WorldWideScience

Sample records for ancestry-sensitive dna markers

  1. Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans

    NARCIS (Netherlands)

    P. Kersbergen (Paula); K. van Duijn (Kate); A. Kloosterman (Ate); J.T. den Dunnen (Johan); M.H. Kayser (Manfred); P. de Knijff (Peter)

    2009-01-01

    textabstractBackground: The identification and use of Ancestry-Sensitive Markers (ASMs), i.e. genetic polymorphisms facilitating the genetic reconstruction of geographical origins of individuals, is far from straightforward. Results: Here we describe the ascertainment and application of five differe

  2. Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans

    Directory of Open Access Journals (Sweden)

    den Dunnen Johan T

    2009-10-01

    Full Text Available Abstract Background The identification and use of Ancestry-Sensitive Markers (ASMs, i.e. genetic polymorphisms facilitating the genetic reconstruction of geographical origins of individuals, is far from straightforward. Results Here we describe the ascertainment and application of five different sets of 47 single nucleotide polymorphisms (SNPs allowing the inference of major human groups of different continental origin. For this, we first used 74 cell lines, representing human males from six different geographical areas and screened them with the Affymetrix Mapping 10K assay. In addition to using summary statistics estimating the genetic diversity among multiple groups of individuals defined by geography or language, we also used the program STRUCTURE to detect genetically distinct subgroups. Subsequently, we used a pairwise FST ranking procedure among all pairs of genetic subgroups in order to identify a single best performing set of ASMs. Our initial results were independently confirmed by genotyping this set of ASMs in 22 individuals from Somalia, Afghanistan and Sudan and in 919 samples from the CEPH Human Genome Diversity Panel (HGDP-CEPH Conclusion By means of our pairwise population FST ranking approach we identified a set of 47 SNPs that could serve as a panel of ASMs at a continental level.

  3. DNA methylation markers for breast cancer prognosis

    OpenAIRE

    Dedeurwaerder, Sarah; Fuks, François

    2012-01-01

    Currently, most of the prognostic and predictive gene expression signatures emerging for breast cancer concern the tumor component. In Dedeurwaerder et al. we show that DNA methylation profiling of breast tumors is a particularly sensitive means of capturing features of the immune component of breast tumors. Most importantly, correlation is observed between T-cell marker genes and breast cancer clinical outcome.

  4. Prognostic DNA Methylation Markers for Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Siri H. Strand

    2014-09-01

    Full Text Available Prostate cancer (PC is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181 and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.

  5. Prognostic DNA methylation markers for prostate cancer.

    Science.gov (United States)

    Strand, Siri H; Orntoft, Torben F; Sorensen, Karina D

    2014-01-01

    Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC. PMID:25238417

  6. Pollen dispersal analysis using DNA markers

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    2014-01-01

    Full Text Available Modes of pollen dispersal are important for plant ecology, conservation, and evolutionary biology as pollen-mediated gene flow connects one generation of sexually-reproducing plants to the next. With the development of DNA molecular techniques, molecular markers (especially microsatellite markers have replaced traditional physical markers for pollen flow analysis. Methods of paternity assignment with maximum likelihood and Bayesian inference have greatly improved the estimation of pollen flow characteristics with regard to direction, distance, and strength. Pollen dispersal curves have been characterized by single parameter, two-parameter, multi-parameter, and two-component composite models to better evaluate the shape of dispersal distributions. These innovative techniques and methods have been successfully applied to assess pollination patterns in studies of plant sexual polymorphism, population connectivity, and natural hybridization, which, in turn, have provided important insights into basic theories of evolution, ecology, and conservation. In the coming years, high-throughput sequencing technologies are expected to accelerate the application of molecular marker-based pollen flow analysis across a wide range of plant taxa.

  7. Utilization of Cotton DNA Markers in Cotton Breeding

    Institute of Scientific and Technical Information of China (English)

    CANTRELL Roy G; XIAO Jin-hua

    2008-01-01

    @@ Informative,portable,and efficient DNA markers have the potential to accelerate genetic gain in cotton breeding.Discovery and widespread application of DNA markers to cotton has traditionally lagged behind other major crop species.The reasons are well known to ICGI participants.The foundation for widespread development and application of DNA markers has been laid by ICGI and research within the private sector.

  8. Evaluation of DNA markers for fish identification

    Directory of Open Access Journals (Sweden)

    Maria Vittoria Riina

    2013-02-01

    Full Text Available Species substitution is a common commercial fraud, mainly applied to fish species. It is thus important to have analytical methods for species identification. DNA analysis can be a suitable technique: some mitochondrial genes are actually recognized as valuable markers for species discrimination. Aim of this work was thus to evaluate the capability of cytb and COI genes to discriminate the species of fish (n=89 which are commonly substituted. In the last four years of activity on field, the laboratory analysed, using the FINS method (Forensically Informative Nucleotide Sequencing, 146 samples, belonging to several fish species, sent by veterinary officers in the frame of their activities of control: in this work, results about number and kind of fraud are reported. Additionally, samples directly purchased by the lab were examined. The obtained results showed that the genetic markers have a high discriminatory power and that the method is highly suitable. The frequent detection of species substitution in the samples collected on field showed the importance of controlling this kind of frauds in the fish market.

  9. Statistics of DNA Markers - RGP gmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available RGP gmap Statistics of DNA Markers Data detail Data name Statistics of DNA Markers Description of data conte...ate History of This Database Site Policy | Contact Us Statistics of DNA Markers - RGP gmap | LSDB Archive ...

  10. Sexing birds using random amplified polymorphic DNA (RAPD) markers

    NARCIS (Netherlands)

    Lessells, C.M.; Mateman, A.C.

    1998-01-01

    We used random amplified polymorphic DNA (RAPD) markers to sex birds from small tissue (usually blood) samples. Arbitrarily chosen 10-mer PCR primers were screened with DNA from known-sex individuals for the production of a bright female-specific band. Suitable primers were found for seven bird spec

  11. Generation and application of VNTR DNA markers to fruit trees

    International Nuclear Information System (INIS)

    Multilocus and single locus variable number of tandem repeat (VNTR) DNA markers have been used to identify individuals and races as well as to detect genetic linkage with genes coding for the traits of interest. Multilocus VNTR markers are advantageous for identification, while single locus markers are suitable for linkage analysis. DNA fingerprint information was used to identify mango cultivars and to analyse the genetic relatedness of 20 mango cultivars. Individual specific patterns were obtained for each cultivar and the probability of obtaining a similar pattern for two different cultivars was found to be 9.4 x 10-6. Individual specific patterns were also obtained for the Carica species and for the tomato and avocado cultivars. Evolutionary trees, based on genetic distances, were established for mango cultibars, for tomato cultivars and accessions, and for several Persea species and avocado races. Genetic analysis aimed at detecting allelic and linked bands were carried out using VNTR multilocus probes in the family structures of avocado and mango. Using this tool, a very high level of heterozygosity was detected in these loci in avocado. By applying several methodologies of linkage analysis, a specific avocado DNA fingerprint band (p8) was identified as being genetically linked to a gene coding for avocado fruit skin colour. The complexity of linkage analysis of the multiband pattern led us to generate simple sequence repeat (SSR) single locus DNA markers to identify linkage with the traits of interest in avocado. Because of their characteristics, these SSRs are the markers of choice for human geneticists. The generation scheme for SSR markers, as well as their evaluation, are presented. The avocado SSR markers are now being mapped. (author). 16 refs, 2 figs, 2 tabs

  12. Male-specific DNA markers from African catfish (Clarias gariepinus).

    Science.gov (United States)

    Kovács, B; Egedi, S; Bártfai, R; Orbán, L

    2000-01-01

    We searched for sex-specific DNA sequences in the male and female genomes of African catfish, Clarias gariepinus (Burchell, 1822) by comparative random amplified polymorphic DNA (RAPD) assays performed on pooled DNA samples. Two sex-linked RAPD markers were identified from the male DNA pool and confirmed on individual samples, showing good agreement with phenotypic sex. Both markers were isolated, cloned and characterized. The first marker (CgaY1) was nearly 2.6 kb long, while the length of second one (CgaY2) was 458 bp. Southern blot analysis with a CgaY1 probe showed strong hybridizing fragments only in males and not in females under stringent conditions, indicating the presence of multiple copies of CgaY1 in the male genome. When tested by zoo blot on the genomes of two closely related species from the Clariidae family, CgaY1 hybridized to the DNA of Heterobranchus longifilis and generated a faint male-specific band at low stringency. CgaY2 produced similar hybridization pattern in both sexes of C. gariepinus, C. macrocephalus and H. longifilis. Specific primers were designed to the sequences and the markers were amplified in multiplex PCR reactions together with a control band common to all individuals. This allowed for rapid, molecular sexing of the species on the basis of a simple three band (male) versus one band (female) pattern. According to our knowledge these are the first sex-specific DNA markers isolated from a siluroid fish species. PMID:11766847

  13. DNA markers provide insight about common lime in historicalplantings

    DEFF Research Database (Denmark)

    Hansen, Ole Kim; Thomsen, Pernille; Rasmussen, Christine Waage

    2014-01-01

    As part of the restoration process of an avenue of common lime (Tilia × europaea) from 1760 in the Royal Danish Gardens, all remaining trees were genotyped with DNA markers before they were felled. As such, information about the nature of the plant material (clonal versus non-clonal) and mode...

  14. Selection Of Drought Resistant Mutants In Rice Using DNA Markers

    International Nuclear Information System (INIS)

    In recent years, the marker - assisted selection (MAS) strategy have been used for selection of traits that are difficult and costly performed measurement and score. Selection for a well-developed root system could improve the drought resistance of rice as the plant would avoid water stress by absorbing water from the soil. There were several reports on map construction and identification of the markers tightly linked to morphological and physiological traits related to drought resistance in rice, in particular, root traits in upland and lowland rice (Champoux et al., 1995; Ray et al., 1996; Price et al., 1997, 2000; Yadav et al., 1997). In this report, we present the results on selection of drought resistance mutants in rice using the DNA markers tightly linked to root traits favorable for drought resistance. The mutant rice lines were obtained from irradiated seeds and calluses by gamma ray. The selection was performed at M2 mutants using the DNA markers linked to maximum root length (MRL), root weight to shoot weight ratio (RW/SR), and weight of deep root to shoot weight ratio (DRW/SR). The obtained results showed that there were many lines possessed drought resistant markers. In addition, there is a number of lines have altered genome. Several lines having drought markers proved to be more resistant to drought in green-house test. These lines could be useful for further test and development of drought resistant varieties. (author)

  15. DNA fingerprinting of safflower irradiation induced mutants by RAPD markers

    International Nuclear Information System (INIS)

    RAPD markers were utilized to identify the genetic differences and the genetic relationship between 8 safflower genotypes i.e. seven induced mutants namely Mut 1 H, Mut 2 H2 , Mut3, Mut4, Mut 5 , Mut6, Mut 7 and the parental variety Giza 1. Ten arbitrary primers were used; different primers generated polymorphic RAPD profiles. The number of amplified DNA amplicons across the ten primers ranged from seven amplicons for the primer OBC-18 to 17 amplicons for the primersOPA-03 and OPA-04. However the number of polymorphic amplicons ranged from 1 for the primer OPB-3 to 14 amplicons for the primers OPA-03 and OPA-17. The percentage of polymorphism ranged from 9.09 % for the primer OPB- 03 to 100% for the primer OPC-17.The highest genetic similarity (94%) was found between Mut 4 and Mut 7 and the lowest (79.0%) was found between Mut 1 and Giza 1. Seventeen positive and four negative unique RAPD markers were identified across the 8 safflower genotypes. The parent Giza 1 was characterized by one positive unique marker amplified by OPA-03 primer at the molecular weight of 2000 bp as well as, two negative unique markers generated by the OPB-6 and OPB-5 primers at the molecular weights of 1150 and 800 bp., respectively. The mutant 1 showed highest number of positive unique markers (8) generated by OPA-3 primer at the molecular weights of 1400, 800 ,700 and 600 bp, OPB-04 at the molecular weight 2000 bp., OPB-06 primers at the molecular weight of 900 bp., OPB-05 primer at the molecular weight of 500 bp., and OPA-04 primer at the molecular weight of 600 bp. Mut 2 was identified by two positive unique markers generated by the OPB-05 and OPA-03 primers at the molecular weights of 1500 and 500 bp respectively, However the Mut 3 was characterized by one positive unique marker amplified by OPC-17 primer at the molecular weight 550 bp., there is no unique number was found to characterize the mutant 4. The Mut 5 identified by one positive uniquemarker generated by OPA-04 Primer at the

  16. Development, distribution and application of DNA markers for cereal research

    International Nuclear Information System (INIS)

    DNA probes and primers are important resources for molecular genetic research and molecular breeding. Presently, more than 2500 wheat probes, 400 barley probes, 800 foxtail, pearl millet and finger millet probes, and approximately 150 wheat microsatellite (SSR) primer pairs have been developed and maintained in our DNA Resource Centre at the John Innes Centre (JIC). To accelerate probe and primer distribution, an 'anchor set' and a 'supplementary anchor set', containing 73 and 31 wheat RFLP probes, respectively, and a standard set of 42 primer pairs for wheat SSR markers were selected. Similarly, a set of 52 pearl millet probes has been selected for distribution. More than 8000 wheat RFLP probes, 2000 wheat SSR primer pairs, 700 millet probes and 200 barley probes have been distributed to more than 250 research groups in 40 countries. Our wheat and millet probes and other grass cDNA probes have been used for comparative genetic studies. The revealed conservation of gene content and gene order has been used to construct maps of many grass species and to predict the locations of key genes from one crop species to another. Developed SSR and AFLP markers in wheat, barley and millet are particularly suited for genetic diversity analyses and map construction. (author)

  17. RECRUITMENT OF GROUPER BROODSTOCK ON THE BASIS OF SINGLE LOCUS DNA MARKERS

    OpenAIRE

    Rodrigues Kenneth Francis; Zaidi Ahmad Tani; Syarul Nataqain Baharum

    2016-01-01

    The manuscript describes the development and application of molecular markers for the selection of broodstock of two species of Groupers Epinephelus fuscoguttatus and E. corallicola using single locus DNA markers. The article presents a database of verified DNA markers which can be applied for fish breeding and genetic selection.

  18. Identification of Epinephelus malabaricus and Epinephelus coioides using DNA markers

    Institute of Scientific and Technical Information of China (English)

    WANG Shifeng; DU Jiaying; WANG Jun; DING Shaoxiong

    2007-01-01

    Using multi-molecular marker technologies and based on morphological criteria, the genetic relationship between Epinepheelus malabaricus and E.coioides was examined in the hope of resolving the long-standing issue of identifying these two species.Results showed that: (1) E.coioides and E.malabaricus should be identified as two species, the consistency of mitochondrial DNA cytochrome b gene sequence between E.malabaricus and E.coioides is 94.4%, and the genetic similarity by AFLP was 0.753 9; (2) Hybridization exists between E.malabaricus and E.coioides, the specific RAPD and AFLP fragments are found to be useful in the identification of these two species, and the genetic properties (both with exterior and inheritance) of hybrid is significantly biased to the male parents; and (3) AFLP was a potentially powerful tool in constructing the genetic linkage map for these two groupers.

  19. Detailed information of DNA markers - RGP gmap2000 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available iosciencedbc.jp/togodb/view/rgp_gmap2000_marker#en Data acquisition method As the source of polymorphic DNA markers for map construct...ion, we used two types of cDNA clones (callus and roots)

  20. Intelligent DNA-based molecular diagnostics using linked genetic markers

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  1. Optimizing reproducibility evaluation for random amplified polymorphic DNA markers.

    Science.gov (United States)

    Ramos, J R; Telles, M P C; Diniz-Filho, J A F; Soares, T N; Melo, D B; Oliveira, G

    2008-01-01

    The random amplified polymorphic DNA (RAPD) technique is often criticized because it usually shows low levels of repeatability; thus it can generate spurious bands. These problems can be partially overcome by rigid laboratory protocols and by performing repeatability tests. However, because it is expensive and time-consuming to obtain genetic data twice for all individuals, a few randomly chosen individuals are usually selected for a priori repeatability analysis, introducing a potential bias in genetic parameter estimates. We developed a procedure to optimize repeatability analysis based on RAPD data, which was applied to evaluate genetic variability in three local populations of Tibochina papyrus, an endemic Cerrado plant found in elevated rocky fields in Brazil. We used a simulated annealing procedure to select the smallest number of individuals that contain all bands and repeated the analyses only for those bands that were reproduced in these individuals. We compared genetic parameter estimates using HICKORY and POPGENE softwares on an unreduced data set and on data sets in which we eliminated bands based on repeatability of individuals selected by simulated annealing and based on three randomly selected individuals. Genetic parameter estimates were very similar when we used the optimization procedure to reduce the number of bands analyzed, but as expected, selecting only three individuals to evaluate the repeatability of bands produced very different estimates. We conclude that the problems of repeatability attributed to RAPD markers could be due to bias in the selection of loci and primers and not necessarily to the RAPD technique per se. PMID:19065774

  2. Platelet mitochondrial DNA methylation: a potential new marker of cardiovascular disease

    OpenAIRE

    Baccarelli, Andrea A.; Byun, Hyang-Min

    2015-01-01

    Background: Platelets are critical in the etiology of cardiovascular disease (CVD), and the mitochondria in these cells serve as an energy source for platelet function. Epigenetic factors, especially DNA methylation, have been employed as markers of CVD. Unlike nuclear DNA methylation, mitochondrial DNA (mtDNA) methylation has not been widely studied, in part, due to debate about its existence and role. In this study, we examined platelet mtDNA methylation in relation to CVD. Results: We meas...

  3. Genetic diversity of sago palm in Indonesia based on chloroplast DNA (cpDNA markers

    Directory of Open Access Journals (Sweden)

    MEMEN SURAHMAN

    2010-07-01

    Full Text Available Abbas B, Renwarin Y, Bintoro MH, Sudarsono, Surahman M, Ehara H (2010 Genetic diversity of sago palm in Indonesia based on chloroplast DNA (cpDNA markers. Biodiversitas 11: 112-117. Sago palm (Metroxylon sagu Rottb. was believed capable to accumulate high carbohydrate content in its trunk. The capability of sago palm producing high carbohydrate should be an appropriate criterion for defining alternative crops in anticipating food crisis. The objective of this research was to study genetic diversity of sago palm in Indonesia based on cpDNA markers. Total genome extraction was done following the Qiagen DNA isolation protocols 2003. Single Nucleotide Fragments (SNF analyses were performed by using ABI Prism GeneScanR 3.7. SNF analyses detected polymorphism revealing eleven alleles and ten haplotypes from total 97 individual samples of sago palm. Specific haplotypes were found in the population from Papua, Sulawesi, and Kalimantan. Therefore, the three islands will be considered as origin of sago palm diversities in Indonesia. The highest haplotype numbers and the highest specific haplotypes were found in the population from Papua suggesting this islands as the centre and the origin of sago palm diversities in Indonesia. The research had however no sufficient data yet to conclude the Papua origin of sago palm. Genetic hierarchies and differentiations of sago palm samples were observed significantly different within populations (P=0.04574, among populations (P=0.04772, and among populations within the island (P=0.03366, but among islands no significant differentiations were observed (P= 0.63069.

  4. Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers.

    Science.gov (United States)

    Fahner, Nicole A; Shokralla, Shadi; Baird, Donald J; Hajibabaei, Mehrdad

    2016-01-01

    In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding. PMID:27310720

  5. DNA marker mining of ILSTS035 microsatellite locus on chromosome 6 of Hanwoo cattle

    Indian Academy of Sciences (India)

    Jung-Sou Yeo; Jea-Young Lee; Jae-Woo Kim

    2004-12-01

    We describe tests for detecting and locating quantitative trait loci (QTL) for traits in Hanwoo cattle. From results of a permutation test to detect QTL for marbling, we selected the microsatellite locus ILSTS035 on chromosome 6 for further analysis. -means clustering analysis applied to five traits and nine DNA markers in ILSTS035 resulted in three cluster groups. Finally we employed the bootstrap test method to calculate confidence intervals using the resampling method to find major DNA markers. We conclude that the major markers of ILSTS035 locus on chromosome 6 of Hanwoo cattle are markers 235 bp and 266 bp.

  6. Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars.

    Science.gov (United States)

    Kawamura, Kazutaka; Kawanabe, Takahiro; Shimizu, Motoki; Okazaki, Keiichi; Kaji, Makoto; Dennis, Elizabeth S; Osabe, Kenji; Fujimoto, Ryo

    2016-03-01

    Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia, and most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system. Self-incompatibility is successfully used for the production of F1 hybrid seeds in B. rapa vegetables to avoid contamination by non-hybrid seeds, and the strength of self-incompatibility is important for harvesting a highly pure F1 seeds. Prediction of agronomically important traits such as disease resistance based on DNA markers is useful. In this dataset, we identified the S haplotypes by DNA markers and evaluated the strength of self-incompatibility in Chinese cabbage inbred lines. The data described the predicted disease resistance to Fusarium yellows or clubroot in 22 Chinese cabbage inbred lines using gene associated or gene linked DNA markers. PMID:26862564

  7. Validation and use of DNA markers for sex determination in papaya (Carica papaya)

    International Nuclear Information System (INIS)

    Profitable papaya production requires female and hermaphrodite plants in higher number than male plants. This is only possible if sex of plants is determined at an early growth stage. The present study was conducted to validate sex-linked DNA markers using plants from two Pakistani papaya varieties and subsequently utilize them for determination of sex in juvenile papaya plants. One hundred and five plants (including 49 male and 56 female) of two Pakistani Papaya varieties at flowering stage were screened with six DNA markers viz., W-11, T12, SDP, Napf-76Napf-76, PKBT4 and PKBT5. All male plants exhibited amplification of sex-linked alleles with markers T12 and W11, whereas, 96% and 95% of female plants showed the absence of sex-linked allele with these markers, respectively. Markers SDP, PKBT5 and Napf-76 showed the presence of sex-linked alleles in 98%, 96% and 93% of male plants, respectively, whereas the same markers showed the absence of sex-linked alleles in 100%, 96% and 94% of female plants. One marker, PKBT4 could not produce expected PCR amplification reported previously. The five DNA markers were further used to screen 171 papaya seedlings. These markers clearly differentiated male and female sex types in the studied papaya plants. Results of our study are likely to facilitate Pakistani papaya breeders and growers to incorporate DNA based screening at juvenile stage to determine sex at early stage and to ensure profitable papaya production. (author)

  8. Development of Random Amplified Polymorphism DNA Markers Linked to Powdery Mildew Resistance Gene in Melon

    Directory of Open Access Journals (Sweden)

    Budi Setiadi Daryono

    2015-11-01

    Full Text Available A random amplified polymorphic DNA (RAPD marker linked to powdery mildew resistance gene (Pm-I in melon PI 371795 was reported. However, the RAPD marker has problem in scoring. To detect powdery mildew resistance gene (Pm-I in melon accurately, the RAPD marker was cloned and sequenced to design sequence characterized amplified region (SCAR markers. SCAPMAR5 marker derived from pUBC411 primer yielded a single DNA band at 1061 bp. Segregation of SCAPMAR5 marker in bulk of F2 plants demonstrated that the marker was co-segregated with RAPD marker from which the SCAR marker was originated. Moreover, results of SCAR analysis in diverse melons showed SCAPMAR5 primers obtained a single 1061 bp linked to Pm-I in resistant melon PI 371795 and PMAR5. On the other hand, SCAPMAR5 failed to detect Pm-I in susceptible melons. Results of this study revealed that SCAR analysis not only confirmed melons that had been clearly scored for resistance to Pm-I evaluated by RAPD markers, but also clarified the ambiguous resistance results obtained by the RAPD markers.   Key words: Cucumis melo L., Pm-I, RAPD, SCAPMAR5

  9. A Novel Selection Marker for Efficient DNA Cloning and Recombineering in E. coli

    OpenAIRE

    Chuan-Wei Jang; Terry Magnuson

    2013-01-01

    Production of recombinant DNA in bacterial cells is an essential technique in molecular biology. Plasmids are usually maintained in an E. coli host by antibiotic selection. However, there are only a few antibiotic-resistance markers available in common use. Here we report the adoption of a novel selection marker, mfabI (mutant fabI) for plasmid propagation in E. coli. mfabI expands the limited repertoire of selection markers and allows for more efficient molecular manipulation and plasmid pro...

