    The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55–83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes. PMID:26606051

  20. The use of random amplified polymorphic DNA (RAPD) analysis for studies of genetic variation in populations of Coccinella septempunctata in Belgium.

    PubMed

    Haubruge, Eric; Vanlerberghe-Masutti, Flavie; Collignon, Pierre; Francis, Frédéric

    2002-01-01

    The movement and dispersion of Coccinella septempunctata and its efficacy as aphid control agent over large areas is not really understood because of the difficulty in identifying the origins of predators. To quantify the genetic diversity within the species and monitor the spatial foraging, populations were sampled from Belgium and analysed for RAPD DNA variation. Twenty decamer primers generated more than hundred polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei and Li, then used to construct a radial neighbour-joining dendrogram and examine intra- and inter-population variance coefficients, by analysis of molecular variation (AMOVA). This study shows that while a number of factors can complicate the use and interpretation of RAPD fragments as genetic markers, RAPD analysis can be a valuable technique for studies of intra-specific genetic variation in C. septempunctata.

  1. Spatiotemporal variations in metal accumulation, RNA/DNA ratio and energy reserve in Perna viridis transplanted along a marine pollution gradient in Hong Kong.

    PubMed

    Yeung, Jamius W Y; Zhou, Guang-Jie; Leung, Kenneth M Y

    2017-01-21

    We examined spatiotemporal variations of metal levels and three growth related biomarkers, i.e., RNA/DNA ratio (RD), total energy reserve (Et) and condition index (CI), in green-lipped mussels Perna viridis transplanted into five locations along a pollution gradient in the marine environment of Hong Kong over 120days of deployment. There were significant differences in metal levels and biomarker responses among the five sites and six time points. Mussels in two clean sites displayed better CI and significantly lower levels of Ag, Cu, Pb and Zn in their tissues than the other sites. Temporal patterns of RD in P. viridis were found to be site-specific. Across all sites, Et decreased in P. viridis over the deployment period, though the rate of decrease varied significantly among the sites. Therefore, temporal variation of biomarkers should be taken to consideration in mussel-watch programs because such information can help discriminate pollution-induced change from natural variation.

  2. Identification of mitochondrial DNA sequence variation and development of single nucleotide polymorphic markers for CMS-D8 in cotton.

    PubMed

    Suzuki, Hideaki; Yu, Jiwen; Wang, Fei; Zhang, Jinfa

    2013-06-01

    Cytoplasmic male sterility (CMS), which is a maternally inherited trait and controlled by novel chimeric genes in the mitochondrial genome, plays a pivotal role in the production of hybrid seed. In cotton, no PCR-based marker has been developed to discriminate CMS-D8 (from Gossypium trilobum) from its normal Upland cotton (AD1, Gossypium hirsutum) cytoplasm. The objective of the current study was to develop PCR-based single nucleotide polymorphic (SNP) markers from mitochondrial genes for the CMS-D8 cytoplasm. DNA sequence variation in mitochondrial genes involved in the oxidative phosphorylation chain including ATP synthase subunit 1, 4, 6, 8 and 9, and cytochrome c oxidase 1, 2 and 3 subunits were identified by comparing CMS-D8, its isogenic maintainer and restorer lines on the same nuclear genetic background. An allelic specific PCR (AS-PCR) was utilized for SNP typing by incorporating artificial mismatched nucleotides into the third or fourth base from the 3' terminus in both the specific and nonspecific primers. The result indicated that the method modifying allele-specific primers was successful in obtaining eight SNP markers out of eight SNPs using eight primer pairs to discriminate two alleles between AD1 and CMS-D8 cytoplasms. Two of the SNPs for atp1 and cox1 could also be used in combination to discriminate between CMS-D8 and CMS-D2 cytoplasms. Additionally, a PCR-based marker from a nine nucleotide insertion-deletion (InDel) sequence (AATTGTTTT) at the 59-67 bp positions from the start codon of atp6, which is present in the CMS and restorer lines with the D8 cytoplasm but absent in the maintainer line with the AD1 cytoplasm, was also developed. A SNP marker for two nucleotide substitutions (AA in AD1 cytoplasm to CT in CMS-D8 cytoplasm) in the intron (1,506 bp) of cox2 gene was also developed. These PCR-based SNP markers should be useful in discriminating CMS-D8 and AD1 cytoplasms, or those with CMS-D2 cytoplasm as a rapid, simple, inexpensive, and

  3. Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

    PubMed Central

    Grundberg, Elin; Meduri, Eshwar; Sandling, Johanna K.; Hedman, Åsa K.; Keildson, Sarah; Buil, Alfonso; Busche, Stephan; Yuan, Wei; Nisbet, James; Sekowska, Magdalena; Wilk, Alicja; Barrett, Amy; Small, Kerrin S.; Ge, Bing; Caron, Maxime; Shin, So-Youn; Ahmadi, Kourosh R.; Ainali, Chrysanthi; Barrett, Amy; Bataille, Veronique; Bell, Jordana T.; Buil, Alfonso; Deloukas, Panos; Dermitzakis, Emmanouil T.; Dimas, Antigone S.; Durbin, Richard; Glass, Daniel; Grundberg, Elin; Hassanali, Neelam; Hedman, Åsa K.; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lindgren, Cecilia M.; Lowe, Christopher E.; McCarthy, Mark I.; Meduri, Eshwar; di Meglio, Paola; Min, Josine L.; Montgomery, Stephen B.; Nestle, Frank O.; Nica, Alexandra C.; Nisbet, James; O’Rahilly, Stephen; Parts, Leopold; Potter, Simon; Sandling, Johanna; Sekowska, Magdalena; Shin, So-Youn; Small, Kerrin S.; Soranzo, Nicole; Spector, Tim D.; Surdulescu, Gabriela; Travers, Mary E.; Tsaprouni, Loukia; Tsoka, Sophia; Wilk, Alicja; Yang, Tsun-Po; Zondervan, Krina T.; Lathrop, Mark; Dermitzakis, Emmanouil T.; McCarthy, Mark I.; Spector, Timothy D.; Bell, Jordana T.; Deloukas, Panos

    2013-01-01

    Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h2median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner. PMID:24183450

  4. RNA/DNA ratios in American glass eels (Anguilla rostrata): evidence for latitudinal variation in physiological status and constraints to oceanic migration?

    PubMed Central

    Laflamme, Simon; Côté, Caroline; Gagnaire, Pierre-Alexandre; Castonguay, Martin; Bernatchez, Louis

    2012-01-01

    During their larval leptocephalus phase, newly hatched American eels undergo an extensive oceanic migration from the Sargasso Sea toward coastal and freshwater habitats. Their subsequent metamorphosis into glass eel is accompanied by drastic morphological and physiological changes preceding settlement over a wide geographic range. The main objective of this study was to compare RNA/DNA ratios and condition factor among glass eels in order to test the null hypothesis of no difference in physiological status and metabolic activity of glass eels at the outcome of their oceanic migration. This was achieved by analyzing glass eel samples collected at the mouth of 17 tributaries covering a latitudinal gradient across the species distribution range from Florida to Gaspésie (Québec). Our main observations were (i) a latitudinal increase in mean total length; (ii) a latitudinal variation in mean RNA/DNA ratios, which was best explained by a quadratic model reaching its minimum in the central range of sampling locations; and (iii) a latitudinal variation in Fulton's condition factor, which was best explained by a quadratic model reaching its maximum in the central range of sampling locations. Below we discuss the possible links between latitudinal variation in glass eel physiological status and variable energetic and environmental constraints to oceanic migration as a function of latitudinal distribution. PMID:22837833

  5. Genetic variations of CYP2B6 gene were associated with plasma BPDE-Alb adducts and DNA damage levels in coke oven workers.

    PubMed

    Huang, Guoxiang; Guo, Huan; Wu, Tangchun

    2012-06-20

    Polycyclic aromatic hydrocarbons (PAHs), the main components of coke oven emissions, can induce activation of cytochrome P450 (CYP) enzymes, which metabolize PAHs and result in DNA damage by forming adducts. This study was designed to know whether genetic variants of CYP genes are associated with plasma benzo[a]pyrene-7,8-diol-9,10-epoxide-albumin (BPDE-Alb) adducts and DNA damage in coke oven workers. In this study, 298 workers were divided into four groups according to the environmental PAHs exposure levels. The concentrations of plasma BPDE-Alb adducts were detected by reverse-phase high-performance liquid chromatography and the DNA damage levels were measured using comet assay. Twelve tag single nucleotide polymorphisms (tagSNPs) of 4 CYP genes were selected and genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In the top group, workers with CYP2B6 rs3760657GA genotype have lower BPDE-Alb adducts and DNA damage levels than those with rs3760657GG genotype (P<0.05). In the control group, the DNA damage levels of subjects with CYP1A1 rs4646421AA or GA+AA genotypes were lower than those with GG genotype (P<0.05). However, no such effects were shown for the other tagSNPs. These results suggested that genetic variations of CYP2B6 might be associated with low BPDE-Alb adducts and DNA damage levels in worker with high exposure to PAHs.

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

    PubMed

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

    2013-09-01

    A number of α,β-unsaturated aldehydes are present in food both as natural constituents and as flavouring agents. Their reaction with DNA due to their electrophilic α,β-unsaturated aldehyde moiety may result in genotoxicity as observed in some in vitro models, thereby raising a safety concern. A question that remains is whether in vivo detoxification would be efficient enough to prevent DNA adduct formation and genotoxicity. In this study, a human physiologically based kinetic/dynamic (PBK/D) model of trans-2-hexenal (2-hexenal), a selected model α,β-unsaturated aldehyde, was developed to examine dose-dependent detoxification and DNA adduct formation in humans upon dietary exposure. The kinetic model parameters for detoxification were quantified using relevant pooled human tissue fractions as well as tissue fractions from 11 different individual subjects. In addition, a Monte Carlo simulation was performed so that the impact of interindividual variation in 2-hexenal detoxification on the DNA adduct formation in the population as a whole could be examined. The PBK/D model revealed that DNA adduct formation due to 2-hexenal exposure was 0.039 adducts/10⁸ nucleotides (nt) at the estimated average 2-hexenal dietary intake (0.04 mg 2-hexenal/kg bw) and 0.18 adducts/10⁸ nt at the 95th percentile of the dietary intake (0.178 mg 2-hexenal/kg bw) in the most sensitive people. These levels are three orders of magnitude lower than natural background DNA adduct levels that have been reported in disease-free humans (6.8-110 adducts/10⁸ nt), suggesting that the genotoxicity risk for the human population at realistic dietary daily intakes of 2-hexenal may be negligible.

  7. Genetic variation in DNMT3B and increased global DNA methylation is associated with suicide attempts in psychiatric patients.

    PubMed

    Murphy, T M; Mullins, N; Ryan, M; Foster, T; Kelly, C; McClelland, R; O'Grady, J; Corcoran, E; Brady, J; Reilly, M; Jeffers, A; Brown, K; Maher, A; Bannan, N; Casement, A; Lynch, D; Bolger, S; Buckley, A; Quinlivan, L; Daly, L; Kelleher, C; Malone, K M

    2013-02-01

    Recently, a significant epigenetic component in the pathology of suicide has been realized. Here we investigate candidate functional SNPs in epigenetic-regulatory genes, DNMT1 and DNMT3B, for association with suicide attempt (SA) among patients with co-existing psychiatric illness. In addition, global DNA methylation levels [5-methyl cytosine (5-mC%)] between SA and psychiatric controls were quantified using the Methylflash Methylated DNA Quantification Kit. DNA was obtained from blood of 79 suicide attempters and 80 non-attempters, assessed for DSM-IV Axis I disorders. Functional SNPs were selected for each gene (DNMT1; n = 7, DNMT3B; n = 10), and genotyped. A SNP (rs2424932) residing in the 3' UTR of the DNMT3B gene was associated with SA compared with a non-attempter control group (P = 0.001; Chi-squared test, Bonferroni adjusted P value = 0.02). Moreover, haplotype analysis identified a DNMT3B haplotype which differed between cases and controls, however this association did not hold after Bonferroni correction (P = 0.01, Bonferroni adjusted P value = 0.56). Global methylation analysis showed that psychiatric patients with a history of SA had significantly higher levels of global DNA methylation compared with controls (P = 0.018, Student's t-test). In conclusion, this is the first report investigating polymorphisms in DNMT genes and global DNA methylation quantification in SA risk. Preliminary findings suggest that allelic variability in DNMT3B may be relevant to the underlying diathesis for suicidal acts and our findings support the hypothesis that aberrant DNA methylation profiles may contribute to the biology of suicidal acts. Thus, analysis of global DNA hypermethylation in blood may represent a biomarker for increased SA risk in psychiatric patients.

  8. Paramecium putrinum (Ciliophora, Protozoa): the first insight into the variation of two DNA fragments - molecular support for the existence of cryptic species.

    PubMed

    Tarcz, Sebastian; Rautian, Maria; Potekhin, Alexey; Sawka, Natalia; Beliavskaya, Alexandra; Kiselev, Andrey; Nekrasova, Irina; Przyboś, Ewa

    2014-04-01

    Paramecium putrinum (Claparede & Lachmann 1858) is one of the smallest (80-140 μm long) species of the genus Paramecium. Although it commonly occurs in freshwater reservoirs, no molecular studies of P. putrinum have been conducted to date. Herein we present an assessment of molecular variation in 27 strains collected from widely separated populations by using two selected DNA fragments (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA). Both the trees and haplotype networks reconstructed for both genome fragments show that the studied strains of P. putrinum form five main haplogroups. The mean distance between the studied strains is p-distance=0.007/0.068 (rDNA/COI) and exhibits similar variability as that between P. bursaria syngens. Based on these data, one could hypothesize that the clusters revealed in the present study may correspond to previously reported syngens and that there are at least five cryptic species within P. putrinum.

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

    PubMed Central

    AL-Huqail, Asma A.; Abdelhaliem, Ekram

    2015-01-01

    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. PMID:26180815

  10. Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings

    PubMed Central

    Gao, Guizhen; Li, Jun; Li, Hao; Li, Feng; Xu, Kun; Yan, Guixin; Chen, Biyun; Qiao, Jiangwei; Wu, Xiaoming

    2014-01-01

    DNA methylation is responsive to various biotic and abiotic stresses. Heat stress is a serious threat to crop growth and development worldwide. Heat stress results in an array of morphological, physiological and biochemical changes in plants. The relationship between DNA methylation and heat stress in crops is relatively unknown. We investigated the differences in methylation levels and changes in the cytosine methylation patterns in seedlings of two rapeseed genotypes (heat-sensitive and heat-tolerant) under heat stress. Our results revealed that the methylation levels were different between a heat-tolerant genotype and a heat-sensitive one under control conditions. Under heat treatment, methylation increased more in the heat-sensitive genotype than in the heat-tolerant genotype. More DNA demethylation events occurred in the heat-tolerant genotype, while more DNA methylation occurred in the heat-sensitive genotype. A large and diverse set of genes were affected by heat stress via cytosine methylation changes, suggesting that these genes likely play important roles in the response and adaption to heat stress in Brassica napus L. This study indicated that the changes in DNA methylation differed between heat-tolerant and heat-sensitive genotypes of B. napus in response to heat stress, which further illuminates the molecular mechanisms of the adaption to heat stress in B. napus. PMID:24987298

  11. High sensitivity of the single-strand conformation polymorphism method for detecting sequence variations in the low-density lipoprotein receptor gene validated by DNA sequencing.

    PubMed

    Jensen, H K; Jensen, L G; Hansen, P S; Faergeman, O; Gregersen, N

    1996-08-01

    We designed oligonucleotide primer pairs to amplify the promoter region, the translated exon sequences, and the flanking intron sequences of all 18 exons of the LDL receptor gene to compare the ability of the PCR single-strand conformation polymorphism (PCR-SSCP) method with semiautomated solid-phase genomic DNA sequencing to detect sequence variations. In 20 apparently unrelated Danish patients with a clinical diagnosis of heterozygous familial hypercholesterolemia (FH), we identified 13 different mutations in the LDL receptor gene: two silent (C331C, N494 N); five missense (W66G, E119K, T383P, W556S, T7051); one nonsense (W23X); three splice-site (313 + 1G-->A, 1061-8T-->C, 1846-1G-->A); and two frameshift (335del10, 1650delG) mutations. Four of these mutations, N494 N, T383P, 1061-8T-->C, and W556S, have not been reported earlier. The pathogenicity of the T383P, 1061-8T-->C, and W556S mutations remains to be established by in vitro mutagenesis and transfection studies. One patient had three mutations (335del10, 1061-8T-->C, and T705I) on the same allele. Further, nine well-known polymorphisms were detectable with this methodological setup. Direct DNA sequencing of the PCR products used for the SSCP analysis did not reveal any sequence variations not detected by the PCR-SSCP method. In two patients we did not detect any mutation by either method. We conclude that the PCR-SSCP analysis, performed as described here, is as sensitive and efficient as DNA sequencing in the ability to identify the sequence variations in the LDL receptor gene of the patients with heterozygous FH of this study.

  12. Possible conservation units of the sun bear (Helarctos malayanus) in Sarawak based on variation of mtDNA control region.

    PubMed

    Onuma, Manabu; Suzuki, Masatsugu; Ohtaishi, Noriyuki

    2006-11-01

    The mitochondrial DNA control region of the sun bear (Helarctos malayanus) was sequenced using 21 DNA samples collected from confiscated sun bears to identify conservation units, such as evolutionarily significant units and management units, in Sarawak, Borneo Island. A total of 10 haplotypes were observed, indicating the presence of at least two lineages in the sun bear population in Sarawak. Presumably, these two lineages could represent evolutionarily significant units. However, the geographical distributions of the two lineages remained unknown due to the lack of information regarding the exact capture locations of the confiscated sun bears. It is essential to elucidate the geographical distributions of these lineages in order to create a proper conservation plan for the sun bears in Sarawak. Therefore, further studies examining the haplotype distributions using DNA samples from known localities are essential.

  13. [Genetic structure of the sable Martes zibellina L. populations from magadan oblast as inferred from mitochondrial DNA variation].

    PubMed

    Petrovskaia, A V

    2007-04-01

    Restriction polymorphism of the mtDNA cytochrome b gene was studied in nine sable Martes zibellina L. populations from three introduction foci of Khabarovsk and Kamchatka sables in Magadan oblast: Olya, Kolyma, and Omolon. For comparison, similar studies were performed with the populations of central Kamchatka and Khabarovsk krai. In total, 444 DNA specimens were examined. Three mtDNA haplotypes (A, B, and C) proved to occur at various frequencies in the populations under study. The sable population system displayed high differentiation (FST = 22.3%). The populations of the Olya focus were most similar genetically to the populations of Kamchatka; those of the Omolon focus were similar to the Khabarovsk populations, and those of the Kolyma focus occupied an intermediate place. The observed spatial heterogeneity of the sable populations of Magadan oblast was explained in terms of the formation of the introduction foci of Kamchatka and Khabarovsk sables, starting from the 1950s.

  14. Variation in Mitochondrial Cytochrome c Oxidase I DNA Can Successfully Identify Culex (Melanoconion) pedroi (Diptera: Culicidae) and Culex (Melanoconion) ribeirensis (Diptera: Culicidae).

    PubMed

    Araki, A S; Maia, D A; Gil-Santana, H R; de Mello, C F; Martins, A de J; Alencar, J

    2016-12-22

    Culex (Melanoconion) pedroi Sirivanakarn & Belkin 1980 and Culex (Melanoconion) ribeirensis Forattini & Sallum 1985 are two morphologically very similar species of the Pedroi subgroup of mosquitoes in the Spissipes section of the subgenus Melanoconion of the genus Culex L. 1758. We carried out an analysis of the mitochondrial cytochrome c oxidase I (COI) DNA variation between these two species. The recent observation of sympatric coexistence in a forested area of Rio de Janeiro State (Brazil) triggered the need to validate these two species previously identified based on morphology. We concluded that the COI is a useful tool for identification of Cx. pedroi and Cx. ribeirensis.