  10. Identification of DNA markers linked to a blast resistance gene in rice

    International Nuclear Information System (INIS)

    Identification of DNA markers closely linked to a blast (Pyricularia oryzae Cav.) resistance gene and establishment of an indirect selection method for the blast resistance gene based on linked DNA markers are reported. A pair of near isogenic lines, K80R and K79S, were developed using a local Chinese indica rice cultivar, Hong-jiao-zhan, as the resistant donor and IR24 as the recurrent parent. Ten putatitvely positive markers were identified by screening 177 mapped DNA markers. Using 143 plants composed of the F2 population of K80R/K79S, three restriction fragment length polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were verified to be closely linked to the blast resistance gene. The resistance genotypes of each F2 resistant individual were determined by inoculation of the F3 lines. RG869 was found to be most closely linked to the resistance gene, with a genetic distance of 5.1 cM. To fine map this gene with more DNA markers, the bulk segregation analysis procedure was employed to identify the random amplified polymorphic DNA (RAPD) markers linked to the resistance gene. Six of 199 arbitrary primers were able to produce positive RAPD bands. Tight linkage between the resistance gene and the three RAPD bands, each from a different primer, was confirmed after amplification of the DNA of all the F2 individuals. The linked DNA fragments were cloned and sequenced. The results of specific amplification were in agreement with those of RAPD analysis. The half-seed RAPD analysis procedure for blast resistance detection was established. The amplified DNA patterns on the extract from the endosperm half of the mature seeds were identical to those of the total DNA from the leaves. (author). 13 refs, 3 figs

  11. Identification of body fluid-specific DNA methylation markers for use in forensic science.

    Science.gov (United States)

    Park, Jong-Lyul; Kwon, Oh-Hyung; Kim, Jong Hwan; Yoo, Hyang-Sook; Lee, Han-Chul; Woo, Kwang-Man; Kim, Seon-Young; Lee, Seung-Hwan; Kim, Yong Sung

    2014-11-01

    DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science.

  12. Identification of body fluid-specific DNA methylation markers for use in forensic science.

    Science.gov (United States)

    Park, Jong-Lyul; Kwon, Oh-Hyung; Kim, Jong Hwan; Yoo, Hyang-Sook; Lee, Han-Chul; Woo, Kwang-Man; Kim, Seon-Young; Lee, Seung-Hwan; Kim, Yong Sung

    2014-11-01

    DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science. PMID:25128690

  13. Blood-derived DNA methylation markers of cancer risk.

    Science.gov (United States)

    Marsit, Carmen; Christensen, Brock

    2013-01-01

    The importance of somatic epigenetic alterations in tissues targeted for carcinogenesis is now well recognized and considered a key molecular step in the development of a tumor. Particularly, alteration of gene-specific and genomic DNA methylation has been extensively characterized in tumors, and has become an attractive biomarker of risk due to its specificity and stability in human samples. It also is clear that tumors do not develop as isolated phenomenon in their target tissue, but instead result from altered processes affecting not only the surrounding cells and tissues, but other organ systems, including the immune system. Thus, alterations to DNA methylation profiles detectable in peripheral blood may be useful not only in understanding the carcinogenic process and response to environmental insults, but can also provide critical insights in a systems biological view of tumorigenesis. Research to date has generally focused on how environmental exposures alter genomic DNA methylation content in peripheral blood. More recent work has begun to translate these findings to clinically useful endpoints, by defining the relationship between DNA methylation alterations and cancer risk. This chapter highlights the existing research linking the environment, blood-derived DNA methylation alterations, and cancer risk, and points out how these epigenetic alterations may be contributing fundamentally to carcinogenesis.

  14. Development of DNA marker for Fusarium resistance in Pisang Berangan

    International Nuclear Information System (INIS)

    Fusarium wilt (Panama disease), a disease caused by a soil-bome fungus Fusarium oxysporum f. sp. cubense, is regarded as one of the most significant threats to banana (Musa spp.) production worldwide. In Malaysia, it is affecting the Cavendish as well as Pisang Berangan which are widely planted for export as well as for local consumption. Pisang Berangan mutant line (MB96) which was obtained through induced mutation by gamma irradiation has showed certain degree of tolerance towards the disease. Attempts were made to utilise Polymerase Chain Reaction (PCR) based techniques i.e. RAPD (Random Amplified Polymorphic DNA) to screen for unique DNA sequences that are associated or closely linked to these tolerance characteristics. Four single 1 Obp primers and five duplex 1 Obp primers combinations were used to detect polymorphism between the DNA of control and 4 mutant lines micropropagated from MB96. As further control, DNA of Pisang Mas was included. Duplex arbitrary primer combinations 11-89 and single primer OPA-3 have produced DNA fragments that are polymorphic between cultivar, Pisang Berangan and Pisang Mas. However the RAPD analysis failed to show any polymorphism between the control and the mutant lines or in between the mutant lines

  15. A Simple DNA Preparation Method for PCR Amplifications in Marker-Assisted Selection of Wheat

    Institute of Scientific and Technical Information of China (English)

    WANG Shu; R E Knox; R M DePauw; J M Clarke; WANG Bo-lun

    2005-01-01

    An important, but often limiting step in marker-assisted breeding is the efficient isolation of plant DNA for polymerase chain reaction (PCR) amplification. A simple method using an alkali treatment to extract wheat DNA for marker-assisted selection (MAS) in wheat breeding programs was compared to a commercial kit and cetyltrimethylammonium bromide (CTAB) extraction. DNA concentration from the alkali extraction was higher than the other two methods but purity was lower than CTAB extraction. The alkali extraction method was used on breeding lines to determine its usefulness. The alkali-extracted DNA samples were suitable for several PCR-based procedures, including random amplified polymorphic DNA (RAPD), microsatellite (simple sequence repeat, i.e., SSR) and sequence characterized amplified region (SCAR)analyses.

  16. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer

    Directory of Open Access Journals (Sweden)

    Laird Peter W

    2008-07-01

    Full Text Available Abstract Background Lung cancer is the leading cause of cancer death in men and women in the United States and Western Europe. Over 160,000 Americans die of this disease every year. The five-year survival rate is 15% – significantly lower than that of other major cancers. Early detection is a key factor in increasing lung cancer patient survival. DNA hypermethylation is recognized as an important mechanism for tumor suppressor gene inactivation in cancer and could yield powerful biomarkers for early detection of lung cancer. Here we focused on developing DNA methylation markers for squamous cell carcinoma of the lung. Using the sensitive, high-throughput DNA methylation analysis technique MethyLight, we examined the methylation profile of 42 loci in a collection of 45 squamous cell lung cancer samples and adjacent non-tumor lung tissues from the same patients. Results We identified 22 loci showing significantly higher DNA methylation levels in tumor tissue than adjacent non-tumor lung. Of these, eight showed highly significant hypermethylation in tumor tissue (p Conclusion We have identified 22 DNA methylation markers for squamous cell lung cancer, several of which have not previously been reported to be methylated in any type of human cancer. The top eight markers show great promise as a sensitive and specific DNA methylation marker panel for squamous cell lung cancer.

  17. Genetic diversity and phylogenetic relationship of Chinese cashmere goats based on microsatellite DNA markers

    OpenAIRE

    Ran Di; Xiaohong He; Jianlin Han; Weijun Guan; Yabin Pu; Qianjun Zhao; Baoling Fu; Yuehui Ma

    2007-01-01

    Genetic diversity of nine indigenous Chinese cashmere goat populations and one West African breed were investigated using 19 microsatellite DNA markers and fluorescence PCR. The aim was to investigate the status of the genetic resources of Chinese cashmere goats. Fourteen of the microsatellite loci were highly polymorphic and effective markers for analysis of genetic diversity and relationship among goat populations. Analysis of polymorphic information content and genetic heterozygosity showe...

  18. Capillary electrophoresis of miniSTR markers to genotype highly degraded DNA samples.

    Science.gov (United States)

    Coble, Michael D

    2012-01-01

    The amplification of short tandem repeat (STR) markers throughout the human nuclear DNA genome are used to associate crime scene evidence to the perpetrator's profile in criminal investigations. For highly challenged or compromised materials such as stains exposed to the elements, skeletal remains from missing persons cases, or fragmented and degraded samples from mass disasters, obtaining a full STR profile may be difficult if not impossible. With the introduction of short amplicon STR or "miniSTR" typing, it is possible to obtain STR genetic information from highly challenged samples without the need to sequence the hypervariable regions of the mitochondrial DNA (mtDNA) genome. Non-Combined DNA Index System (CODIS) STR markers have been developed to obtain information beyond the core CODIS loci. This chapter will focus on the steps necessary to prepare and use one of the non-CODIS (NC) multiplexes, NC01 (Coble and Butler 2005), for analysis on capillary electrophoresis instrumentation.

  19. Introduction of T-DNA into Watermelon by Stigma Smeared Method and Its Molecular Marker Research

    Institute of Scientific and Technical Information of China (English)

    MA Shuang-wu; BAO Wen-feng; WANG Ji-ming; SHANG Jian-li; WANG Xiao-jun

    2011-01-01

    [Objective] The aim was to introduce T-DNA into watermelon for its molecular marker research. [Method] Based on the method of foreign DNA introduced to Arabidopsis thaliana via dipping flowers, the stigma smear was used to transfer T-DNA into watermelon and its molecular marker research was carried out. [ Result] The ideal transformed species was ZXG01078 for the highest fruit setting rate and the most deviant seedlings. The best concentration of kanamycin for treating watermelon seeds was 500 -700 mg/L with differences among the species. The best position was spire leaf or young leaf and the best concentration of kanamycin for treating the watermelon leaf was 4 000 -8 000 mg/L with no significant difference among species. The steadily variation appearing of growing pointless and conjoined twin seedlings indicated that the normal growth had been interfered by foreign DNA in the progeny. [ Conclusion] This study had provided basis for the further research on watermelon.

  20. Low Cost DNA Molecular Weight Marker: Primer-Directed Synthesis from pGEM-T Easy Vector

    Directory of Open Access Journals (Sweden)

    Siriporn RIYAJAN

    2011-06-01

    Full Text Available A low cost DNA molecular weight marker was produced by a marker primer-directed synthetic method using pGEM-T Easy vector as the DNA template. Seven primers were used to amplify eight different DNA fragments, which were 150, 300, 375, 500, 700, 1,000, 1,200 and 1,625 bp, from bacterial culture containing pGEM-T Easy vector. Polymerase chain reactions (PCR for all marker loci required the same optimal annealing temperature, which allowed all the PCR to be completed in a single run. To obtain the molecular weight marker, the PCR product of each locus was mixed together and directly used as marker without any further purification. This custom made molecular weight marker was found to be approximately 17 to 49 times less expensive than other commercial 100 bp DNA ladder markers.Graphical abstract

  1. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana).

    Science.gov (United States)

    Carim, Kellie J; Christianson, Kyle R; McKelvey, Kevin M; Pate, William M; Silver, Douglas B; Johnson, Brett M; Galloway, Bill T; Young, Michael K; Schwartz, Michael K

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth.

  2. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana)

    Science.gov (United States)

    Carim, Kellie J.; Christianson, Kyle R.; McKelvey, Kevin M.; Pate, William M.; Silver, Douglas B.; Johnson, Brett M.; Galloway, Bill T.; Young, Michael K.; Schwartz, Michael K.

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth. PMID:27551919

  3. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana).

    Science.gov (United States)

    Carim, Kellie J; Christianson, Kyle R; McKelvey, Kevin M; Pate, William M; Silver, Douglas B; Johnson, Brett M; Galloway, Bill T; Young, Michael K; Schwartz, Michael K

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth. PMID:27551919

  4. Detection of Y STR markers of male fetal dna in maternal circulation

    OpenAIRE

    Nair Seema; Peter Sam; Pillay V; Remya U; Krishnaprasad R; Rajammal B

    2007-01-01

    Background: Circulating fetal cells and cell free DNA in the maternal blood has been shown to help in prenatal diagnosis of genetic disorders without relying on invasive procedures leading to significant risk of pregnancy loss. Aim: The current study was undertaken to detect the male fetal population using Y STR markers DYS 19, DYS 385 and DYS 392 and also to study the extent of persistence of fetal DNA in the mother following delivery. Materials and Methods: Blinded study was conducted ...

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

    Directory of Open Access Journals (Sweden)

    Hyang-Min Byun

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

  6. Dyes as bifunctional markers of DNA hybridization on surfaces and mutation detection.

    Science.gov (United States)

    García-Mendiola, Tania; Cerro, María Ramos; López-Moreno, José María; Pariente, Félix; Lorenzo, Encarnación

    2016-10-01

    The interaction of small molecules with DNA has found diagnostic and therapeutic applications. In this work, we propose the use of two different dyes, in particular Azure A and Safranine, as bifunctional markers of on-surface DNA hybridization and potent tools for screening of specific gene mutations directly in real DNA PCR amplicons extracted from blood cells. By combining spectroscopic and electrochemical methods we demonstrate that both dyes can interact with single and double stranded DNA to a different extent, allowing reliable hybridization detection. From these data, we have also elucidated the nature of the interaction. We conclude that the binding mode is fundamentally intercalative with an electrostatic component. The dye fluorescence allows their use as nucleic acid stains for the detection of on-surfaces DNA hybridization. Its redox activity is exploited in the development of selective electrochemical DNA biosensors. PMID:27317997

  7. Tagging genes for drought resistance by DNA markers in wheat (abstract)

    International Nuclear Information System (INIS)

    Wheat families (F/sub 3) raised from the seed of drought resistant and susceptible F/sub 2/ plants developed from the cross of drought resistant and susceptible parents were grown under greenhouse conditions in polyethylene tubes filled with soil and sand mixture. Drought stress was imposed and monitored at the seedling stage. The relative water content and net photosynthesis was recorded with increasing drought stress until a significant part of the seedling population had zero or negative net photosynthesis. The seedling with zero or negative net photosynthesis were named as drought susceptible and the seedlings at the same drought stress showing net photosynthesis were named as drought resistance. Twenty each of the most susceptible and resistant seedlings were selected for DNA extraction. Random Amplified Polymorphic DNA (RAPD) technique using bulked segregant analysis was used to identify DNA markers linked to drought resistance. The primers OPJ-05, OPJ-14, OPI-20 and OPA-19 produced polymorphic DNA fragments between the contrasting bulks. The polymorphic DNA fragment of 1.55kb produced by the primer OPA-19 was found linked to drought resistance. This DNA marker can be used in markers-assisted selection for drought resistance or to clone drought resistance gene. (author)

  8. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    Directory of Open Access Journals (Sweden)

    Wimalanathan Kokulapalan

    2011-01-01

    Full Text Available Abstract Background Previous loblolly pine (Pinus taeda L. genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats, also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs and 149 were from non-transcribed genomic sequences (genomic-SSRs. Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO terms. Duplicate (i.e., redundant accessory and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped

  9. Alu repeats as markers for forensic DNA analyses

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Kass, D.H. [Louisiana State Univ., New Orleans, LA (United States)] [and others

    1994-01-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 98.9% nucleotide identity with the HS subfamily consensus sequence, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 inch and 3 inch unique flanking DNA sequences from each HS Alu that allow the locus to be assayed for the presence or absence of the Alu repeat. The dimorphic HS Alu sequences probably inserted in the human genome after the radiation of modem humans (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project. HS Alu family member insertions differ from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) in that polymorphisms due to Alu insertions arise as a result of a unique event which has occurred only one time in the human population and spread through the population from that point. Therefore, individuals that share HS Alu repeats inherited these elements from a common ancestor. Most VNTR and RFLP polymorphisms may arise multiple times in parallel within a population.

  10. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects.

    Science.gov (United States)

    Elbrecht, Vasco; Taberlet, Pierre; Dejean, Tony; Valentini, Alice; Usseglio-Polatera, Philippe; Beisel, Jean-Nicolas; Coissac, Eric; Boyer, Frederic; Leese, Florian

    2016-01-01

    Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate. PMID:27114891

  11. cpDNA Microsatellite Markers for Lemna minor (Araceae: Phylogeographic Implications

    Directory of Open Access Journals (Sweden)

    Gowher A. Wani

    2014-07-01

    Full Text Available Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

  12. Genetic management of broodstock populations with DNA markers in rainbow trout

    Science.gov (United States)

    DNA markers are very useful for aquaculture and fisheries broodstock management. They have been used for parentage assignment when spawning families share common environments, and to evaluate genetic parameters in broodstock populations. The selective breeding program at the National Center for Cool...

  13. An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat

    Science.gov (United States)

    The stem rust resistance gene Sr2 has provided broad-spectrum protection against stem rust (Puccinia graminis) since its wide spread deployment in wheat from the 1940s. Because Sr2 confers partial resistance which is difficult to select under field conditions, a DNA marker is desirable that accurate...

  14. Detection of Y STR markers of male fetal dna in maternal circulation

    Directory of Open Access Journals (Sweden)

    Nair Seema

    2007-01-01

    Full Text Available Background: Circulating fetal cells and cell free DNA in the maternal blood has been shown to help in prenatal diagnosis of genetic disorders without relying on invasive procedures leading to significant risk of pregnancy loss. Aim: The current study was undertaken to detect the male fetal population using Y STR markers DYS 19, DYS 385 and DYS 392 and also to study the extent of persistence of fetal DNA in the mother following delivery. Materials and Methods: Blinded study was conducted on 50 mothers delivering male and female babies. Cellular and cell free DNA was extracted from maternal and fetal cord blood and amplified for Y STR markers by PCR. Results: The amplification sensitivity of Y specific STR, DYS19 was 100% (22/22 in the male fetal DNA samples. The incidence of other STRs, i.e., DYS385 and DYS392 were 91% (20/22 each. Analysis of results revealed that thirteen of the twenty six women had detectable male fetal DNA at the time of delivery. However fetal DNA was not detectable twenty four hours after delivery. Conclusion: Preliminary results show that the separation of fetal cell-free DNA in the maternal circulation is a good low-cost approach for the future development of novel strategies to provide non-invasive techniques for early prenatal diagnosis.

  15. A novel selection marker for efficient DNA cloning and recombineering in E. coli.

    Directory of Open Access Journals (Sweden)

    Chuan-Wei Jang

    Full Text Available Production of recombinant DNA in bacterial cells is an essential technique in molecular biology. Plasmids are usually maintained in an E. coli host by antibiotic selection. However, there are only a few antibiotic-resistance markers available in common use. Here we report the adoption of a novel selection marker, mfabI (mutant fabI for plasmid propagation in E. coli. mfabI expands the limited repertoire of selection markers and allows for more efficient molecular manipulation and plasmid propagation in E. coli. We show that mfabI is not only an efficient plasmid selection marker, but it also possesses unique activity that may facilitate molecular manipulation of unstable sequences. Furthermore, we have incorporated mfabI in the recombineering tool kit for generating mouse gene targeting vectors and demonstrate the advantage of using mfabI-containing recombineering vectors.

  16. Linkage analysis of neurofibromatosis type I, using chromosome 17 DNA markers.

    OpenAIRE

    Kittur, S D; Bagdon, M M; Lubs, M L; Phillips, J. A.; Murray, J C; Slaugenhaupt, S A; Chakravarti, A; Adler, W. H.

    1989-01-01

    The gene for von Recklinghausen neurofibromatosis type 1 (NF1) has recently been mapped to the pericentromeric region of human chromosome 17. To further localize the NF1 gene, linkage analysis using chromosome 17 DNA markers was performed on 11 multigeneration families with 175 individuals, 57 of whom were affected. The markers used were D17Z1 (p17H8), D17S58 (EW301), D17S54 (EW203), D17S57 (EW206), D17S73 (EW207), CRI-L946, HOX-2, and growth hormone. Tight linkage was found between NF1 and D...

  17. Circulating cell-free DNA: an up-coming molecular marker in exercise physiology.

    Science.gov (United States)

    Breitbach, Sarah; Tug, Suzan; Simon, Perikles

    2012-07-01

    The phenomenon of circulating cell-free DNA (cfDNA) concentrations is of importance for many biomedical disciplines including the field of exercise physiology. Increases of cfDNA due to exercise are described to be a potential hallmark for the overtraining syndrome and might be related to, or trigger adaptations of, immune function induced by strenuous exercise. At the same time, exercise provides a practicable model for studying the phenomenon of cfDNA that is described to be of pathophysiological relevance for different topics in clinical medicine like autoimmune diseases and cancer. In this review, we are summarizing the current knowledge of exercise-based acute and chronic alterations in cfDNA levels and their physiological significance. The effects of acute exercise on cfDNA concentrations have been investigated in resistance exercises and in continuous, stepwise and interval endurance exercises of different durations. cfDNA concentrations peaked immediately after acute exercise and showed a rapid return to baseline levels. Typical markers of skeletal muscle damage (creatine kinase, uric acid, C-reactive protein) show delayed kinetics compared with the cfDNA peak response. Exercise parameters such as intensity, duration or average energy expenditure do not explain the extent of increasing cfDNA concentrations after strenuous exercise. This could be due to complex processes inside the human organism during and after physical activity. Therefore, we hypothesize composite effects of different physiological stress parameters that come along with exercise to be responsible for increasing cfDNA concentrations. We suggest that due to acute stress, cfDNA levels increase rapidly by a spontaneous active or passive release mechanism that is not yet known. As a result of the rapid and parallel increase of cfDNA and lactate in an incremental treadmill test leading to exhaustion within 15-20 minutes, it is unlikely that cfDNA is released into the plasma by typical necrosis

  18. RPS8--a new informative DNA marker for phylogeny of Babesia and Theileria parasites in China.

    Directory of Open Access Journals (Sweden)

    Zhan-Cheng Tian

    Full Text Available Piroplasmosis is a serious debilitating and sometimes fatal disease. Phylogenetic relationships within piroplasmida are complex and remain unclear. We compared the intron-exon structure and DNA sequences of the RPS8 gene from Babesia and Theileria spp. isolates in China. Similar to 18S rDNA, the 40S ribosomal protein S8 gene, RPS8, including both coding and non-coding regions is a useful and novel genetic marker for defining species boundaries and for inferring phylogenies because it tends to have little intra-specific variation but considerable inter-specific difference. However, more samples are needed to verify the usefulness of the RPS8 (coding and non-coding regions gene as a marker for the phylogenetic position and detection of most Babesia and Theileria species, particularly for some closely related species.

  19. Elevated levels of urinary markers of oxidatively generated DNA and RNA damage in bipolar disorder

    DEFF Research Database (Denmark)

    Munkholm, Klaus; Poulsen, Henrik Enghusen; Kessing, Lars Vedel;

    2015-01-01

    investigated oxidatively generated damage to DNA and RNA in patients with bipolar disorder and its relationship with the affective phase compared with healthy control subjects. METHODS: Urinary excretion of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-oxo-7,8-dihydroguanosine (8-oxoGuo), markers...... of oxidatively generated DNA and RNA damage, respectively, was measured in 37 rapid cycling patients with bipolar disorder and in 40 age- and gender-matched healthy control subjects. Employing a longitudinal design, repeated measurements of both markers were evaluated in various affective phases in patients...... with bipolar disorder during a six- to 12-month period and compared with repeated measurements in healthy control subjects. RESULTS: In linear mixed models, adjusting for demographical, metabolic, and lifestyle factors, the excretion of 8-oxodG and 8-oxoGuo was significantly elevated in euthymic patients...

  20. Association between Urinary Excretion of Cortisol and Markers of Oxidatively Damaged DNA and RNA in Humans

    DEFF Research Database (Denmark)

    Joergensen, Anders; Broedbaek, Kasper; Weimann, Allan;

    2011-01-01

    Chronic psychological stress is associated with accelerated aging, but the underlying biological mechanisms are not known. Prolonged elevations of the stress hormone cortisol is suspected to play a critical role. Through its actions, cortisol may potentially induce oxidatively generated damage...... to cellular constituents such as DNA and RNA, a phenomenon which has been implicated in aging processes. We investigated the relationship between 24 h excretion of urinary cortisol and markers of oxidatively generated DNA and RNA damage, 8-oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydroguanosine......, in a sample of 220 elderly men and women (age 65 - 83 years). We found a robust association between the excretion of cortisol and the oxidation markers (R(2)¿=¿0.15, P...

  1. Optimization Of ISSR Markers For DNA Fingerprinting In Stevia Rebaudiana Bertoni

    International Nuclear Information System (INIS)

    ISSR or inter-simple sequence repeat is PCR based markers which required no prior DNA sequence knowledge of the studied organism. It has been proved to overcome limitations in other genetic marker techniques. In this study, 100 ISSR primers which comprised of 80 specific primers and 20 degenerate primers were used. All of the primers were tested on gradient temperatures from 45-55 degree Celsius. For positive amplification, 62 specific primers (77.5 %) and 18 degenerate primers (90.0 %) were recorded as working primers. The most efficient temperature for 25 primers was 55 degree Celsius. Marker derived from ISSR profiling is a powerful approach for identification and molecular classification of Stevia rebaudiana bertoni. (author)

  2. Rapid Characterization of Garlic Clones with Locus-Specific DNA Markers

    OpenAIRE

    İPEK, Meryem; İPEK, AHMET; Simon, Philipp W

    2008-01-01

    Maintenance of redundant garlic (Allium sativum L.) accessions is expensive due to the necessity of yearly regenerating garlic accessions in germplasm centers. Therefore, rapid characterization of garlic accessions is important for avoiding duplicated genotypes. For this purpose we developed several locus-specific polymerase chain reaction (PCR)-based DNA markers, and tested them for the characterization of garlic clones that were previously analyzed using amplified fragment length polymorphi...

  3. Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma

    OpenAIRE

    Hagen Jeffrey A; Cozen Wendy; Turla Sally; Laird Peter W; Siegmund Kimberly D; Galler Janice S; Tsou Jeffrey A; Koss Michael N; Laird-Offringa Ite A

    2007-01-01

    Abstract Background Lung cancer is the number one cancer killer of both men and women in the United States. Three quarters of lung cancer patients are diagnosed with regionally or distantly disseminated disease; their 5-year survival is only 15%. DNA hypermethylation at promoter CpG islands shows great promise as a cancer-specific marker that would complement visual lung cancer screening tools such as spiral CT, improving early detection. In lung cancer patients, such hypermethylation is dete...

  4. Classification of plant associated bacteria using RIF, a computationally derived DNA marker.

    Directory of Open Access Journals (Sweden)

    Kevin L Schneider

    Full Text Available A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF. Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS. Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF

  5. Optimization of ISSR Markers for Molecular DNA Fingerprinting in Aquilaria sp

    International Nuclear Information System (INIS)

    Aquilaria sp. belongs to the Thymelaeaceae family and well distributed to Asia region. The species is a multipurpose use from root to shoot and becoming an economic important crop, which generates wide interest in understanding the genetic diversity of the species. Understanding of the effectiveness in differentiating DNA-based markers is an important step towards plant germplasm characterization and evaluation. It is becoming a prerequisite for more effective application of molecular marker techniques in breeding and mapping programs. Polymerase Chain Reaction (PCR)-based approaches are in demanding as its simplicity and requirement for only small quantities of sample genomic DNA. Inter-simple sequence repeats (ISRR) requires no prior genomic information as anchor template in producing multi-loci markers of tandem repeats for polymorphic patterns by PCR amplification which becoming a key of advantageous of ISSR primers. ISSR markers have shown rapid, simple, reproducible and inexpensive means in molecular taxonomy, conservation breeding and genetic diversity analysis. The ISSR for marker applications are essential to facilitate management, conservation and genetic improvement programs towards improvement of standard resin quality for perfume and or pharmaceutical industries. In this paper, a total of 100 ISSR primers were optimized by using Aquilaria malaccensis. Primers optimization resulted, 38 ISSR primers affirmative for the polymorphism evaluation study, which encountered both from specific and degenerate ISSR primers. Marker derived from ISSR profiling is a powerful method for identification and molecular classification of Aquilaria sp from species to accessions and further will useful in identifying any mutant lines derived from nature and/or mutagenesis activities. (author)

  6. Germplasm and breeding research of tea plant based on DNA marker approaches

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Tea is the most popular non-alcoholic and healthy beverage worldwide.Tea production contributes greatly to the economy and the job opportunities for many countries in Asia and Africa.Meanwhile,the germplasm of tea,with a huge potential for the future of the whole tea industry,is presently one of the most valuable and fundamental materials for tea breeding and tea biotechnology.DNA molecular markers have been proven to be robust and valuable approaches in the studies of genetic diversity and variation,molecular identification,molecular phylogenetics,genetic stability and integrity of tea germplasm,and the genetic linkage map for breeding of tea.In this paper,a brief prospect on the molecular marker studies of tea has been summarized.The purpose is to provide an effective way for undertaking a massive tea germplasm appraisal and evaluation,to develop new applicable and cheap DNA markers,to establish a high density genetic linkage map and analyze the agronomically important QTLs,and finally,to facilitate the marker assisted early selection and shorten breeding procedures in tea.

  7. Integrating microsatellite DNA markers and otolith geochemistry to assess population structure of European hake (Merluccius merluccius)

    Science.gov (United States)

    Tanner, Susanne E.; Pérez, Montse; Presa, Pablo; Thorrold, Simon R.; Cabral, Henrique N.

    2014-04-01

    Population structure and natal origins of European hake were investigated using microsatellite DNA markers and otolith geochemistry data. Five microsatellites were sequenced and otolith core geochemical composition was determined from age-1 hake collected in the northeast Atlantic Ocean and the Mediterranean Sea. Microsatellites provided evidence of a major genetic split in the vicinity of the Strait of Gibraltar, separating the Atlantic and the Mediterranean populations, with the exception of the Gulf of Cádiz. Based on classification models using otolith core geochemical values, individual natal origins were identified, although with an increased error rate. Coupling genotype and otolith data increased the classification accuracy of individuals to their potential natal origins while providing evidence of movement between the northern and southern stock units in the Atlantic Ocean. Information obtained by the two natural markers on population structure of European hake was complementary as the two markers act at different spatio-temporal scales. Otolith geochemistry provides information over an ecological time frame and on a fine spatial scale, while microsatellite DNA markers report on gene flow over evolutionary time scales and therefore act on a broader spatio-temporal resolution. Thus, this study confirmed the value of otolith geochemistry to complement the assessment of early life stage dispersal in populations with high gene flow and low genetic divergence.

  8. Evaluation of five microbial and four mitochondrial DNA markers for tracking human and pig fecal pollution in freshwater

    Science.gov (United States)

    He, Xiwei; Liu, Peng; Zheng, Guolu; Chen, Huimei; Shi, Wei; Cui, Yibin; Ren, Hongqiang; Zhang, Xu-Xiang

    2016-10-01

    This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84.0–88.8%) except Pig-2-Bac (100%). Specificities of the human mtDNA markers (99.1 and 98.1%) were higher than those of the human-associated microbial ones (57.0–88.8%). But this pattern was not observed in the pig-associated markers where Pig-2-Bac had 100% specificity. The reliability of H-ND6 and H-ND5 was further evidenced to identify locations of the most polluted within the Taihu Lake watershed of China. In general, the microbial DNA markers demonstrated a higher fecal concentration than the mtDNA ones; increasing temperature and sunlight exposure accelerated significantly the decay of all the DNA markers. Results of this study suggest that DNA markers H-ND6, H-ND5, and Pig-2-Bac may be among the best for fecal source tracking in water.

  9. Genetic diversity and DNA fingerprinting in jute (Corchorus spp. based on SSR markers

    Directory of Open Access Journals (Sweden)

    Liwu Zhang

    2015-10-01

    Full Text Available Genetic diversity analysis and DNA finger printing are very useful in breeding programs, seed conservation and management. Jute (Corchorus spp. is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties (Huangma 179 and Kuanyechangguo from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with CoSSR305-120 and CoSSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  10. Genetic diversity and DNA fingerprinting in jute(Corchorus spp.) based on SSR markers

    Institute of Scientific and Technical Information of China (English)

    Liwu; Zhang; Rongrong; Cai; Minhang; Yuan; Aifen; Tao; Jiantang; Xu; Lihui; Lin; Pingping; Fang; Jianmin; Qi

    2015-01-01

    Genetic diversity analysis and DNA finger printing are very useful in breeding programs,seed conservation and management. Jute(Corchorus spp.) is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties(Huangma 179 and Kuanyechangguo) from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with Co SSR305-120 and Co SSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

  11. Paternity testing using microsatellite DNA markers in captive Adélie penguins (Pygoscelis adeliae).

    Science.gov (United States)

    Sakaoka, Ken; Suzuki, Isao; Kasugai, Naeko; Fukumoto, Yohei

    2014-01-01

    We investigated the paternity of 39 Adélie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n = 26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ≥4 years old in the exhibit tank during each reproductive season; n = 9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations.

  12. Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp.

    Science.gov (United States)

    Willows-Munro, Sandi; Robinson, Terence J; Matthee, Conrad A

    2005-06-01

    Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting, gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock, are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini. PMID:15878131

  13. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement?

    Science.gov (United States)

    Ferri, G; Corradini, B; Ferrari, F; Santunione, A L; Palazzoli, F; Alu', M

    2015-03-01

    The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for

  14. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory

    OpenAIRE

    Slankster, Eryn E.; Chase, Jillian M.; Jones, Lauren A.; Wendell, Douglas L.

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tand...

  15. Mitochondrial DNA Marker EST00083 Is Not Associated with High vs. Average IQ in a German Sample.

    Science.gov (United States)

    Moises, Hans W.; Yang, Liu; Kohnke, Michael; Vetter, Peter; Neppert, Jurgen; Petrill, Stephen A.; Plomin, Robert

    1998-01-01

    Tested the association of a mitochondrial DNA marker (EST00083) with high IQ in a sample of 47 German adults with high IQ scores and 77 adults with IQs estimated at lower than 110. Results do not support the hypothesis that high IQ is associated with this marker. (SLD)

  16. Mitochondrial DNA variant at HVI region as a candidate of genetic markers of type 2 diabetes

    Science.gov (United States)

    Gumilar, Gun Gun; Purnamasari, Yunita; Setiadi, Rahmat

    2016-02-01

    Mitochondrial DNA (mtDNA) is maternally inherited. mtDNA mutations which can contribute to the excess of maternal inheritance of type 2 diabetes. Due to the high mutation rate, one of the areas in the mtDNA that is often associated with the disease is the hypervariable region I (HVI). Therefore, this study was conducted to determine the genetic variants of human mtDNA HVI that related to the type 2 diabetes in four samples that were taken from four generations in one lineage. Steps being taken include the lyses of hair follicles, amplification of mtDNA HVI fragment using Polymerase Chain Reaction (PCR), detection of PCR products through agarose gel electrophoresis technique, the measurement of the concentration of mtDNA using UV-Vis spectrophotometer, determination of the nucleotide sequence via direct sequencing method and analysis of the sequencing results using SeqMan DNASTAR program. Based on the comparison between nucleotide sequence of samples and revised Cambridge Reference Sequence (rCRS) obtained six same mutations that these are C16147T, T16189C, C16193del, T16127C, A16235G, and A16293C. After comparing the data obtained to the secondary data from Mitomap and NCBI, it were found that two mutations, T16189C and T16217C, become candidates as genetic markers of type 2 diabetes even the mutations were found also in the generations of undiagnosed type 2 diabetes. The results of this study are expected to give contribution to the collection of human mtDNA database of genetic variants that associated to metabolic diseases, so that in the future it can be utilized in various fields, especially in medicine.

  17. Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer

    Science.gov (United States)

    Tsyba, Liudmyla; Onyshchenko, Kateryna; Kashparova, Olena; Nikolaienko, Oleksii; Panasenko, Grigory; Vozianov, Sergii; Romanenko, Alina; Rynditch, Alla

    2016-01-01

    The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for the LRRC3B (74.1%), APC (51.9%), FHIT (55.6%), and RASSF1 (62.9%) genes in patients with renal cancer. Promoter methylation of VHL and ITGA9 genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands of RASSF1A, FHIT, and APC genes in blood plasma can be used as noninvasive diagnostic markers of cancer.

  18. Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Hagen Jeffrey A

    2007-10-01

    Full Text Available Abstract Background Lung cancer is the number one cancer killer of both men and women in the United States. Three quarters of lung cancer patients are diagnosed with regionally or distantly disseminated disease; their 5-year survival is only 15%. DNA hypermethylation at promoter CpG islands shows great promise as a cancer-specific marker that would complement visual lung cancer screening tools such as spiral CT, improving early detection. In lung cancer patients, such hypermethylation is detectable in a variety of samples ranging from tumor material to blood and sputum. To date the penetrance of DNA methylation at any single locus has been too low to provide great clinical sensitivity. We used the real-time PCR-based method MethyLight to examine DNA methylation quantitatively at twenty-eight loci in 51 primary human lung adenocarcinomas, 38 adjacent non-tumor lung samples, and 11 lung samples from non-lung cancer patients. Results We identified thirteen loci showing significant differential DNA methylation levels between tumor and non-tumor lung; eight of these show highly significant hypermethylation in adenocarcinoma: CDH13, CDKN2A EX2, CDX2, HOXA1, OPCML, RASSF1, SFPR1, and TWIST1 (p-value Conclusion The identification of eight CpG island loci showing highly significant hypermethylation in lung adenocarcinoma provides strong candidates for evaluation in patient remote media such as plasma and sputum. The four most highly ranked loci, CDKN2A EX2, CDX2, HOXA1 and OPCML, which show significant DNA methylation even in stage IA tumor samples, merit further investigation as some of the most promising lung adenocarcinoma markers identified to date.

  19. Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers

    Science.gov (United States)

    Sziszkosz, Nikolett; Mihók, Sándor; Jávor, András

    2016-01-01

    The Gidran is a native Hungarian horse breed that has approached extinction several times. Phylogenetic analysis of two mitochondrial markers (D-loop and cytochrome-b) was performed to determine the genetic characterization of the Gidran for the first time as well as to detect errors in the management of the Gidran stud book. Sequencing of 686 bp of CYTB and 202 bp of the D-loop in 260 mares revealed 24 and 32 haplotypes, respectively, among 31 mare families. BLAST analysis revealed six novel CYTB and four D-loop haplotypes that have not been previously reported. The Gidran mares showed high haplotype (CYTB: 0.8735 ± 0.011; D-loop: 0.9136 ± 0.008) and moderate nucleotide (CYTB: 0.00472 ± 0.00017; D-loop: 0.02091 ± 0.00068) diversity. Of the 31 Gidran mare families, only 15 CYTB (48.4%) and 17 D-loop (54.8%) distinct haplotypes were formed using the two markers separately. Merged markers created 24 (77.4%) mare families, which were in agreement with the mare families in the stud book. Our key finding was that the Gidran breed still possesses high genetic diversity despite its history. The obtained haplotypes are mostly consistent with known mare families, particularly when the two mtDNA markers were merged. Our results could facilitate conservation efforts for preserving the genetic diversity of the Gidran. PMID:27168959

  20. Intraspecific differentiation of Hancornia speciosa revealed by simple sequence repeat and random amplified polymorphic DNA markers.

    Science.gov (United States)

    Nogueira, C A; Stafuzza, N B; Ribeiro, T P; Prado, A D L; Menezes, I P P; Peixoto, N; Gonçalves, P J; Almeida, L M

    2015-01-01

    Hancornia speciosa, popularly known as mangabeira, is a fruit tree native to the Brazilian Cerrado that shows great economic potential, due to its multiple uses. Intraspecific classification of this species is difficult because it shows high morphological diversity. An early study of the species reported that there are six botanic varieties that differ morphologically mainly in the shapes of their leaves and flowers. Except to note the wide morphological variation and economic potential of this species, few studies have been published about the genetic diversity of mangabeira. Knowledge of the genetic variability of this species among populations would be useful for genetic conservation and breeding programs. Therefore, we tested the transferability of 12 simple sequence repeats from expressed sequence tags (EST-SSRs) from Catharanthus roseus to H. speciosa and used 10 random amplified polymorphic DNA markers to evaluate the genetic variability among botanical varieties of H. speciosa. We obtained a high transferability frequency of EST-SSR markers from C. roseus to H. speciosa (75%). However, EST-SSR markers showed low heterozygosity and locus variability (two or three alleles by locus), which suggest low genetic diversity in the mangabeira samples. The Jaccard dissimilarity index and an examination of geographic distances indicated a non-spatial structuring of the genetic variability. Our markers were unable to distinguish H. speciosa botanical varieties. PMID:26662392

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

    Directory of Open Access Journals (Sweden)

    Wales Richard

    2001-07-01

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

  2. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

    Directory of Open Access Journals (Sweden)

    Tike Sartika

    2000-06-01

    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  3. Differential utility of the Bacteroidales DNA and RNA markers in the tiered approach for microbial source tracking in subtropical seawater.

    Science.gov (United States)

    Liu, Rulong; Cheng, Ken H F; Wong, Klaine; Cheng, Samuel C S; Lau, Stanley C K

    2015-07-01

    Source tracking of fecal pollution is an emerging component in water quality monitoring. It may be implemented in a tiered approach involving Escherichia coli and/or Enterococcus spp. as the standard fecal indicator bacteria (FIB) and the 16S rRNA gene markers of Bacteroidales as source identifiers. The relative population dynamics of the source identifiers and the FIB may strongly influence the implementation of such approach. Currently, the relative performance of DNA and RNA as detection targets of Bacteroidales markers in the tiered approach is not known. We compared the decay of the DNA and RNA of the total (AllBac) and ruminant specific (CF128) Bacteroidales markers with those of the FIB in seawater spiked with cattle feces. Four treatments of light and oxygen availability simulating the subtropical seawater of Hong Kong were tested. All Bacteroidales markers decayed significantly slower than the FIB in all treatments. Nonetheless, the concentrations of the DNA and RNA markers and E. coli correlated significantly in normoxic seawater independent of light availability, and in hypoxic seawater only under light. In hypoxic seawater without light, the concentrations of RNA but not DNA markers correlated with that of E. coli. Generally, the correlations between Enterococcus spp. and Bacteroidales were insignificant. These results suggest that either DNA or RNA markers may complement E. coli in the tiered approach for normoxic or hypoxic seawater under light. When light is absent, either DNA or RNA markers may serve for normoxic seawater, but only the RNA markers are suitable for hypoxic seawater. PMID:25652655

  4. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    Science.gov (United States)

    Schoch, Conrad L.; Seifert, Keith A.; Huhndorf, Sabine; Robert, Vincent; Spouge, John L.; Levesque, C. André; Chen, Wen; Bolchacova, Elena; Voigt, Kerstin; Crous, Pedro W.; Miller, Andrew N.; Wingfield, Michael J.; Aime, M. Catherine; An, Kwang-Deuk; Bai, Feng-Yan; Barreto, Robert W.; Begerow, Dominik; Bergeron, Marie-Josée; Blackwell, Meredith; Boekhout, Teun; Bogale, Mesfin; Boonyuen, Nattawut; Burgaz, Ana R.; Buyck, Bart; Cai, Lei; Cai, Qing; Cardinali, G.; Chaverri, Priscila; Coppins, Brian J.; Crespo, Ana; Cubas, Paloma; Cummings, Craig; Damm, Ulrike; de Beer, Z. Wilhelm; de Hoog, G. Sybren; Del-Prado, Ruth; Dentinger, Bryn; Diéguez-Uribeondo, Javier; Divakar, Pradeep K.; Douglas, Brian; Dueñas, Margarita; Duong, Tuan A.; Eberhardt, Ursula; Edwards, Joan E.; Elshahed, Mostafa S.; Fliegerova, Katerina; Furtado, Manohar; García, Miguel A.; Ge, Zai-Wei; Griffith, Gareth W.; Griffiths, K.; Groenewald, Johannes Z.; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Guo, Liang-Dong; Hagen, Ferry; Hambleton, Sarah; Hamelin, Richard C.; Hansen, Karen; Harrold, Paul; Heller, Gregory; Herrera, Cesar; Hirayama, Kazuyuki; Hirooka, Yuuri; Ho, Hsiao-Man; Hoffmann, Kerstin; Hofstetter, Valérie; Högnabba, Filip; Hollingsworth, Peter M.; Hong, Seung-Beom; Hosaka, Kentaro; Houbraken, Jos; Hughes, Karen; Huhtinen, Seppo; Hyde, Kevin D.; James, Timothy; Johnson, Eric M.; Johnson, Joan E.; Johnston, Peter R.; Jones, E.B. Gareth; Kelly, Laura J.; Kirk, Paul M.; Knapp, Dániel G.; Kõljalg, Urmas; Kovács, Gábor M.; Kurtzman, Cletus P.; Landvik, Sara; Leavitt, Steven D.; Liggenstoffer, Audra S.; Liimatainen, Kare; Lombard, Lorenzo; Luangsa-ard, J. Jennifer; Lumbsch, H. Thorsten; Maganti, Harinad; Maharachchikumbura, Sajeewa S. N.; Martin, María P.; May, Tom W.; McTaggart, Alistair R.; Methven, Andrew S.; Meyer, Wieland; Moncalvo, Jean-Marc; Mongkolsamrit, Suchada; Nagy, László G.; Nilsson, R. Henrik; Niskanen, Tuula; Nyilasi, Ildikó; Okada, Gen; Okane, Izumi; Olariaga, Ibai; Otte, Jürgen; Papp, Tamás; Park, Duckchul; Petkovits, Tamás; Pino-Bodas, Raquel; Quaedvlieg, William; Raja, Huzefa A.; Redecker, Dirk; Rintoul, Tara L.; Ruibal, Constantino; Sarmiento-Ramírez, Jullie M.; Schmitt, Imke; Schüßler, Arthur; Shearer, Carol; Sotome, Kozue; Stefani, Franck O.P.; Stenroos, Soili; Stielow, Benjamin; Stockinger, Herbert; Suetrong, Satinee; Suh, Sung-Oui; Sung, Gi-Ho; Suzuki, Motofumi; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M. Teresa; Tretter, Eric; Untereiner, Wendy A.; Urbina, Hector; Vágvölgyi, Csaba; Vialle, Agathe; Vu, Thuy Duong; Walther, Grit; Wang, Qi-Ming; Wang, Yan; Weir, Bevan S.; Weiß, Michael; White, Merlin M.; Xu, Jianping; Yahr, Rebecca; Yang, Zhu L.; Yurkov, Andrey; Zamora, Juan-Carlos; Zhang, Ning; Zhuang, Wen-Ying; Schindel, David

    2012-01-01

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups. PMID:22454494

  5. Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications.

    Science.gov (United States)

    Avettand-Fènoël, Véronique; Hocqueloux, Laurent; Ghosn, Jade; Cheret, Antoine; Frange, Pierre; Melard, Adeline; Viard, Jean-Paul; Rouzioux, Christine

    2016-10-01

    HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis. PMID:27559075

  6. Highly polymorphic DNA markers in an Africanized honey bee population in Costa Rica

    Directory of Open Access Journals (Sweden)

    Lobo Segura Jorge Arturo

    2000-01-01

    Full Text Available Two genetic markers (the mtDNA COI-COII intergenic region and the microsatellite A7 with high levels of variability in South African and European honey bees were analyzed in wild swarms of Africanized honey bees (Apis mellifera from Costa Rica. Allelic or haplotypic frequencies revealed high levels of genetic variability at these loci in this population. Most of the alleles were African alleles, although some European-derived alleles were also present. Differences in the frequencies of African alleles between African and Africanized samples were minor, which could be explained by founder effects occurring during the introduction of African honey bee populations into South America.

  7. Random amplified polymorphic DNA (RAPD) markers readily distinguish cryptic mosquito species (Diptera: Culicidae: Anopheles).