  15. [Intraspecific structure of sable Martes zibellina inferred from nucleotide variation of the mitochondrial DNA cytochrome b gene].

    PubMed

    Maliarchuk, B A; Petrovskaia, A V; Derenko, M V

    2010-01-01

    A fragment of the mitochondrial DNA (mtDNA) cytochrome b gene was sequences in sable from Magadan oblast, Khabarovsk krai, and Kamchatka. Using phylogenetic analysis, the presence of two clusters (A and BC), with the divergence value of 1.4%, was demonstrated. Analysis of the cytochrome b gene median networks indicated that split of the ancestral population took place in early Pleistocene (about one Myr ago), while expansion of its more young phylogenetic group A occurred in late Pleistocene, about 120,000 years ago.

  16. Mitochondrial DNA sequence variation and phylogeography of Pimelia darkling beetles on the island of Tenerife (Canary Islands).

    PubMed

    Juan, C; Ibrahim, K M; Oromi, P; Hewitt, G M

    1996-12-01

    Four morphological taxa of the beetle genus Pimelia (Coleoptera, Tenebrionidae) are known to exist on the Atlantic island of Tenerife. We have obtained DNA sequences for 61 individuals from these taxa across the island for a 200 bp long fragment of the mitochondrial COI gene. In addition, a restriction site polymorphism in the nuclear rRNA ITS-1 sequence was identified and screened in a sample of these individuals using the enzyme Kpn2I. The results were analysed using approaches which allow inferences to be made about the population genetic structure and the mitochondrial genealogy of these closely related beetles. The mtDNA haplotype distribution and the estimates of sequence divergence revealed the presence of two ancient mtDNA lineages which coincide with the disjunct volcanic evolution of the island. The ITS-1 polymorphism was found to be diagnostic of these two lineages. However, the morphological and mitochondrial phylogenies were found to be discordant. We argue that this is possibly the result of rapid morphological change, produced by selection in different habitats, which has been recently superimposed on an older mitochondrial DNA divergence.

  17. Intra-Monozygotic Twin Pair Discordance and Longitudinal Variation of Whole-Genome Scale DNA Methylation in Adults

    PubMed Central

    Zhang, Su-Hua; Chen, Jinzhong; Lu, Daru; Shen, Min; Li, Chengtao

    2015-01-01

    Monozygotic twins share identical genomic DNA and are indistinguishable using conventional genetic markers. Increasing evidence indicates that monozygotic twins are epigenetically distinct, suggesting that a comparison between DNA methylation patterns might be useful to approach this forensic problem. However, the extent of epigenetic discordance between healthy adult monozygotic twins and the stability of CpG loci within the same individual over a short time span at the whole-genome scale are not well understood. Here, we used Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles using blood collected from 10 pairs of monozygotic twins and 8 individuals sampled at 0, 3, 6, and 9 months. Using an effective and unbiased method for calling differentially methylated (DM) CpG sites, we showed that 0.087%–1.530% of the CpG sites exhibit differential methylation in monozygotic twin pairs. We further demonstrated that, on whole-genome level, there has been no significant epigenetic drift within the same individuals for up to 9 months, including one monozygotic twin pair. However, we did identify a subset of CpG sites that vary in DNA methylation over the 9-month period. The magnitude of the intra-pair or longitudinal methylation discordance of the CpG sites inside the CpG islands is greater than those outside the CpG islands. The CpG sites located on shores appear to be more suitable for distinguishing between MZ twins. PMID:26248206

  18. MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa

    PubMed Central

    2013-01-01

    Background The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/’hoansi, !Xun, /Gui+//Gana, Khwe, ≠Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record. Results The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/’hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: ≠Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other

  19. Seasonal variations in the levels of PAH–DNA adducts in young adults living in Mexico City

    PubMed Central

    García-Suástegui, W. A.; Huerta-Chagoya, A.; Carrasco-Colín, K. L.; Pratt, M. M.; John, K.; Petrosyan, P.; Rubio, J.; Poirier, M. C.; Gonsebatt, M. E.

    2011-01-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous components of polluted air. The Mexico City Metropolitan Area (MCMA), one of the most densely populated areas in the world, is 2240 m above sea level. At this altitude, less oxygen is available, making combustion less efficient and therefore producing more PAH pollutants. According to the Automatic Monitoring Network in Mexico City (RAMA, for its Spanish initials; http://www.sma.df.gob.mx/simat2/informaciontecnica/index.php?opcion=5&opciondifusion_bd=90), which performs environmental monitoring, the critical air pollutants in Mexico City are ozone and particulate matter (PM). PM emissions increase during the dry season (winter to spring) and decrease during the rainy season (summer to autumn). The bioactivation of some PAHs produces reactive metabolites that bind to DNA, and the presence of elevated levels of PAH–DNA adducts in tissues such as blood lymphocytes represents an elevated risk for the development of cancer. We have compared the levels of PAH–DNA adducts and the percentage of cells with chromosomal aberrations (CWAs) using a matched set of peripheral blood lymphocytes obtained on two separate occasions from young non-smoking inhabitants of the MCMA (n = 92) during the 2006 dry season and the following rainy season. PAH–DNA adducts were analysed using the r7, t8-dihydroxy-t-9, 10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE)–DNA chemiluminescence immunoassay (CIA). The percentages of CWA were determined in cultured lymphocytes from the same individuals. Both DNA adduct levels and chromosomal aberrations were tested for correlation with lifestyle and the polymorphisms of cytochromes P450 CYP1A1 and CYP1B1 as well as glutathione-S-transferases GSTM1 and GSTT1. The levels of PAH–DNA adducts were significantly higher (P < 0.001) in the dry season (10.66 ± 3.05 per 109 nt, n = 92) than during the rainy season (9.50 ± 2.85 per 109 nt, n = 92) and correlated with the seasonal levels of particulate

  20. [Variation in mitochondrial DNA in Far Eastern mullet pilengas, Liza haematocheilus Temminck and Schlegel, acclimatized in the Azov-Black Sea basin].

    PubMed

    Salmenkova, E A; Gordeeva, N V; Omel'chenko, V T; Makhotkin, M A; Dudkin, S I

    2007-09-01

    This study continues the investigation of genetic variation in the populations of native and acclimatized in the Azov-Black Sea basin pilengas from the Sea of Japan. The previous comparison based on allozyme analysis was supplemented by analysis of restriction polymorphism of a mitochondrial DNA fragment containing the cytochrome b gene and the D-loop. Five out of fifteen endonucleases tested detected polymorphic sites. In the samples of native and acclimatized pilengas, five common haplotypes were found; ten and three "population-specific" haplotypes were detected in the Far Eastern and the Azov populations, respectively. The differences in haplotype distributions between these populations were highly significant (P < 0.001). The mtDNA variation was lower in the Azov than in the Far Eastern population (haplotype diversity mu respectively 6.35 +/- 0.27 and 9.14 +/- 0.55), which is in good agreement with the decrease in the number of polymorphic loci and the mean number of alleles per locus, found earlier for allozyme markers in this population. The reasons for these differences in the acclimatized population are discussed.

  1. Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy

    PubMed Central

    Wang, Haibin; Qi, Xiangyu; Chen, Sumei; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Jiang, Jiafu; Chen, Fadi

    2015-01-01

    Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5′-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation. PMID:26379692

  2. Genetic variation of rice (Oryza sativa L.) germplasm in Myanmar based on genomic compositions of DNA markers

    PubMed Central

    Wunna; Watanabe, Kazuo N.; Ohsawa, Ryo; Obara, Mitsuhiro; Yanagihara, Seiji; Aung, Pa Pa; Fukuta, Yoshimichi

    2016-01-01

    The genetic diversity of 175 rice accessions from Myanmar, including landraces and improved types from upland and lowland ecosystems in five different areas—Western (hilly), Northern (mountainous), North and South-eastern (plateau), and Southern (plain)—was evaluated on the basis of polymorphism data for 65 DNA markers and phenol reactions. On the basis of the DNA polymorphism data, high genetic diversity was confirmed to conserve in the accessions from each ecosystem and area. And the accessions were classified into two cluster groups I and II, which corresponded to Indica Group and Japonica Group, respectively. Cluster group I accessions were distributed mainly in upland ecosystems; group II were distributed in lowland in the Southern area, and the distributions of dominant groups differed among areas. Rice germplasm in Myanmar has maintained high genetic diversity among ecosystems and areas. This information will be used for advanced studies in germplasm and rice breeding in Myanmar. PMID:28163592

  3. Restarting and recentering genetic algorithm variations for DNA fragment assembly: The necessity of a multi-strategy approach.

    PubMed

    Hughes, James Alexander; Houghten, Sheridan; Ashlock, Daniel

    2016-12-01

    DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. This study focuses on the overlap-layout-consensus approach. Heuristics and computational intelligence methods are combined to exploit their respective benefits. These algorithm combinations were able to produce high quality results surpassing the best results obtained by a number of competitive algorithms specially designed and tuned for this problem on thirteen of sixteen popular benchmarks. This work also reinforces the necessity of using multiple search strategies as it is clearly observed that algorithm performance is dependent on problem instance; without a deeper look into many searches, top solutions could be missed entirely.

  4. Early life adversity and serotonin transporter gene variation interact to affect DNA methylation of the corticotropin-releasing factor gene promoter region in the adult rat brain.

    PubMed

    van der Doelen, Rick H A; Arnoldussen, Ilse A; Ghareh, Hussein; van Och, Liselot; Homberg, Judith R; Kozicz, Tamás

    2015-02-01

    The interaction between childhood maltreatment and the serotonin transporter (5-HTT) gene linked polymorphic region has been associated with increased risk to develop major depression. This Gene × Environment interaction has furthermore been linked with increased levels of anxiety and glucocorticoid release upon exposure to stress. Both endophenotypes are regulated by the neuropeptide corticotropin-releasing factor (CRF) or hormone, which is expressed by the paraventricular nucleus of the hypothalamus, the bed nucleus of the stria terminalis, and the central amygdala (CeA). Therefore, we hypothesized that altered regulation of the expression of CRF in these areas represents a major neurobiological mechanism underlying the interaction of early life stress and 5-HTT gene variation. The programming of gene transcription by Gene × Environment interactions has been proposed to involve epigenetic mechanisms such as DNA methylation. In this study, we report that early life stress and 5-HTT genotype interact to affect DNA methylation of the Crf gene promoter in the CeA of adult male rats. Furthermore, we found that DNA methylation of a specific site in the Crf promoter significantly correlated with CRF mRNA levels in the CeA. Moreover, CeA CRF mRNA levels correlated with stress coping behavior in a learned helplessness paradigm. Together, our findings warrant further investigation of the link of Crf promoter methylation and CRF expression in the CeA with behavioral changes that are relevant for psychopathology.

  5. [Variation of the mitochondrial DNA control region in the populations of southern form of Dolly Varden (Salvelinus malma krascheninnikovi) from Sakhalin].

    PubMed

    Osinov, A G; Miuge, N S

    2008-12-01

    Analysis of a 551-bp segment of the mitochondrial DNA control region in 23 individuals from nine populations of Dolly Varden from Sakhalin and three individuals from the Shikaribetsu Lake (Hokkaido) revealed the presence of seven haplotypes of southern form, along with one haplotype of northern form of Dolly Varden. All seven haplotypes of southern Dolly Varden were earlier described in the populations from Hokkaido. Nested analysis of molecular variance (AMOVA) based on the haplotype frequencies, performed using literature data, suggested that, during the glacial epoch, there were three regional population groups of Dolly Varden (from eastern and western coasts of Sakhalin, and from Southern Primorye). Population groups from Sakhalin and Primorye were clearly separated. The differences between two Sakhalin population groups in the mtDNA haplotype frequencies were not statistically significant. However, relative to the earlier obtained data on microsatellite loci, these differences were statistically significant. For the populations of Sakhalin Dolly Varden, the data on mitochondrial and microsatellite DNA variation supplement each other.

  6. Patterns of variation in the intergenic spacers of ribosomal DNA in Drosophila melanogaster support a model for genetic exchanges during X-Y pairing.

    PubMed Central

    Polanco, C; González, A I; Dover, G A

    2000-01-01

    Detailed analysis of variation in intergenic spacer (IGS) and internal transcribed spacer (ITS) regions of rDNA drawn from natural populations of Drosophila melanogaster has revealed contrasting patterns of homogenization although both spacers are located in the same rDNA unit. On the basis of the role of IGS regions in X-Y chromosome pairing, we proposed a mechanism of single-strand exchanges at the IGS regions, which can explain the different evolutionary trajectories followed by the IGS and the ITS regions. Here, we provide data from the chromosomal distribution of selected IGS length variants, as well as the detailed internal structure of a large number of IGS regions obtained from specific X and Y chromosomes. The variability found in the different internal subrepeat regions of IGS regions isolated from X and Y chromosomes supports the proposed mechanism of genetic exchanges and suggests that only the "240" subrepeats are involved. The presence of a putative site for topoisomerase I at the 5' end of the 18S rRNA gene would allow for the exchange between X and Y chromosomes of some 240 subrepeats, the promoter, and the ETS region, leaving the rest of the rDNA unit to evolve along separate chromosomal lineages. The phenomenon of localized units (modules) of homogenization has implications for multigene family evolution in general. PMID:10880483

  7. Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris.

    PubMed

    Padhi, Abinash

    2014-03-15

    The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity.

  8. Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.

    PubMed

    Gernandt, D S; Liston, A; Piñero, D

    2001-12-01

    The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.

  9. Mammalian DNA δ15N exhibits 40‰ intramolecular variation and is unresponsive to dietary protein level

    PubMed Central

    Strable, Maggie S.; Tschanz, Carolyn L.; Varamini, Behzad; Chikaraishi, Yoshito; Ohkouchi, Naohiko; Brenna, J. Thomas

    2014-01-01

    We report the first high precision characterization of molecular and intramolecular δ15N of nucleosides derived from mammalian DNA. The influence of dietary protein level on brain amino acids and deoxyribonucleosides was determined to investigate whether high protein turnover would alter amino acid 15N or 13C. Pregnant guinea pig dams were fed control diets, or high or low levels of dietary protein throughout gestation, and all pups were fed control diets. Cerebellar DNA of offspring was extracted at 2 and 120 days of life, nucleosides isolated and δ15N and δ13C characterized. Mean diet δ15N = 0.45±0.33‰, compared to cerebellar whole tissue and DNA δ15N = +4.1±0.7‰ and −4.5±0.4‰, respectively. Cerebellar deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), and deoxyguanosine (dG) δ15N were +1.4±0.4, −2.1±0.9, −7.2±0.3, and −10.4±0.5‰, respectively. There were no changes in amino acid or deoxyribonucleoside δ15N due to dietary protein level. Using known metabolic relationships, we developed equations to calculate the intramolecular δ15N originating from aspartate (asp) in purines (pur) or pyrimidines (pyr), glutamine (glu), and glycine (gly) to be δ15NASP-PUR, δ15NASP-PYR, δ15NGLN, and δ15NGLY +11.9±2.3‰, +7.0±2.0‰, −9.1±2.4‰, and −31.8±8.9‰, respectively. A subset of twelve amino acids from food and brain had mean δ15N of 4.3±3.2‰ and 13.8±3.1‰, respectively, and δ15N for gly and asp were 12.6±2.2‰ and 15.2±0.8‰, respectively. A separate isotope tracer study detected no significant turnover of cerebellar DNA in the first six months of life. The large negative δ15N difference between gly and cerebellar purine N at the gly (7) position implies either that there is a major isotope effect during DNA synthesis, or that in utero gly has a different isotope ratio during rapid growth and metabolism than in adult life. Our data show that cerebellar nucleoside intramolecular δ15N vary over more than

  10. Variation in whole DNA methylation in red maple (Acer rubrum) populations from a mining region: association with metal contamination and cation exchange capacity (CEC) in podzolic soils.

    PubMed

    Kalubi, K N; Mehes-Smith, M; Spiers, G; Omri, A

    2017-02-15

    Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications. The estimated CEC values varied significantly among sites, ranging between 1.8 and 10.5 cmol(+) kg(-1), with a strong relationship being observed between CEC and pH (r = 0.96**). Cation exchange capacity, significantly lower in highly metal contaminated sites compared to both reference and less contaminated sites, was higher in the higher organic matter limed compared to unlimed sites. There was a significant variation in the level of cytosine methylation among the metal-contaminated sites. Significant and strong negative correlations between [5mdC]/[dG] and bioavailable nickel (r = -0.71**) or copper (r = -0.72**) contents were observed. The analysis of genomic DNA for adenine methylation in this study showed a very low level of [6N-mdA]/dT] in Acer rubrum plants analyzed ranging from 0 to 0.08%. Significant and very strong positive correlation was observed between [6N-mdA]/dT] and soil bioavailable nickel (r = 0.78**) and copper (r = 0.88**) content. This suggests that the increased bioavailable metal levels associated with contamination by nickel and copper particulates are associated with cytosine and adenine methylation.

  11. 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

    PubMed Central

    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

  12. FOX-superroots of Lotus corniculatus, overexpressing Arabidopsis full-length cDNA, show stable variations in morphological traits.

    PubMed

    Himuro, Yasuyo; Tanaka, Hidenori; Hashiguchi, Masatsugu; Ichikawa, Takanari; Nakazawa, Miki; Seki, Motoaki; Fujita, Miki; Shinozaki, Kazuo; Matsui, Minami; Akashi, Ryo; Hoffmann, Franz

    2011-01-15

    Using the full-length cDNA overexpressor (FOX) gene-hunting system, we have generated 130 Arabidopsis FOX-superroot lines in bird's-foot trefoil (Lotus corniculatus) for the systematic functional analysis of genes expressed in roots and for the selection of induced mutants with interesting root growth characteristics. We used the Arabidopsis-FOX Agrobacterium library (constructed by ligating pBIG2113SF) for the Agrobacterium-mediated transformation of superroots (SR) and the subsequent selection of gain-of-function mutants with ectopically expressed Arabidopsis genes. The original superroot culture of L. corniculatus is a unique host system displaying fast root growth in vitro, allowing continuous root cloning, direct somatic embryogenesis and mass regeneration of plants under entirely hormone-free culture conditions. Several of the Arabidopsis FOX-superroot lines show interesting deviations from normal growth and morphology of roots from SR-plants, such as differences in pigmentation, growth rate, length or diameter. Some of these mutations are of potential agricultural interest. Genomic PCR analysis revealed that 100 (76.9%) out of the 130 transgenic lines showed the amplification of single fragments. Sequence analysis of the PCR fragments from these 100 lines identified full-length cDNA in 74 of them. Forty-three out of 74 full-length cDNA carried known genes. The Arabidopsis FOX-superroot lines of L. corniculatus, produced in this study, expand the FOX hunting system and provide a new tool for the genetic analysis and control of root growth in a leguminous forage plant.

  13. Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm

    PubMed Central

    Jin, Jingjing; Lee, May; Bai, Bin; Sun, Yanwei; Qu, Jing; Rahmadsyah; Alfiko, Yuzer; Lim, Chin Huat; Suwanto, Antonius; Sugiharti, Maria; Wong, Limsoon; Ye, Jian; Chua, Nam-Hai; Yue, Gen Hua

    2016-01-01

    Oil palm is the world’s leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits. PMID:27426468

  14. Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

    PubMed

    Jin, Jingjing; Lee, May; Bai, Bin; Sun, Yanwei; Qu, Jing; Rahmadsyah; Alfiko, Yuzer; Lim, Chin Huat; Suwanto, Antonius; Sugiharti, Maria; Wong, Limsoon; Ye, Jian; Chua, Nam-Hai; Yue, Gen Hua

    2016-12-01

    Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.

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

    PubMed

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

    2015-12-22

    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.

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

    PubMed

    Barbieri, Chiara; Vicente, Mário; Oliveira, Sandra; Bostoen, Koen; Rocha, Jorge; Stoneking, Mark; Pakendorf, Brigitte

    2014-01-01

    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.