    Science.gov (United States)

    Wilkerson, R C; Parsons, T J; Albright, D G; Klein, T A; Braun, M J

    1993-01-01

    The usefulness of random amplified polymorphic DNA (RAPD) was examined as a potential tool to differentiate cryptic mosquito species. It proved to be a quick, effective means of finding genetic markers to separate two laboratory populations of morphologically indistinguishable African malaria vectors, Anopheles gambiae and An. arabiensis. In an initial screening of fifty-seven RAPD primers, 377 bands were produced, 295 of which differed between the two species. Based on criteria of interpretability, simplicity and reproducibility, thirteen primers were chosen for further screening using DNA from thirty individuals of each species. Seven primers produced diagnostic bands, five of which are described here. Some problematic characteristics of RAPD banding patterns are discussed and approaches to overcome these are suggested. PMID:8269099

  8. DNA-based genetic markers for Rapid Cycling Brassica rapa (Fast Plants type designed for the teaching laboratory.

    Directory of Open Access Journals (Sweden)

    Eryn E. Slankster

    2012-06-01

    Full Text Available We have developed DNA-based genetic markers for rapid-cycling Brassica rapa (RCBr, also known as Fast Plants. Although markers for Brassica rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP based markers and 14 variable number tandem repeat (VNTR-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a nongenic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

  9. Coelomocyte-derived fluorescence and DNA markers of composting earthworm species.

    Science.gov (United States)

    Rorat, Agnieszka; Kachamakova-Trojanowska, Neli; Jozkowicz, Alicja; Kruk, Jerzy; Cocquerelle, Claude; Vandenbulcke, Franck; Santocki, Michal; Plytycz, Barbara

    2014-01-01

    Supravital species identification of morphologically similar syntopic earthworms inhabiting dung and compost heaps or those from commercial cultures is difficult. The aim of the studies was to find out non-invasive species-specific markers for proper segregation of earthworm species from a dense mixed colony of waste decomposers. Worms were segregated according to external characteristics into Eisenia andrei, Eisenia fetida, and Dendrobaena veneta, and left for reproduction and analysis of non-invasively retrieved coelomocyte-containing coelomic fluid and/or species-specific partial sequences of cytochrome c oxidase subunit I (COI) gene in DNA extracted from amputated tail tips of adults and their offspring. Flow cytometric analysis of coelomocyte samples revealed that amount of nuclear DNA increases in order D. veneta ≪ E. andrei Eisenia spp. Spectrofluorimetry of coelomocyte lysates revealed that the amount of eleocyte-stored riboflavin is significantly lower in coelomocyte lysates from D. veneta than from Eisenia spp., and the emission peak of X-fluorophore is much more distinct in D. veneta than in Eisenia spp. Coelomic fluid of E. andrei exhibits a very distinct spectra of MUG fluorophore which are absent in D. veneta and in the majority of E. fetida, while some E. fetida possess MUG-like fluorophore. Sequences of the COI gene in the DNA of the worms from the mixed colony and their offspring confirmed species identity. In conclusion, species-specific coelomocyte-derived markers may be a useful complement to morphological and DNA-based taxonomy during studies on syntopic earthworms. PMID:24115405

  10. Analysis of relationship between tumor markers and quantification of free DNA in serum of lung cancer patients

    International Nuclear Information System (INIS)

    To evaluate the diagnostic value and relationship between five tumor markers (CA19- 9,CA125,CYFRA21-1 ,CEA,NSE) and free DNA in serum for lung cancer detection and try to find a new and more efficient tumor marker, the amounts of CA19-9, CA125, CYFRA21-1, CEA, NSE were determined by RIA and free DNA was determined by the use of quantitative real time PCR amplification of the human epidermal growth factor receptor (EGFR) in 52 lung cancer patients and 8 cases of benign pulmonary disease and 10 healthy controls. The resulls showed that average concentration of free DNA in serum of lung cancer patients, benign pulmo- nary disease and healthy controls was 107.6ng/mL, 76.86ng/mL and 18.8ng/mL, respective- ly. The diagnostic sensitivity, specificity and accuracy of free DNA for lung cancer were 71. 2%, 50% and 68.3%, same as the diagnostic value of combined detection of five tumor markers. The sensitivity, specificity and accuracy of the five tumor markers and free DNA combinend detection for lung cancer were 94.2%, 25% and 85%, respectively. The free DNA in the serum of lung cancer patients may be a new and better tumor marker. (authors)

  11. Genetic Relatedness among Duku, Kokosan, and Pisitan in Indonesia Based on Random Amplified Polymorphic DNA Markers

    Directory of Open Access Journals (Sweden)

    Laila Hanum

    2015-11-01

    Full Text Available Genetic relatedness among duku, kokosan, and pisitan from Indonesia were investigated using random amplified polymorphic DNA (RAPD markers. Eleven primers (OPA-01, OPA-02, OPA-10, OPB-07, OPB-11, OPB-12, OPB-15, OPT-16, OPU-14, OPU-19, and OPU-20 were used for amplification and yielded a total of 174 DNA bands, of which 167 were polymorphic. Primer OPA-10, OPB-11, OPB-12, OPB-15, and OPU-19 produced all of the polymorphic DNA bands. The size of the amplified DNA fragments ranged from 41-1546 bp. The dendrogram separated into two clusters at a genetic similarity coefficient of 0.76. The cluster 1 consisted of subclusters duku and several pisitan (pisitan OKI, pisitan Sleman, pisitan Hatu, pisitan Punggur, and pisitan Tanjung, and cluster 2 consisted of subclusters kokosan and pisitan. In the kokosan subclusters, including duku Drendan. Dendrogram supported the determination of taxonomic status of duku, kokosan, and pisitan as one species, namely Lansium domesticum Corr. and its divided into two groups, namely L. domesticum ’duku group’ and L. domesticum ’pisitan-kokosan group’. Thus, RAPD analysis was useful tool for determining the genetic variation and the genetics relatedness among duku, kokosan, and pisitan in Indonesia.Key words: duku, kokosan, pisitan/langsat, genetic relatedness, RAPD

  12. Blood DNA methylation markers in prospectively identifiedhepatocellular carcinoma cases and controls from Taiwan

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    AIM To determine if gene-specific DNA methylation inprospectively collected blood samples is associated withlater development of hepatocellular carcinoma (HCC).METHODS: Comparing genome-wide DNA methylationprofiles using Illumina Human methylation 450Karrays, we previously identified a list of loci that weredifferentially methylated between tumor and adjacentnontumor tissues. To examine if dysregulation of DNA methylation patterns observed in tumor tissues can bedetected in white blood cell (WBC) DNA, we conducteda prospective case-control study nested within acommunity-based cancer screening cohort in Taiwanwith 16 years of follow up. We measured methylationlevels in ninety-six loci that were aberrant in DNAmethylation in HCC tumor tissues compared to adjacenttissues. Baseline WBC DNA from 159 HCC cases and 312matched controls were bisulfite treated and assayed byIllumina BeadArray. We used the χ 2 test for categoricalvariables and student's t -test for continuous variables toassess the difference in selected characteristics betweencases and controls. To estimate associations with HCCrisk, we used conditional logistic regression modelsstratified on the matching factors to calculate odds ratios(OR) and 95%CI.RESULTS: We found that high methylation level incg10272601 in WNK2 was associated with increasedrisk of HCC, with an OR of 1.91 (95%CI: 1.27-2.86).High methylation levels in both cg12680131 in TPO andcg22511877 in MYT1L , however, were associated withdecreased risk. The ORs (95%CI) were 0.59 (0.39-0.87)and 0.50 (0.33-0.77), respectively, for those with methylationlevels of cg12680131 and cg22511877 abovethe median compared with those with levels belowthe median. These associations were still statisticallysignificant in multivariable conditional logistic regressionmodels after adjusting for hepatitis B virus infection andalcohol consumption.CONCLUSION: These findings support the measurementof methylation markers in WBC DNA

  13. DNA methylation in serum of breast cancer patients: an independent prognostic marker.

    Science.gov (United States)

    Müller, Hannes M; Widschwendter, Andreas; Fiegl, Heidi; Ivarsson, Lennart; Goebel, Georg; Perkmann, Elisabeth; Marth, Christian; Widschwendter, Martin

    2003-11-15

    Changes in the status of DNA methylation are one of the most common molecular alterations in human neoplasia. Because it is possible to detect these epigenetic alterations in the bloodstream of patients, we investigated whether aberrant DNA methylation in patient pretherapeutic sera is of prognostic significance in breast cancer. Using MethyLight, a high-throughput DNA methylation assay, we analyzed 39 genes in a gene evaluation set, consisting of 10 sera from metastasized patients, 26 patients with primary breast cancer, and 10 control patients. To determine the prognostic value of genes identified within the gene evaluation set, we finally analyzed pretreatment sera of 24 patients having had no adjuvant treatment (training set) to determine their prognostic value. An independent test set consisting of 62 patients was then used to test the validity of genes and combinations of genes, which in the training set were found to be good prognostic markers. In the gene evaluation set we identified five genes (ESR1, APC, HSD17B4, HIC1, and RASSF1A). In the training set, patients with methylated serum DNA for RASSF1A and/or APC had the worst prognosis (P < 0.001). This finding was confirmed by analyzing serum samples from the independent test set (P = 0.007). When analyzing all 86 of the investigated patients, multivariate analysis showed methylated RASSF1A and/or APC serum DNA to be independently associated with poor outcome, with a relative risk for death of 5.7. DNA methylation of particular genes in pretherapeutic sera of breast cancer patients, especially of RASSF1A/APC, is more powerful than standard prognostic parameters.

  14. DNA分子标记在中药鉴定中的应用进展%DNA Molecular Marker in Progress in the Application of Chinese Medicine Identification

    Institute of Scientific and Technical Information of China (English)

    海学忠

    2012-01-01

    DNA molecular markers including molecular hybrid (southern hybridization) as the foundation of DNA molecular markers, PCR-based DNA molecular markers and DNA sequence to the basis of molecular markers and DNA sequencing by technology. This paper summarizes the commonly used DNA molecular markers on the features of DNA molecular markers in recent years Chinese medicine identification in this paper reviewed the application.%DNA分子标记包括以分子杂交(southern杂交)为基础的DNA分子标记技术、以PCR为基础的DNA分子标记技术和以DNA序列为基础的分子标记技术和DNA序列测定技术。本文概述了常用DNA分子标记技术的特点,对近年来DNA分子标记在中药鉴定中的应用进行了综述。

  15. Determination of the nucleosidic structural parameters by means of DNA vibrational markers

    Science.gov (United States)

    Ghomi, M.; Letellier, R.; Taillandier, E.

    1990-10-01

    Normal mode calculations based on the GF-Wilson method and a reliable force field allow the vibrational markers arising from the deoxyadenosine (dA) and deoxyguanosine (dG) residues in DNA double helical chains (right- and left-handed conformations) to be reproduced. To do this, a fast, optimized code running on a CRAY-2 computer has been performed. The normal modes of these nucleosides have been calculated as a function of their structural parameters, on the basis of a non-redundant set of internal coordinates. This study permits a better understanding of the behaviour of the main nucleosidic markers used experimentally to determine the conformation of an oligonucleotide or polynucleotide in the crystalline phase and in solution. Taking account of the calculated data, we propose a reliable set of values for the nucleosidic structural parameters which are in good agreement with those estimated by other techniques such as X-ray diffraction or nuclear magnetic resonance (NMR) spectroscopy. We have extended this study to follow the evolution of the nucleosidic vibrational markers as a function of the sugar conformation and the glycosidic torsion angle.

  16. A candidate metastasis-associated DNA marker for ductal mammary carcinoma

    International Nuclear Information System (INIS)

    Molecular genetic markers to identify the 13% lymph node-negative mammary carcinomas that are prone to develop metastases would clearly be of considerable value in indicating those cases in need of early aggressive therapy. Representational difference analysis was used in an attempt to identify genetic alterations related to breast cancer metastasis by comparing genomic DNA from microdissected normal cells and from metastatic cells of ductal breast carcinoma patients. Representational difference analysis products yielded 10 unique metastasis-associated DNA sequences (MADS), i.e. products apparently lost in metastatic cell DNA. Of these sequences, MADS-IX was found to be lost in the transition from primary to metastasis in two out of five ductal breast carcinoma cases. This sequence was localized on chromosome 10q21 by radiation hybrid mapping and fluorescence in situ hybridization. The PTEN gene, which is also located on chromosome 10q, was detected to be present by PCR in all five cases. On the contrary, a breast carcinoma cell line, HCC-1937, which has homozygous loss of a region encompassing the PTEN gene, showed the presence of MADS-IX. PCR screening of three additional breast carcinoma cell lines with known losses in specific chromosomal regions also showed the presence of MADS-IX. These data suggest that MADS-IX possibly is part of a novel candidate metastasis-associated gene located close to the PTEN gene on chromosome 10q. The first set of PCR screening in five patient samples indicates that it could be used as a molecular marker for ductal mammary metastasis

  17. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies.

    Science.gov (United States)

    Gallagher, William M; Bergin, Orla E; Rafferty, Mairin; Kelly, Zoë D; Nolan, Ilse-Maria; Fox, Edward J P; Culhane, Aedin C; McArdle, Linda; Fraga, Mario F; Hughes, Linda; Currid, Caroline A; O'Mahony, Fiona; Byrne, Aileen; Murphy, Alison A; Moss, Catherine; McDonnell, Susan; Stallings, Raymond L; Plumb, Jane A; Esteller, Manel; Brown, Robert; Dervan, Peter A; Easty, David J

    2005-11-01

    The incidence of melanoma is increasing rapidly, with advanced lesions generally failing to respond to conventional chemotherapy. Here, we utilized DNA microarray-based gene expression profiling techniques to identify molecular determinants of melanoma progression within a unique panel of isogenic human melanoma cell lines. When a poorly tumorigenic cell line, derived from an early melanoma, was compared with two increasingly aggressive derivative cell lines, the expression of 66 genes was significantly changed. A similar pattern of differential gene expression was found with an independently derived metastatic cell line. We further examined these melanoma progression-associated genes via use of a tailored TaqMan Low Density Array (LDA), representing the majority of genes within our cohort of interest. Considerable concordance was seen between the transcriptomic profiles determined by DNA microarray and TaqMan LDA approaches. A range of novel markers were identified that correlated here with melanoma progression. Most notable was TSPY, a Y chromosome-specific gene that displayed extensive down-regulation in expression between the parental and derivative cell lines. Examination of a putative CpG island within the TSPY gene demonstrated that this region was hypermethylated in the derivative cell lines, as well as metastatic melanomas from male patients. Moreover, treatment of the derivative cell lines with the DNA methyltransferase inhibitor, 2'-deoxy-5-azacytidine (DAC), restored expression of the TSPY gene to levels comparable with that found in the parental cells. Additional DNA microarray studies uncovered a subset of 13 genes from the above-mentioned 66 gene cohort that displayed re-activation of expression following DAC treatment, including TSPY, CYBA and MT2A. DAC suppressed tumor cell growth in vitro. Moreover, systemic treatment of mice with DAC attenuated growth of melanoma xenografts, with consequent re-expression of TSPY mRNA. Overall, our data support

  18. Molecular authentication of the medicinal herb Ruta graveolens (Rutaceae) and an adulterant using nuclear and chloroplast DNA markers.

    Science.gov (United States)

    Al-Qurainy, F; Khan, S; Tarroum, M; Al-Hemaid, F M; Ali, M A

    2011-11-10

    Dried parts of different plant species often look alike, especially in powdered form, making them very difficult to identify. Ruta graveolens, sold as a dried medicinal herb, can be adulterated with Euphorbia dracunculoides. The genomic DNA was isolated from the leaf powder (100 mg each) using the modified CTAB method. Internal transcribed spacer sequences of nuclear ribosomal DNA (nrDNA-ITS), and chloroplast spacer sequences (rpoB and rpoC1) are regarded as potential genes for plant DNA barcoding. We amplified and sequenced these spacer sequences and confirmed the sequences with a BLAST search. Sequence alignment was performed using ClustalX to look for differences in the sequences. A DNA marker was developed based on rpoB and rpoC1 of the nrDNA-ITS for the identification of the adulterant E. dracunculoides in samples of R. graveolens that are sold in local herbal markets. Sequence-characterized amplified region markers of 289 and 264 bp for R. graveolens and 424 bp for E. dracunculoides were developed from dissimilar sequences of this nrDNA-ITS to speed up the authentication process. This marker successfully distinguished these species in extracted samples with as little as 5 ng DNA/μL extract.

  19. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples.

    Science.gov (United States)

    Dong, Chun-Nan; Yang, Ya-Dong; Li, Shu-Jin; Yang, Ya-Ran; Zhang, Xiao-Jing; Fang, Xiang-Dong; Yan, Jiang-Wei; Cong, Bin

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these "nucleosome protected STRs" (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  20. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

    Science.gov (United States)

    Dong, Chun-nan; Yang, Ya-dong; Li, Shu-jin; Yang, Ya-ran; Zhang, Xiao-jing; Fang, Xiang-dong; Yan, Jiang-wei; Cong, Bin

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types. PMID:27189082

  1. Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina.

    Directory of Open Access Journals (Sweden)

    Bryn T M Dentinger

    Full Text Available DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species has not been established. We succeeded in generating 167 partial COI sequences (~450 bp representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30% with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.

  2. Urine Cell-Free DNA Integrity as a Marker for Early Prostate Cancer Diagnosis: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Valentina Casadio

    2013-01-01

    Full Text Available Circulating cell-free DNA has been recognized as an accurate marker for the diagnosis of prostate cancer, whereas the role of urine cell-free DNA (UCF DNA has never been evaluated in this setting. It is known that normal apoptotic cells produce highly fragmented DNA while cancer cells release longer DNA. We thus verified the potential role of UCF DNA integrity for early prostate cancer diagnosis. UCF DNA was isolated from 29 prostate cancer patients and 25 healthy volunteers. Sequences longer than 250 bp (c-Myc, BCAS1, and HER2 were quantified by real-time PCR to verify UCF DNA integrity. Receiver operating characteristic (ROC curve analysis revealed an area under the curve of 0.7959 (95% CI 0.6729–0.9188. At the best cut-off value of 0.04 ng/μL, UCF DNA integrity analysis showed a sensitivity of 0.79 (95% CI 0.62–0.90 and a specificity of 0.84 (95% CI 0.65–0.94. These preliminary findings indicate that UCF DNA integrity could be a promising noninvasive marker for the early diagnosis of prostate cancer and pave the way for further research into this area.

  3. Action of booster immunization with E2 CSFV on immune response elicited by marker DNA-vaccine against CSF

    Directory of Open Access Journals (Sweden)

    Deryabina O. G.

    2012-04-01

    Full Text Available The aim was to study the influence of booster immunization with recombinant fragment of E2 CSFV on humoral immune response, elicited by candidate marker DNA-vaccine against CSF. Methods. The fragment of E2 CSFV gene has been detected by PCR, and the expression of encoded protein – by immunohistochemical analysis. The anti-E2 antibodies in blood serum after immunization have been detected by ELISA. Results. It has been shown that candidate marker DNA-vaccine transfected myocytes of murine biceps in situ. The data of immuno-histochemical analysis revealed the expression of fragment of glycoprotein E2 CSFV from the plasmid introduced. The booster immunization with recombinant E2 led to the significant increase of the titer of antibodies specific to the antigen studied. Conclusions. The data obtained show that boosting with recombinant E2 enhances humoral immune response elicited by the candidate marker DNA-vaccine against CSF.

  4. Introgression evidence and phylogenetic relationships among three (ParaMisgurnus species as revealed by mitochondrial and nuclear DNA markers

    Directory of Open Access Journals (Sweden)

    Jakovlić I.

    2013-01-01

    Full Text Available The taxonomy of (ParaMisgurnus genera is still debated. We therefore used mitochondrial and nuclear DNA markers to analyze the phylogenetic relationships among Misgurnus anguillicaudatus, Paramisgurnus dabryanus and Misgurnus fossilis. Differing phylogenetic signals from mitochondrial and nuclear marker data suggest an introgression event in the history of M. anguillicaudatus and M. mohoity. No substantial genetic evidence was found that Paramisgurnus dabryanus should be classified as a separate genus.

  5. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

  6. [Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

    Science.gov (United States)

    Pesik, V Yu; Fedunin, A A; Agdzhoyan, A T; Utevska, O M; Chukhraeva, M I; Evseeva, I V; Churnosov, M I; Lependina, I N; Bogunov, Yu V; Bogunova, A A; Ignashkin, M A; Yankovsky, N K; Balanovska, E V; Orekhov, V A; Balanovsky, O P

    2014-06-01

    We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA. PMID:25715463

  7. THE RAPID DIAGNOSTICS OF SEX OF SALMONIDS USING DNA-MARKERS

    Directory of Open Access Journals (Sweden)

    Yu. P. Rud

    2014-12-01

    Full Text Available Based on nucleotide sequences of sex-specific DNA-markers of salmonid fishes the oligonucleotide primers for polymerase chain reaction were selected with purpose on rapid diagnostic of sex in rainbow trout Onchorhynchus mykiss, brown trout Salmo trutta, huchen Hucho hucho and grayling Thymallus thymallus. The specify of amplification was determined by nucleotide sequence analysis of PCR-products. All amplified fragments were referred to sex-specific locuses of Y chromosomes in males of investigated fish species. The PCR-products were in size of 880, 607, 521 and 558 for rainbow trout, brown trout, grayling and huchen respectively. Thus the sex determination in above mentioned fish species and identification of genotypic males under process of hormonal sex reversion can be provided using conventional PCR. Present method relates to rapid diagnostics because the data analysis and return of results back to fish farm take one single day.

  8. DNA barcoding in Atlantic Forest plants: what is the best marker for Sapotaceae species identification?

    Directory of Open Access Journals (Sweden)

    Caio Vinicius Vivas

    2014-12-01

    Full Text Available The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region -ITS in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122, followed by trnH-psbA (0.019, matK (0.008 and rbcL (0.002. For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.

  9. A linkage between DNA markers on the X chromosome and male sexual orientation.

    Science.gov (United States)

    Hamer, D H; Hu, S; Magnuson, V L; Hu, N; Pattatucci, A M

    1993-07-16

    The role of genetics in male sexual orientation was investigated by pedigree and linkage analyses on 114 families of homosexual men. Increased rates of same-sex orientation were found in the maternal uncles and male cousins of these subjects, but not in their fathers or paternal relatives, suggesting the possibility of sex-linked transmission in a portion of the population. DNA linkage analysis of a selected group of 40 families in which there were two gay brothers and no indication of nonmaternal transmission revealed a correlation between homosexual orientation and the inheritance of polymorphic markers on the X chromosome in approximately 64 percent of the sib-pairs tested. The linkage to markers on Xq28, the subtelomeric region of the long arm of the sex chromosome, had a multipoint lod score of 4.0 (P = 10(-5), indicating a statistical confidence level of more than 99 percent that at least one subtype of male sexual orientation is genetically influenced. PMID:8332896

  10. A linkage between DNA markers on the X chromosome and male sexual orientation

    Energy Technology Data Exchange (ETDEWEB)

    Hamer, D.H.; Hu, S.; Magnuson, V.L.; Hu, N.; Pattatucci, A.M.L.

    1993-07-16

    The role of genetics in male sexual orientation was investigated by pedigree and linkage analyses on 114 families of homosexual men. Increased rates of same-sex orientation were found in the maternal uncles and male cousins of these subjects, but not in their fathers or paternal relatives, suggesting the possibility of sex-linked transmission in a portion of the population. DNA linkage analysis of a selected group of 40 families in which there were two gay brothers and no indication of nonmaternal transmission revealed a correlation between homosexual orientation and the inheritance of polymorphic markers on the X chromosome in approximately 64 percent of the sib-pairs tested. The linkage to markers on Xq28, the subtelomeric region of the long arm of the sex chromosome, had a multipoint lod score of 4.0(P = 10[sup [minus]5]), indicating a statistical confidence level of more than 99 percent that at least one subtype of male sexual orientation is genetically influenced.

  11. Mapping of the vaccinia virus DNA polymerase gene by marker rescue and cell-free translation of selected RNA

    International Nuclear Information System (INIS)

    The previous demonstration that a phosphonoacetate (PAA)-resistant (PAA/sup r/) vaccinia virus mutant synthesized an altered DNA polymerase provided the key to mapping this gene. Marker rescue was performed in cells infected with wild-type PAA-sensitive (PAA/sup s/) vaccinia by transfecting with calcium phosphate-precipitated DNA from a PAA/sup r/ mutant virus. Formation of PAA/sup r/ recombinants was measured by plaque assay in the presence of PAA. Of the 12 HindIII fragments cloned in plasmid or cosmid vectors, only fragment E conferred the PAA/sup r/ phenotype. Successive subcloning of the 15-kilobase HindIII fragment E localized the marker within a 7.5-kilobase BamHI-HindIII fragment and then within a 2.9-kilobase EcoRI fragment. The location of the DNA polymerase gene, about 57 kilobases from the left end of the genome, was confirmed by cell-free translation of mRNA selected by hybridization to plasmids containing regions of PAA/sup r/ vaccinia DNA active in marker rescue. A 100,000-dalton polypeptide that comigrated with authentic DNA polymerase was synthesized. Correspondence of the in vitro translation product with purified vaccinia DNA polymerase was established by peptide mapping

  12. Interspecific introgression in cetaceans: DNA markers reveal post-F1 status of a pilot whale.

    Directory of Open Access Journals (Sweden)

    Laura Miralles

    Full Text Available Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region and eight nuclear loci (microsatellites as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain, one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.

  13. DEVELOPMENT OF MULTIPLEX DNA-MARKER SET FOR IDENTIFICATION OF RICE BLAST RESISTANCE GENES Pi -40 AND Pi-b

    Directory of Open Access Journals (Sweden)

    Suprun I. I.

    2013-12-01

    Full Text Available Multiplex DNA-marker set for PCR identification for rice blast resistance genes Pi-40 and Pi-b was developed in this study. Optimal primers combinations and PCR conditions allows to identify both abovementioned genes in the single PCR

  14. Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease-digested DNA: identification of markers tightly linked to the supernodulation locus in soybean.

    Science.gov (United States)

    Caetano-Anollés, G; Bassam, B J; Gresshoff, P M

    1993-10-01

    Multiple endonuclease digestion of template DNA or amplification products can increase significantly the detection of polymorphic DNA in fingerprints generated by multiple arbitrary amplicon profiling (MAAP). This coupling of endonuclease cleavage and amplification of arbitrary stretches of DNA, directed by short oligonucleotide primers, readily allowed distinction of closely related fungal and bacterial isolates and plant cultivars. MAAP analysis of cleaved template DNA enabled the identification of molecular markers linked to a developmental locus of soybean (Glycine max L. Merrill). Ethyl methane sulfonate (EMS)-induced supernodulating, near-isogenic lines altered in the nts locus, which controls nodule formation, could be distinguished from each other and from the parent cultivar by amplification of template pre-digested with 2-3 restriction enzymes. A total of 42 DNA polymorphisms were detected using only 19 octamer primers. In the absence of digestion, 25 primers failed to differentiate these soybean genotypes. Several polymorphic products co-segregated tightly with the nts locus in F2 families from crosses between the allelic mutants nts382 and nts1007 and the ancestral G. soja Sieb. & Succ. PI468.397. Our results suggest that EMS is capable of inducing extensive DNA alterations, probably around discrete mutational hot-spots. EMS-induced DNA polymorphisms may constitute sequence-tagged markers diagnostic of specific genomic regions.

  15. Identification of Random Amplified Polymorphic DNA Markers Linked to Sex Determination in Calamus simplicifolius C. F. Wei

    Institute of Scientific and Technical Information of China (English)

    Hua YANG; Si-Ming GAN; Guang-Tian YIN; Huang-Can XU

    2005-01-01

    The random amplified polymorphic DNA (RAPD) molecular marker technique was used to determine the sex of Calamus simplicifolius C. F. Wei In the present study, DNA samples were extracted individually from 10 male and 10 female plants. After a total of 1 040 decamer primers had been tested, an approximate 500-bp male-specific DNA fragment was generated with the S1443 primer. It is feasible to identify sex at the early stages of plant life, which is beneficial for improving breeding programs of this dioecious species. In addition, we have obtained a proper RAPD protocol that is useful for other species of rattan.

  16. Use of RAPD marker for identification of DNA polymorphism in gamma rays treated Jatropha Curcas L

    International Nuclear Information System (INIS)

    The aim of this study is to examine the discriminatory power of random amplified polymorphic DNA (RAPD) marker in Jatropha curcas, and to determine the effect of various dose exposures (0, 5, 10, f, 20 and 25 Kr) of gamma rays on J. curcas, at molecular level. All the ten random primers used produced reproducible polymorphic bands. PCR products of mutant genome revealed a total of 40 bands, out of which 27 were polymorphic. Polymorphism information content (PIC) values were ranged from 0.00 to 0.40 and the highest PIC value of 0.40 was observed in primer OPU-13 followed by primers OPAL-II and OPT-18 (0.30) while no PIC value were reported in primers OPH-18 and OPM-13. Jaccard's coefficient of similarity varied from 0.476 to 0.723, indicative of high level of genetic variation among the mutants studied. UPGMA cluster analysis indicated three distinct clusters, one comprising control while the second included four mutants viz., 10, 15, 25 and 20 Kr. The mutant 5 Kr remained distinct and formed third cluster indicating its higher genetic diversity from the rest of the mutants and control. The primer OPU-13 produced maximum number of bands (8) showed highest discriminatory power and PIC (0.40) by showing maximum number of polymorphic bands (5) when compared to other primers used. The study reveals that RAPD molecular markers can be used to assess polymorphism among the mutants and can be a useful tool to supplement the distinctness, uniformity and stability analysis for plant varietal identification and protection. (author)

  17. Identification of Nonpoint Sources of Fecal Pollution in Coastal Waters by Using Host-Specific 16S Ribosomal DNA Genetic Markers from Fecal Anaerobes

    OpenAIRE

    Bernhard, Anne E.; Field, Katharine G.

    2000-01-01

    We describe a new PCR-based method for distinguishing human and cow fecal contamination in coastal waters without culturing indicator organisms, and we show that the method can be used to track bacterial marker sequences in complex environments. We identified two human-specific genetic markers and five cow-specific genetic markers in fecal samples by amplifying 16S ribosomal DNA (rDNA) fragments from members of the genus Bifidobacterium and the Bacteroides-Prevotella group and performing leng...

  18. Characterization of microsatellite DNA libraries from three mealybug species and development of microsatellite markers for Pseudococcus viburni (Hemiptera: Pseudococcidae).

    Science.gov (United States)

    Correa, M C G; Zaviezo, T; Le Maguet, J; Herrbach, E; Malausa, T

    2014-04-01

    Mealybugs (Hemiptera: Pseudococcidae) are important pests for crops worldwide. Different species, cryptic taxa under the same species name or even populations within a species can differ in biological characteristics, such as phenology, resistance to insecticides, virus transmission and susceptibility to natural enemies. Therefore, their management efficacy depends on their accurate identification. Microsatellite genetic markers are efficient in revealing the fine-scale taxonomic status of insects, both at inter- and intra-specific level. Despite their potential uses, microsatellites have been developed only for one mealybug species so far. Hence, it is unclear whether microsatellites may be useful to assess mealybug population differentiation and structuring. In this work, we tested the feasibility of developing microsatellite markers in mealybugs by: (i) producing and characterizing microsatellite DNA libraries for three species: Pseudococcus viburni, Pseudococcus comstocki and Heliococcus bohemicus, and (ii) by developing and testing markers for Ps. viburni. The obtained libraries contained balanced percentages of dinucleotide (ranging from 15 to 25%) and trinucleotide (from 5 to 17%) motifs. The marker setup for Ps. viburni was successful, although 70% of the primers initially tested were discarded for a lack of polymorphism. Finally, 25 markers were combined in two multiplex polymerase chain reactions with 21 displaying no evidence of deviation from Hardy-Weinberg equilibrium. Ps. viburni markers were tested on one population from France and one from Chile. The markers revealed a significant genetic differentiation between the two populations with an Fst estimate of 0.266.

  19. Potential markers of tongue tumor progression selected by cDNA microarray.

    Science.gov (United States)

    Carinci, F; Lo Muzio, L; Piattelli, A; Rubini, C; Chiesa, F; Ionna, F; Palmieri, A; Maiorano, E; Pastore, A; Laino, G; Dolci, M; Pezzetti, F

    2005-01-01

    Squamous cell carcinoma (SCC), the most frequent malignant tumor of the oral cavity, generally exhibits a poor prognosis and metastases are the main cause of death. This tumor often arises from pre-malignant lesions. To date, it is difficult to predict if and which pre-malignant lesions may progress into oral SCC using traditional methods. For these reasons, several studies are trying to identify markers useful in the progression of pre-malignant lesions and tumors. To define the genetic expression profile of tongue tumor progression we compared 9 dysplasias (DS), 8 tumors without metastasis (TWM), 11 metastasizing SCCs (MT) of the tongue, and a baseline of 11 normal tissues by using cDNA microarray containing 19.2 K clones. We initially applied hierarchical agglomerative clustering based on information from all 6026 clones. Results were obtained by performing a two steps analysis: a Significance Analysis of Microarray (SAM) and a Gene Ontology search. One hundred and five clones have statistically significant different expression levels (FDR ADAMTS2 and cathepsin O). Additionally, under-expressed genes encoded apoptosis-related proteins (PDCD4 and CASP4). In conclusion, we identified several genes differentially expressed in tumor progression which can potentially help in better classifying pre-malignant lesions and tongue SCCs. PMID:16164832

  20. Use of radioisotopes in agriculture: DNA based molecular markers in crop improvement

    International Nuclear Information System (INIS)

    Agriculture has always benefited from the use of radioisotopes in many ways. In the beginning radioisotopes were mostly used for physiological studies to measure photosynthetic efficiency, nutrient uptake, and for mutation breeding. Radioisotopes have now become a part of the biotechnological tools that are being increasingly used in improving crops and production systems. The tools of biotechnology are being increasingly used to hasten breeding and address problems of biotic and abiotic stresses. Some of the non-radioactive methods have replaced radiotracer techniques and thus led to automation often at high cost. However, still there remain many applications where radioisotopes seem almost indispensable. For some of the applications like comparative genome mapping, the confirmation of transgenics, and establishment of gene copy number, use of RFLP with radioisotopes is essential. The following research areas at ICRISAT use radioisotopes: (1) physiological basis of adaptation to abiotic stresses (ii) development and use of appropriate DNA markers crop improvement; (iii) characterization of cytoplasmic male sterile systems and genetic diversity of breeding materials, land races and the wild relatives and (iv) molecular basis of disease resistance; (v) comparative genome mapping across cereals, (vi) isolation and characterization of genes of potential value to genetic improvement and (vii) verification of genetic transformation events. (author)

  1. Investigation of five polymorphic DNA markers associated with late onset Alzheimer disease

    Directory of Open Access Journals (Sweden)

    Gharesouran Jalal

    2013-01-01

    Full Text Available Alzheimer's disease is a complex neurodegenerative disorder characterized by memory and cognitive impairment and is the leading cause of dementia in the elderly. The aim of our study was to examine the polymorphic DNA markers CCR2 (+190 G/A, CCR5Δ32, TNF-α (-308 G/A, TNF-α (-863 C/A and CALHM1 (+394 C/T to determine the relationship between these polymorphisms and the risk of late onset Alzheimer's disease in the population of Eastern Azerbaijan of Iran. A total of 160 patient samples and 163 healthy controls were genotyped by PCR-RFLP and the results confirmed using bidirectional sequencing. Statistical analysis of obtained data revealed non-significant difference between frequency of CCR5Δ32 in case and control groups. The same result was observed for TNF-α (-863 C/A genotype and allele frequencies. Contrary to above results, significant differences were detected in frequency of TNF-α (-308 G/A and CCR2-64I genotypes between the cases and healthy controls. A weak significant difference observed between allele and genotype frequencies of rs2986017 in CALHM1 (+394 C/T; P86L in patient and control samples. It can be concluded that the T allele of P86L variant in CALHM1 & +190 G/A allele of CCR2 have a protective role against abnormal clinical features of Alzheimer's disease.

  2. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

    Science.gov (United States)

    Jan, Catherine

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

  3. New STS molecular markers for assessment of genetic diversity and DNA fingerprinting in hop (Humulus lupulus L.).

    Science.gov (United States)

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

    Molecular markers have been increasingly used in genetic studies of crop species for their applicability in breeding programs. In this work, we report on the development of new sequence-tagged site (STS) markers based on sequence information from several identified hop (Humulus lupulus L.) genes. We demonstrate the usefulness of these STS markers and compare them to SSRs for identifying hop genotypes and estimating genetic diversity in a collection of 68 hop cultivars from around the world. We found 3 individual gene variants (A, B, C) of the chs_H1 gene in this collection. The most frequent gene variant, B (AJ304877), was not detected in Mt. Hood, Glacier, and Horizon (US) cultivars. Gene variant A came from an American germplasm through wild hops. We found length polymorphism in intron 1 of the chs2 gene, and 4 different amplified markers were detected in PCRs. The chs3 gene was found in only one third of the cultivars. None of the variants of the studied CHS genes were found in Humulus japonicus. We detected 5 major gene variants of DNA-binding protein in the collection of H. lupulus cultivars and 2 others in H. japonicus. We also found 3 individual gene variants of an endochitinase gene. The distribution of gene variants did not correlate with any resistance. We proved that developed STS markers can be successfully used for the analysis of genetic diversity and can substitute and supplement SSR markers in hop. PMID:17546067

  4. Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos genome and cross-amplification in other birds

    Directory of Open Access Journals (Sweden)

    Xu Ke

    2005-07-01

    Full Text Available Abstract In order to study duck microsatellites, we constructed a library enriched for (CAn, (CAGn, (GCCn and (TTTCn. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97 was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04 at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%. The polymorphism information content (PIC of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose.

  5. Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics

    OpenAIRE

    Pośpiech, Ewelina; Karłowska-Pik, Joanna; Ziemkiewicz, Bartosz; Kukla, Magdalena; Skowron, Małgorzata; Wojas-Pelc, Anna; Branicki, Wojciech

    2016-01-01

    The genetics of eye colour has been extensively studied over the past few years, and the identified polymorphisms have been applied with marked success in the field of Forensic DNA Phenotyping. A picture that arises from evaluation of the currently available eye colour prediction markers shows that only the analysis of HERC2-OCA2 complex has similar effectiveness in different populations, while the predictive potential of other loci may vary significantly. Moreover, the role of gender in the ...

  6. Genetic Dissection of New Genotypes of Drumstick Tree (Moringa oleifera Lam.) Using Random Amplified Polymorphic DNA Marker

    OpenAIRE

    Shamsuddeen Rufai; Hanafi, M. M.; Rafii, M. Y.; Ahmad, S; Arolu, I. W.; Jannatul Ferdous

    2013-01-01

    The knowledge of genetic diversity of tree crop is very important for breeding and improvement program for the purpose of improving the yield and quality of its produce. Genetic diversity study and analysis of genetic relationship among 20 Moringa oleifera were carried out with the aid of twelve primers from, random amplified polymorphic DNA marker. The seeds of twenty M. oleifera genotypes from various origins were collected and germinated and raised in nursery before transplanting to the fi...

  7. Virulence Genes and Neutral DNA Markers of Helicobacter pylori Isolates from Different Ethnic Communities of West Bengal, India

    OpenAIRE

    Datta, Simanti; Chattopadhyay, Santanu; G. Balakrish Nair; Mukhopadhyay, Asish K.; Hembram, Jabaranjan; Berg, Douglas E.; Rani Saha, Dhira; Khan, Asis; Santra, Amal; S.K. Bhattacharya; Chowdhury, Abhijit

    2003-01-01

    Virulence-associated genes and neutral DNA markers of Helicobacter pylori strains from the Santhal and Oroan ethnic minorities of West Bengal, India, were studied. These people have traditionally been quite separate from other Indians and differ culturally, genetically, and linguistically from mainstream Bengalis, whose H. pylori strains have been characterized previously. H. pylori was found in each of 49 study participants, although none had peptic ulcer disease, and was cultured from 31 of...

  8. North-south population subdivision of Juniperus seravschanica in Kyrgyzstan revealed through novel plastid DNA markers

    Institute of Scientific and Technical Information of China (English)

    Ormon SULTANGAZIEV; Heino KONRAD; Silvio SCHUELER; Thomas GEBUREK

    2012-01-01

    Junipers are main components of semiarid forests in Central Asia.Conservation of these plant genetic resources should be based on an understanding of factors that have shaped species-level genetic variation.We used Juniperus seravschanica Kom.as a model species to investigate patterns and processes that may be associated with these factors.Novel plastid DNA markers (two minisatellites,one transversion,one indel) were identified and applied to investigate haplotype diversity and population structure in Kyrgyzstan.In total,540 individuals from 15 populations were analyzed and 11 haplotypes detected.Strong divergence between populations from northern and southern Kyrgyzstan was evident from the haplotype distribution.Gene diversity within populations ranged from 0.083 to 0.765,and was on average higher in southern (0.687) than in northern populations (0.540).A similar pattern was detected in allelic richness.Analysis of molecular variance (AMOVA) revealed that 11.9% of the total genetic variation was due to differences among regions,1.5% among populations,and 86.6% within populations.NST was not significantly different from GST (0.125),suggesting no evidence of a phylogeographic pattern.A Mantel test detected a weak but significant isolation-by-distance pattern for the whole dataset and southern populations separately.These results suggest that the north of Kyrgyzstan was relatively recently colonized by migrants from southern populations,probably associated with favorable conditions during the early Holocene.The humid Fergana Valley and Fergana Range are probable ecological barriers to gene flow between northern and southern populations.

  9. Impact of deep coalescence on the reliability of species tree inference from different types of DNA markers in mammals.

    Directory of Open Access Journals (Sweden)

    Alejandro Sánchez-Gracia

    Full Text Available An important challenge for phylogenetic studies of closely related species is the existence of deep coalescence and gene tree heterogeneity. However, their effects can vary between species and they are often neglected in phylogenetic analyses. In addition, a practical problem in the reconstruction of shallow phylogenies is to determine the most efficient set of DNA markers for a reliable estimation. To address these questions, we conducted a multilocus simulation study using empirical values of nucleotide diversity and substitution rates obtained from a wide range of mammals and evaluated the performance of both gene tree and species tree approaches to recover the known speciation times and topological relationships. We first show that deep coalescence can be a serious problem, more than usually assumed, for the estimation of speciation times in mammals using traditional gene trees. Furthermore, we tested the performance of different sets of DNA markers in the determination of species trees using a coalescent approach. Although the best estimates of speciation times were obtained, as expected, with the use of an increasing number of nuclear loci, our results show that similar estimations can be obtained with a much lower number of genes and the incorporation of a mitochondrial marker, with its high information content. Thus, the use of the combined information of both nuclear and mitochondrial markers in a species tree framework is the most efficient option to estimate recent speciation times and, consequently, the underlying species tree.

  10. 5S rDNA characterization in twelve Sciaenidae fish species (Teleostei, Perciformes: depicting gene diversity and molecular markers

    Directory of Open Access Journals (Sweden)

    Fernanda A. Alves-Costa

    2008-01-01

    Full Text Available In order to extend the genetic data on the Sciaenidae fish family, the present study had the purpose to characterize PCR-generated 5S rDNA repeats of twelve species of this group through PAGE (Polyacrylamide Gel Electrophoresis analysis. The results showed the occurrence of at least two different 5S rDNA size classes in all the species. Moreover, 5S rDNA repeats of one of the studied species - Isopisthus parvipinnis - were cloned and subjected to nucleotide sequencing and Southern blot membrane hybridization analyses, which permitted to confirm the existence of two major 5S rDNA classes. Phylogenetic analysis based on the nucleotide sequences of different 5S rDNA repeats of I. parvipinnis lead to their separation into two major clusters. These results may reflect the high dynamism that rules the evolution rate of 5S rDNA repeats. The obtained data suggest that 5S rDNA can be useful in genetic analyses to identify species-specific markers and determine relationships among species of the Sciaenidae group.

  11. A new nuclear DNA marker from ubiquitin ligase gene region for genetic diversity detection of walnut germplasm resources

    Directory of Open Access Journals (Sweden)

    Zhili Suo

    2015-03-01

    Full Text Available Development of more sensitive nuclear DNA markers for identification of species, particularly closely allied taxa has been a challenging task that has attracted interest from scientists in fields of biotechnological development and genetic diversity detection. In this study, the sequence of the ubiquitin ligase gene (UBE3 region of nuclear DNA was tested for applicability and efficacy in revealing genetic diversity of walnut resources, with an emphasis on inter- and intra-specific levels. Analysis on genetic relationship among the taxa was conducted with the neighbor-joining (NJ method. The number of variable bases in the UBE3 region was 20 sites. All nine taxa (species/variety/cultivars were distinguished using the UBE3 sequence. In addition, each taxon was characterized molecularly with a unique nucleotide molecular formula using ten variable base sites derived from the nuclear DNA UBE3 gene sequence. This study presents a good complementary methodology for developing new DNA markers for identification of genus Juglans.

  12. The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae

    Directory of Open Access Journals (Sweden)

    Marco Ballardini

    2013-12-01

    Full Text Available The genus Phoenix (Arecaceae comprises 14 species distributed from Cape Verde Islands to SE Asia. It includes the economically important species Phoenix dactylifera. The paucity of differential morphological and anatomical useful characters, and interspecific hybridization, make identification of Phoenix species difficult. In this context, the development of reliable DNA markers for species and hybrid identification would be of great utility. Previous studies identified a 12 bp polymorphic chloroplast minisatellite in the trnG(GCC-trnfM(CAU spacer, and showed its potential for species identification in Phoenix. In this work, in order to develop an efficient DNA barcode marker for Phoenix, a longer cpDNA region (700 bp comprising the mentioned minisatellite, and located between the psbZ and trnfM(CAU genes, was sequenced. One hundred and thirty-six individuals, representing all Phoenix species except P. andamanensis, were analysed. The minisatellite showed 2-7 repetitions of the 12 bp motif, with 1-3 out of seven haplotypes per species. Phoenix reclinata and P. canariensis had species-specific haplotypes. Additional polymorphisms were found in the flanking regions of the minisatellite, including substitutions, indels and homopolymers. All this information allowed us to identify unambiguously eight out of the 13 species, and overall 80% of the individuals sampled. Phoenix rupicola and P. theophrasti had the same haplotype, and so had P. atlantica, P. dactylifera, and P. sylvestris (the “date palm complex” sensu Pintaud et al. 2013. For these species, additional molecular markers will be required for their unambiguous identification. The psbZ-trnfM(CAU region therefore could be considered as a good basis for the establishment of a DNA barcoding system in Phoenix, and is potentially useful for the identification of the female parent in Phoenix hybrids.

  13. Highly Informative Single-Copy Nuclear Microsatellite DNA Markers Developed Using an AFLP-SSR Approach in Black Spruce (Picea mariana) and Red Spruce (P. rubens)

    OpenAIRE

    Yong-Zhong Shi; Natascha Forneris; Rajora, Om P

    2014-01-01

    Background Microsatellites or simple sequence repeats (SSRs) are highly informative molecular markers for various biological studies in plants. In spruce (Picea) and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana)...

  14. DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India.

    Science.gov (United States)

    Rebijith, K B; Asokan, R; Kumar, N K Krishna; Srikumar, K K; Ramamurthy, V V; Bhat, P Shivarama

    2012-10-01

    Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed <1% intraspecific divergence for all four species examined, whereas the interspecific distances ranged from 7 to 13%. This study showed that the DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any. PMID:23068182

  15. Evolution and perspectives of cultivar identification and traceability from tree to oil and table olives by means of DNA markers.

    Science.gov (United States)

    Pasqualone, Antonella; Montemurro, Cinzia; di Rienzo, Valentina; Summo, Carmine; Paradiso, Vito Michele; Caponio, Francesco

    2016-08-01

    In recent years, an increasing number of typicality marks has been awarded to high-quality olive oils produced from local cultivars. In this case, quality control requires effective varietal checks of the starting materials. Moreover, accurate cultivar identification is essential in vegetative-propagated plants distributed by nurseries and is a pre-requisite to register new cultivars. Food genomics provides many tools for cultivar identification and traceability from tree to oil and table olives. The results of the application of different classes of DNA markers to olive with the purpose of checking cultivar identity and variability of plant material are extensively discussed in this review, with special regard to repeatability issues and polymorphism degree. The characterization of olive germplasm from all countries of the Mediterranean basin and from less studied geographical areas is described and innovative high-throughput molecular tools to manage reference collections are reviewed. Then the transferability of DNA markers to processed products - virgin olive oils and table olives - is overviewed to point out strengths and weaknesses, with special regard to (i) the influence of processing steps and storage time on the quantity and quality of residual DNA, (ii) recent advances to overcome the bottleneck of DNA extraction from processed products, (iii) factors affecting whole comparability of DNA profiles between fresh plant materials and end-products, (iv) drawbacks in the analysis of multi-cultivar versus single-cultivar end-products and (v) the potential of quantitative polymerase chain reaction (PCR)-based techniques. © 2016 Society of Chemical Industry. PMID:26991131

  16. Production of marker-free and RSV-resistant transgenic rice using a twin T-DNA system and RNAi

    Indian Academy of Sciences (India)

    Yayuan Jiang; Lin Sun; Mingsong Jiang; Kaidong Li; Yunzhi Song; Changxiang Zhu

    2013-09-01

    A twin T-DNA system is a convenient strategy for creating selectable marker-free transgenic plants. The standard transformation plasmid, pCAMBIA 1300, was modified into a binary vector consisting of two separate T-DNAs, one of which contained the hygromycin phosphotransferase (hpt) marker gene. Using this binary vector, we constructed two vectors that expressed inverted-repeat (IR) structures targeting the rice stripe virus (RSV) coat protein (CP) gene and the special-disease protein (SP) gene. Transgenic rice lines were obtained via Agrobacterium-mediated transformation. Seven independent clones harbouring both the hpt marker gene and the target genes (RSV CP or SP) were obtained in the primary transformants of pDTRSVCP and pDTRSVSP, respectively. The segregation frequencies of the target gene and the marker gene in the T1 plants were 8.72% for pDTRSVCP and 12.33% for pDTRSVSP. Two of the pDTRSVCP lines and three pDTRSVSP lines harbouring the homozygous target gene, but not the hpt gene, were strongly resistant to RSV. A molecular analysis of the resistant transgenic plants confirmed the stable integration and expression of the target genes. The resistant transgenic plants displayed lower levels of the transgene transcripts and specific small interfering RNAs, suggesting that RNAi induced the viral resistance.