  17. Copy Number Variation of Mitochondrial DNA Genes in Pneumocystis jirovecii According to the Fungal Load in BAL Specimens

    PubMed Central

    Valero, Clara; Buitrago, María José; Gits-Muselli, Maud; Benazra, Marion; Sturny-Leclère, Aude; Hamane, Samia; Guigue, Nicolas; Bretagne, Stéphane; Alanio, Alexandre

    2016-01-01

    Pneumocystis jirovecii is an unculturable fungus and the causative agent of Pneumocystis pneumonia, a life-threatening opportunistic infection. Although molecular diagnosis is often based on the detection of mtLSU rRNA mitochondrial gene, the number of copies of mitochondrial genes had not been investigated. We developed and optimized six real-time PCR assays in order to determine the copy number of four mitochondrial genes (mtSSU rRNA, mtLSU rRNA, NAD1, and CYTB) in comparison to nuclear genome (DHPS and HSP70) and tested 84 bronchoalveolar fluids of patients at different stages of the infection. Unexpectedly, we found that copy number of mitochondrial genes varied from gene to gene with mtSSU rRNA gene being more represented (37 copies) than NAD1 (23 copies), mtLSU rRNA (15 copies) and CYTB (6 copies) genes compared to nuclear genome. Hierarchical clustering analysis (HCA) allowed us to define five major clusters, significantly associated with fungal load (p = 0.029), in which copy number of mitochondrial genes was significantly different among them. More importantly, copy number of mtLSU rRNA, NAD1, and CYTB but not mtSSU rRNA differed according to P. jirovecii physiological state with a decreased number of copies when the fungal load is low. This suggests the existence of a mixture of various subspecies of mtDNA that can harbor different amplification rates. Overall, we revealed here an unexpected variability of P. jirovecii mtDNA copy number that fluctuates according to P. jirovecii’s physiological state, except for mtSSU that is the most stable and the most present mitochondrial gene. PMID:27672381

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

    PubMed Central

    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

  19. Intrageneric phylogenetics based on mitochondrial DNA variation among fifteen harpactorine assassin bugs with four ecotypes and three morphs (Hemiptera: Reduviidae: Harpactorinae).

    PubMed

    Ambrose, Dunston P; Lenin, E Arockia; Kiruba, D Angeline

    2014-03-19

    Available mitochondrial DNA sequences viz., 16S, Cyt b, Cyt c oxidase subunit - I, and Cyt c subunit-like - I gene of Rhynocoris (Kolenati) species were subjected to phylogenetic analysis to understand the intrageneric and intraspecific variations and the role of geographical isolation on speciation; using CLUSTAL W in MEGA version 5.1. This analysis includes fifteen species and four ecotypes of R. kumarii Ambrose and Livingstone and three morphs of R. marginatus (Fabricius) from four countries viz., Canada, China, Korea, and South Africa. The pairwise genetic distances were calculated and phylograms were constructed using Maximum Likelihood, Maximum Parsimony, and Neighbor-Joining methods. These preliminary analyses not only demarcated the fifteen species of Rhynocoris, the four ecotypes of R. kumarii, and the three morphs of R. marginatus, but also revealed phylogenetic relationships and the role of geographical isolation and polymorphism on speciation.

  20. 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)

    USGS Publications Warehouse

    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.                   

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

    PubMed

    Andersen, L W; Born, E W; Gjertz, I; Wiig, O; Holm, L E; Bendixen, C

    1998-10-01

    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 northwest (NW) Greenland, east (E) Greenland, Svalbard and Franz Joseph Land. Two of the 10 haplotypes detected in the four samples were diagnostic for the NW Greenland sample, which implied that the group of walruses in this area is evolutionary distinct from walruses in the other three areas. One individual sampled in E Greenland exhibited a Pacific haplotype, which proved a connection between the Pacific walrus and walruses in eastern Greenland. The Franz Joseph Land, Svalbard and E Greenland samples shared the most common haplotype, indicating very little differentiation at the mtDNA level. Gene flow (Nm) estimates among the four areas indicated a very restricted exchange of female genes between NW Greenland and the more eastern Atlantic Arctic samples, and a closer relationship between the three samples composing the eastern Atlantic Arctic. The genetic variation at 11 polymorphic microsatellite loci grouped individuals into three populations, NW Greenland, E Greenland and a common Franz Joseph Land-Svalbard population, which were connected by moderate gene flow.

  2. Agro-ecological variations of sheath rot disease of rice caused by Sarocladium oryzae and DNA fingerprinting of the pathogen's population structure.

    PubMed

    Tajul Islam Chowdhury, M; Salim Mian, M; Taher Mia, M A; Rafii, M Y; Latif, M A

    2015-12-28

    To examine the impact of regional and seasonal variations on the incidence and severity of sheath rot, a major seed-borne disease of rice caused by Sarocladium oryzae, data on incidence and severity were collected from 27 selected fields in the Gazipur, Rangpur, Bogra, Chittagong, Comilla, Gopalgonj, Jessore, Manikgonj, and Bhola districts of Bangladesh in rain-fed and irrigated conditions. Cultural variability of 29 pathogen isolates obtained from 8 different locations was studied on potato dextrose agar (PDA) and genetic variability was determined by DNA fingerprinting using variable number tandem repeat-polymerase chain reaction markers. Overall, disease incidence and severity were higher in irrigated rice. Disease incidence and severity were highest in the Bhola district in rain-fed rice and lowest in irrigated rice. Mycelial growth of 29 representative isolates was found to vary on PDA and the isolates were divided into 6 groups. The range of the overall size of conidia of the selected isolates was 2.40-7.20 x 1.20-2.40 μm. Analysis of the DNA fingerprint types of the 29 isolates of S. oryzae, obtained from the amplification reactions, revealed 10 fingerprinting types (FPTs) that were 80% similar. FPT-1 was the largest group and included 13 isolates (44.8%), while FPT-2 was the third largest group and included 3 isolates. Each of FPT-3, 4, 5, and 6 included only 1 isolate. We observed no relationship between cultural and genetic groupings.

  3. Human longevity and variation in DNA damage response and repair: study of the contribution of sub-processes using competitive gene-set analysis.

    PubMed

    Debrabant, Birgit; Soerensen, Mette; Flachsbart, Friederike; Dato, Serena; Mengel-From, Jonas; Stevnsner, Tinna; Bohr, Vilhelm A; Kruse, Torben A; Schreiber, Stefan; Nebel, Almut; Christensen, Kaare; Tan, Qihua; Christiansen, Lene

    2014-09-01

    DNA-damage response and repair are crucial to maintain genetic stability, and are consequently considered central to aging and longevity. Here, we investigate whether this pathway overall associates to longevity, and whether specific sub-processes are more strongly associated with longevity than 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 the competitive gene-set analysis by Wang et al indicated that BER, HRR and RECQ associated stronger with longevity than the respective remaining genes of the pathway (P-values=0.004-0.048). For HRR and RECQ, only one gene contributed to the significance, whereas for BER several genes contributed. These associations did, however, generally not pass correction for multiple testing. Still, these findings indicate that, of the entire pathway, variation in BER might influence longevity the most. These modest sized P-values were not replicated in a German sample. This might, though, be due to differences in genotyping procedures and investigated SNPs, potentially inducing differences in the coverage of gene regions. Specifically, five genes were not covered at all in the German data. Therefore, investigations in additional study populations are needed before final conclusion can be drawn.

  4. Reprint of "Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)".

    PubMed

    Kooken, Jennifer; Fox, Karen; Fox, Alvin; Altomare, Diego; Creek, Kim; Wunschel, David; Pajares-Merino, Sara; Martínez-Ballesteros, Ilargi; Garaizar, Javier; Oyarzabal, Omar; Samadpour, Mansour

    2014-01-01

    This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.

  5. [The variation in chum salmon Oncorhynchus keta (Walbaum) mitochondrial DNA and its connection with the paleogeographic events in the Northwest Pacific].

    PubMed

    Poliakova, N E; Semina, A V; Brykov, V A

    2006-10-01

    The results of examining mtDNA variation in populations of chum salmon Oncorhynchus keta from the rivers of the basins of the seas of Japan and Okhotsk and in the chum salmon seasonal races of the Amur River are presented. A significant level of polymorphism between the majority of the populations studied was detected. The groups of chum salmon from the Japan and Okhotsk Seas displayed the most pronounced differences. Analysis of genetic variation demonstrated that periodic paleontologic and climatic changes in the past of this region were the most probable factor that caused the divergence of these populations. The advances and retreats of glaciers and the accompanying regressions and transgressions of the ocean level caused isolation of chum salmon in the refugia belonging hypothetically to the paleo-Suifun and paleo-Amur regions. These population groups diverged presumably 350-450 thousand years ago. Differences between the seasonal races of the Amur chum salmon are insignificant, and their emergence dates back to the period of the last Wisconsin glaciation. Probably, the main isolation factor now is the genetically determined time of spawning.

  6. Diurnal variation in bacterioplankton composition and DNA damage in the microbial community from an Andean oligotrophic lake.

    PubMed

    Fernández-Zenoff, María V; Estévez, María C; Farías, María E

    2014-01-01

    Laguna Azul is an oligotrophic lake situated at 4,560 m above sea level and subject to a high level of solar radiation. Bacterioplankton community composition (BCC) was analysed by denaturing gradient gel electrophoresis and the impact of solar ultraviolet radiation was assessed by measuring cyclobutane pyrimidine dimers (CPD). Furthermore, pure cultures of Acinetobacter johnsonii A2 and Rhodococcus sp. A5 were exposed simultaneously and CPD accumulation was studied. Gel analyses generated a total of 7 sequences belonging to Alpha-proteobacteria (1 band), Beta-proteobacteria (1 band), Bacteroidetes (2 bands), Actinobacteria (1 band), and Firmicutes (1 band). DGGE profiles showed minimal changes in BCC and no CPD was detected even though a high level of damage was found in biodosimeters. A. johnsonii A2 showed low level of DNA damage while Rhodococcus sp. A5 exhibited high resistance since no CPD were detected under natural UV-B exposure, suggesting that the bacterial community is well adapted to this highly solar irradiated environment.

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

    PubMed

    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.

  8. Gene flow versus local adaptation in the northern acorn barnacle, Semibalanus balanoides: insights from mitochondrial DNA variation.

    PubMed

    Brown, A F; Kann, L M; Rand, D M

    2001-10-01

    In reciprocal transplant experiments, Bertness and Gaines (1993) found that Semibalanus balanoides juveniles that had settled in an upper Narragansett Bay estuary survived better in that estuary that did juveniles from coastal localities. The observed pattern of survivorship led to the claim that local adaptation may result from a combination of limited gene flow between and strong selection within these habitats. Here we test the hypothesis that limited gene flow has led to habitat-specific population differentiation using sequence and restriction fragment length polymorphism analyses of the mitochondrial DNA D-loop region of S. balanoides. Samples were analyzed from replicated coastal and estuary localities in both Narragansett Bay, Rhode Island, and Damariscotta River, Maine. The patterns of F(ST) indicate that gene flow between coast and estuary is extensive (Nm > 100) and is not lower in the estuary with lower flushing rates (Narragansett Bay). Given the high estimate of genetic exchange, adaptations for unpredictable environments seem more likely than local adaptation in this species because loci that respond to selection in one generation are essentially homogenized by the next seasons' settlement. Nevertheless, these estimates of neutral gene flow can help identify the strength of selection necessary for local adaptation to accumulate in Semibalanus.

  9. A preliminary report on the genetic variation in pointed gourd (Trichosanthes dioica Roxb.) as assessed by random amplified polymorphic DNA.

    PubMed

    Adhikari, S; Biswas, A; Bandyopadhyay, T K; Ghosh, P D

    2014-06-01

    Pointed gourd (Trichosanthes dioica Roxb.) is an economically important cucurbit and is extensively propagated through vegetative means, viz vine and root cuttings. As the accessions are poorly characterized it is important at the beginning of a breeding programme to discriminate among available genotypes to establish the level of genetic diversity. The genetic diversity of 10 pointed gourd races, referred to as accessions was evaluated. DNA profiling was generated using 10 sequence independent RAPD markers. A total of 58 scorable loci were observed out of which 18 (31.03%) loci were considered polymorphic. Genetic diversity parameters [average and effective number of alleles, Shannon's index, percent polymorphism, Nei's gene diversity, polymorphic information content (PIC)] for RAPD along with UPGMA clustering based on Jaccard's coefficient were estimated. The UPGMA dendogram constructed based on RAPD analysis in 10 pointed gourd accessions were found to be grouped in a single cluster and may represent members of one heterotic group. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd.

  10. Contrasting patterns of population subdivision and historical demography in three western Mediterranean lizard species inferred from mitochondrial DNA variation.

    PubMed

    Pinho, C; Harris, D J; Ferrand, N

    2007-03-01

    Pleistocene climatic oscillations were a major force shaping genetic variability in many taxa. We analyse the relative effects of the ice ages across a latitudinal gradient in the Western Mediterranean region, testing two main predictions: (i) species with historical distributions in northern latitudes should have experienced greater loss of suitable habitat, resulting in higher extinction of historical lineages than species distributed in southern latitudes, where the effects of the ice ages were not as drastic. This would be reflected in the observation of lower diversity and number of differentiated lineages in northern areas. (ii) a signature of demographic expansion following the climate amelioration should be obvious in northern species, whereas in the south evidence of long-term effective population size stability should be observed. We used as models three species of wall lizards (Podarcis bocagei, Podarcis carbonelli and Podarcis vaucheri) that replace each other along the study area. We investigated the patterns of mitochondrial DNA diversity and subdivision and obtained demographic parameter estimates for each species. Our results suggest that P. bocagei, the northernmost species, bears low genetic diversity, a shallow coalescent history and marks of a demographic expansion. In contrast, P. vaucheri, the species with a southernmost distribution, shows deeper coalescence events, complex geographical substructure and no evidence for population growth. The species with an intermediate distribution, P. carbonelli, shows average levels of diversity, substructure and population growth. Taken together, these results conform to our main predictions and are explained by a differential influence of the ice ages on distinct latitudes.

  11. The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility

    PubMed Central

    Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

    2014-01-01

    National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma. PMID:23860041

  12. Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

    PubMed Central

    Ruck, Elizabeth C.; Nakov, Teofil; Jansen, Robert K.; Theriot, Edward C.; Alverson, Andrew J.

    2014-01-01

    Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages. PMID:24567305

  13. Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos Taurus and Bos Indicus)

    PubMed Central

    MacHugh, D. E.; Shriver, M. D.; Loftus, R. T.; Cunningham, P.; Bradley, D. G.

    1997-01-01

    Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (taurine) and humped (zebu) cattle, providing strong support for a separate origin for domesticated zebu cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and taurine cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African cattle afforded a high resolution perspective on the hybrid nature of African cattle populations and also suggested that certain West African populations of valuable disease-tolerant taurine cattle are under threat of genetic absorption by migrating zebu herds. PMID:9215909

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

    PubMed Central

    Armstead, Ian; Huang, Lin; King, Julie; Ougham, Helen; Thomas, Howard; King, Ian

    2007-01-01

    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. PMID:17708759

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

    PubMed Central

    Roy, Pritesh Sundar; Rao, Gundimeda Jwala Narasimha; 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

  16. The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs.

    PubMed

    Kin, Katherine; Chen, Xi; Gonzalez-Garay, Manuel; Fakhouri, Walid D

    2016-04-15

    Non-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predicted target genes for COMs showed that the majority are involved in DNA damage, apoptosis, cell cycle regulation, and RNA processing. EMSA results showed that both cMYC and P53 bind to cis-overlapping motifs within a ChIP-seq co-occupied region in Chr12. In vitro functional analysis of selected co-occupied elements verified enhancer activity, and also showed that the occurrence of SNPs within three COMs significantly altered enhancer activity. We identified a list of COM-associated functional SNPs that are in close proximity to SNPs associated with common diseases in large population studies. These results suggest a potential molecular mechanism to identify etiologic regulatory mutations associated with common diseases.

  17. Genetic variations of ND5 gene of mtDNA in populations of Anopheles sinensis (Diptera: Culicidae) malaria vector in China

    PubMed Central

    2013-01-01

    Background Anopheles sinensis is a principal vector for Plasmodium vivax malaria in most parts of China. Understanding of genetic structure and genetic differentiation of the mosquito should contribute to the vector control and malaria elimination in China. Methods The present study investigated the genetic structure of An. sinensis populations using a 729 bp fragment of mtDNA ND5 among 10 populations collected from seven provinces in China. Results ND5 was polymorphic by single mutations within three groups of An. sinensis that were collected from 10 different geographic populations in China. Out of 140 specimens collected from 10 representative sites, 84 haplotypes and 71 variable positions were determined. The overall level of genetic differentiation of An. sinensis varied from low to moderate across China and with a FST range of 0.00065 – 0.341. Genealogy analysis clustered the populations of An. sinensis into three main clusters. Each cluster shared one main haplotype. Pairwise variations within populations were higher (68.68%) than among populations (31.32%) and with high fixation index (FST = 0.313). The results of the present study support population growth and expansion in the An. sinensis populations from China. Three clusters of An. sinensis populations were detected in this study with each displaying different proportion patterns over seven Chinese provinces. No correlation between genetic and geographic distance was detected in overall populations of An. sinensis (R2 = 0.058; P = 0.301). Conclusions The results indicate that the ND5 gene of mtDNA is highly polymorphic in An. sinensis and has moderate genetic variability in the populations of this mosquito in China. Demographic and spatial results support evidence of expansion in An. sinensis populations. PMID:24192424

  18. Variations of SSU rDNA group I introns in different isolates of Cordyceps militaris and the loss of an intron during cross-mating.

    PubMed

    Lian, Tiantian; Yang, Tao; Sun, Junde; Guo, Suping; Yang, Huaijun; Dong, Caihong

    2014-08-01

    Cordyceps militaris, the type species of genus Cordyceps, is one of the most popular mushrooms and a nutraceutical in eastern Asia. It is considered a model organism for the study of Cordyceps species because it can complete its life cycle when cultured in vitro. In the present study, the occurrence and sequence variation of SSU rDNA group I introns, Cmi.S943 and Cmi.S1199, among different isolates of C. militaris were analyzed. Based on the secondary structure predictions, the Cmi.S943 intron has been placed in subgroup IC1, and the Cmi.S1199 intron has been placed in subgroup IE. No significant similarity between Cmi.S943 and Cmi.S1199 suggested different origins. Three genotypes, based on the frequency and distribution of introns, were described to discriminate the 57 surveyed C. militaris strains. It was found that the genotype was related to the stroma characteristics. The stromata of all of the genotype II strains, which possessed only Cmi.S943, could produce perithecium. In contrast, the stromata of all genotype III strains, which had both Cmi.S943 and Cmi.S1199, could not produce perithecium. Cmi.S1199 showed the lowest level of intra-specific variation among the tested strains. Group I introns can be lost during strain cross-mating. Therefore, we presumed that during cross-mating and recombination, intron loss could be driven by positive Darwinian selection due to the energetic cost of transcribing long introns.

  19. Mitochondrial DNA variation in the malaria vector Anopheles minimus across China, Thailand and Vietnam: evolutionary hypothesis, population structure and population history.

    PubMed

    Chen, B; Pedro, P M; Harbach, R E; Somboon, P; Walton, C; Butlin, R K

    2011-02-01

    The effects of Pleistocene environmental fluctuations on the distribution and diversity of organisms in Southeast Asia are much less well known than in Europe and North America. In these regions, the combination of palaeoenvironmental reconstruction and inferences about population history from genetic data has been very powerful. In Southeast Asia, mosquitoes are good candidates for the genetic approach, with the added benefit that understanding the relative contributions of historical and current processes to population structure can inform management of vector species. Genetic variation among populations of Anopheles minimus was examined using 144 mtDNA COII sequences from 23 sites in China, Thailand and Vietnam. Haplotype diversity was high, with two distinct lineages that have a sequence divergence of over 2% and exhibit different geographical distributions. We compare alternative hypotheses concerning the origin of this pattern. The observed data deviate from the expectations based on a single-panmictic population with or without growth, or a stable but spatially structured population. However, they can be readily accommodated by a model of past fragmentation into eastern and western refugia, followed by growth and range expansion. This is consistent with the palaeoenvironmental reconstructions currently available for the region.

  20. Mitochondrial DNA variation in the malaria vector Anopheles minimus across China, Thailand and Vietnam: evolutionary hypothesis, population structure and population history

    PubMed Central

    Chen, B; Pedro, P M; Harbach, R E; Somboon, P; Walton, C; Butlin, R K

    2011-01-01

    The effects of Pleistocene environmental fluctuations on the distribution and diversity of organisms in Southeast Asia are much less well known than in Europe and North America. In these regions, the combination of palaeoenvironmental reconstruction and inferences about population history from genetic data has been very powerful. In Southeast Asia, mosquitoes are good candidates for the genetic approach, with the added benefit that understanding the relative contributions of historical and current processes to population structure can inform management of vector species. Genetic variation among populations of Anopheles minimus was examined using 144 mtDNA COII sequences from 23 sites in China, Thailand and Vietnam. Haplotype diversity was high, with two distinct lineages that have a sequence divergence of over 2% and exhibit different geographical distributions. We compare alternative hypotheses concerning the origin of this pattern. The observed data deviate from the expectations based on a single-panmictic population with or without growth, or a stable but spatially structured population. However, they can be readily accommodated by a model of past fragmentation into eastern and western refugia, followed by growth and range expansion. This is consistent with the palaeoenvironmental reconstructions currently available for the region. PMID:20517346

  1. One species or several? Discordant patterns of geographic variation between allozymes and mtDNA sequences among spiders in the genus Metepeira (Araneae: Araneidae).

    PubMed

    Piel, W H; Nutt, K J

    2000-06-01

    Paradoxically, an allozyme study of Metepeira "spinipes" (sensu lato) demonstrated extensive gene flow among four populations whose members are nevertheless morphologically and behaviorally distinct. Initially, the authors tentatively concluded that the populations exhibited panmixis and suggested that local environmental effects accounted for the apparent morphological and behavioral differences. However, they later concluded that such differences were too great to be accounted for by the environment alone and that the four populations actually represented three different species. To confirm that the allozyme results were, in fact, artifactual, we reexamined the relationships among these populations by sequencing a portion of the 12S mtDNA ribosomal subunit. In contrast to the allozyme result, our results demonstrate good agreement between patterns of genetic and morphological/behavioral variation. We suggest (1) that the allozyme allele frequencies are homogenized by balancing selection, not gene flow as was previously concluded, and therefore (2) that this study provides another instance in which inferences about population structures from allozyme data are misleading.

  2. Variation in copy number of the 28S rDNA of Aspergillus fumigatus measured by droplet digital PCR and analog quantitative real-time PCR.

    PubMed

    Alanio, Alexandre; Sturny-Leclère, Aude; Benabou, Marion; Guigue, Nicolas; Bretagne, Stéphane

    2016-08-01

    Droplet digital PCR (ddPCR) after DNA digestion yielded a 28S rDNA copy number of 61 to 86 copies/genome when testing 10 unrelated Aspergillus fumigatus isolates, higher than with quantitative PCR. Unfortunately, ddPCR after DNA digestion did not improve the sensitivity of our PCR assay when testing serum patients with invasive aspergillosis.

  3. 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

    PubMed Central

    2012-01-01

    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 neutral-to-alkaline streams

  4. DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L.

    PubMed

    González-Martínez, Santiago C; Ersoz, Elhan; Brown, Garth R; Wheeler, Nicholas C; Neale, David B

    2006-03-01

    Genetic association studies are rapidly becoming the experimental approach of choice to dissect complex traits, including tolerance to drought stress, which is the most common cause of mortality and yield losses in forest trees. Optimization of association mapping requires knowledge of the patterns of nucleotide diversity and linkage disequilibrium and the selection of suitable polymorphisms for genotyping. Moreover, standard neutrality tests applied to DNA sequence variation data can be used to select candidate genes or amino acid sites that are putatively under selection for association mapping. In this article, we study the pattern of polymorphism of 18 candidate genes for drought-stress response in Pinus taeda L., an important tree crop. Data analyses based on a set of 21 putatively neutral nuclear microsatellites did not show population genetic structure or genomewide departures from neutrality. Candidate genes had moderate average nucleotide diversity at silent sites (pi(sil) = 0.00853), varying 100-fold among single genes. The level of within-gene LD was low, with an average pairwise r2 of 0.30, decaying rapidly from approximately 0.50 to approximately 0.20 at 800 bp. No apparent LD among genes was found. A selective sweep may have occurred at the early-response-to-drought-3 (erd3) gene, although population expansion can also explain our results and evidence for selection was not conclusive. One other gene, ccoaomt-1, a methylating enzyme involved in lignification, showed dimorphism (i.e., two highly divergent haplotype lineages at equal frequency), which is commonly associated with the long-term action of balancing selection. Finally, a set of haplotype-tagging SNPs (htSNPs) was selected. Using htSNPs, a reduction of genotyping effort of approximately 30-40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought tolerance in pine.

  5. CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis

    PubMed Central

    McCaffrey, Jennifer; Sibert, Justin; Zhang, Bin; Zhang, Yonggang; Hu, Wenhui; Riethman, Harold; Xiao, Ming

    2016-01-01

    We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences. This labeling strategy is very powerful in targeting repetitive sequences as well as in barcoding genomic regions and structural variants not amenable to current labeling methods that rely on uneven distributions of restriction site motifs in the DNA. Importantly, it renders the labeled double-stranded DNA available in long intact stretches for high-throughput analysis in nanochannel arrays as well as for lower throughput targeted analysis of labeled DNA regions using alternative methods for stretching and imaging the labeled long DNA molecules. Thus, this method will dramatically improve both automated high-throughput genome-wide mapping as well as targeted analyses of complex regions containing repetitive and structurally variant DNA. PMID:26481349

  6. CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis.

    PubMed

    McCaffrey, Jennifer; Sibert, Justin; Zhang, Bin; Zhang, Yonggang; Hu, Wenhui; Riethman, Harold; Xiao, Ming

    2016-01-29

    We have developed a new, sequence-specific DNA labeling strategy that will dramatically improve DNA mapping in complex and structurally variant genomic regions, as well as facilitate high-throughput automated whole-genome mapping. The method uses the Cas9 D10A protein, which contains a nuclease disabling mutation in one of the two nuclease domains of Cas9, to create a guide RNA-directed DNA nick in the context of an in vitro-assembled CRISPR-CAS9-DNA complex. Fluorescent nucleotides are then incorporated adjacent to the nicking site with a DNA polymerase to label the guide RNA-determined target sequences. This labeling strategy is very powerful in targeting repetitive sequences as well as in barcoding genomic regions and structural variants not amenable to current labeling methods that rely on uneven distributions of restriction site motifs in the DNA. Importantly, it renders the labeled double-stranded DNA available in long intact stretches for high-throughput analysis in nanochannel arrays as well as for lower throughput targeted analysis of labeled DNA regions using alternative methods for stretching and imaging the labeled long DNA molecules. Thus, this method will dramatically improve both automated high-throughput genome-wide mapping as well as targeted analyses of complex regions containing repetitive and structurally variant DNA.

  7. BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.

    PubMed

    Chae, Heejoon; Lee, Sangseon; Seo, Seokjun; Jung, Daekyoung; Chang, Hyeonsook; Nephew, Kenneth P; Kim, Sun

    2016-12-01

    Measuring gene expression, DNA sequence variation, and DNA methylation status is routinely done using high throughput sequencing technologies. To analyze such multi-omics data and explore relationships, reliable bioinformatics systems are much needed. Existing systems are either for exploring curated data or for processing omics data in the form of a library such as R. Thus scientists have much difficulty in investigating relationships among gene expression, DNA sequence variation, and DNA methylation using multi-omics data. In this study, we report a system called BioVLAB-mCpG-SNP-EXPRESS for the integrated analysis of DNA methylation, sequence variation (SNPs), and gene expression for distinguishing cellular phenotypes at the pairwise and multiple phenotype levels. The system can be deployed on either the Amazon cloud or a publicly available high-performance computing node, and the data analysis and exploration of the analysis result can be conveniently done using a web-based interface. In order to alleviate analysis complexity, all the process are fully automated, and graphical workflow system is integrated to represent real-time analysis progression. The BioVLAB-mCpG-SNP-EXPRESS system works in three stages. First, it processes and analyzes multi-omics data as input in the form of the raw data, i.e., FastQ files. Second, various integrated analyses such as methylation vs. gene expression and mutation vs. methylation are performed. Finally, the analysis result can be explored in a number of ways through a web interface for the multi-level, multi-perspective exploration. Multi-level interpretation can be done by either gene, gene set, pathway or network level and multi-perspective exploration can be explored from either gene expression, DNA methylation, sequence variation, or their relationship perspective. The utility of the system is demonstrated by performing analysis of phenotypically distinct 30 breast cancer cell line data set. BioVLAB-mCpG-SNP-EXPRESS is

  8. The influence of history and contemporary stream hydrology on the evolution of genetic diversity within species: an examination of microsatellite DNA variation in bull trout, Salvelinus confluentus (Pisces: Salmonidae).

    PubMed

    Costello, A B; Down, T E; Pollard, S M; Pacas, C J; Taylor, E B

    2003-02-01

    An understanding of the relative roles of historical and contemporary factors in structuring genetic variation is a fundamental, but understudied aspect of geographic variation. We examined geographic variation in microsatellite DNA allele frequencies in bull trout (Salvelinus confluentus, Salmonidae) to test hypotheses concerning the relative roles of postglacial dispersal (historical) and current landscape features (contemporary) in structuring genetic variability and population differentiation. Bull trout exhibit relatively low intrapopulation microsatellite variation (average of 1.9 alleles per locus, average He = 0.24), but high levels of interpopulation divergence (F(ST) = 0.39). We found evidence of historical influences on microsatellite variation in the form of a decrease in the number of alleles and heterozygosities in populations on the periphery of the range relative to populations closer to putative glacial refugia. In addition, one region of British Columbia that was colonized later during deglaciation and by more indirect watershed connections showed less developed and more variable patterns of isolation by distance than a similar region colonized earlier and more directly from refugia. Current spatial and drainage interconnectedness among sites and the presence of migration barriers (falls and cascades) within individual streams were found to be important contemporary factors influencing historical patterns of genetic variability and interpopulation divergence. Our work illustrates the limited utility of equilibrium models to delineate population structure and patterns of genetic diversity in recently founded populations or those inhabiting highly heterogeneous environments, and it highlights the need for approaches incorporating a landscape context for population divergence. Substantial microsatellite DNA divergence among bull trout populations may also signal divergence in traits important to population persistence in specific environments.

  9. Variation in DNA binding constants with a change in geometry of ternary copper(II) complexes with N2O donor Schiff base and cyanate or dicyanamide

    NASA Astrophysics Data System (ADS)

    Jana, Subrata; Santra, Ramesh Chandra; Das, Saurabh; Chattopadhyay, Shouvik

    2014-09-01

    Two new copper(II) complexes, [Cu(L)(OCN)] (1) and [CuL(dca)]n (2), where HL = 2-(-(2-(diethylamino)ethylimino)methyl)naphthalen-1-ol, dca = N(CN)2-, have been synthesized and characterized by elemental analysis, IR, UV-VIS spectroscopy and single crystal X-ray diffraction studies. Complex 1 has square planar and complex 2 square pyramidal geometries in solid state around metal centre. Interactions of the complexes with calf thymus DNA (CT DNA) were studied by UV-VIS spectroscopy. Binding constant and site size of interaction were determined. Binding site size and intrinsic binding constant K revealed complex 1 interacted with calf thymus DNA better than complex 2.

  10. Alternative splicing in the fiddler crab cognate ecdysteroid receptor: variation in receptor isoform expression and DNA binding properties in response to hormone.

    PubMed

    Durica, David S; Das, Sunetra; Najar, Fares; Roe, Bruce; Phillips, Barret; Kappalli, Sudha; Anilkumar, Gopinathan

    2014-09-15

    RXR cDNA cloning from three Uca species led to the identification of 4 conserved isoforms, indicative of alternative splicing in the hinge and ligand binding domains (LBD). Sequencing of overlapping clones from a Ucapugilator genomic library identified EcR isoforms matching previously identified cDNA variants; in addition, a cryptic exon in the LBD was detected and evidence for expression of this new isoform was obtained from next-generation sequencing. RNA-seq analysis also identified a new amino terminal EcR variant. EcR and RXR transcript abundance increases throughout ovarian maturation in U. pugilator, while cognate receptor transcript abundance remains constant in a related Indo-Pacific species with a different reproductive strategy. To examine if crab RXR LBD isoforms have different physical properties in vitro, electromobility shift assays were performed with different EcR isoforms. The cognate crab and fruit fly receptors differ in their responses to hormone. Ecdysteroids did not increase DNA binding for the crab heterodimers, while ecdysteroids stimulate binding for Drosophilamelanogaster EcR/USP heterodimers. In swapping experiments, UpEcR/USP heterodimers did not show ligand-responsive differences in DNA binding; both crab RXR LBD isoforms, however, conferred ligand-responsive increases in DNA binding with DmEcRs. These data indicate that both UpRXR LBD isoforms can heterodimerize with the heterologous DmEcR receptors and promote ligand and DNA binding. Unresponsiveness of the cognate receptors to ecdysteroid, however, suggest additional factors may be required to mediate endogenous, perhaps isoform-specific, differences in EcR conformation, consistent with previously reported effects of UpRXR isoforms on UpEcR ligand-binding affinities.

  11. Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA.

    PubMed

    Yannic, Glenn; Basset, Patrick; Büchi, Lucie; Hausser, Jacques; Broquet, Thomas

    2012-06-01

    We investigated sex specificities in the evolutionary processes shaping Y chromosome, autosomes, and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal, and biparentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it was mostly due to genetic variance among populations within valleys, whereas the opposite was observed on other markers. In addition, there was no pattern of isolation by distance for the Y, whereas there was strong isolation by distance on mtDNA and autosomes. We use a hierarchical island model of coancestry dynamics to discuss the relative roles of the microevolutionary forces that may induce such patterns. We conclude that sex-biased dispersal is the most important driver of the observed genetic structure, but with an intriguing twist: it seems that dispersal is strongly male biased at large spatial scale, whereas it is mildly biased in favor of females at local scale. These results add to recent reports of scale-specific sex-biased dispersal patterns, and emphasize the usefulness of the Y chromosome in conjunction with mtDNA and autosomes to infer sex specificities.

  12. Variation in mitochondrial DNA and allozymes discriminates early and late forms of Chinook salmon Oncorhynchus tshawytscha in the Kenai and Kasilof Rivers, AK

    USGS Publications Warehouse

    Adams, Noah S.; Spearman, William J.; Burger, Carl V.; Currens, Kenneth P.; Schreck, Carl B.; Li, Hiram W.

    1994-01-01

    Genetic differences between early and late forms of Alaskan chinook salmon (Oncorhynchus tshawytscha) were identified using two genetic approaches: mitochondrial DNA (mtDNA) analysis, and protein electrophoresis. Study populations consisted of early and late runs in each of the Kenai and Kasilof rivers in Alaska, and a population from the Minam River, Oregon. Two segments of mtDNA were amplified using the polymerase chain reaction (PCR) and digested with 14–16 restriction enzymes. Results showed that early runs were genetically similar to each other but different from the late runs. The late runs were different from each other based on the frequency of the common haplotypes. Frequency differences in shared haplotypes together with the presence of a unique haplotype separated the Minam River stock from those in Alaska. In the protein analysis, each population was examined at 30 allozyme loci. Based on 14 polymorphic loci, Minam River salmon were genetically distinct from the Alaskan populations. Within the Alaskan populations, early runs were most similar to each other but different from the late runs; the late runs were also genetically most similar to each other. Both mtDNA and allozyme analysis suggest that chinook salmon may segregate into genetically different early and late forms within a drainage.

  13. Genomic variation in maize

    SciTech Connect

    Rivin, C.J.

    1990-01-01

    We have endeavored to learn to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in F1 hybrids, tissue culture cells and regenerated plants.

  14. Temporal genetic variation of mitochondrial DNA and the female effective population size of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico.

    PubMed

    1999-07-01

    We studied genetic drift of mitochondrial DNA (mtDNA) haplotype frequencies in a natural population of red drum (Sciaenops ocellatus) from the northern Gulf of Mexico (Gulf). The amount of genetic drift observed across temporally adjacent year classes (1986-89) was used to estimate variance effective (female) population size (Nef). Nef was estimated to be 14 308 and the ratio of female effective size to adult female census size was approximately 0.004, which is among the lowest value reported for vertebrate animals. Low effective size relative to census size among red drum in the northern Gulf may result from yearly fluctuations in the number of breeding females, high variance in female reproductive success, or both. Despite low genetic effective size relative to census size, the genetic effective population size of red drum in the northern Gulf appears sufficiently large to preclude potentially deleterious effects of inbreeding.

  15. Intraspecific Genetic Variation and Phylogenetic Analysis of Dirofilaria immitis Samples from Western China Using Complete ND1 and 16S rDNA Gene Sequences

    PubMed Central

    Liu, Tianyu; Liang, Yinan; Zhong, Xiuqin; Wang, Ning; Hu, Dandan; Zhou, Xuan; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

    2014-01-01

    Dirofilaria immitis (heartworm) is the causative agent of an important zoonotic disease that is spread by mosquitoes. In this study, molecular and phylogenetic characterization of D. immitis were performed based on complete ND1 and 16S rDNA gene sequences, which provided the foundation for more advanced molecular diagnosis, prevention, and control of heartworm diseases. The mutation rate and evolutionary divergence in adult heartworm samples from seven dogs in western China were analyzed to obtain information on genetic diversity and variability. Phylogenetic relationships were inferred using both maximum parsimony (MP) and Bayes methods based on the complete gene sequences. The results suggest that D. immitis formed an independent monophyletic group in which the 16S rDNA gene has mutated more rapidly than has ND1. PMID:24639299

  16. Internal repetition and intraindividual variation in the rDNA ITS1 of the anopheles punctulatus group (Diptera: Culicidae): multiple units and rates of turnover.

    PubMed

    Bower, James E; Cooper, Robert D; Beebe, Nigel W

    2009-01-01

    The rapid divergence of repetitive sequences makes them desirable markers for phylogenetic studies of closely related groups, provided that a high level of sequence homogeneity has been maintained within species. Intraspecific polymorphisms are found in an increasing number of studies now, and this highlights the need to determine why these occur. In this study we examined intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) from a group of cryptic mosquito species. Individuals of the Anopheles punctulatus group contained multiple ITS1 length variants that ranged from 1.2 to 8.0 kb. Nucleotide and copy number variation for several homologous internal repeats is common, yet the intraspecific sequence divergence of cloned PCR isolates is comparable to that of other mosquito species (~0.2-1.5%). Most of the length variation is comprised of a 5'-ITS1 repeat that was identified as a duplication of a conserved ITS2 region. Secondary structure conservation for this repeat is pronounced and several repeat types that are highly homogenized have formed. Significant interspecific divergence indicates a high rate of evolutionary change for this spacer. A maximum likelihood tree constructed here was congruent with previous phylogenetic hypotheses and suggests that concerted evolution is also accompanied by interpopulation divergence. The lack of interindividual differences and the presence of homogenized internal repeats suggest that a high rate of turnover has reduced the overall level of variation. However, the intraindividual variation also appears to be maintained by the absence of a single turnover rate and the complex dynamics of ongoing recombination within the spacer.

  17. The effects of structural variations of thiophene-containing Ru(II) complexes on the acid-base and DNA binding properties.