  17. Human migration, diversity and disease association: a convergent role of established and emerging DNA markers

    OpenAIRE

    Guha, Pokhraj; Sanjeev K. Srivastava; Bhattacharjee, Soumen; Chaudhuri, Tapas K.

    2013-01-01

    With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it’s excellence in unveiling answers to the questions regarding the migration pattern of human across different geographical regions. As a bonus these markers proved very much beneficial in solv...

  18. HUMAN MIGRATION, DIVERSITY AND DISEASE ASSOCIATION: A CONVERGENT ROLE OF ESTABLISHED AND EMERGING DNA MARKERS

    OpenAIRE

    Pohhraj eGuha; Sanjeev Kumar Srivastava; Soumen eBhattacharjee; Chaudhuri, Tapas K.

    2013-01-01

    With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it’s excellence in unveiling answers to the questions regarding the migration pattern of human across different geographical regions. As a bonus these markers proved very much beneficial in sol...

  19. Using DNA Microarrays To Identify Library-Independent Markers for Bacterial Source Tracking

    OpenAIRE

    Soule, Marilyn; Kuhn, Edward; Loge, Frank; Gay, John; Call, Douglas R.

    2006-01-01

    Bacterial source tracking is used to apportion fecal pollution among putative sources. Within this context, library-independent markers are genetic or phenotypic traits that can be used to identify the host origin without a need for library-dependent classification functions. The objective of this project was to use mixed-genome Enterococcus microarrays to identify library-independent markers. Separate shotgun libraries were prepared for five host groups (cow, dog, elk/deer, human, and waterf...

  20. Circulating Cell Free DNA as the Diagnostic Marker for Ovarian Cancer: A Systematic Review and Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Quan Zhou

    Full Text Available Quantitative analyses of circulating cell-free DNA (cfDNA are potential methods for the detection of ovarian cancer. Many studies have evaluated these approaches, but the results were too inconsistent to be conclusive. This study is the first to systematically evaluate the accuracy of circulating cfDNA for the diagnosis of ovarian cancer by conducting meta-analysis.We searched PubMed, Embase, Cochrane Library and the Chinese National Knowledge Infrastructure (CNKI databases systematically for relevant literatures up to December 10, 2015. All analyses were conducted using Meta-DiSc1.4 and Stata 12.0 software. Sensitivity, specificity and other measures of accuracy of circulating cfDNA for the diagnosis of ovarian cancer were pooled. Meta-regression was performed to identify the sources of heterogeneity.This meta-analysis included a total of 9 studies, including 462 ovarian cancer patients and 407 controls. The summary estimates for quantitative analysis of circulating cfDNA in ovarian cancer screen were as follows: sensitivity, 0.70 (95% confidence interval (CI, 0.65-0.74; specificity, 0.90 (95% CI, 0.87-0.93; positive likelihood ratio, 6.60 (95% CI, 3.90-11.17; negative likelihood ratio, 0.34 (95% CI, 0.25-0.47; diagnostic odds ratio, 26.05 (95% CI, 14.67-46.26; and area under the curve, 0.89 (95% CI, 0.83-0.95, respectively. There was no statistical significance for the evaluation of publication bias.Current evidence suggests that quantitative analysis of cfDNA has unsatisfactory sensitivity but acceptable specificity for the diagnosis of ovarian cancer. Further large-scale prospective studies are required to validate the potential applicability of using circulating cfDNA alone or in combination with conventional markers as diagnostic biomarker for ovarian cancer and explore potential factors that may influence the accuracy of ovarian cancer diagnosis.

  1. DNA methylation mediated silencing of microRNA-145 is a potential prognostic marker in patients with lung adenocarcinoma

    OpenAIRE

    Wenjie Xia; Qiang Chen; Jie Wang; Qixing Mao; Gaochao Dong; Run Shi; YanYan Zheng; Lin Xu; Feng Jiang

    2015-01-01

    The molecular mechanism of down-regulated microRNA-145 (miR-145) expression in lung adenocarcinoma (LAC) remains largely unknown. We hypothesized that aberrant hyper-methylation of the CpG sites silenced the expression of miR-145 in LAC. In consideration of its pivotal role in LAC development and progression, we also evaluated the clinical utility of miR-145 as a prognostic marker. We assessed the DNA methylation status of the miR-145 promoter region in 20 pairs of LAC and the matched non-tum...

  2. Complete mitochondrial genome of Dendronephthya putteri (Octocorallia, Alcyonacea) and useful candidate for developing DNA barcode markers of Dendronephthya species.

    Science.gov (United States)

    Kwak, Hyeon Sook; Choi, Eun Hwa; Jang, Kuem Hee; Ryu, Shi Hyun; Kim, Young Shin; Hwang, Ui Wook

    2015-08-01

    The mitochondrial genome of Dendronephthya putteri (Octocorallia, Alcyonacea) which is an endangered species was completely sequenced. It is 18,853 bp in length and identical to those of Dendronephthya species in its gene arrangement and genome organization. Nucleotide sequence comparison of the mitochondrial genomes of the two D. putteri individuals obtained from this study and the previously reported one (GenBank accession number JQ290079) showed that they are identical perfectly. We found useful candidate for DNA barcode markers for D. putteri species identification. PMID:24083972

  3. Identifying the North American plum species phylogenetic signal using nuclear, mitochondrial, and chloroplast DNA markers

    Science.gov (United States)

    Premise of the study: Prunus L. phylogeny has extensively studied using cpDNA sequences. CpDNA has a slow rate of evolution which is beneficial to determine species relationships at a deeper level. However, a limitation of the chloroplast based phylogenies is its transfer by interspecific hybridizat...

  4. RFLP analysis of forensic DNA samples with single-locus VNTR genetic markers.

    Science.gov (United States)

    Bing, D H; Bieber, F R

    2001-05-01

    This unit covers the many and varied methods for extracting DNA from such diverse specimens as blood, tissue, stamps and envelopes, and cigarette butts, among others. Modifications to the methods that allow the DNA to be used for either PCR or Southern blotbased analyses are also included.

  5. HUMAN MIGRATION, DIVERSITY AND DISEASE ASSOCIATION: A CONVERGENT ROLE OF ESTABLISHED AND EMERGING DNA MARKERS

    Directory of Open Access Journals (Sweden)

    Pohhraj eGuha

    2013-08-01

    Full Text Available With the gradual development of intelligence, human got curious to know his origin and evolutionary background. Historical statements and anthropological findings were his primary tool for solving the puzzles of his own origin, until came the golden era of molecular markers which took no time to prove it’s excellence in unveiling answers to the questions regarding the migration pattern of human across different geographical regions. As a bonus these markers proved very much beneficial in solving criminal offences and in understanding the etiology of many dreaded diseases and to design their prevention. In this review, we have aimed to throw light on some of the promising molecular markers which are very much in application now-a-days for not only understanding the evolutionary background and ancient migratory routes of humans but also in the field of forensics and human health.

  6. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Directory of Open Access Journals (Sweden)

    Chodon Sass

    Full Text Available Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL, and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS, were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  7. The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.

    Science.gov (United States)

    Wilcox, Taylor M; Carim, Kellie J; McKelvey, Kevin S; Young, Michael K; Schwartz, Michael K

    2015-01-01

    Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri), and rainbow trout (O. mykiss), which are of conservation interest both as native species and as invasive species across each other's native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah) prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.

  8. The Dual Challenges of Generality and Specificity When Developing Environmental DNA Markers for Species and Subspecies of Oncorhynchus.

    Directory of Open Access Journals (Sweden)

    Taylor M Wilcox

    Full Text Available Environmental DNA (eDNA sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi, Yellowstone cutthroat trout (O. clarkii bouvieri, and rainbow trout (O. mykiss, which are of conservation interest both as native species and as invasive species across each other's native ranges. We found that local polymorphisms within westslope cutthroat trout and rainbow trout posed a challenge to designing assays that are generally applicable across the range of these widely-distributed species. Further, poorly-resolved taxonomies of Yellowstone cutthroat trout and Bonneville cutthroat trout (O. c. utah prevented design of an assay that distinguishes these recognized taxa. The issues of intraspecific polymorphism and unresolved taxonomy for eDNA assay design addressed in this study are likely to be general problems for closely-related taxa. Prior to field application, we recommend that future studies sample populations and test assays more broadly than has been typical of published eDNA assays to date.

  9. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  10. Urinary 8-hydroxy-2'-deoxyguanosine as a biological marker of in vivo oxidative DNA damage

    International Nuclear Information System (INIS)

    DNA is subject to constant oxidative damage from endogenous oxidants. The oxidized DNA is continuously repaired and the oxidized bases are excreted in the urine. A simple routine analytical procedure is described for urinary 8-hydroxy-2'-deoxyguanosine, an oxidative DNA damage adduct, as an indicator of oxidative damage in humans and rodents. This adduct was purified from human urine and characterized. The described assay employs a series of solid-phase extraction steps that separate 8-hydroxy-2'-deoxyguanosine from other urinary constituents, followed by analysis by gradient reversed-phase HPLC coupled to a dual-electrode high-efficient electrochemical detection system. Analysis of urine from three species by this method indicates that mice excrete approximately 3.3-fold more 8-hydroxy-2'-deoxyguanosine than humans (582 vs. 178 residues per cell day), a result that supports the proposal that oxidative damage to DNA increases in proportion to species-specific basal metabolic rates

  11. Identification of Bacterial DNA Markers for the Detection of Human and Cattle Fecal Pollution - SLIDES

    Science.gov (United States)

    Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

  12. IDENTIFICATION OF BACTERIAL DNA MARKERS FOR THE DETECTION OF HUMAN AND CATTLE FECAL POLLUTION

    Science.gov (United States)

    Technological advances in DNA sequencing and computational biology allow scientists to compare entire microbial genomes. However, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for most laborato...

  13. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

    Science.gov (United States)

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  14. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN CATTLE FECAL SAMPLES - ABSTRACT

    Science.gov (United States)

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

  15. Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

    Science.gov (United States)

    Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

  16. DNA polymorphisms in chickpea accessions as revealed by PCR-based markers.

    Science.gov (United States)

    Yadav, P; Koul, K K; Shrivastava, N; Mendaki, M J; Bhagyawant, S S

    2015-01-01

    Chickpea is a food legume which is alleged to be a preferred source of protein next only to milk. Germplasm of cultivated chickpea available is deficient in desired genetic variation. Genetic manipulations therefore, necessitate the genetic exploitation of its related annual and wild species. 42 RAPD and 41 ISSR markers were employed to ascertain polymorphism across 20 genotypes which were collected from 10 different geographical areas of the world. RAPD marker detected 51% genetic polymorphisms while ISSR marker detected 54 %. With an average of 6.5 each RAPD primer amplified 5—8 bands. Similarly with an average of 7.9 each ISSR primer amplified 4—12 bands. The cluster dendrogram demonstrated a similarity coefficient range from 0.80 to 0.92 due to RAPD markers, whereas with ISSR primers the cluster dendrogram showed similarity coefficient of 0.60 to 1.00. Accessions from same geographical area seem to be genetically similar than those from geographically distant and isolated ones. When however compared, interestingly the ISSR dendrogram showed more correlation with pedigree data than the RAPD dendrogram. The variability index worked out in the present study ranges from 0.79 to 0.96. Since the ultimate reason for such studies is selection of diverse genetic accessions for their recommendation to breeding programmers, the accessions like ICC6263, ICC6306 and ICC17160 can be recommended as parents. Further breeding programmes can therefore be planned to procure additional variation complexes in chickpea genetic stocks. PMID:26516116

  17. DNA markers to disentangle complexes of cryptic taxa in mealybugs (Hemiptera: Pseudococcidae)

    Science.gov (United States)

    Mealybugs (Hemiptera: Pseudococcidae) are major pests of a wide range of crops and ornamental plants worldwide. Their high degree of morphological similarity makes them difficult to identify and limits their study and management. We aimed to identify a set of markers for the genetic characterization...

  18. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples

    OpenAIRE

    Chun-nan Dong; Ya-dong Yang; Shu-jin Li; Ya-ran Yang; Xiao-jing Zhang; Xiang-dong Fang; Jiang-wei Yan; Bin Cong

    2016-01-01

    In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and ident...

  19. Circulating cell-free DNA and its integrity as a prognostic marker for breast cancer

    OpenAIRE

    Iqbal, Sobuhi; Vishnubhatla, Sreenivas; Raina, Vinod; Sharma, Surabhi; Gogia, Ajay; Suryanarayana S.V. Deo; Mathur, Sandeep; Shukla, Nutan Kumar

    2015-01-01

    The aim of our study was to look for alternative predictive biomarkers for breast cancer management in limited resource setup. A comprehensive analysis of circulating cell-free DNA (CCFD) in serum at baseline was performed to assess its prognostic potential. Quantitative polymerase chain reaction (qPCR) of ALU sequences using ALU115 and ALU247 primers was carried out in patients (N: baseline 148, postoperative 47) and 51 healthy controls. Mean serum DNA integrity, levels of ALU 247 and levels...

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    A. Helmi

    2011-01-01

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

  2. Assessment of genetic diversity in Mucuna species of India using randomly amplified polymorphic DNA and inter simple sequence repeat markers.

    Science.gov (United States)

    Patil, Ravishankar R; Pawar, Kiran D; Rane, Manali R; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

    2016-04-01

    Genus Mucuna which is native to China and Eastern India comprises of perennial climbing legume with long slender branches, trifoliate leaves and bear green or brown pod covered with soft or rigid hairs that cause intense irritation. The plants of this genus are agronomically and economically important and commercially cultivated in India, China and other regions of the world. The high degrees of taxonomical confusions exist in Mucuna species that make authentic identification and classification difficult. In the present study, the genetic diversity among the 59 accessions of six species and three varieties of M. pruriens has been assessed using DNA fingerprinting based molecular markers techniques namely randomly amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and combined dataset of RAPD and ISSR. Also, genetic relationship among two endemic species of Mucuna namely M. imbricata and M. macrocarpa and two varieties namely IIHR hybrid (MHR) and Dhanwantari (MD) with other species under study was investigated by using cluster analysis and principal coordinate analysis. The cluster analysis of RAPD, ISSR and combined dataset of RAPD and ISSR clearly demonstrated the existence of high interspecific variation than intra-specific variation in genus Mucuna. The utility and efficacy of RAPD and ISSR for the study of intra species and interspecies genetic diversity was evident from AMOVA and PCoA analysis. This study demonstrates the genetic diversity in Mucuna species and indicates that these markers could be successfully used to assess genetic variation among the accessions of Mucuna species. PMID:27436912

  3. A Unique Procedure to Identify Cell Surface Markers Through a Spherical Self-Organizing Map Applied to DNA Microarray Analysis.

    Science.gov (United States)

    Sugii, Yuh; Kasai, Tomonari; Ikeda, Masashi; Vaidyanath, Arun; Kumon, Kazuki; Mizutani, Akifumi; Seno, Akimasa; Tokutaka, Heizo; Kudoh, Takayuki; Seno, Masaharu

    2016-01-01

    To identify cell-specific markers, we designed a DNA microarray platform with oligonucleotide probes for human membrane-anchored proteins. Human glioma cell lines were analyzed using microarray and compared with normal and fetal brain tissues. For the microarray analysis, we employed a spherical self-organizing map, which is a clustering method suitable for the conversion of multidimensional data into two-dimensional data and displays the relationship on a spherical surface. Based on the gene expression profile, the cell surface characteristics were successfully mirrored onto the spherical surface, thereby distinguishing normal brain tissue from the disease model based on the strength of gene expression. The clustered glioma-specific genes were further analyzed by polymerase chain reaction procedure and immunocytochemical staining of glioma cells. Our platform and the following procedure were successfully demonstrated to categorize the genes coding for cell surface proteins that are specific to glioma cells. Our assessment demonstrates that a spherical self-organizing map is a valuable tool for distinguishing cell surface markers and can be employed in marker discovery studies for the treatment of cancer.

  4. Concordance of nuclear and mitochondrial DNA markers in detecting a founder event in Lake Clark sockeye salmon

    Science.gov (United States)

    Ramstad, Kristina M.; Woody, Carol Ann; Habicht, Chris; Sage, G. Kevin; Seeb, James E.; Allendorf, Fred W.

    2007-01-01

    Genetic bottleneck effects can reduce genetic variation, persistence probability, and evolutionary potential of populations. Previous microsatellite analysis suggested a bottleneck associated with a common founding of sock-eye salmon Oncorhynchus nerka populations of Lake Clark, Alaska, about 100 to 400 generations ago. The common foundingevent occurred after the last glacial recession and resulted in reduced allelic diversity and strong divergence of Lake Clarksockeye salmon relative to neighboring Six Mile Lake and LakeIliamna populations. Here we used two additional genetic marker types (allozymes and mtDNA) to examine these patterns further. Allozyme and mtDNA results were congruent with the microsatellite data in suggesting a common founder event in LakeClark sockeye salmon and confirmed the divergence of Lake Clarkpopulations from neighboring Six Mile Lake and Lake Iliamna populations. The use of multiple marker types provided better understanding of the bottleneck in Lake Clark. For example, the Sucker Bay Lake population had an exceptionally severe reduction in allelic diversity at microsatellite loci, but not at mtDNA. This suggests that the reduced microsatellite variation in Sucker Bay Lake fish is due to consistently smaller effective population size than other Lake Clark populations, rather than a more acute or additional bottleneck since founding. Caution is urged in using reduced heterozygosity as a measure of genetic bottleneck effects because stochastic variance among loci resulted in an overall increase in allozyme heterozygosity within bottlenecked Lake Clark populations. However, heterozygosity excess, which assesses heterozygosity relative to allelic variation, detected genetic bottleneck effects in both allozyme and microsatellite loci. 

  5. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers.

    Directory of Open Access Journals (Sweden)

    Han-Jun Jin

    Full Text Available BACKGROUND: The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary. METHODOLOGY AND RESULTS: We analyzed mitochondrial DNA (mtDNA sequence variation in the hypervariable segments I and II (HVS-I and HVS-II and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing, Vietnamese and Thais. In addition, published mtDNA haplogroup data (N = 3307, mtDNA HVS-I sequences (N = 2313, Y chromosome haplogroup data (N = 1697 and Y chromosome STR data (N = 2713 were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations. CONCLUSION: The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.

  6. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

    Science.gov (United States)

    Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

    2007-01-01

    Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

  7. 16S partial gene mitochondrial DNA and internal transcribed spacers ribosomal DNA as differential markers of Trichuris discolor populations.

    Science.gov (United States)

    Callejón, R; Halajian, A; de Rojas, M; Marrugal, A; Guevara, D; Cutillas, C

    2012-05-25

    Comparative morphological, biometrical and molecular studies of Trichuris discolor isolated from Bos taurus from Spain and Iran was carried out. Furthermore, Trichuris ovis isolated from B. taurus and Capra hircus from Spain has been, molecularly, analyzed. Morphological studies revealed clear differences between T. ovis and T. discolor isolated from B. taurus but differences were not observed between populations of T. discolor isolated from different geographical regions. Nevertheless, the molecular studies based on the amplification and sequencing of the internal transcribed spacers 1 and 2 ribosomal DNA and 16S partial gene mitochondrial DNA showed clear differences between both populations of T. discolor from Spain and Iran suggesting two cryptic species. Phylogenetic studies corroborated these data. Thus, phylogenetic trees based on ITS1, ITS2 and 16S partial gene sequences showed that individuals of T. discolor from B. taurus from Iran clustered together and separated, with high bootstrap values, of T. discolor isolated from B. taurus from Spain, while populations of T. ovis from B. taurus and C. hircus from Spain clustered together but separated with high bootstrap values of both populations of T. discolor. Furthermore, a comparative phylogenetic study has been carried out with the ITS1and ITS2 sequences of Trichuris species from different hosts. Three clades were observed: the first clustered all the species of Trichuris parasitizing herbivores (T. discolor, T. ovis, Trichuris leporis and Trichuris skrjabini), the second clustered all the species of Trichuris parasitizing omnivores (Trichuris trichiura and Trichuris suis) and finally, the third clustered species of Trichuris parasitizing carnivores (Trichuris muris, Trichuris arvicolae and Trichuris vulpis).

  8. Authentication of Cordyceps sinensis by DNA Analyses: Comparison of ITS Sequence Analysis and RAPD-Derived Molecular Markers.

    Science.gov (United States)

    Lam, Kelly Y C; Chan, Gallant K L; Xin, Gui-Zhong; Xu, Hong; Ku, Chuen-Fai; Chen, Jian-Ping; Yao, Ping; Lin, Huang-Quan; Dong, Tina T X; Tsim, Karl W K

    2015-01-01

    Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM). In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS) sequences and the random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps. PMID:26694332

  9. Authentication of Cordyceps sinensis by DNA Analyses: Comparison of ITS Sequence Analysis and RAPD-Derived Molecular Markers

    Directory of Open Access Journals (Sweden)

    Kelly Y. C. Lam

    2015-12-01

    Full Text Available Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM. In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS sequences and the random amplified polymorphic DNA (RAPD-sequence characterized amplified region (SCAR were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps.

  10. Molecular and functional diversity of PGPR fluorescent Pseudomonads based on 16S rDNA-RFLP and RAPD markers.

    Science.gov (United States)

    Singh, Bhim Pratap

    2015-09-01

    The genetic and functional diversity of plant growth promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with chickpea (Cicer arietinum L.) rhizosphere was analyzed. In total, 34 isolates along with two reference isolates were screened for various plant growth promoting traits (phosphorous solubilization, ACC deaminase, HCN, IAA and siderophore productions) and antagonist activity against four fungal phytopathogens and three bacterial pathogens. Most of the isolates, that showed PGPR activity, also showed antagonistic activity against all the three fungal pathogens. The genetic relationship was assessed by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (16S rDNA-RFLP). Relationship between both the markers was analyzed based on mantel test and a negative correlation was observed. The study concluded that PGPR traits appeared to be strain specific rather than specific to any phylogenetic group. The study also reported that 16S rDNA based profiling differentiated PGPR fluorescent Pseudomonas on the basis of location rather than biological trait. RAPD profiling could be useful to differentiate among the closely related isolates. The genetic and functional diversity of fluorescent pseudomonads, associated with the chickpea rhizosphere, has useful ecological role and potential utilization in sustainable agriculture.