    PubMed

    Yuan, Cui-Li; Zhang, An-Guo; Zheng, Ze-Bo; Wang, Ke-Zhi

    2013-03-01

    A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)₂(Hbptip)](PF₆)₂ {bpy = 2,2'-bipyridine, Hbptip = 2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid-base properties of the complex were studied by UV-visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK(a1) = 1.31 ± 0.09 and pK(a2) = 5.71 ± 0.11 with the pK(a2) associated deprotonation/protonation process occurring over 3 pK(a) units more acidic than thiophenyl-free parent complex of [Ru(bpy)₂(Hpip)]²⁺ {Hpip = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)₂(Hbptip)]²⁺ in Tris-HCl buffer (pH 7.1 and 50 mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV-visible and emission spectroscopy techniques of UV-visible and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)₂(Hip)]²⁺, [Ru(bpy)₂(Htip)]²⁺, and [Ru(bpy)₂(Haptip)]²⁺ {Hip = 1H-imidazo[4,5-f][1,10]phenanthroline, Htip = 2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip = 2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}.

  18. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution

    PubMed Central

    Modahl, Cassandra M.; Mackessy, Stephen P.

    2016-01-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  19. Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution.

    PubMed

    Modahl, Cassandra M; Mackessy, Stephen P

    2016-06-01

    Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides

  20. Genetic diversity of Histoplasma capsulatum strains isolated from Argentina based on nucleotide sequence variations in the internal transcribed spacer regions of rDNA.

    PubMed

    Landaburu, Fernanda; Cuestas, María Luján; Rubio, Andrea; Elías, Nahuel Alejandro; Daneri, Gabriela Lopez; Veciño, Cecilia; Iovannitti, Cristina A; Mujica, María Teresa

    2014-05-01

    The internal transcribed spacer (ITS) regions of rDNA genes of 49 Histoplasma capsulatum (48 from clinical samples and one from soil) isolates were examined. Nucleotide sequence heterogeneity within this region was useful for phylogenetic classification of H. capsulatum and species identification. Thus, in 45 of 49 isolates we observed higher percentages of identity in the nucleotide sequences of ITS regions when the isolates studied herein were compared with those reported in our country in the South America B clade. Phylogenetic analyses of rDNA sequences corresponding to the 537 bp of the ITS region obtained from H. capsulatum isolates assigned South America type B clade (45 isolates), North America type 1 and Asia clade (2 isolates each one). H. capsulatum strains isolated from soil and from patients living in Argentina (45 of 49) clustered together with the H. capsulatum isolates of the South America B clade. The high level of genetic similarity among our isolates suggests that almost one genetic population is present in the microenvironment. Isolates described as H. capsulatum var. capsulatum or var. farciminosum (2 isolates) did not form a monophyletic group and were found in the Asia clade. Subsequent studies are needed to properly identify these isolates.

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

    PubMed

    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.

  2. Selenite-induced variation in glutathione peroxidase activity of three mammalian cell lines: no effect on radiation-induced cell killing or DNA strand breakage

    SciTech Connect

    Sandstroem, B.E.C.; Carlsson, J.; Marklund, S.L.

    1989-02-01

    The selenium-dependent glutathione peroxidase activities of three mammalian cell lines, HT29, P31, and N-18, cultured in medium with low serum content, increased about 2-, 5-, and 40-fold, respectively, after supplementation with 100 nM selenite. Catalase, CuZn superoxide dismutase, and Mn superoxide dismutase activities were not generally influenced by selenite supplementation, and there was only a minor nonselenium-dependent glutathione peroxidase activity in the investigated cell lines. Gamma-irradiated control and selenite-supplemented cells showed no changes in the surviving fractions, as estimated by clonogenic survival or (/sup 3/H)-thymidine uptake, nor were there any significant differences between the two groups in the induction of DNA strand breaks after gamma irradiation under repairing (37 degrees C) or nonrepairing (0 degrees C) conditions. The results suggest that selenium-dependent glutathione peroxidase does not contribute significantly to the radiation resistance of cultured mammalian cells.

  3. Intraspecific variation in Radopholus similis isolates assessed with restriction fragment length polymorphism and DNA sequencing of the internal transcribed spacer region of the ribosomal RNA cistron.

    PubMed

    Elbadri, Gamal A A; De Ley, Paul; Waeyenberge, Lieven; Vierstraete, Andy; Moens, Maurice; Vanfleteren, Jacques

    2002-02-01

    Restriction fragment length polymorphism and direct sequencing of the internal transcribed spacer rDNA region of 19 isolates of Radopholus similis yielded significant diversity, both among isolates and within some individuals. Restriction fragment length polymorphism with HaeIII, AluI and Tru9I yielded two sets of patterns. Digestion with RsaI revealed one or two supernumerary bands in single nematodes from five isolates, and sequencing confirmed microheterogeneity in four of these. Phylogenetic analysis grouped most isolates closely together, except for the five isolates with additional bands for RsaI. Our data reveal more population structure than previously found and lend further support to the synonymy of R. similis and 'Radopholus citrophilus'.

  4. Genetic variation in one-carbon metabolism in relation to genome-wide DNA methylation in breast tissue from heathy women.

    PubMed

    Song, Min-Ae; Brasky, Theodore M; Marian, Catalin; Weng, Daniel Y; Taslim, Cenny; Llanos, Adana A; Dumitrescu, Ramona G; Liu, Zhenua; Mason, Joel B; Spear, Scott L; Kallakury, Bhaskar V S; Freudenheim, Jo L; Shields, Peter G

    2016-03-09

    Single nucleotide polymorphisms (SNPs) in one-carbon metabolism genes and lifestyle factors (alcohol drinking and breast folate) may be determinants of whole-genome methylation in the breast. DNA methylation profiling was performed using the Illumina Infinium HumanMethylation450 BeadChip in 81 normal breast tissues from women undergoing reduction mammoplasty and no history of cancer. ANCOVA, adjusting for age, race and BMI, was used to identify differentially-methylated (DM) CpGs. Gene expression, by the Affymetrix GeneChip Human Transcriptome Array 2.0, was correlated with DM. Biological networks of DM genes were assigned using Ingenuity Pathway Analysis. Fifty-seven CpG sites were DM in association with eight SNPs in FTHFD, MTHFD1, MTHFR, MTR, MTRR, and TYMS (P <5.0 x 10(-5)); 56% of the DM CpGs were associated with FTHFD SNPs, including DM within FTHFD. Gene expression was negatively correlated with FTHFD methylation (r=-0.25, P=0.017). Four DM CpGs identified by SNPs in MTRR, MTHFR, and FTHFD were significantly associated with alcohol consumption and/or breast folate. The top biological network of DM CpGs was associated with Energy Production, Molecular Transportation, and Nucleic Acid Metabolism. This is the first comprehensive study of the association between SNPs in one-carbon metabolism genes and genome-wide DNA methylation in normal breast tissues. These SNPs, especially FTHFD, as well as alcohol intake and folate exposure, appear to affect DM in breast tissues of healthy women. The finding that SNPs in FTHFD and MTR are associated with their own methylation is novel and highlights a role for these SNPs as cis-methylation quantitative trait loci.

  5. Evolution of the polyploid north-west Iberian Leucanthemum pluriflorum clan (Compositae, Anthemideae) based on plastid DNA sequence variation and AFLP fingerprinting

    PubMed Central

    Greiner, Roland; Vogt, Robert; Oberprieler, Christoph

    2013-01-01

    Background and Aims The genus Leucanthemum is a species-rich polyploid complex from southern and central Europe, comprising 41 species with ploidy ranging from 2x to 22x. The present contribution aims at reconstructing the evolutionary history of a geographically isolated species group (the L. pluriflorum clan) from the north-west Iberian Peninsula comprising the diploid L. pluriflorum, the tetraploids L. ircutianum subsp. pseudosylvaticum and L. × corunnense (a putative hybrid taxon based on crossing between L. pluriflorum and L. merinoi), and the hexaploids L. sylvaticum and L. merinoi. Methods Chromosome number variation (determined flow cytometrically) and sequence variation were analysed for two intergenic spacer regions on the plastid genome (psbA-trnH and trnC-petN) for individuals from 54 populations in combination with amplified fragment length polymorphism (AFLP) fingerprinting of 246 representative individuals from these populations. Key Results Plastid sequence data revealed that all surveyed members of the L. pluriflorum clan possess plastid haplotypes that are closely related to each other and distinctly separated from other Leucanthemum species. AFLP fingerprinting resulted in allopolyploid fragment patterns for most of the polyploid populations, except for the tetraploid L. × corunnense and a further tetraploid population in northern Galicia, which cluster with the diploids rather than with the other polyploids. In silico modelling of (auto)tetraploid AFLP genotypes further corroborates the allopolyploid nature of L. ircutianum subsp. pseudosylvaticum, L. sylvaticum and L. merinoi. Conclusions The present study provides evidence for recognizing one diploid (L. pluriflorum), one autotetraploid (L. corunnense), one allotetraploid (L. pseudosylvaticum) and one allohexaploid (L. sylvaticum with the two geographically and ecologically differentiated subspecies subsp. sylvaticum and subsp. merinoi) in the L. pluriflorum clan. It also has implications

  6. 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.

    PubMed

    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'.

  7. Variation of DNA Fragmentation Levels During Density Gradient Sperm Selection for Assisted Reproduction Techniques: A Possible New Male Predictive Parameter of Pregnancy?

    PubMed

    Muratori, Monica; Tarozzi, Nicoletta; Cambi, Marta; Boni, Luca; Iorio, Anna Lisa; Passaro, Claudia; Luppino, Benedetta; Nadalini, Marco; Marchiani, Sara; Tamburrino, Lara; Forti, Gianni; Maggi, Mario; Baldi, Elisabetta; Borini, Andrea

    2016-05-01

    Predicting the outcome of in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) is one main goal of the present research on assisted reproduction. To understand whether density gradient centrifugation (DGC), used to select sperm, can affect sperm DNA integrity and impact pregnancy rate (PR), we prospectively evaluated sperm DNA fragmentation (sDF) by TUNEL/PI, before and after DGC. sDF was studied in a cohort of 90 infertile couples the same day of IVF/ICSI treatment. After DGC, sDF increased in 41 samples (Group A, median sDF value: 29.25% [interquartile range, IQR: 16.01-41.63] in pre- and 60.40% [IQR: 32.92-93.53] in post-DGC) and decreased in 49 (Group B, median sDF value: 18.84% [IQR: 13.70-35.47] in pre- and 8.98% [IQR: 6.24-15.58] in post-DGC). PR was 17.1% and 34.4% in Group A and B, respectively (odds ratio [OR]: 2.58, 95% confidence interval [CI]: 0.95-7.04, P = 0.056). After adjustment for female factor, female and male age and female BMI, the estimated OR increased to 3.12 (95% CI: 1.05-9.27, P = 0.041). According to the subgroup analysis for presence/absence of female factor, heterogeneity in the association between the Group A and B and PR emerged (OR: 4.22, 95% CI: 1.16-15.30 and OR: 1.53, 95% CI: 0.23-10.40, respectively, for couples without, n = 59, and with, n = 31, female factor).This study provides the first evidence that the DGC procedure produces an increase in sDF in about half of the subjects undergoing IVF/ICSI, who then show a much lower probability of pregnancy, raising concerns about the safety of this selection procedure. Evaluation of sDF before and after DGC configures as a possible new prognostic parameter of pregnancy outcome in IVF/ICSI. Alternative sperm selection strategies are recommended for those subjects who undergo the damage after DGC.

  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.

    PubMed

    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.

  9. Population Structure of mtDNA Variation due to Pleistocene Fluctuations in the South American Maned Wolf (Chrysocyon brachyurus, Illiger, 1815): Management Units for Conservation.

    PubMed

    González, Susana; Cosse, Mariana; Franco, María del Rosario; Emmons, Louise; Vynne, Carly; Duarte, José Maurício Barbanti; Beccacesi, Marcelo D; Maldonado, Jesús E

    2015-01-01

    The maned wolf (Chrysocyon brachyurus) is one of the largest South American canids, and conservation across this charismatic carnivore's large range is presently hampered by a lack of knowledge about possible natural subdivisions which could influence the population's viability. To elucidate the phylogeographic patterns and demographic history of the species, we used 2 mtDNA markers (D-loop and cytochrome b) from 87 individuals collected throughout their range, in Argentina, Bolivia, Brazil, and Uruguay. We found moderate levels of haplotype and nucleotide diversity, and the 14 D-loop haplotypes were closely related. Genetic structure results revealed 4 groups, and when coupled with model inferences from a coalescent analysis, suggested that maned wolves have undergone demographic fluctuations due to changes in climate and habitat during the Pleistocene glaciation period approximately 24000 years before present (YBP). This genetic signature points to an event that occurred within the timing estimated for the start of the contraction of the Cerrado around 50000 YBP. Our results reveal a genetic signature of population size expansion followed by contraction during Pleistocene interglaciations, which had similar impacts on other South American mammals. The 4 groups should for now be considered management units, within which future monitoring efforts should be conducted independently.

  10. Rescue of the highly virulent classical swine fever virus strain "Koslov" from cloned cDNA and first insights into genome variations relevant for virulence.

    PubMed

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Risager, Peter Christian; Nielsen, Jens; Belsham, Graham J; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun

    2014-11-01

    Classical swine fever virus (CSFV) strain "Koslov" is highly virulent with a mortality rate of up to 100% in pigs. In this study, we modified non-functional cDNAs generated from the blood of Koslov virus infected pigs by site-directed mutagenesis, removing non-synonymous mutations step-by-step, thereby producing genomes encoding the consensus amino acid sequence. Viruses rescued from the construct corresponding to the inferred parental form were highly virulent, when tested in pigs, with infected animals displaying pronounced clinical symptoms leading to high mortality. The reconstruction therefore gave rise to a functional cDNA corresponding to the highly virulent Koslov strain of CSFV. It could be demonstrated that two single amino acid changes (S763L and P968H) in the surface structural protein E2 resulted in attenuation in the porcine infection system while another single amino acid change within the nonstructural protein NS3 (D2183G) reduced virus growth within cells in vitro.

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

    PubMed

    Rapson, Sara; Wu, Man; Okada, Shoko; Das, Alpana; Shrestha, Pushkar; Zhou, Xue-Rong; Wood, Craig; Green, Allan; Singh, Surinder; Liu, Qing

    2015-01-01

    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 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.

  12. Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains.

    PubMed

    Wang, Bin; Jiang, Jianping; Xie, Feng; Li, Cheng

    2013-03-01

    Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.

  13. [The genetic structure of chum salmon (Oncorhynchus keta Walbaum) populations inferred from the nucleotide variation of the mitochondrial DNA cytochrome b gene].

    PubMed

    Bachevskaia, L T; Pereverzeva, V A; Malinina, T V

    2011-11-01

    The nucleotide sequences of a fragment of the mitochondrial DNA cytochrome b gene were determined in 12 chum salmon populations from the Russian Far East. The level of genetic diversity in the chum salmon populations from the Iturup Island, northern coast of the Sea of Okhotsk, and Anadyr' River was found to be higher than in the populations from Kamchatka and Sakhalin, which may be related to the history of their origin and dispersal. The proportions of intrapopulation genetic variability (F(ct)) and interpopulation genetic variability within the groups (F(sc)) account for 90.87 and 0.9%, respectively, and the intergroup component (F(st)) comprises 8.23%. The predominance of one haplotype, B1, which is common for all populations studied, and a low share of intergroup variability suggest the beginning of colonization by the species of the given region from a common source (group of founders) and a relatively recent time of divergence of the chum salmon populations from the region examined.

  14. Chloroplast DNA analysis of Tunisian cork oak populations (Quercus suber L.): sequence variations and molecular evolution of the trnL (UAA)-trnF (GAA) region.

    PubMed

    Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi

    2016-10-24

    Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.

  15. Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

    PubMed Central

    Zarrin, Majid; Erfaninejad, Maryam

    2016-01-01

    Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates. PMID:27588085

  16. Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus).

    PubMed

    Marks, Ben D; Hackett, Shannon J; Capparella, Angelo P

    2002-07-01

    Studies of the distribution of South American taxa have identified several areas of endemism that may have contributed to the historical diversification of the region. We constructed a phylogeny of Glyphorynchus spirurus (Aves: Dendrocolaptidae) populations using mtDNA sequence data from portions of cytochrome b, NADH dehydrogenase subunit II (ND2), and complete NADH dehydrogenase subunit III (ND3). Using this phylogeny we evaluate five previous hypotheses of area-relationships, two based on phylogenetic studies of morphological characters in birds and three based on parsimony analysis of endemism in birds and primates. Maximum likelihood and maximum parsimony analyses recovered two phylogenetic hypotheses that differed in the placement of one of the areas. Within each of the areas of endemism, the two analyses support the same clades. Neither of the phylogenetic hypotheses for Glyphorynchus exactly matches any of the five previous hypotheses of area-relationships, although ambiguous support exists for one of them. Five areas-Central America, Inambari, Napo, Pará, and Rondônia-are supported as composites with component taxa having phylogenetic affinities with more than one area. Data reported here also indicate high levels of sequence divergence within Glyphorynchus. Genetic breaks within Glyphorynchus are only partially congruent with subspecific taxonomy. The regional sampling design used makes this study the largest scale genetic assay of a widespread Neotropical avian taxon published to date.

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

    PubMed

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

    2015-11-24

    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.

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

    PubMed Central

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

    2015-01-01

    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

  19. (Genomic variation in maize)

    SciTech Connect

    Rivin, C.J.

    1991-01-01

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  20. Identification of structural variation in mouse genomes

    PubMed Central

    Keane, Thomas M.; Wong, Kim; Adams, David J.; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

    2014-01-01

    Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation. PMID:25071822

  1. 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.

    PubMed

    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.

  2. [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)].

    PubMed

    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.

  3. Variational filtering.

    PubMed

    Friston, K J

    2008-07-01

    This note presents a simple Bayesian filtering scheme, using variational calculus, for inference on the hidden states of dynamic systems. Variational filtering is a stochastic scheme that propagates particles over a changing variational energy landscape, such that their sample density approximates the conditional density of hidden and states and inputs. The key innovation, on which variational filtering rests, is a formulation in generalised coordinates of motion. This renders the scheme much simpler and more versatile than existing approaches, such as those based on particle filtering. We demonstrate variational filtering using simulated and real data from hemodynamic systems studied in neuroimaging and provide comparative evaluations using particle filtering and the fixed-form homologue of variational filtering, namely dynamic expectation maximisation.

  4. FROG - Fingerprinting Genomic Variation Ontology.

    PubMed

    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.

  5. Identification and characterization of a catechol-o-methyltransferase cDNA in the catfish Heteropneustes fossilis: Tissue, sex and seasonal variations, and effects of gonadotropin and 2-hydroxyestradiol-17β on mRNA expression.

    PubMed

    Chaube, R; Rawat, A; Inbaraj, R M; Bobe, J; Guiguen, Y; Fostier, A; Joy, K P

    2016-12-08

    Catechol-O-methyltransferase (COMT) is involved in the methylation and inactivation of endogenous and xenobiotic catechol compounds, and serves as a common biochemical link in the catecholamine and catecholestrogen metabolism. Studies on cloning, sequencing and function characterization comt gene in lower vertebrates like fish are fewer. In the present study, a full-length comt cDNA of 1442bp with an open-reading frame (ORF) of 792bp, and start codon (ATG) at nucleotide 162 and stop codon (TAG) at nucleotide 953 was isolated and characterized in the stinging catfish Heteropneustes fossilis (accession No. KT597925). The ORF codes for a protein of 263 amino acid residues, which is also validated by the catfish transcriptome data analysis. The catfish Comt shared conserved putative structural regions important for S-adenosyl methionine (AdoMet)- and catechol-binding, transmembrane regions, two glycosylation sites (N-65 and N-91) at the N-terminus and two phosphorylation sites (Ser-235 and Thr-240) at the C-terminus. The gene was expressed in all tissues examined and the expression showed significant sex dimorphic distribution with high levels in females. The transcript was abundant in the liver, brain and gonads and low in muscles. The transcripts showed significant seasonal variations in the brain and ovary, increased progressively to the peak levels in spawning phase and then declined. The brain and ovarian comt mRNA levels showed periovulatory changes after in vivo and in vitro human chorionic gonadotropin (hCG) treatments with high fold increases at 16 and 24h in the brain and at 16h in the ovary. The catecholestrogen 2-hydroxyE2 up regulated ovarian comt expression in vitro with the highest fold increase at 16h. The mRNA and protein was localized in the follicular layer of the vitellogenic follicles and in the cytoplasm of primary follicles. The data were discussed in relation to catecholamine and catecholestrogen-mediated functions in the brain and ovary of the

  6. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    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. PMID:26244889

  7. DNA Nanotechnology

    NASA Astrophysics Data System (ADS)

    Taniguchi, Masateru; Kawai, Tomoji

    2002-11-01

    DNA is one candidate of promising molecules for molecular electronic devices, since it has the double helix structure with pi-electron bases for electron transport, the address at 0.4 nm intervals, and the self-assembly. Electrical conductivity and nanostructure of DNA and modified DNA molecules are investigated in order to research the application of DNA in nanoelectronic devices. It has been revealed that DNA is a wide-gap semiconductor in the absence of doping. The conductivity of DNA has been controlled by chemical doping, electric field doping, and photo-doping. It has found that Poly(dG)[middle dot]Poly(dC) has the best conductivity and can function as a conducting nanowire. The pattern of DNA network is controlled by changing the concentration of the DNA solution.

  8. Mitochondrial DNA.

    ERIC Educational Resources Information Center

    Wright, Russell G.; Bottino, Paul J.

    1986-01-01

    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  9. Dna Sequencing

    DOEpatents

    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.

  10. Multivalent Lipid--DNA Complexes: Distinct DNA Compaction Regimes

    NASA Astrophysics Data System (ADS)

    Evans, Heather M.; Ahmad, A.; Ewert, K.; Safinya, C. R.

    2004-03-01

    Cationic liposomes (CL), while intrinsically advantageous in comparison to viruses, still have limited success for gene therapy and require more study. CL spontaneously self-assemble with DNA via counterion release, forming small particles approximately 200nm in diameter. X-ray diffraction reveals CL-DNA structures that are typically a multilamellar organization of lipids with DNA intercalated between the layers. We explore the structural properties of CL-DNA complexes formed with new multivalent lipids (Ewert et al, J. Med. Chem. 2002; 45:5023) that range from 2+ to 16+. Contrary to a simple prediction for the DNA interaxial spacing d_DNA based on a geometrical space-filling model, these lipids show dramatic DNA compaction, down to d_DNA ˜ 25 ÅVariations in the membrane charge density, σ _M, lead to distinct spacing regimes. We propose that this DNA condensation is controlled by a unique locking mechanism between the DNA double helix and the large, multivalent lipid head groups. Funded by NSF DMR-0203755 and NIH GM-59288.

  11. High resolution optical DNA mapping

    NASA Astrophysics Data System (ADS)

    Baday, Murat

    Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

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

    PubMed

    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.

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

    SciTech Connect

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

    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.

  14. DNA Immunization

    PubMed Central

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed. PMID:24510291

  15. Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA

    SciTech Connect

    Tsodikov, Oleg V.; Biswas, Tapan

    2011-09-06

    An essential protein, DnaA, binds to 9-bp DNA sites within the origin of replication oriC. These binding events are prerequisite to forming an enigmatic nucleoprotein scaffold that initiates replication. The number, sequences, positions, and orientations of these short DNA sites, or DnaA boxes, within the oriCs of different bacteria vary considerably. To investigate features of DnaA boxes that are important for binding Mycobacterium tuberculosis DnaA (MtDnaA), we have determined the crystal structures of the DNA binding domain (DBD) of MtDnaA bound to a cognate MtDnaA-box (at 2.0 {angstrom} resolution) and to a consensus Escherichia coli DnaA-box (at 2.3 {angstrom}). These structures, complemented by calorimetric equilibrium binding studies of MtDnaA DBD in a series of DnaA-box variants, reveal the main determinants of DNA recognition and establish the [T/C][T/A][G/A]TCCACA sequence as a high-affinity MtDnaA-box. Bioinformatic and calorimetric analyses indicate that DnaA-box sequences in mycobacterial oriCs generally differ from the optimal binding sequence. This sequence variation occurs commonly at the first 2 bp, making an in vivo mycobacterial DnaA-box effectively a 7-mer and not a 9-mer. We demonstrate that the decrease in the affinity of these MtDnaA-box variants for MtDnaA DBD relative to that of the highest-affinity box TTGTCCACA is less than 10-fold. The understanding of DnaA-box recognition by MtDnaA and E. coli DnaA enables one to map DnaA-box sequences in the genomes of M. tuberculosis and other eubacteria.

  16. DNA ligases.

    PubMed

    Tabor, S

    2001-05-01

    DNA ligases catalyze the formation of phosphodiester bonds between juxtaposed 5' phosphate and a 3'-hydroxyl terminus in duplex DNA. This activity can repair single-stranded nicks in duplex DNA and join duplex DNA restriction fragments having either blunt ends or homologous cohesive ends. Two ligases are used for nucleic acid research and their reaction conditions and applications are described in this unit: E. coli ligase and T4 ligase. These enzymes differ in two important properties. One is the source of energy: T4 ligase uses ATP, while E. coli ligase uses NAD. Another important difference is their ability to ligate blunt ends; under normal reaction conditions, only T4 DNA ligase will ligate blunt ends.

  17. Intra-individual internal transcribed spacer 1 (ITS1) and ITS2 ribosomal sequence variation linked with multiple rDNA loci: a case of triploid Atractolytocestus huronensis, the monozoic cestode of common carp.

    PubMed

    Králová-Hromadová, Ivica; Stefka, Jan; Spakulová, Marta; Orosová, Martina; Bombarová, Marta; Hanzelová, Vladimíra; Bazsalovicsová, Eva; Scholz, Tomás

    2010-02-01

    Complete sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) and karyological characters of the monozoic (unsegmented) tapeworm Atractolytocestus huronensis Anthony, 1958 (Cestoda: Caryophyllidea) from Slovakia were analysed, revealing considerable intra-genomic variability and triploidy in all analysed specimens. Analysis of 20 sequences of each ITS1 and ITS2 spacer yielded eight and 10 different sequence types, respectively. In individual tapeworms, two to four ITS1 and three to four ITS2 sequence types were found. Divergent intra-genomic ITS copies were mostly induced by nucleotide substitutions and different numbers of short repetitive motifs within the sequence. In addition, triploidy was found to be a common feature of A. huronensis. The karyotype of Slovakian A. huronensis possesses three sets of chromosomes (3n=24, n=4m+3st+1minute chromosome), similar to the previously described triploidy in conspecific tapeworms from North America. Fluorescent in situ hybridisation (FISH) with a ssrDNA probe revealed two distinct rDNA clusters for each homologue of the triplet number 2. To date, A. huronensis is the only cestode species in which intra-individual ITS sequence variants were found in parallel with its triploid nature and multiple rDNA loci. Some of these molecular and genetic features were observed in several other species of basal or nearly basal tapeworms of the orders Caryophyllidea and Diphyllobothriidea, which indicates that the phenomena may be characteristic for evolutionarily lower tapeworms and deserve more attention in future studies.

  18. Natural transformation and phase variation modulation in Neisseria meningitidis.

    PubMed

    Alexander, Heather L; Richardson, Anthony R; Stojiljkovic, Igor

    2004-05-01

    Neisseria meningitidis has evolved the ability to control the expression-state of numerous genes by phase variation. It has been proposed that the process aids this human pathogen in coping with the diversity of microenvironments and host immune systems. Therefore, increased frequencies of phase variation may augment the organism's adaptability and virulence. In this study, we found that DNA derived from various neisserial co-colonizers of the human nasopharynx increased N. meningitidis switching frequencies, indicating that heterologous neisserial DNA modulates phase variation in a transformation-dependent manner. In order to determine whether the effect of heterologous DNA was specific to the Hb receptor, HmbR, we constructed a Universal Rates of Switching cassette (UROS). With this cassette, we demonstrated that heterologous DNA positively affects phase variation throughout the meningococcal genome, as UROS phase variation frequencies were also increased in the presence of neisserial DNA. Overexpressing components of the neisserial mismatch repair system partially alleviated DNA-induced changes in phase variation frequencies, thus implicating mismatch repair titration as a cause of these transformation-dependent increases in switching. The DNA-dependent effect on phase variation was transient and may serve as a mechanism for meningococcal genetic variability that avoids the fitness costs encountered by global mutators.

  19. Patenting DNA.

    PubMed

    Bobrow, Martin; Thomas, Sandy

    2002-12-01

    The protection of inventions based on human DNA sequences has been achieved mainly through application of the patent system. Over the past decade, there has been continuing debate about whether this use of intellectual property rights is acceptable. Companies and universities have been active during this period in filing thousands of patent applications. Although many have argued that to claim a DNA sequence in a patent is to claim a discovery, patent law allows discoveries that are useful to be claimed as part of an invention. As the technology to isolate DNA sequences has advanced, the criterion for inventiveness, necessary for any invention to be eligible for filing, has become more difficult to justify in the case of claims to DNA sequences. Moreover, the discovery that a gene is associated with a particular disease is, it is argued, to discover a fact about the world and undeserving of the status of an invention. Careful examination of the grounds for allowing the patenting of DNA sequences as research tools suggests such rewards will rarely be justified. The patenting of DNA sequences as chemical intermediates necessary for the manufacture of therapeutic proteins is, however, reasonable given that the information within the sequence is applied to produce a tangible substance which has application as a medicine. Despite the legal, technical and political complexities of applying the flexibilities with the current law, it is argued that much could be achieved in the area of patenting DNA by raising the thresholds for patentability.

  20. DNA-DNA interaction beyond the ground state

    NASA Astrophysics Data System (ADS)

    Lee, D. J.; Wynveen, A.; Kornyshev, A. A.

    2004-11-01

    The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic “snap-shot” recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a “torsional alignment transition,” which is first order for nonhomologous DNA and weaker order for homologous sequences.

  1. DNA-DNA interaction beyond the ground state.

    PubMed

    Lee, D J; Wynveen, A; Kornyshev, A A

    2004-11-01

    The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic "snap-shot" recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a "torsional alignment transition," which is first order for nonhomologous DNA and weaker order for homologous sequences.

  2. Genomic variation in maize. Progress report, 1990

    SciTech Connect

    Rivin, C.J.

    1990-12-31

    We have endeavored to learn to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in F1 hybrids, tissue culture cells and regenerated plants.

  3. Dancing DNA.

    ERIC Educational Resources Information Center

    Pennisi, Elizabeth

    1991-01-01

    An imaging technique that uses fluorescent dyes and allows scientists to track DNA as it moves through gels or in solution is described. The importance, opportunities, and implications of this technique are discussed. (KR)

  4. Characterization of group A Streptococcus strains recovered from Mexican children with pharyngitis by automated DNA sequencing of virulence-related genes: unexpectedly large variation in the gene (sic) encoding a complement-inhibiting protein.

    PubMed Central

    Mejia, L M; Stockbauer, K E; Pan, X; Cravioto, A; Musser, J M

    1997-01-01

    Sequence variation was studied in several target genes in 54 strains of group A Streptococcus (GAS) cultured from children with pharyngitis in Mexico City. Although 16 distinct emm alleles were identified, only 4 had not been previously described. Virtually all bacteria (31 of 33 [94%] with the streptococcal pyrogenic exotoxin gene (speA) had emm1-related, emm3, or emm6 alleles. The gene (sic) encoding an extracellular GAS protein that inhibits complement function was unusually variable among isolates with the emm1 family of alleles, with a total of seven variants identified. The data suggest that many GAS strains infecting Mexican children are genetically similar to organisms commonly encountered in the United States and western Europe. Sequence variation in the sic gene is useful for rapid differentiation among GAS isolates with the emm1 family of alleles. PMID:9399523

  5. DNA adductomics.

    PubMed

    Balbo, Silvia; Turesky, Robert J; Villalta, Peter W

    2014-03-17

    Systems toxicology is a broad-based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term exposome has been employed to refer to the totality of all exposures, and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics, and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the (32)P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. Although triple quadrupole and ion trap mass spectrometry, particularly when using multistage scanning (LC-MS(n)), have shown promise in the field of DNA adductomics, it is anticipated that high-resolution and accurate-mass LC-MS(n) instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should also benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other -omics tools will contribute greatly to the field of systems toxicology.

  6. Fleet DNA (Presentation)

    SciTech Connect

    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.

  7. What Is Mitochondrial DNA?

    MedlinePlus

    ... 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 ...

  8. Final report [DNA Repair and Mutagenesis - 1999

    SciTech Connect

    Walker, Graham C.

    2001-05-30

    The meeting, titled ''DNA Repair and Mutagenesis: Mechanism, Control, and Biological Consequences'', was designed to bring together the various sub-disciplines that collectively comprise the field of DNA Repair and Mutagenesis. The keynote address was titled ''Mutability Doth Play Her Cruel Sports to Many Men's Decay: Variations on the Theme of Translesion Synthesis.'' Sessions were held on the following themes: Excision repair of DNA damage; Transcription and DNA excision repair; UmuC/DinB/Rev1/Rad30 superfamily of DNA polymerases; Cellular responses to DNA damage, checkpoints, and damage tolerance; Repair of mismatched bases, mutation; Genome-instability, and hypermutation; Repair of strand breaks; Replicational fidelity, and Late-breaking developments; Repair and mutation in challenging environments; and Defects in DNA repair: consequences for human disease and aging.

  9. DNA vaccines

    NASA Astrophysics Data System (ADS)

    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.

  10. Ancient DNA

    PubMed Central

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets. PMID:15875564

  11. Perturbation of DNA tertiary structure by physical and chemical carcinogens: effects on DNA repair processes.

    PubMed

    Pedrini, A M; Tornaletti, S; Barabino, S; Menichini, P; Fronza, G; Abbondandolo, A

    1989-01-01

    DNA within the cell is organized into higher-order structures characterized by negative supercoiling. Supercoiling is a property of any DNA molecule lacking ends capable of rotation. Parameters defining the properties of supercoiled DNA are significant for the description of the reactive state of DNA molecules. We have investigated whether physical and chemical DNA modifying agents alter the parameters describing the DNA tertiary structure. The variations in DNA tertiary structure of partially relaxed topoisomers obtained from plasmid DNA have been studied by one dimensional agarose gel electrophoresis, a technique allowing the measurement of alterations in the degree of supercoiling equivalent to fractions of superhelical turns. Unwinding angles of 8.5 degrees for pyrimidine dimers and of 8.5 degrees for acetyl-4-hydroxyaminoquinoline-I-oxide (Ac-4-HAQO) adducts have been determined by titrating for each topoisomers the number of damaged sites necessary to reduce the superhelical turns by one. Analogous unwinding was observed for topoisomers obtained from in vivo irradiated plasmid DNA. We have also shown that local alterations in DNA structure caused by UV irradiation inhibit bacterial type I DNA topoisomerases. In addition, we have demonstrated that E. coli mutants lacking DNA topoisomerase I are sensitive to UV light. The pronounced inhibition of DNA synthesis as well as the chromosome instability observed after UV irradiation of this strain, suggest that DNA topoisomerase I might be involved in those cellular responses elicited by the proximity of damaged bases to sites of active replication.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. Individual epigenetic variation: When, why, and so what?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. DNA Music.

    ERIC Educational Resources Information Center

    Miner, Carol; della Villa, Paula

    1997-01-01

    Describes an activity in which students reverse-translate proteins from their amino acid sequences back to their DNA sequences then assign musical notes to represent the adenine, guanine, cytosine, and thymine bases. Data is obtained from the National Institutes of Health (NIH) on the Internet. (DDR)

  14. DNA Investigations.

    ERIC Educational Resources Information Center

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  15. Synthetic DNA

    PubMed Central

    O’ Driscoll, Aisling; Sleator, Roy D.

    2013-01-01

    With world wide data predicted to exceed 40 trillion gigabytes by 2020, big data storage is a very real and escalating problem. Herein, we discuss the utility of synthetic DNA as a robust and eco-friendly archival data storage solution of the future. PMID:23514938

  16. Disorder in DNA-Linked Gold Nanoparticle Assemblies

    NASA Astrophysics Data System (ADS)

    Harris, Nolan

    2005-03-01

    We report experimental observations of the effects of disorder on the phase behavior of DNA-linked nanoparticle networks. Variation in DNA linker lengths results in different melting temperatures, and hence stabilities, of DNA-linked nanoparticle assemblies. We discovered an unusual trend in the melting temperatures, resulting from the introduction of linker DNA which produced unequal DNA duplex lengths between particles. Comparison with DNA thermodynamics proves that such an anomaly does not exist for free DNA duplex melting, and suggests the influence of disorder on the collective behavior of DNA-linked nanoparticle assemblies. This disorder, brought about by the presence of two duplexes of different length and energy between each particle pair lowers the overall stability of the network formed. 1. C.-H. Kiang, ``Phase Transition of DNA-Linked Gold Nanoparticles,'' Physica A 321 (2003) 164--169.2. N. C. Harris and C. H. Kiang, ``Disorder in DNA-Linked Gold Nanoparticle Assemblies,'' submitted (2004).

  17. Disorder in DNA-Linked Gold Nanoparticle Assemblies

    NASA Astrophysics Data System (ADS)

    Harris, Nolan C.; Kiang, Ching-Hwa

    2005-07-01

    We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a nonmonotonic “zigzag” pattern in the melting temperature as a function of DNA linker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.

  18. Establishing epigenetic variation during genome reprogramming

    PubMed Central

    2013-01-01

    Transgenerational reprogramming of DNA methylation is important for transposon silencing and epigenetic inheritance. A stochastic regulation of methylation states in the germline may lead to epigenetic variation and the formation of epialleles that contribute to phenotypic variation. In Arabidopsis thaliana inbred lines, the frequency of single base variation of DNA methylation is much higher than genetic mutation and, interestingly, variable epialleles are pre-methylated in the male germline. However, these same alleles are targeted for demethylation in the pollen vegetative nucleus, by a mechanism that seems to contribute to the accumulation of small RNAs that reinforce transcriptional gene silencing in the gametes. These observations are paving the way toward understanding the extent of epigenetic reprogramming in higher plants, and the mechanisms regulating the stability of acquired epigenetic states across generations. PMID:23774895

  19. Standardization of anti-DNA antibody assays.

    PubMed

    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.

  20. Diversity within the genus Elymus (Poaceae: Triticeae) II: analyses of variation within 5S nrDNA restrict membership in the genus to species with StH genomes.

    PubMed

    Baum, Bernard R; Edwards, Tara; Johnson, Douglas A

    2016-02-01

    The genus Elymus is a repository for a large number of species that have been difficult to classify by traditional techniques due to their remarkable levels of polymorphism. Following the genome analyses of Yen and Yang (Genus Elymus 5:58-362, 2013), we used sequences of the nr5SDNA to investigate diversity within those 24 species having St and H haplomes (Baum et al. Mol Genet Genomics 290:329-42, 2015) and for which the genome status was known. The present work extends this analysis to include eight species for which there was no information on genomic status. Our results show that these eight have nr5SDNA sequences that can be assigned to unit classes of orthologous sequences found in St and H haplomes, suggesting that the presence of St and H haplomes is characteristic of the genus. We then carried out a set of canonical discriminant analyses based on 247 DNA new sequences from these 8 species plus the 1054 sequences previously identified from 24 Elymus species. Sequences were analyzed to answer the following questions: Do the species integrate or are they different? Are the tetraploids different from the higher-ploid species? Are the species united within sections, or the same within regions? How do the species fare when divided according to sections? The main results of the canonical discriminant analyses are that the species are united within the tetraploids and within the hexaploids, within each region and within each section. In addition, a series of classificatory discriminant analyses showed that the identification tests are different, although not sufficiently useful for the discrimination of all the species. We also demonstrate the power of our approach by showing that the voucher for Elymus mobilis is not Elymus at all, but Leymus.