  11. Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing

    NARCIS (Netherlands)

    A. Vidaki (Athina); F. Giangasparo (Federica); D. Syndercombe-Court (Denise)

    2016-01-01

    textabstractThe presence of specific body fluids at crime scenes could be linked with particular types of crime, therefore attributing a DNA profile to a specific tissue could increase the evidential significance of a match with a suspect. Current methodologies such as tissue-specific mRNA profiling

  12. Graft-Derived Cell-Free DNA as a Marker of Transplant Graft Injury.

    Science.gov (United States)

    Oellerich, Michael; Walson, Philip D; Beck, Julia; Schmitz, Jessica; Kollmar, Otto; Schütz, Ekkehard

    2016-04-01

    Although short-term success after solid organ transplantation is good, long-term graft and recipient survival are both not satisfactory. Despite therapeutic drug monitoring (TDM) of immunosuppressive drugs (ISDs), both excessive and insufficient immunosuppression still do occur. There is a need for new biomarkers that, when combined with TDM, can be used to provide more effective and less toxic, personalized immunosuppression to improve long-term survival. Currently used methods are insufficient to rapidly, cost-effectively, and directly interrogate graft integrity after solid organ transplantation. However, because organ transplants are also genome transplants, measurement of graft-derived circulating cell-free DNA (GcfDNA) has shown promise as a way to improve both graft and recipient outcomes after solid organ transplantation through the early detection of severe graft injury, enabling an early intervention. A newly developed droplet digital polymerase chain reaction (ddPCR) method has advantages over expensive high-throughput sequencing methods to rapidly quantify GcfDNA percentages and absolute amounts. This procedure does not require donor DNA and therefore can be applied to any organ donor/recipient pair. The droplet digital polymerase chain reaction method allows for the early, sensitive, specific, and cost-effective direct assessment of graft integrity and can be used to define individual responses to ISDs including the minimal ISD exposures necessary to prevent rejection. This is especially important in patients undergoing ISD switches due to ISD toxicity, infections, or malignancies. Although prospective, multicenter clinical trials in liver, heart, and kidney transplantation have not been completed, early results suggest that GcfDNA can be combined with TDM to guide changes in immunosuppression to provide more effective, and less toxic treatment. Personalized immunosuppression will shift emphasis in transplantation from reaction to prevention and could

  13. Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.

    Science.gov (United States)

    Soto-Calderón, Iván Darío; Clark, Nicholas Jonathan; Wildschutte, Julia Vera Halo; DiMattio, Kelly; Jensen-Seaman, Michael Ignatius; Anthony, Nicola Mary

    2014-12-01

    The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts

  14. Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.

    Science.gov (United States)

    Soto-Calderón, Iván Darío; Clark, Nicholas Jonathan; Wildschutte, Julia Vera Halo; DiMattio, Kelly; Jensen-Seaman, Michael Ignatius; Anthony, Nicola Mary

    2014-12-01

    The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts

  15. Characterization of microsatellite DNA markers for the alligator snapping turtle, Macrochelys temminckii: Primer note

    Science.gov (United States)

    Hackler, J.C.; Van Den Bussche, Ronald A.; Leslie, David M., Jr.

    2007-01-01

    Two trinucleotide and seven tetranucleotide microsatellite loci were isolated from an alligator snapping turtle Macrochelys temminckii. To assess the degree of variability in these nine microsatellite loci, we genotyped 174 individuals collected from eight river drainage basins in the southeastern USA. These markers revealed a moderate degree of allelic diversity (six to 16 alleles per locus) and observed heterozygosity (0.166-0.686). These polymorphic microsatellite loci provide powerful tools for population genetic studies for a species that is afforded some level of conservation protection in every state in which it occurs. ?? 2006 The Authors.

  16. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata

    Directory of Open Access Journals (Sweden)

    Amirul Firdaus Jamaluddin Jamsari

    2011-01-01

    Full Text Available Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae, a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07 was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.

  17. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata.

    Science.gov (United States)

    Jamsari, Amirul Firdaus Jamaluddin; Min-Pau, Tan; Siti-Azizah, Mohd Nor

    2011-04-01

    Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.

  18. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata.

    Science.gov (United States)

    Jamsari, Amirul Firdaus Jamaluddin; Min-Pau, Tan; Siti-Azizah, Mohd Nor

    2011-04-01

    Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata. PMID:21734840

  19. Role of hazelnut consumption on DNA damage and lipid-related markers in children with primary dyslipidemia

    Directory of Open Access Journals (Sweden)

    Cristian Del Bo'

    2015-06-01

    Sixty children (11.5 ± 2.5 years have participated in an 8-week controlled, parallel, dietary intervention study with hazelnuts (0.43 g/kg body weight per day. Subjects received dietary guidelines and were randomized in 3 groups: 1- hazelnuts with skin; 2- hazelnut without skin; 3- control (without hazelnuts. Before and after intervention, blood samples were collected and used to evaluate the levels of formamidopyrimidine-DNA glycosylase (FPG-sensitive sites and H2O2-induced DNA damage in peripheral blood mononuclear cells (by comet assay, serum lipid profile (by automatic analyzer and erythrocyte membrane phospholipids composition (by gas chromatography analysis. Preliminary results in a subgroup (5 subjects receiving hazelnut with skin and 5 controls show a reduction in the FPG-sensitive sites (from 13.8 ± 3.16% to 7.88 ± 2.98% and H2O2-induced DNA damage (from 44.4 ± 3.1% to 35.7 ± 7.6% following 8-week hazelnut consumption, while no effect seems to occur in the control group. Hazelnut decreases serum LDL-C level (-11.2%; p= 0.01 and seems to affect erythrocyte membrane phospholipids composition compared to baseline, while no difference in triglycerides, total and HDL-C levels has been documented in the subgroup analyzed. These preliminary results show a tendency towards a decrease in the levels of FPG-sensitive sites, H2O2-induced DNA damage and serum LDL-C after an 8-week hazelnut intervention. Data elaboration on the complete group of subjects will help understanding the effect of hazelnut consumption on lipid profile and markers of oxidative stress in children affected by primary dyslipidemia.

  20. Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Pedram Kashiani

    2012-01-01

    Full Text Available A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon's information index (I and Nei's gene diversity coefficient (Nei, Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703, while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456. Based on linkage disequilibrium (LD measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even so, there was a high proportion of genetic variation in Chromosomes 4, 5, 8, 9 and 10, thereby revealing their appropriateness for use in the genetic diversity investigations among tropical sweet corn lines. Chromosome 4, with the highest number of loci in linkage disequilibrium, was considered the best for marker-phenotype association and QTL mapping, followed by Chromosomes 5, 8, 9 and 10.

  1. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer

    OpenAIRE

    Laird Peter W; Weisenberger Daniel J; Campan Mihaela; Turla Sally; Hagen Jeffrey A; Koss Michael N; Galler Janice S; Anglim Paul P; Siegmund Kimberly D; Laird-Offringa Ite A

    2008-01-01

    Abstract Background Lung cancer is the leading cause of cancer death in men and women in the United States and Western Europe. Over 160,000 Americans die of this disease every year. The five-year survival rate is 15% – significantly lower than that of other major cancers. Early detection is a key factor in increasing lung cancer patient survival. DNA hypermethylation is recognized as an important mechanism for tumor suppressor gene inactivation in cancer and could yield powerful biomarkers fo...

  2. Blood DNA methylation markers in potentially identified Chinese patients with hepatocellular carcinoma.

    Science.gov (United States)

    Liu, Zongying; Yan, Haixiu; Zhang, Jinshu

    2016-07-01

    To determine whether blood DNA methylation is associated with hepatocellular carcinoma (HCC) for Chinese patients, we used genome-wide DNA methylation detection to access the blood samples of Chinese patients by Illumina Human methylation 450K arrays. Sixty potentially gene locis which had different methylated levels significantly among tumor and adjacent normal tissues would be tested in this study. A previous study was conducted in China communities and followed with 7 years. The DNA from white blood cells (WBC) from 192 patients with HCC and 215 matched controls were assayed in this study. The χ2 test was used to measure data to categorize variables and t -test was used to evaluate the different characteristics among groups. Besides, odds ratios (OR) and 95%CI was calculated for matching factors by conditional logistic regression models. We found that high methylation in WNK2 was related to increased risk of HCC, and high methylation in TPO were related to decreased risk of HCC. In our multivariable conditional logistic regression models, these results all exist. Those findings support the methylated changes of WNK2 and TPO may become a new detection index for HCC patients in clinical laboratory. However, the results should be replicated in additional prospective studies with lager samples. PMID:27592479

  3. Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.

    Science.gov (United States)

    Peijnenburg, K T C A; Fauvelot, C; Breeuwer, J A J; Menken, S B J

    2006-10-01

    Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations. PMID:16968273

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

    Directory of Open Access Journals (Sweden)

    Yasodha Perumal

    2009-01-01

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

  5. Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers.

    Science.gov (United States)

    Hama-Ali, Emad Omer; Alwee, Sharifah Shahrul Rabiah Syed; Tan, Soon Guan; Panandam, Jothi Malar; Ling, Ho Chai; Namasivayam, Parameswari; Peng, Hoh Boon

    2015-05-01

    Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method. PMID:25399079

  6. Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan.

    Directory of Open Access Journals (Sweden)

    Erhan Bilal

    Full Text Available We report results from the analysis of complete mitochondrial DNA (mtDNA sequences from 112 Japanese semi-supercentenarians (aged above 105 years combined with previously published data from 96 patients in each of three non-disease phenotypes: centenarians (99-105 years of age, healthy non-obese males, obese young males and four disease phenotypes, diabetics with and without angiopathy, and Alzheimer's and Parkinson's disease patients. We analyze the correlation between mitochondrial polymorphisms and the longevity phenotype using two different methods. We first use an exhaustive algorithm to identify all maximal patterns of polymorphisms shared by at least five individuals and define a significance score for enrichment of the patterns in each phenotype relative to healthy normals. Our study confirms the correlations observed in a previous study showing enrichment of a hierarchy of haplogroups in the D clade for longevity. For the extreme longevity phenotype we see a single statistically significant signal: a progressive enrichment of certain "beneficial" patterns in centenarians and semi-supercentenarians in the D4a haplogroup. We then use Principal Component Spectral Analysis of the SNP-SNP Covariance Matrix to compare the measured eigenvalues to a Null distribution of eigenvalues on Gaussian datasets to determine whether the correlations in the data (due to longevity arises from some property of the mutations themselves or whether they are due to population structure. The conclusion is that the correlations are entirely due to population structure (phylogenetic tree. We find no signal for a functional mtDNA SNP correlated with longevity. The fact that the correlations are from the population structure suggests that hitch-hiking on autosomal events is a possible explanation for the observed correlations.

  7. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification.

    Science.gov (United States)

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry. PMID:27471732

  8. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification

    Science.gov (United States)

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry.

  9. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification.

    Science.gov (United States)

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry.

  10. Virulence genes and neutral DNA markers of Helicobacter pylori isolates from different ethnic communities of West Bengal, India.

    Science.gov (United States)

    Datta, Simanti; Chattopadhyay, Santanu; Balakrish Nair, G; Mukhopadhyay, Asish K; Hembram, Jabaranjan; Berg, Douglas E; Rani Saha, Dhira; Khan, Asis; Santra, Amal; Bhattacharya, S K; Chowdhury, Abhijit

    2003-08-01

    Virulence-associated genes and neutral DNA markers of Helicobacter pylori strains from the Santhal and Oroan ethnic minorities of West Bengal, India, were studied. These people have traditionally been quite separate from other Indians and differ culturally, genetically, and linguistically from mainstream Bengalis, whose H. pylori strains have been characterized previously. H. pylori was found in each of 49 study participants, although none had peptic ulcer disease, and was cultured from 31 of them. All strains carried the cag pathogenicity island and potentially toxigenic s1 alleles of vacuolating cytotoxin gene (vacA) and were resistant to at least 8 micro g of metronidazole per ml. DNA sequence motifs in vacA mid-region m1 alleles, cagA, and an informative insertion or deletion motif next to cagA from these strains were similar to those of strains from ethnic Bengalis. Three mobile elements, IS605, IS607, and ISHp608, were present in 29, 19, and 10%, respectively, of Santhal and Oroan strains, which is similar to their prevalence in Bengali H. pylori. Thus, there is no evidence that the gene pools of H. pylori of these ethnic minorities differ from those of Bengalis from the same region. This relatedness of strains from persons of different ethnicities bears on our understanding of H. pylori transmission between communities and genome evolution. PMID:12904384

  11. Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification

    Science.gov (United States)

    Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

    2016-01-01

    The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry. PMID:27471732

  12. Intravital imaging of fluorescent markers and FRET probes by DNA tattooing

    Directory of Open Access Journals (Sweden)

    Spencer David M

    2007-01-01

    Full Text Available Abstract Background Advances in fluorescence microscopy and mouse transgenesis have made it possible to image molecular events in living animals. However, the generation of transgenic mice is a lengthy process and intravital imaging requires specialized knowledge and equipment. Here, we report a rapid and undemanding intravital imaging method using generally available equipment. Results By DNA tattooing we transfect keratinocytes of living mice with DNA encoding fluorescent biosensors. Subsequently, the behavior of individual cells expressing these biosensors can be visualized within hours and using conventional microscopy equipment. Using this "instant transgenic" model in combination with a corrected coordinate system, we followed the in vivo behavior of individual cells expressing either FRET- or location-based biosensors for several days. The utility of this approach was demonstrated by assessment of in vivo caspase-3 activation upon induction of apoptosis. Conclusion This "instant skin transgenic" model can be used to follow the in vivo behavior of individual cells expressing either FRET- or location-based probes for several days after tattooing and provides a rapid and inexpensive method for intravital imaging in murine skin.

  13. Monitoring of transplanted liver health by quantification of organ-specific genomic marker in circulating DNA from receptor.

    Directory of Open Access Journals (Sweden)

    Hada C Macher

    Full Text Available BACKGROUND: Health assessment of the transplanted organ is very important due to the relationship of long-term survival of organ transplant recipients and health organ maintenance. Nowadays, the measurement of cell-free DNA from grafts in the circulation of transplant recipients has been considered a potential biomarker of organ rejection or transplant associated complications in an attempt to replace or reduce liver biopsy. However, methods developed to date are expensive and extremely time-consuming. Our approach was to measure the SRY gene, as a male organ biomarker, in a setting of sex-mismatched female recipients of male donor organs. METHODS: Cell-free DNA quantization of the SRY gene was performed by real-time quantitative PCR beforehand, at the moment of transplantation during reperfusion (day 0 and during the stay at the intensive care unit. Beta-globin cell-free DNA levels, a general cellular damage marker, were also quantified. RESULTS: Beta-globin mean values of patients, who accepted the graft without any complications during the first week after surgery, diminished from day 0 until patient stabilization. This decrease was not so evident in patients who suffered some kind of post-transplantation complications. All patients showed an increase in SRY levels at day 0, which decreased during hospitalization. Different complications that did not compromise donated organs showed increased beta-globin levels but no SRY gene levels. However, when a donated organ was damaged the patients exhibited high levels of both genes. CONCLUSION: Determination of a SRY gene in a female recipient's serum is a clear and specific biomarker of donated organs and may give us important information about graft health in a short period of time by a non-expensive technique. This approach may permit clinicians to maintain a close follow up of the transplanted patient.

  14. DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance

    Institute of Scientific and Technical Information of China (English)

    Jie-hong ZHAO; Ji-shun ZHANG; Yi WANG; Ren-gang WANG; Chun WU; Long-jiang FAN; Xue-liang REN

    2011-01-01

    DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth,development,and polyploidization.However,there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative characteristics.We studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco,Nicotiana tabacum,using a methylation-sensitive amplified polymorphism (MSAP) technique.The results showed that methylation existed at a high level among tobacco accessions,among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic.A cluster analysis revealed distinct patterns of geography-specific groups.In addition,three polymorphic sites significantly related to tobacco mosaic virus (TMV) resistance were explored.This suggests that tobacco breeders should pay more attention to epigenetic traits.

  15. DNA markers as a tool for genetic traceability of primary product in agri-food chains

    Directory of Open Access Journals (Sweden)

    Daria Scarano

    2012-11-01

    Full Text Available The agri-food components of the Made in Italy are well known all over the world, therefore they may significantly contribute to the Italian economy. However, also owing to a large number of cases of improper labelling, the Italian agro-food industry faces an ever-increasing competition. For this reason, there is a decline of consumers’ confidence towards food production systems and safety controls. To prevent erroneous classification of products and to protect consumers from false instore information, it is important to develop and validate techniques that are able to detect mislabelling at any stage of the food-chain. This paper describes some examples of genetic traceability of primary products in some important plant food chains such as durum wheat, olive and tomato, based on DNA analysis both of raw material and of processed food (pasta, olive oil, and peeled tomato.

  16. Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa)

    Science.gov (United States)

    Gor, Mian Chee; Mantri, Nitin; Pang, Edwin

    2016-09-01

    A Fragaria Discovery Panel (FDP; strawberry-specific SDA) containing 287 features was constructed by subtracting the pooled gDNA of nine non-angiosperm species from the pooled gDNA of five strawberry genotypes. This FDP was used for Bulk Segregant Analysis (BSA) to enable identification of molecular markers associated with day-neutrality. Analysis of hybridisation patterns of a short day (SD) DNA bulk and three day-neutral (DN) DNA bulks varying in flowering strength allowed identification of a novel feature, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. The signal intensities of FaP2E11 feature obtained from the strong DN bulk (DN1) is three fold higher than the short day bulk (SD), indicating that the putative marker may linked to a CKX1 variant allele with lower enzyme activity. We propose a model for flowering regulation based on the hypothesis that flowering strength may be regulated by the copy number of FaP2E11-linked CKX1 alleles. This study demonstrates the feasibility of the SDA-based BSA approach for the identification of molecular markers associated with day-neutrality in strawberry. This innovative strategy is an efficient and cost-effective approach for molecular marker discovery.

  17. Concordance of Hypermethylated DNA and the Tumor Markers CA 15-3, CEA, and TPA in Serum during Monitoring of Patients with Advanced Breast Cancer

    DEFF Research Database (Denmark)

    Kristiansen, Søren; Jørgensen, Lars Mønster; Høgh Hansen, Morten;

    2015-01-01

    The serological protein tumor markers CA 15-3, CEA, and TPA are frequently used to monitor tumor burden among metastatic breast cancer patients. Breast cancer is associated with global DNA hypomethylation and hypermethylation of some promoter regions. No monitoring study has yet investigated the ...

  18. Application of subtracted gDNA microarray-assisted Bulked Segregant Analysis for rapid discovery of molecular markers associated with day-neutrality in strawberry (Fragaria x ananassa).

    Science.gov (United States)

    Gor, Mian Chee; Mantri, Nitin; Pang, Edwin

    2016-01-01

    A Fragaria Discovery Panel (FDP; strawberry-specific SDA) containing 287 features was constructed by subtracting the pooled gDNA of nine non-angiosperm species from the pooled gDNA of five strawberry genotypes. This FDP was used for Bulk Segregant Analysis (BSA) to enable identification of molecular markers associated with day-neutrality. Analysis of hybridisation patterns of a short day (SD) DNA bulk and three day-neutral (DN) DNA bulks varying in flowering strength allowed identification of a novel feature, FaP2E11, closely linked to CYTOKININ OXIDASE 1 (CKX1) gene possibly involved in promoting flowering under non-inductive condition. The signal intensities of FaP2E11 feature obtained from the strong DN bulk (DN1) is three fold higher than the short day bulk (SD), indicating that the putative marker may linked to a CKX1 variant allele with lower enzyme activity. We propose a model for flowering regulation based on the hypothesis that flowering strength may be regulated by the copy number of FaP2E11-linked CKX1 alleles. This study demonstrates the feasibility of the SDA-based BSA approach for the identification of molecular markers associated with day-neutrality in strawberry. This innovative strategy is an efficient and cost-effective approach for molecular marker discovery. PMID:27586242

  19. The Aspergillus nidulans amdS gene as a marker for the identification of multicopy T-DNA integration events in Agrobacterium-mediated transformation of Aspergillus awamori

    NARCIS (Netherlands)

    Michielse, C.B.; Ram, A.F.J.; Hondel, C.A.M.J.J. van den

    2004-01-01

    The Aspergillus nidulans amdS selection marker was used for the identification of multicopy T-DNA insertions in Agrobacterium-mediated transformation of Asp. awamori. The selection of transformants on agar plates containing acetamide as sole nitrogen source and hygromycin resulted in a six-fold decr

  20. DNA分子标记技术在果树上的应用%APPLICATIONS OF DNA MOLECULAR MARKERS TO FRUIT TREES

    Institute of Scientific and Technical Information of China (English)

    马翠兰; 刘星辉; 张玉兰

    2001-01-01

    近20年来,随着分子生物学技术的发展,出现了一类重要的遗传标记--DNA分子标记。本文综述了DNA分子标记技术的原理、特点及其在果树上的研究进展,并对其存在问题和解决途径及应用前景进行了讨论。%Some significant DNA molecular markers have been developed bymolecular biology as one of the types of genetic markers during the past two decades.The principles and characteristics and the progress of research in fruit trees on several main DNA molecular marker techniques were reviewed.And problems,the way to settle them and the practical prospects were also discussed.

  1. Genetic diversity and phylogenetic relationship of Indonesian Local goats using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    M Syamsul Arifin Zein

    2012-03-01

    Full Text Available Genetic diversity is important information in the process of conservation and sustainable utilization of animal genetic resources. Thirteen microsatellite markers were used to estimate the degree of genetic diversity on five Indonesian local goats. Results showed the highest average allele diversity present in the locus MAF70 (5.6 ± 2.9, and the lowest was in the locus MAF035 (1.6 ± 0.6, the average number of alleles per locus was 6 ± 2.3. The lowest average alleles diversity present was in the Gembrong goat (2.2 ± 1.1 and the highest was in the Jawarandu goat (4.9 ± 2.2. There is a unique alleles at loci MCM527 and present in all Indonesian local goat with the highest allele frequency on Peranakan Etawa (37.2% and lowest in Gembrong goat (7.9%. H0 ranged from 0.372 ± 0.173 (Gembrong to 0.540 ± 0.204 (Peranakan Etawa, and HE ranging from 0.249 ± 0.196 (Gembrong to 0.540 ± 0.212 (Peranakan Etawa.The genetic differentiation for inbreeding among population (FIS, within population (FIT, and average genetic differention (FST were 0,0208 (2,08%, 0,1532 (15,32%, and 0,1352 (13,52%, respectively. Locus ILSTS029, BMS1494, MAF035 and INRA0132 had a low PIC value (PIC 0.5. Phylogenetic relationship was consistent with the history of its development based on Kacang goat except was for Gembrong Goat. This research information can be used for conservation strategies and breeding programs on each population of Indonesian local goat.

  2. Molecular characterization of Saudi local chicken strains using mitochondrial DNA markers.

    Science.gov (United States)

    Yacoub, H A; Ramadan, H A I; Baeshen, Nabih A; Sadek, Mahmoud Abdel; Abou Alsoud, M E

    2015-08-01

    The current study was carried out to investigate and estimate the genetic diversity of native breeds based on cytochrome b (cyt-b) gene of mitochondrial DNA information. The obtained sequences of cyt-b gene segment have TAA as a stop codon at 488 position with no insertions or deletion in all individuals of both native chicken strains. The blast results showed that no variation was found among individuals within both native chicken strains, but when a comparison was established among them and other species of genus Gallus the variation is exploring, additionally many mutant sites were detected as single nucleotide polymorphisms (SNPs) in different sites. The phylogenetic trees exhibited three different groups. The results revealed that the native chicken strains were closely related to the cluster of Gallus gallus and subspecies of Gallus, suggesting that they may be separated from the same origin. According to this result and previously studies, the native chicken strains are genetically closer to Gallus gallus and it could be successfully distinguished from the other wild types of Gallus chicken based on cyt-b gene information. We recommended that the governmental concerns for native chicken strain should be enhanced to screen its genetic structure for large scale in the Kingdom of Saudi Arabia.

  3. Genetic characterization of Golden mahseer (Tor putitora) populations using mitochondrial DNA markers.

    Science.gov (United States)

    Sati, Jyoti; Kumar, Rohit; Sahoo, Prabhati Kumari; Patiyal, Rabindar S; Ali, Shahnawaz; Barat, Ashoktaru

    2015-02-01

    Golden Mahseer (Tor putitora) is an economically important fish of India and Southeast Asia. The present study examined the genetic variations between seven geographically isolated populations of T. putitora using Cyt b (Cytochrome b) and ATPase6/8 gene sequences of mitochondrial DNA. Analysis of 133 sequences of Cyt b (1141 bp) and 130 sequences of ATPase6/8 gene (842 bp) revealed 47 and 44 haplotypes, respectively. The estimated haplotype and nucleotide diversity was high in River Jia Bhoreli (Bhalukpong) population (h = 1.00000, π = 0.007121 for Cyt b and h = 0.90441 π = 0.004867 for ATPase6/8). Results of AMOVA indicated that majority of the genetic variations in both genes were due to variation among populations (60.79% for Cyt b and 51.41% for ATPase6/8 gene). The pairwise F(ST) comparison and neighbor-joining tree revealed high genetic divergence of River Jia Bhoreli population from other populations. The understanding of genetic variations of T. putitora populations will play a key role in conservation and management of this endangered fish species.