  1. DNA nanostructure immobilization to lithographic DNA arrays

    NASA Astrophysics Data System (ADS)

    Negrete, Omar D.

    Although DNA is well known for its genetic role in biology, DNA has also been sought-after as a material for the self-assembly of biological and electronic devices. Examples of DNA nanostructure construction include DNA tiled self-assembly and DNA Origami, where by controlling the sequence and concentration of DNA molecules, the rational design of geometric DNA nanostructures is possible. The assembly of DNA nanostructures takes place in solution and thus they are in disorder and require further organization to construct circuitry or devices. Hence, it is essential for future applications of this technology to develop methods to direct the placement of DNA nanostructures on a surface. To address this challenge my research examines the use of DNA microarrays to capture DNA nanostructures via DNA hybridization. Modern DNA arrays offer a high-density of sequence-specific molecular recognition sites where the addressable placement of DNA nanostructures can be achieved. Using Maskless Array Synthesizer (MAS) technology, I have characterized photolithographic DNA arrays for the hybridization of DNA complexes like large DNA molecules (> 1 kb), DNA-gold nanoparticle conjugates, and DNA Origami. Although modern photolithographic DNA arrays can possess a high-density of sequence (106/cm2), the printed DNA areas are on the order of tens of microns. Thus, I have also developed a method to reduce the DNA array spot size to nanoscale dimensions through the combined use of electron beam lithography with photolithographic DNA synthesis. This work addresses the key elements towards developing a surface patterning technology that takes advantage of DNA base-pairing for both molecular sub-assembly and surface patterning.

  2. Atomic Force Microscopy for DNA SNP Identification

    NASA Astrophysics Data System (ADS)

    Valbusa, Ugo; Ierardi, Vincenzo

    The knowledge of the effects of single-nucleotide polymorphisms (SNPs) in the human genome greatly contributes to better comprehension of the relation between genetic factors and diseases. Sequence analysis of genomic DNA in different individuals reveals positions where variations that involve individual base substitutions can occur. Single-nucleotide polymorphisms are highly abundant and can have different consequences at phenotypic level. Several attempts were made to apply atomic force microscopy (AFM) to detect and map SNP sites in DNA strands. The most promising approach is the study of DNA mutations producing heteroduplex DNA strands and identifying the mismatches by means of a protein that labels the mismatches. MutS is a protein that is part of a well-known complex of mismatch repair, which initiates the process of repairing when the MutS binds to the mismatched DNA filament. The position of MutS on the DNA filament can be easily recorded by means of AFM imaging.

  3. Antigenic variation in African trypanosomes

    PubMed Central

    Horn, David

    2014-01-01

    Studies on Variant Surface Glycoproteins (VSGs) and antigenic variation in the African trypanosome, Trypanosoma brucei, have yielded a remarkable range of novel and important insights. The features first identified in T. brucei extend from unique to conserved-among-trypanosomatids to conserved-among-eukaryotes. Consequently, much of what we now know about trypanosomatid biology and much of the technology available has its origin in studies related to VSGs. T. brucei is now probably the most advanced early branched eukaryote in terms of experimental tractability and can be approached as a pathogen, as a model for studies on fundamental processes, as a model for studies on eukaryotic evolution or often all of the above. In terms of antigenic variation itself, substantial progress has been made in understanding the expression and switching of the VSG coat, while outstanding questions continue to stimulate innovative new approaches. There are large numbers of VSG genes in the genome but only one is expressed at a time, always immediately adjacent to a telomere. DNA repair processes allow a new VSG to be copied into the single transcribed locus. A coordinated transcriptional switch can also allow a new VSG gene to be activated without any detectable change in the DNA sequence, thereby maintaining singular expression, also known as allelic exclusion. I review the story behind VSGs; the genes, their expression and switching, their central role in T. brucei virulence, the discoveries that emerged along the way and the persistent questions relating to allelic exclusion in particular. PMID:24859277

  4. Child Development and Structural Variation in the Human Genome

    ERIC Educational Resources Information Center

    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…

  5. Prokaryotic DNA ligases unwind superhelical DNA.

    PubMed

    Ivanchenko, M; van Holde, K; Zlatanova, J

    1996-09-13

    We have studied the effect on DNA topology of binding of prokaryotic DNA ligases (T4 and E. coli) to superhelical or nicked circular DNA. Performing topoisomerase I-mediated relaxation in the presence of increasing amounts of T4 ligase led to a shift in the topoisomer distribution to increasingly more negative values. This result suggested that T4 ligase unwound the DNA and was further substantiated by ligation of nicked circular molecules by E. coli DNA ligase in the presence of increasing amounts of T4 ligase. Such an experiment was possible since the two DNA ligases require different cofactors for enzymatic activity. Performing a similar experiment with reverse partners, using E. coli DNA ligase as ligand, and T4 ligase as sealing agent, we observed that the E. coli enzyme also unwound the DNA. Thus, prokaryotic DNA ligases can be added to an ever-growing list of DNA-binding proteins that unwind the DNA upon binding.

  6. Free-Floating DNA: A New Strand of Technology from the Old Spool of Thought.

    ERIC Educational Resources Information Center

    Wegmann, Larry

    1989-01-01

    A procedure for extracting DNA from yeast using common reagents and equipment is given. Suggestions for variations are provided. A second activity for building a model of DNA from toothpicks is included. (CW)

  7. First evidence of DNA methylation in insect Tribolium castaneum: environmental regulation of DNA methylation within heterochromatin.

    PubMed

    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.

  8. [Genomic variation in maize]. Final project report

    SciTech Connect

    Rivin, C.J.

    1991-12-31

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  9. Application of DNA fingerprinting in medicolegal practice.

    PubMed

    Raina, Anupuma; Dogra, T D

    2002-12-01

    Fingerprinting is thought to establish the identify of an individual in forensic cases. The technique is extensively used for forensic purposes. Deoxyribonucleic acid (DNA) is the vehicle of generational transference of heritable unit. While arching markers for genetic disease professor Alec Jeffreys discovered that certain regions of DNA showed variations in the number of tandem repeats known as variable number of tandem repeats (VNTRs). Thus DNA fingerprint was named by observing the number of repeated sequences which differ from individual to individual. The structure of DNA is quite flexible, within the nucleus of each cell resides an identical copy of the individual's genetic material, DNA. The coding regions of the genomic DNA are known as genes. The DNA fingerprinting in forensic science has generated considerable excitement in the criminal justice community. DNA fingerprinting can be applied to identify an individual in criminal and civil cases. Polymerase chain reaction has revolutionised molecular biology it has an ability to amplify (usually fewer than 3000 bp) a particular sequence of DNA into million of copies in a very short period. Consequently only a very tiny amount of an organism's DNA needs to be available originally. This property of polymerase chain reaction has enabled to analyse many forensic samples particularly which are degraded. Microsatellite DNA or commonly as short tandem repeats are scattered throughout the human genome and occur on an average of every 10,000 nucleotides. Microsatellite markers are considered to be the most powerful genetic markers. Collection, preservation and handling are the integral part of DNA fingerprinting analysis. There are various methods to isolate DNA from different biological materials but presently most of the laboratories prefer using FTA paper. The age of humans can be estimated by using DNA based on telomere shortening.

  10. Monitoring the Bending Stiffness of DNA

    NASA Astrophysics Data System (ADS)

    Yuan, Chongli; Lou, Xiongwen; Rhoades, Elizabeth; Chen, Huimin; Archer, Lynden

    2007-03-01

    In eukaryotic cells, the accessibility of genomic sequences provides an inherent regulation mechanism for gene expression through variations in bending stiffness encoded by the nucleic acid sequence. Cyclization of dsDNA is the prevailing method for determining DNA bending stiffness. Recent cyclization data for short dsDNA raises several fundamental questions about the soundness of the cyclization method, particularly in cases where the probability of highly bent DNA conformations is low. We herein evaluate the role of T4 DNA ligase in the cyclization reaction by inserting an environmental sensitive base analogue, 2-amino purine, to the DNA molecule. By monitoring the 2-AP fluorescence under standard cyclization conditions, it is found that in addition to trapping highly-bent cyclic DNA conformations, T4 DNA ligase enhances the apparent base pair flip out rate, thus exaggerating the measured flexibility. This result is further confirmed using fluorescence anisotropy experiments. We show that fluorescence resonance energy transfer (FRET) measurements on suitably labeled dsDNA provides an alternative approach for quantifying the bending stiffness of short fragments. DNA bending stiffness results obtained using FRET are compared with literature values.

  11. Structural investigation into physiological DNA phosphorothioate modification

    PubMed Central

    Lan, Wenxian; Hu, Zhongpei; Shen, Jie; Wang, Chunxi; Jiang, Feng; Liu, Huili; Long, Dewu; Liu, Maili; Cao, Chunyang

    2016-01-01

    DNA phosphorothioate (PT) modification, with sulfur replacing a nonbridging phosphate oxygen in a sequence and stereo specific manner, is a novel physiological variation in bacteria. But what effects on DNA properties PT modification has is still unclear. To address this, we prepared three double-stranded (ds) DNA decamers, d(CGPXGCCGCCGA) with its complementary strand d(TCGGCGPXGCCG) (where X = O or S, i.e., PT-free dsDNA, [Sp, Sp]-PT dsDNA or [Rp, Rp]-PT dsDNA) located in gene of Streptomyces lividans. Their melting temperature (Tm) measurement indicates that [Rp, Rp]-PT dsDNA is most unstable. Their electron transfer potential detection presents an order of anti-oxidation properties: Sp-PT DNA > Rp-PT DNA > PT-free DNA. Their NMR structures demonstrate that PT modification doesn’t change their B-form conformation. The sulfur in [Rp, Rp]-PT dsDNA locates in the major groove, with steric effects on protons in the sugar close to modification sites, resulting in its unstability, and facilitating its selectively interactions with ScoMcrA. We thought that PT modification was dialectical to the bacteria. It protects the hosting bacteria by working as antioxidant against H2O2, and acts as a marker, directing restriction enzyme observed in other hosts, like ScoMcrA, to correctly cleave the PT modified DNA, so that bacteria cannot spread and survive. PMID:27169778

  12. Mitochondrial DNA haplotype predicts deafness risk

    SciTech Connect

    Hutchin, T.; Cortopassi, G.

    1995-12-18

    Since mitochondrial DNA (mtDNA) does not recombine in humans, once deleterious variation arises within a particular mtDNA clone it remains linked to that clonal type. An A to G mutation at mtDNA position 1555 confers matrilineal deafness among Asians and others. Two major mtDNA types (I and II) have been defined in Asians by D-loop sequencing. We have determined the D-loop sequence of 8 unrelated deaf Asians bearing the 1555G mutation, and find that 7 are of type II, whereas only one is of type I. Thus the frequency of the 1555G mutation is higher in type II mtDNA than type I (P = 0.035, binomial test), and persons with type II mtDNA are more likely to become deaf. Type II mtDNAs are rare in the Caucasian population, which may explain the rarity of this form of deafness in the United States. Negative Darwinian selection is expected to rapidly eliminate mtDNAs bearing severely deleterious mutations; but mildly deleterious mutations whose phenotype is expressed after reproduction should persist on the mtDNA background in which they arose. Thus determination of mtDNA clonal type has the potential to predict human risk for diseases that are the result of mildly deleterious mtDNA mutations which confer a post-reproductive phenotype. 4 refs., 1 fig.

  13. Forensic DNA methylation profiling from evidence material for investigative leads

    PubMed Central

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-01-01

    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

  14. Forensic DNA methylation profiling from evidence material for investigative leads.

    PubMed

    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].

  15. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

    SciTech Connect

    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.

  16. DNA nanostructure meets nanofabrication.

    PubMed

    Zhang, Guomei; Surwade, Sumedh P; Zhou, Feng; Liu, Haitao

    2013-04-07

    Recent advances in DNA nanotechnology have made it possible to construct DNA nanostructures of almost arbitrary shapes with 2-3 nm of precision in their dimensions. These DNA nanostructures are ideal templates for bottom-up nanofabrication. This review highlights the challenges and recent advances in three areas that are directly related to DNA-based nanofabrication: (1) fabrication of large scale DNA nanostructures; (2) pattern transfer from DNA nanostructure to an inorganic substrate; and (3) directed assembly of DNA nanostructures.

  17. Mobile DNA in the pathogenic Neisseria

    PubMed Central

    Obergfell, Kyle P.; Seifert, H. Steven

    2015-01-01

    The genus Neisseria contains two pathogenic species of notable public health concern: Neisseria gonorrhoeae and Neisseria meningitidis. These pathogens display a notable ability to undergo frequent programmed recombination events. The recombination mediated pathways of transformation and pilin antigenic variation in the Neisseria are well studied systems that are critical for pathogenesis. Here we will detail the conserved and unique aspects of transformation and antigenic variation in the Neisseria. Transformation will be followed from initial DNA binding through recombination into the genome with consideration to the factors necessary at each step. Additional focus is paid to the unique type IV secretion system that mediates donation of transforming DNA in the pathogenic Neisseria. The pilin antigenic variation system uses programed recombinations to alter a major surface determinant which allows immune avoidance and promotes infection. We discuss the trans- and cis- acting factors which facilitate pilin antigenic variation and present the current understanding of the mechanisms involved in the process. PMID:25866700

  18. Alcohol, DNA Methylation, and Cancer

    PubMed Central

    Varela-Rey, Marta; Woodhoo, Ashwin; Martinez-Chantar, Maria-Luz; Mato, José M.; Lu, Shelly C.

    2013-01-01

    Cancer is one of the most significant diseases associated with chronic alcohol consumption, and chronic drinking is a strong risk factor for cancer, particularly of the upper aerodigestive tract, liver, colorectum, and breast. Several factors contribute to alcohol-induced cancer development (i.e., carcinogenesis), including the actions of acetaldehyde, the first and primary metabolite of ethanol, and oxidative stress. However, increasing evidence suggests that aberrant patterns of DNA methylation, an important epigenetic mechanism of transcriptional control, also could be part of the pathogenetic mechanisms that lead to alcohol-induced cancer development. The effects of alcohol on global and local DNA methylation patterns likely are mediated by its ability to interfere with the availability of the principal biological methyl donor, S-adenosylmethionine (SAMe), as well as pathways related to it. Several mechanisms may mediate the effects of alcohol on DNA methylation, including reduced folate levels and inhibition of key enzymes in one-carbon metabolism that ultimately lead to lower SAMe levels, as well as inhibition of activity and expression of enzymes involved in DNA methylation (i.e., DNA methyltransferases). Finally, variations (i.e., polymorphisms) of several genes involved in one-carbon metabolism also modulate the risk of alcohol-associated carcinogenesis. PMID:24313162

  19. Rapid Approaches Towards DNA Damage Analysis

    PubMed Central

    Crews, N.; Paidipalli, Manasa

    2013-01-01

    The severe effects of DNA damage on human health have led to a tremendous amount of research being focused. Owing to the importance of damage detection, different approaches for the detection and quantification of the damaged DNA will be presented. In this work, we have modeled DNA damage using well-known mutagens: UV radiation to create photoproducts and restriction enzyme digestion to create double strand breaks. We will show that quantitative PCR (qPCR), a widely known measure of detecting the presence of the target DNA can be used to quantify photoproducts/intramolecular DNA damage. Our results indicate that a comparison of the initial concentration available in the undamaged and the damaged samples can be used to reveal the effect of damaged DNA in its amplification. By analyzing multiple regions using this technique, their relative susceptibility to damage can be measured. We also show that high-resolution melting analysis (HRMA), a measure of the bond energy between two DNA strands, can be used to quantify double strand breaks. The strand breaks resulted in a change in the overall distribution of the bond energy thus causing variations in the melting profile. HRMA has also been examined to compare DNA damage resulting from UV-A, UV-B and UV-C irradiation. The evaluation techniques demonstrated can potentially be extended to various types of DNA damage.

  20. DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.

    PubMed

    Sucher, Nikolaus J; Hennell, James R; Carles, Maria C

    2012-01-01

    DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

  1. Systematic biases in DNA copy number originate from isolation procedures

    PubMed Central

    2013-01-01

    Background The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal. Results While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing. Conclusion These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses. PMID:23618369

  2. Electro-optical detection of single λ-DNA.

    PubMed

    Liu, Shuo; Wall, Thomas A; Ozcelik, Damla; Parks, Joshua W; Hawkins, Aaron R; Schmidt, Holger

    2015-02-07

    Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.

  3. Variation, "evolution", immortality and genetic instabilities in tumour cells.

    PubMed

    Bignold, L P

    2007-08-18

    The pathological characteristics of tumour cells often include variation of their histopathological features (i.e. "degrees of de-differentiation") between cases of the same tumour type and between different foci within individual tumours. Usually, only a few cell lines from tumours are immortal. Currently, somatic mutation, replicative infidelity of DNA and aneuploidy are suggested as alternative mechanisms of genomic disturbance underlying tumours. Nevertheless, apart from Hansemann's ideas of "anaplasia" and "de-differentiation" (proposed in the 1890s), and supposed "evolutionary themes" in cancer cell biology, little has been published concerning how histopathologic variation and immortality in tumour cells might arise. This paper reviews applications of the concepts of "variation" to tumours, including concepts of "evolution" and "cellular Darwinism". It is proposed that combinations of somatic mutation, DNA replicative infidelity and aneuploidy may explain the variabilities in tumours, and provide immortality in occasional tumour cells. A possible model involves (i) an initial somatic mutation causing reduced replicative fidelity of DNA, which could be variable in intensity, and thus give rise to variations between cases; (ii) a phase of replicative infidelity of DNA causing daughter cells lines to develop various abnormalities to different degrees, and hence provide for variation between areas of the same tumour. As a last event (iii) occasional asymmetric chromosomal distributions (aneuploidy) might "refresh" the ability of a daughter cell to replicate DNA faithfully causing them to become immortal. Thus extensively mutant and variable, hyperploid, and occasionally immortal cells might arise.

  4. DNA ligase I, the replicative DNA ligase.

    PubMed

    Howes, Timothy R L; Tomkinson, Alan E

    2012-01-01

    Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.

  5. Keeping mtDNA in Shape between Generations

    PubMed Central

    Stewart, James B.; Larsson, Nils-Göran

    2014-01-01

    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. PMID:25299061

  6. Genetic engineering compared to natural genetic variations.

    PubMed

    Arber, Werner

    2010-11-30

    By comparing strategies of genetic alterations introduced in genetic engineering with spontaneously occurring genetic variation, we have come to conclude that both processes depend on several distinct and specific molecular mechanisms. These mechanisms can be attributed, with regard to their evolutionary impact, to three different strategies of genetic variation. These are local nucleotide sequence changes, intragenomic rearrangement of DNA segments and the acquisition of a foreign DNA segment by horizontal gene transfer. Both the strategies followed in genetic engineering and the amounts of DNA sequences thereby involved are identical to, or at least very comparable with, those involved in natural genetic variation. Therefore, conjectural risks of genetic engineering must be of the same order as those for natural biological evolution and for conventional breeding methods. These risks are known to be quite low. There is no scientific reason to assume special long-term risks for GM crops. For future agricultural developments, a road map is designed that can be expected to lead, by a combination of genetic engineering and conventional plant breeding, to crops that can insure food security and eliminate malnutrition and hunger for the entire human population on our planet. Public-private partnerships should be formed with the mission to reach the set goals in the coming decades.

  7. DNA modifications: Another stable base in DNA

    NASA Astrophysics Data System (ADS)

    Brazauskas, Pijus; Kriaucionis, Skirmantas

    2014-12-01

    Oxidation of 5-methylcytosine has been proposed to mediate active and passive DNA demethylation. Tracking the history of DNA modifications has now provided the first solid evidence that 5-hydroxymethylcytosine is a stable epigenetic modification.

  8. Photo-thermal effects in gold nanorods/DNA complexes

    NASA Astrophysics Data System (ADS)

    De Sio, Luciano; Caracciolo, Giulio; Annesi, Ferdinanda; Placido, Tiziana; Pozzi, Daniela; Comparelli, Roberto; Pane, Alfredo; Curri, Maria Lucia; Agostiano, Angela; Bartolino, Roberto

    2015-12-01

    An ingenious combination of plasmonic nanomaterials and one of the most relevant biological systems, deoxyribonucleic acid (DNA) is achieved by bioconjugating gold nanorods (GNRs) with DNA via electrostatic interaction between positively charged GNRs and negatively charged short DNA. The obtained system is investigated as a function of DNA concentration by means of gel electrophoresis, zeta-potential, DNA melting and morphological analysis. It turns out that the obtained bioconjugated systems present both effective electric charge and aggregate size that are particularly amenable for gene therapy and nanomedicine applications. Finally, the effect of the localized (photo-thermal heating) and delocalized temperature variation on the DNA melting by performing both light induced bio-transparent optical heating experiments and a thermographic analysis is investigated, demonstrating that the developed system can be exploited for monitoring nanoscale temperature variation under optical illumination with very high sensitivity.

  9. Sperm DNA oxidative damage and DNA adducts

    PubMed Central

    Jeng, Hueiwang Anna; Pan, Chih-Hong; Chao, Mu-Rong; Lin, Wen-Yi

    2015-01-01

    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

  10. Osmylated DNA, a novel concept for sequencing DNA using nanopores

    NASA Astrophysics Data System (ADS)

    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.

  11. Identification of parasite DNA in common bile duct stones by PCR and DNA sequencing

    PubMed Central

    Jang, Ji Sun; Kim, Kyung Ho; Yu, Jae-Ran

    2007-01-01

    We attempted to identify parasite DNA in the biliary stones of humans via PCR and DNA sequencing. Genomic DNA was isolated from each of 15 common bile duct (CBD) stones and 5 gallbladder (GB) stones. The patients who had the CBD stones suffered from cholangitis, and the patients with GB stones showed acute cholecystitis, respectively. The 28S and 18S rDNA genes were amplified successfully from 3 and/or 1 common bile duct stone samples, and then cloned and sequenced. The 28S and 18S rDNA sequences were highly conserved among isolates. Identity of the obtained 28S D1 rDNA with that of Clonorchis sinensis was higher than 97.6%, and identity of the 18S rDNA with that of other Ascarididae was 97.9%. Almost no intra-specific variations were detected in the 28S and 18S rDNA with the exception of a few nucleotide variations, i.e., substitution and deletion. These findings suggest that C. sinensis and Ascaris lumbricoides may be related with the biliary stone formation and development. PMID:18165713

  12. Synthesis of DNA

    DOEpatents

    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.

  13. DNA encoding a DNA repair protein

    DOEpatents

    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.

  14. DNA systematics. Volume II

    SciTech Connect

    Dutta, S.K.

    1986-01-01

    This book discusses the following topics: PLANTS: PLANT DNA: Contents and Systematics. Repeated DNA Sequences and Polyploidy in Cereal Crops. Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species. Chloropast DNA and Phylogenetic Relationships. rDNA: Evolution Over a Billion Years. 23S rRNA-derived Small Ribosomal RNAs: Their Structure and Evolution with Reference to Plant Phylogeny. Molecular Analysis of Plant DNA Genomes: Conserved and Diverged DNA Sequences. A Critical Review of Some Terminologies Used for Additional DNA in Plant Chromosomes and Index.

  15. Intraspecific mitochondrial DNA variation in North American cervids

    USGS Publications Warehouse

    Cronin, M.A.

    1992-01-01

    Symptoms appeared when quail and pheasants were fed diets containing 0.025-0.050% DDT. Symptoms appeared sooner as percentages increased. Young birds seemed more resistant than adults. Median lethal quantity for adult quail was about 1,200 mg./Kg. Young quail showed no ill-effects after ingesting 3,000 mg./Kg. during 10-week period. Adult pheasants died after ingesting 200-300 mg./Kg. Approximately 600 mg./Kg. were required to kill young pheasants. Quantities of DDT stored in tissues were not proportional to amounts administered or to duration of exposure, but were related to severity of symptoms. Concentration of DDT in breast muscles of birds killed by DDT was about 34 micrograms/Gm. in adult quail and 22 micrograms/Gm. in adult pheasants.

  16. Functionalizing Designer DNA Crystals

    NASA Astrophysics Data System (ADS)

    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

  17. Meiosis-Driven Genome Variation in Plants

    PubMed Central

    Cai, Xiwen; Xu, Steven S

    2007-01-01

    Meiosis includes two successive divisions of the nucleus with one round of DNA replication and leads to the formation of gametes with half of the chromosomes of the mother cell during sexual reproduction. It provides a cytological basis for gametogenesis and nheritance in eukaryotes. Meiotic cell division is a complex and dynamic process that involves a number of molecular and cellular events, such as DNA and chromosome replication, chromosome pairing, synapsis and recombination, chromosome segregation, and cytokinesis. Meiosis maintains genome stability and integrity over sexual life cycles. On the other hand, meiosis generates genome variations in several ways. Variant meiotic recombination resulting from specific genome structures induces deletions, duplications, and other rearrangements within the genic and non-genic genomic regions and has been considered a major driving force for gene and genome evolution in nature. Meiotic abnormalities in chromosome segregation lead to chromosomally imbalanced gametes and aneuploidy. Meiotic restitution due to failure of the first or second meiotic division gives rise to unreduced gametes, which triggers polyploidization and genome expansion. This paper reviews research regarding meiosis-driven genome variation, including deletion and duplication of genomic regions, aneuploidy, and polyploidization, and discusses the effect of related meiotic events on genome variation and evolution in plants. Knowledge of various meiosis-driven genome variations provides insight into genome evolution and genetic variability in plants and facilitates plant genome research. PMID:18645601

  18. Small polarons in dry DNA

    NASA Astrophysics Data System (ADS)

    Chacham, Helio; Alexandre, Simone S.; Soler, Jose M.; Artacho, Emilio

    2004-03-01

    The phenomenon of charge transport in DNA has been attracting attention of both biologists and physicists. From the biology side, there are evidences that charge injection can be associated to damage, mutation, and repair processes in DNA. From the physical sciences side, recent developments in nanotechnology now allow the measurement of currents through single DNA molecules in dried samples, which depict semiconductor behavior. Several mechanisms have been proposed for charge migration and transport in DNA. In that respect, detailed electrical transport measurements through DNA molecules containing identical base pairs (poly(dA)-poly(dT) and poly(dG)-poly(dC)) have been recently reported by Yoo et al [1]. These results fit extremely well a model in which the conduction is due to small polaron motion. In particular, these results indicate that the I-V characteristic of poly(dG)-poly(dC) DNA above 200 K is consistent with a small polaron hopping regime with an activation energy of 0.12 eV. In this work [2] we investigate the polaron formation in dry DNA by applying ab initio calculations to both neutral and charged fragments of dry poly(dG)-poly(dC). Our calculations show that the hole polaron in dry poly(dG)-poly(dC) DNA is a clear case of small polaron. This is verified by four basic properties: (i) the small variation of the polaron binding energy as a function of the DNA fragment size, for small fragment sizes, which is an indication of polaron localization; (ii) the fact that the width of the uppermost valence band is an order of magnitude smaller than the polaron binding energy; (iii) the explicit localization of the hole wavefunction for the largest considered fragment (four base pairs), indicated by the fact that about half of the norm of the hole is localized on a single guanine site; (iv) the localization of structural deformations at the nucleotides where the hole is concentrated. Our calculations also give a polaron binding energy of 0.30 eV. This allows

  19. DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

    DOE PAGES

    Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; ...

    2016-03-09

    The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

  20. DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

    SciTech Connect

    Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; Johnson, Reid C.; Leng, Fenfei

    2016-03-09

    The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.

  1. Molecular DNA switches and DNA chips

    NASA Astrophysics Data System (ADS)

    Sabanayagam, Chandran R.; Berkey, Cristin; Lavi, Uri; Cantor, Charles R.; Smith, Cassandra L.

    1999-06-01

    We present an assay to detect single-nucleotide polymorphisms on a chip using molecular DNA switches and isothermal rolling- circle amplification. The basic principle behind the switch is an allele-specific oligonucleotide circularization, mediated by DNA ligase. A DNA switch is closed when perfect hybridization between the probe oligonucleotide and target DNA allows ligase to covalently circularize the probe. Mismatches around the ligation site prevent probe circularization, resulting in an open switch. DNA polymerase is then used to preferentially amplify the closed switches, via rolling-circle amplification. The stringency of the molecular switches yields 102 - 103 fold discrimination between matched and mismatched sequences.

  2. Molecular Darwinism: the contingency of spontaneous genetic variation.

    PubMed

    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.

  3. An integrated epigenetic and genetic analysis of DNA methyltransferase genes (DNMTs) in tumor resistant and susceptible chicken lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Both epigenetic alterations and genetic variations play essential roles in tumorigenesis. The epigenetic modification of DNA methylation is catalyzed and maintained by the DNA methyltransferases (DNMT3a, DNMT3b and DNMT1). DNA mutations and DNA methylation profiles of DNMTs themselves and their rela...

  4. The Role of Methylation of DNA in Environmental Adaptation

    PubMed Central

    Flores, Kevin B.; Wolschin, Florian; Amdam, Gro V.

    2013-01-01

    Methylation of DNA is an epigenetic mechanism that influences patterns of gene expression. DNA methylation marks contribute to adaptive phenotypic variation but are erased during development. The role of DNA methylation in adaptive evolution is therefore unclear. We propose that environmentally-induced DNA methylation causes phenotypic heterogeneity that provides a substrate for selection via forces that act on the epigenetic machinery. For example, selection can alter environmentally-induced methylation of DNA by acting on the molecular mechanisms used for the genomic targeting of DNA methylation. Another possibility is that specific methylation marks that are environmentally-induced, yet non-heritable, could influence preferential survival and lead to consistent methylation of the same genomic regions over time. As methylation of DNA is known to increase the likelihood of cytosine-to-thymine transitions, non-heritable adaptive methylation marks can drive an increased likelihood of mutations targeted to regions that are consistently marked across several generations. Some of these mutations could capture, genetically, the phenotypic advantage of the epigenetic mark. Thereby, selectively favored transitory alterations in the genome invoked by DNA methylation could ultimately become selectable genetic variation through mutation. We provide evidence for these concepts using examples from different taxa, but focus on experimental data on large-scale DNA sequencing that expose between-group genetic variation after bidirectional selection on honeybees, Apis mellifera. PMID:23620251

  5. Single-cell chromatin accessibility reveals principles of regulatory variation.

    PubMed

    Buenrostro, Jason D; Wu, Beijing; Litzenburger, Ulrike M; Ruff, Dave; Gonzales, Michael L; Snyder, Michael P; Chang, Howard Y; Greenleaf, William J

    2015-07-23

    Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. Although recent advances have improved our ability to document cellular phenotypic variation, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the 'regulome'.

  6. DNA Nanotechnology-- Architectures Designed with DNA

    NASA Astrophysics Data System (ADS)

    Han, Dongran

    As the genetic information storage vehicle, deoxyribonucleic acid (DNA) molecules are essential to all known living organisms and many viruses. It is amazing that such a large amount of information about how life develops can be stored in these tiny molecules. Countless scientists, especially some biologists, are trying to decipher the genetic information stored in these captivating molecules. Meanwhile, another group of researchers, nanotechnologists in particular, have discovered that the unique and concise structural features of DNA together with its information coding ability can be utilized for nano-construction efforts. This idea culminated in the birth of the field of DNA nanotechnology which is the main topic of this dissertation. The ability of rationally designed DNA strands to self-assemble into arbitrary nanostructures without external direction is the basis of this field. A series of novel design principles for DNA nanotechnology are presented here, from topological DNA nanostructures to complex and curved DNA nanostructures, from pure DNA nanostructures to hybrid RNA/DNA nanostructures. As one of the most important and pioneering fields in controlling the assembly of materials (both DNA and other materials) at the nanoscale, DNA nanotechnology is developing at a dramatic speed and as more and more construction approaches are invented, exciting advances will emerge in ways that we may or may not predict.

  7. DNA vaccines: a simple DNA sensing matter?

    PubMed

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J

    2013-10-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA plasmid can be expressed in stromal cells (i.e., muscle cells) as well as DCs, where these antigens are processed and presented to naïve CD4 or CD8 T cells either by direct or cross presentation, respectively; and (2) the transfected DNA plasmid itself may bind to an un-identified cytosolic DNA sensor and activate the TBK1-STING pathway and the production of type I interferons (IFNs) which function as an adjuvant. Recent studies investigating double-stranded cytosolic DNA sensor(s) have highlighted new mechanisms in which cytosolic DNA may release secondary metabolites, which are in turn recognized by a novel DNA sensing machinery. Here, we discuss these new metabolites and the possibilities of translating this knowledge into improved immunogenicity for DNA vaccines.

  8. DNA methylation in endometriosis (Review)

    PubMed Central

    KOUKOURA, OURANIA; SIFAKIS, STAVROS; SPANDIDOS, DEMETRIOS A.

    2016-01-01

    Endometriosis is defined by the presence and growth of functional endometrial tissue, outside the uterine cavity, primarily in the ovaries, pelvic peritoneum and rectovaginal septum. Although it is a benign disease, it presents with malignant characteristics, such as invasion to surrounding tissues, metastasis to distant locations and recurrence following treatment. Accumulating evidence suggests that various epigenetic aberrations may play an essential role in the pathogenesis of endometriosis. Aberrant DNA methylation represents a possible mechanism repsonsible for this disease, linking gene expression alterations observed in endometriosis with hormonal and environmental factors. Several lines of evidence indicate that endometriosis may partially be due to selective epigenetic deregulations influenced by extrinsic factors. Previous studies have shed light into the epigenetic component of endometriosis, reporting variations in the epigenetic patterns of genes known to be involved in the aberrant hormonal, immunologic and inflammatory status of endometriosis. Although recent studies, utilizing advanced molecular techniques, have allowed us to further elucidate the possible association of DNA methylation with altered gene expression, whether these molecular changes represent the cause or merely the consequence of the disease is a question which remains to be answered. This review provides an overview of the current literature on the role of DNA methylation in the pathophysiology and malignant evolution of endometriosis. We also provide insight into the mechanisms through which DNA methylation-modifying agents may be the next step in the research of the pharmaceutical treatment of endometriosis. PMID:26934855

  9. DNA Repair by Reversal of DNA Damage

    PubMed Central

    Yi, Chengqi; He, Chuan

    2013-01-01

    Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology. PMID:23284047

  10. Quantitative DNA fiber mapping

    DOEpatents

    Gray, Joe W.; Weier, Heinz-Ulrich G.

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  11. Variations in Sexual Behavior.

    ERIC Educational Resources Information Center

    Juhasz, Anne McCreary

    1983-01-01

    Questions are raised about the difficulty of defining normal and atypical sexual behavior. Variations from normalcy that students, parents, and educators are most likely to encounter are discussed. The importance of dealing with variations in ways that are best for the individual and the group is emphasized. (PP)

  12. Poxvirus DNA Replication

    PubMed Central

    Moss, Bernard

    2013-01-01

    Poxviruses are large, enveloped viruses that replicate in the cytoplasm and encode proteins for DNA replication and gene expression. Hairpin ends link the two strands of the linear, double-stranded DNA genome. Viral proteins involved in DNA synthesis include a 117-kDa polymerase, a helicase–primase, a uracil DNA glycosylase, a processivity factor, a single-stranded DNA-binding protein, a protein kinase, and a DNA ligase. A viral FEN1 family protein participates in double-strand break repair. The DNA is replicated as long concatemers that are resolved by a viral Holliday junction endonuclease. PMID:23838441

  13. Analyzing the dynamics of DNA replication in Mammalian cells using DNA combing.

    PubMed

    Bialic, Marta; Coulon, Vincent; Drac, Marjorie; Gostan, Thierry; Schwob, Etienne

    2015-01-01

    How cells duplicate their chromosomes is a key determinant of cell identity and genome stability. DNA replication can initiate from more than 100,000 sites distributed along mammalian chromosomes, yet a given cell uses only a subset of these origins due to inefficient origin activation and regulation by developmental or environmental cues. An impractical consequence of cell-to-cell variations in origin firing is that population-based techniques do not accurately describe how chromosomes are replicated in single cells. DNA combing is a biophysical DNA fiber stretching method which permits visualization of ongoing DNA synthesis along Mb-sized single-DNA molecules purified from cells that were previously pulse-labeled with thymidine analogues. This allows quantitative measurements of several salient features of chromosome replication dynamics, such as fork velocity, fork asymmetry, inter-origin distances, and global instant fork density. In this chapter we describe how to obtain this information from asynchronous cultures of mammalian cells.

  14. Total variation regularization with bounded linear variations

    NASA Astrophysics Data System (ADS)

    Makovetskii, Artyom; Voronin, Sergei; Kober, Vitaly

    2016-09-01

    One of the most known techniques for signal denoising is based on total variation regularization (TV regularization). A better understanding of TV regularization is necessary to provide a stronger mathematical justification for using TV minimization in signal processing. In this work, we deal with an intermediate case between one- and two-dimensional cases; that is, a discrete function to be processed is two-dimensional radially symmetric piecewise constant. For this case, the exact solution to the problem can be obtained as follows: first, calculate the average values over rings of the noisy function; second, calculate the shift values and their directions using closed formulae depending on a regularization parameter and structure of rings. Despite the TV regularization is effective for noise removal; it often destroys fine details and thin structures of images. In order to overcome this drawback, we use the TV regularization for signal denoising subject to linear signal variations are bounded.

  15. VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.

    PubMed

    Schaafsma, Gerard C P; Vihinen, Mauno

    2016-04-01

    The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences, and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations, VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, that is, all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels, function, structure, and property, annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and evidence code terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP Web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences.

  16. DNA Damage, DNA Repair, Aging, and Neurodegeneration.

    PubMed

    Maynard, Scott; Fang, Evandro Fei; Scheibye-Knudsen, Morten; Croteau, Deborah L; Bohr, Vilhelm A

    2015-09-18

    Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span.

  17. Variational Transition State Theory

    SciTech Connect

    Truhlar, Donald G.

    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.

  18. Tissue culture-induced DNA methylation polymorphisms in repetitive DNA of tomato calli and regenerated plants.

    PubMed

    Smulders, M J; Rus-Kortekaas, W; Vosman, B

    1995-12-01

    The propagation of plants through tissue culture can induce a variety of genetic and epigenetic changes. Variation in DNA methylation has been proposed as a mechanism that may explain at least a part of these changes. In the present study, the methylation of tomato callus DNA was compared with that of leaf DNA, from control or regenerated plants, at MspI/HpaII sites around five middle-repetitive sequences. Although the methylation of the internal cytosine in the recognition sequence CCGG varied from zero to nearly full methylation, depending on the probe used, no differences were found between callus and leaf DNA. For the external cytosine, small differences were revealed between leaf and callus DNA with two probes, but no polymorphisms were detected among DNA samples of calli or DNA samples of leaves of regenerated plants. When callus DNA cut with HindIII was studied with one of the probes, H9D9, most of the signal was found in high-molecular-weight DNA, as opposed to control leaf DNA where almost all the signal was in a fragment of 530 bp. Also, an extra fragment of 630 bp was found in the callus DNA that was not present in control leaf DNA. Among leaves of plants regenerated from tissue culture, the 630-bp fragment was found in 10 of 68 regenerated plants. This 630-bp fragment was present among progeny of only 4 of these 10 plants after selfing, i.e. it was partly inherited. In these cases, the fragment was not found in all progeny plants, indicat