  4. Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae Using mtDNA Marker

    Directory of Open Access Journals (Sweden)

    Vaithilingam RAVITCHANDIRANE

    2012-05-01

    Full Text Available Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ and maximum likelihood (ML trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97. The overall mean Kimura two parameter (K2P distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069 followed by N. peronii (0.050 and N. mesoprion (0.002. This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.

  5. Using DNA marker to identify groundnut hybrid in groundnut rust resistance research

    Directory of Open Access Journals (Sweden)

    Prathepha, P.

    2004-03-01

    Full Text Available There are many important steps in breeding for rust resistant groundnut cultivar e.g. evaluation of resistance levels, and population building. Groundnut is self-pollinated crop, it has a high rate of self- pollination in the breeding program. The use of DNA to classify hybridization would help to make more accurate selection and speed up the progress of work. The population of this study was from crosses of susceptible cultivars (KKU1 and Tainan 9 and resistant cultivar (NC Ac 17090. It was found that in F1, hybrids had many characteristics in between the parentsícharacters. For example, hybrid of Tainan 9 × NC Ac 17090 had no difference from Tainan 9 in seed weight per plant, width and length of pod, but pod per plant and pod weight per plant had higher values than those of Tainan 9 (high yield cultivar. However, hybrid of KKU2 ×NC Ac 17090 had seed weight per plant, width and length of pod values in between those of parents e.g. lower than KKU 1 but higher than NC Ac 17090. From RAPD technique, 120 primers have been screened. Only one primer (OPO11 showed a difference between NC Ac 17090 and susceptible cultivars (KKU1 and Tainan 9 at 1000 base. So, it was introduced as a tool to select F1 hybrid. The results indicated that F1 hybrids were 56.25 and 57.69% from crosses of Tainan 9 × NC Ac 17090 and KKU 1 × NC Ac 17090 respectively. Results from morphological study confirmed that those plants were from hybridization. Correlation of pustule diameter and number of pustules were significant. Results from F2 indicated that the ratio of susceptible to resistant plants was 15: 1 (p>0.05. However, only 50% of plant with small pustule showed O111000 maker.

  6. High DNA methyltransferase DNMT3B levels: a poor prognostic marker in acute myeloid leukemia.

    Directory of Open Access Journals (Sweden)

    Sandrine Hayette

    Full Text Available It has been recently shown that DNA methyl transferase overexpression is correlated with unfavourable prognosis in human malignancies while methylation deregulation remains a hallmark that defines acute myeloid leukemia (AML. The oncogenic transcription factor EVI1 is involved in methylation deregulation and its overexpression plays a major role for predicting an adverse outcome. Moreover, the identification of DNMT3A mutations in AML patients has recently been described as a poor prognostic indicator. In order to clarify relationship between these key actors in methylation mechanisms and their potential impact on patient outcomes, we analysed 195 de novo AML patients for the expression of DNMT3A, 3B (and its non-catalytic variant 3B(NC and their correlations with the outcome and the expression of other common prognostic genetic biomarkers (EVI1, NPM1, FLT3ITD/TKD and MLL in adult AML. The overexpression of DNMT3B/3B(NC is (i significantly correlated with a shorter overall survival, and (ii inversely significantly correlated with event-free survival and DNMT3A expression level. Moreover, multivariate analysis showed that a high expression level of DNMT3B/3B(NC is statistically a significant independent poor prognostic indicator. This study represents the first report showing that the overexpression of DNMT3B/3B(NC is an independent predictor of poor survival in AML. Its quantification should be implemented to the genetic profile used to stratify patients for therapeutical strategies and should be useful to identify patients who may benefit from therapy based on demethylating agents.

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

    Science.gov (United States)

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

    2004-07-13

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  9. Nuclear and mitochondrial DNA markers in traceability of retail beef samples Marcadores de DNA nuclear e mitocondrial para rastreabilidade da carne bovina comercializada

    Directory of Open Access Journals (Sweden)

    Aline S.M. Cesar

    2010-09-01

    Full Text Available Several characteristics are important in a traceability system of animal products, such as age at slaughter, breed composition, besides information of the productive chain. In general, the certification agent records information about the animals and the system which it came from, although cannot guarantee that the slaughtering, meat processing and distribution are error proof. Besides, there is a differential price, at least at the international market, based on sex and breed composition of the animals. Genetic markers allow identification of characteristics controlled in the beef cattle traceability program, as sex and breed composition, in order to correctly identify and appraise the final product for the consumer. The hypothesis of this study was that the majority beef samples retailed in the local market originate from female with a great participation of zebu breeds. Therefore, the objective of this work was to characterize retail beef samples with DNA markers that identify cattle sex and breed composition. Within 10 beef shops localized in Pirassununga, SP, Brazil, 61 samples were collected, all were genotyped as harboring Bos taurus mitochondrial DNA and 18 were positive for the Y chromosome amplification (male. For the marker sat1711b-Msp I the frequency of the allele A was 0.278 and for the marker Lhr-Hha I the frequency of the allele T was 0.417. The results of sat1711b-Msp I and Lhr-Hha I allelic frequencies are suggestive that the proportion of indicus genome compared with the taurine genome in the market meat is smaller than the observed in the Nellore breed. The procedure described in this study identified sex and subspecies characteristics of beef meat samples, with potential application in meat products certification in special as an auxiliary tool in beef cattle traceability programs.Várias características são importantes no sistema de rastreabilidade, como o sexo, a idade, a raça e/ou a composição racial dos animais, al

  10. [Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry].

    Science.gov (United States)

    Stepanov, V A; Vagaitseva, K V; Kharkov, V N; Cherednichenko, A A; Bocharova, A V

    2016-01-01

    Human genetic markers linked with the X chromosome (X-linked) are used in the field of population and medical genetics, as well as for DNA identification of individuals in forensic science and forensic medicine. We proposed an XSNPid panel that consists of 66 unlinked single nucleotide X chromosome markers and developed a protocol for their multiplex genotyping using multilocus PCR and MALDI-TOF mass spectrometry. The XSNPid panel is genotyped within two multiplexes (36 and 30 markers). The developed protocol provides an efficient genotype reading; the fraction of determined genotypes is 98.29%. The high level of gene diversity (0.461) for the X-linked SNPs included in the panel is characteristic of the Russian population. A total of 63 out of 66 markers that provide a high efficiency of genotyping and independent inheritance are suitable for DNA identification purposes. The XSNPid panel is characterized by a very high discriminating ability when studying the Russian population. The probability of genotype coincidence in two unrelated individuals is 9 × 10^(-27) for women and 2 × 10^(-18) for men. Also, the XSNPid panel has a greater multiplex capacity in addition to a higher discriminating ability compared to the other closest analogues of the X chromosome SNP sets, which makes it more cost effective and less time consuming. The XSNPid panel is a convenient tool, not only for individual DNA identification, but also for population genetic studies.

  11. [Panel of X-linked single-nucleotide polymorphic markers for DNA identification (XSNPid) based on multiplex genotyping by multilocus PCR and MALDI-TOF mass spectrometry].

    Science.gov (United States)

    Stepanov, V A; Vagaitseva, K V; Kharkov, V N; Cherednichenko, A A; Bocharova, A V

    2016-01-01

    Human genetic markers linked with the X chromosome (X-linked) are used in the field of population and medical genetics, as well as for DNA identification of individuals in forensic science and forensic medicine. We proposed an XSNPid panel that consists of 66 unlinked single nucleotide X chromosome markers and developed a protocol for their multiplex genotyping using multilocus PCR and MALDI-TOF mass spectrometry. The XSNPid panel is genotyped within two multiplexes (36 and 30 markers). The developed protocol provides an efficient genotype reading; the fraction of determined genotypes is 98.29%. The high level of gene diversity (0.461) for the X-linked SNPs included in the panel is characteristic of the Russian population. A total of 63 out of 66 markers that provide a high efficiency of genotyping and independent inheritance are suitable for DNA identification purposes. The XSNPid panel is characterized by a very high discriminating ability when studying the Russian population. The probability of genotype coincidence in two unrelated individuals is 9 × 10^(-27) for women and 2 × 10^(-18) for men. Also, the XSNPid panel has a greater multiplex capacity in addition to a higher discriminating ability compared to the other closest analogues of the X chromosome SNP sets, which makes it more cost effective and less time consuming. The XSNPid panel is a convenient tool, not only for individual DNA identification, but also for population genetic studies. PMID:27414782

  12. Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics.

    Science.gov (United States)

    Pośpiech, Ewelina; Karłowska-Pik, Joanna; Ziemkiewicz, Bartosz; Kukla, Magdalena; Skowron, Małgorzata; Wojas-Pelc, Anna; Branicki, Wojciech

    2016-07-01

    The genetics of eye colour has been extensively studied over the past few years, and the identified polymorphisms have been applied with marked success in the field of Forensic DNA Phenotyping. A picture that arises from evaluation of the currently available eye colour prediction markers shows that only the analysis of HERC2-OCA2 complex has similar effectiveness in different populations, while the predictive potential of other loci may vary significantly. Moreover, the role of gender in the explanation of human eye colour variation should not be neglected in some populations. In the present study, we re-investigated the data for 1020 Polish individuals and using neural networks and logistic regression methods explored predictive capacity of IrisPlex SNPs and gender in this population sample. In general, neural networks provided higher prediction accuracy comparing to logistic regression (AUC increase by 0.02-0.06). Four out of six IrisPlex SNPs were associated with eye colour in the studied population. HERC2 rs12913832, OCA2 rs1800407 and SLC24A4 rs12896399 were found to be the most important eye colour predictors (p forensics and provided additional evidence for population specific differences in the predictive importance of the IrisPlex SNPs and gender. PMID:27221533

  13. Probabilistic expert systems for forensic inference from DNA markers in horses: applications to confirm genealogies with lack of genetic data.

    Science.gov (United States)

    Dobosz, Marina; Bocci, Chiara; Bonuglia, Margherita; Grasso, Cinzia; Merigioli, Sara; Russo, Alessandra; De Iuliis, Paolo

    2010-01-01

    Microsatellites have been used for parentage testing and individual identification in forensic science because they are highly polymorphic and show abundant sequences dispersed throughout most eukaryotic nuclear genomes. At present, genetic testing based on DNA technology is used for most domesticated animals, including horses, to confirm identity, to determine parentage, and to validate registration certificates. But if genetic data of one of the putative parents are missing, verifying a genealogy could be questionable. The aim of this paper is to illustrate a new approach to analyze complex cases of disputed relationship with microsatellites markers. These cases were solved by analyzing the genotypes of the offspring and other horses' genotypes in the pedigrees of the putative dam/sire with probabilistic expert systems (PESs). PES was especially efficient in supplying reliable, error-free Bayesian probabilities in complex cases with missing pedigree data. One of these systems was developed for forensic purposes (FINEX program) and is particularly valuable in human analyses. We applied this program to parentage analysis in horses, and we will illustrate how different cases have been successfully worked out.

  14. Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers.

    Science.gov (United States)

    Ichikawa, Madoka; Bawn, Saw; Maw, Ni Ni; Htun, Lat Lat; Thein, Myint; Gyi, Aung; Sunn, Kyaw; Katakura, Ken; Itagaki, Tadashi

    2011-12-01

    Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants.

  15. Application of DNA based marker mutations for improvement of cereals and other sexually reproduced crop plants. Proceedings of a final research co-ordination meeting

    International Nuclear Information System (INIS)

    The Co-ordinated Research Programme (CRP) on the Application of DNA Based Marker Mutations for Improvement of Cereals and Other Sexually Reproduced Crop Plants represents the first of three CRPs dealing with the application of molecular markers to mutations and plant breeding and was implemented between 1992 and 1996. A second companion CRP entitled Use of Novel DNA Fingerprinting Techniques for the Detection and Characterization of Genetic Variation in Vegetatively Propagated Crops devoted to the application of molecular markers in vegetatively propagated crops species was implemented between 1993 and 1997. One positive consequence of these two CRPs has been the implementation of a third CRP entitled Radioactively Labeled DNA Probes for Crop Improvement, which began in 1995 and aims to provide enabling technologies, in the form of probes and primers, to laboratories in developing countries. The rapid development of molecular marker technologies has also resulted in a dramatic increase in request from developing Member States for technical co-operation projects utilizing molecular markers to improve local varieties for biotic and abiotic stresses and other traits of relevance. With the intensified use of induced mutations in genetic studies, it will be important to continue the important work of understanding induced mutations at the molecular level. Evidence of the progress made in implementing molecular marker technologies in laboratories around the world is presented in this publication, which contains the results presented by the participants at the fourth and final Research Co-ordination Meeting of the CRP held in Vienna, 4-8 November 1996. The FAO and IAEA wish to express their sincere appreciation to the participants of the meeting for their work during the project period resulting in the summary and scientific reports presented in this publication

  16. Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling.

    Science.gov (United States)

    van den Berge, Margreet; Bhoelai, Bryan; Harteveld, Joyce; Matai, Anuska; Sijen, Titia

    2016-01-01

    The forensic identification of human body fluids and tissues by means of messenger RNA (mRNA) profiling is a long studied methodology that is increasingly applied to casework samples. Previously, we have described an mRNA multiplex system that targets blood, saliva, semen, menstrual secretion, vaginal mucosa and skin (Lindenbergh et al. and van den Berge et al.). In this study we consider various topics to improve this mRNA profiling system or its use and adapt the method accordingly. Bodily secretions that may be encountered at a crime scene whilst not targeted by the multiplex-id est nasal mucosa, sweat, tears, faeces and urine-were examined for false positive signals. The results prompted us to identify a nasal mucosa marker that allows the discrimination of nasal mucosa from saliva or vaginal mucosa and nosebleed blood from peripheral blood. An updated version of the multiplex was prepared to which the nasal mucosa marker was added and in which markers for semen, vaginal mucosa and blood were replaced. Lactobacillus markers were regarded unsuitable as replacement for vaginal mucosa mRNA markers because of background signals on penile swabs that appeared devoid of female DNA. Furthermore, we provide approaches to deal with highly unbalanced mixtures. First, a differential extraction protocol was incorporated into a co-extraction protocol to allow DNA and RNA analysis of separated non-sperm and sperm fractions. In a second approach, besides the standard multiplex, a customized multiplex is used which excludes markers for prevailing cell types. This allows the use of lower cDNA inputs for the prevailing cell types and higher inputs for cell types that appear masked. Additionally, we assessed the relation between the percentage of alleles or markers detected in DNA or RNA profiles when decreasing sample amounts are analysed. While blood, saliva, semen and menstrual secretion show the trend that DNA profiling is more sensitive than RNA profiling, the reverse is seen

  17. Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling.

    Science.gov (United States)

    van den Berge, Margreet; Bhoelai, Bryan; Harteveld, Joyce; Matai, Anuska; Sijen, Titia

    2016-01-01

    The forensic identification of human body fluids and tissues by means of messenger RNA (mRNA) profiling is a long studied methodology that is increasingly applied to casework samples. Previously, we have described an mRNA multiplex system that targets blood, saliva, semen, menstrual secretion, vaginal mucosa and skin (Lindenbergh et al. and van den Berge et al.). In this study we consider various topics to improve this mRNA profiling system or its use and adapt the method accordingly. Bodily secretions that may be encountered at a crime scene whilst not targeted by the multiplex-id est nasal mucosa, sweat, tears, faeces and urine-were examined for false positive signals. The results prompted us to identify a nasal mucosa marker that allows the discrimination of nasal mucosa from saliva or vaginal mucosa and nosebleed blood from peripheral blood. An updated version of the multiplex was prepared to which the nasal mucosa marker was added and in which markers for semen, vaginal mucosa and blood were replaced. Lactobacillus markers were regarded unsuitable as replacement for vaginal mucosa mRNA markers because of background signals on penile swabs that appeared devoid of female DNA. Furthermore, we provide approaches to deal with highly unbalanced mixtures. First, a differential extraction protocol was incorporated into a co-extraction protocol to allow DNA and RNA analysis of separated non-sperm and sperm fractions. In a second approach, besides the standard multiplex, a customized multiplex is used which excludes markers for prevailing cell types. This allows the use of lower cDNA inputs for the prevailing cell types and higher inputs for cell types that appear masked. Additionally, we assessed the relation between the percentage of alleles or markers detected in DNA or RNA profiles when decreasing sample amounts are analysed. While blood, saliva, semen and menstrual secretion show the trend that DNA profiling is more sensitive than RNA profiling, the reverse is seen

  18. Development of New Microsatellite DNA Markers from Apostichopus japonicus and Their Cross-Species Application in Parastichopus parvimensis and Pathallus mollis

    OpenAIRE

    Guiping Chen; Lan Wang; Xiaojun Rong; Bin Li,; Zheng Zhang; Yingeng Wang; Meijie Liao

    2011-01-01

    Twenty microsatellite DNA markers were developed for sea cucumber and used to investigate polymorphisms of 60 wild Apostichopus japonicus individuals collected from China. It revealed that all the markers were polymorphic. A total of 164 alleles were detected at 20 loci. The number of alleles per locus varied from 3 to 17 with an average of 8.2, and the expected heterozygosities of each locus ranged from 0.03 to 0.89 with an average of 0.64. Cross-species amplification was also conducted in P...

  19. Preliminary evaluation of the use of soil bacterial 16S rDNA DNA markers in sediment fingerprinting in two small endorheic lagoons in southern Spain

    Science.gov (United States)

    Gomez, Jose Alfonso; Landa del Castillo, Blanca; Guzman, Gema; Petticrew, Ellen L.; Owens, Phillip N.

    2016-04-01

    Recently, several studies have shown the effect of soil management on the soil microbial community in olive orchards, how this might differ due to a combination of management and soil type, and how these can be identified using DNA markers (Landa et al., 2014). Using DNA markers of soil bacteria seems to have the potential to detect differences in soil properties between different areas (Joe-Strack and Petticrew, 2012), particularly in those that by their location and characteristics might not present differences in other chemical or geochemical soil properties. This presentation describes the preliminary results of an exploratory survey to evaluate the potential of soil bacteria community composition in determining the origin of the sediment in two small endorheic lagoons in southern Spain. Two lagoons (Zoñar and Dulce) in southern Spain with a small contributing area (877 and 263 ha respectively) were selected for this study. These lagoons were chosen because of their environmental relevance and increasing siltation problems. The dominant land use in most of their contributing catchments is rain-fed olive tree cultivation. In May 2015, two small subcatchments within each of the lagoon's contributing area were sampled. At each sampling point, a composite sample was collected of three subsamples taken within a 5 m radiusa. We differentiated between 0-20 and 20-40 cm soil depth. Additionally, in both lagoons samples were taken from the sedimentation of the stream draining the subcatchment into the lagoon shores, at 0-20 -cm depth. Prior to each sampling each of the the two subcatchments were explored for indications of different properties or management that could help divide it into different "homogeneous" units, including: soil management, visual indications of erosion symptoms (e.g. rills, soil mounds around olive trees), colour, and landscape position. As a result, the subcatchment in each lagoon was divided into three areas (referred to as 1, 2 and 3). The

  20. Trypanosoma brucei gambiense Spliced Leader RNA Is a More Specific Marker for Cure of Human African Trypanosomiasis Than T. b. gambiense DNA.

    Science.gov (United States)

    Ilboudo, Hamidou; Camara, Oumou; Ravel, Sophie; Bucheton, Bruno; Lejon, Veerle; Camara, Mamadou; Kaboré, Jacques; Jamonneau, Vincent; Deborggraeve, Stijn

    2015-12-15

    To assess the efficacy of treatment for human African trypanosomiasis, accurate tests that can discriminate relapse from cure are needed. We report the first data that the spliced leader (SL) RNA is a more specific marker for cure of human African trypanosomiasis than parasite DNA. In blood samples obtained from 61 patients in whom human African trypanosomiasis was cured, SL RNA detection had specificities of 98.4%-100%, while DNA detection had a specificity of only 77%. Data from our proof-of-concept study show that SL RNA detection has high potential as a test of cure.

  1. Development of New Microsatellite DNA Markers from Apostichopus japonicus and Their Cross-Species Application in Parastichopus parvimensis and Pathallus mollis

    Directory of Open Access Journals (Sweden)

    Guiping Chen

    2011-09-01

    Full Text Available Twenty microsatellite DNA markers were developed for sea cucumber and used to investigate polymorphisms of 60 wild Apostichopus japonicus individuals collected from China. It revealed that all the markers were polymorphic. A total of 164 alleles were detected at 20 loci. The number of alleles per locus varied from 3 to 17 with an average of 8.2, and the expected heterozygosities of each locus ranged from 0.03 to 0.89 with an average of 0.64. Cross-species amplification was also conducted in Parastichopus parvimensis collected from the United States and Pathallus mollis collected from Peru. The result showed that 17 loci amplified Parastichopus parvimensis DNAs while only 4 loci could amplify Pathallus mollis DNAs. All of the polymorphic markers would be useful for future genetic breeding and the assessment of genetic variation within sea cucumbers.

  2. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    Science.gov (United States)

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption. PMID:27411901

  3. Comparison between different markers for sperm quality in the cat: Diff-Quik as a simple optical technique to assess changes in the DNA of feline epididymal sperm

    OpenAIRE

    Mota, Paula C.; Ramalho-Santos, João

    2006-01-01

    The majority of wild felids, as well as some domestic cats, have low sperm concentration in their ejaculates, and a high proportion of abnormal spermatozoa. We have employed several possible semen quality markers to further characterize cat epididymal sperm. Methods included possible apoptotic reporters, such as the annexin V assay to monitor exposure of phosphatidylserine (PS) on the outer leaflet of the plasma membrane, as well as cell integrity; and the TUNEL assay to quantify DNA breaks. ...

  4. Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

    OpenAIRE

    Schönhals, E. M.; Ortega, F.; Barandalla, L.; Aragones, A.; Ruiz de Galarreta, J.I.; Liao, J.-C.; Sanetomo, R.; Walkemeier, B.; Tacke, E.; Ritter, E.; Gebhardt, C.

    2016-01-01

    Key message SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Abstract Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of ge...

  5. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    Science.gov (United States)

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption.

  6. Relationships between sperm DNA fragmentation, sperm apoptotic markers and serum levels of CB-153 and p,p'-DDE in European and Inuit populations

    DEFF Research Database (Denmark)

    Stronati, A; Manicardi, G C; Cecati, M;

    2006-01-01

    Persistent organochlorine pollutants (POPs) are suspected to interfere with hormone activity and the normal homeostasis of spermatogenesis. We investigated the relationships between sperm DNA fragmentation, apoptotic markers identified on ejaculated spermatozoa and POP levels in the blood of 652......, but not in the highly exposed Inuit men. Additional issues (genetic background, lifestyle habits and characterization of total xeno-hormonal activities) need to be investigated in order to fully assess the population variations observed....

  7. Transformation of Azotobacter vinelandii OP with a broad host range plasmid containing a cloned chromosomal nif-DNA marker.

    Science.gov (United States)

    Bingle, W H

    1988-05-01

    The non-nitrogen-fixing (Nif-) strain UW10 of Azotobacter vinelandii OP (UW) was naturally induced to competence and transformed with broad host range plasmid pKT210 containing the cloned wild-type nif-10 locus from A. vinelandii UW (Nif+); this marker was unable to complement the nif-10 mutation in trans, but could through recombination with the chromosome. The most frequent type of transformation event observed was recombination between the homologous regions of the plasmid and chromosome (producing Nif+ transformants) with loss of the plasmid vector. At a substantially lower frequency, transformants expressing the plasmid-encoded antibiotic resistance determinants were isolated which were phenotypically Nif-. Agarose gel electrophoresis showed that these transformants contained a plasmid migrating with the same mobility as the original donor plasmid. During culture these transformants acquired a Nif+ phenotype without the loss of the plasmid, as judged by the use of a hybridization probe specific for the cloned nif-DNA fragment. These data indicate that plasmids carrying sequences homologous to chromosomal sequences could be maintained in recombination-proficient A. vinelandii UW. The introduction of plasmids containing sequences homologous to chromosomal sequences was facilitated by prelinearization of the plasmid using a restriction endonuclease generating cohesive ends. Because the site of linearization could be chosen outside the region of shared homology, it was unlikely that the route of plasmid establishment occurred via a homology-facilitated transformation mechanism. The data also indicated that A. vinelandii UW could harbor broad host range cloning vectors based on plasmid RSF1010 without significant impairment of its nitrogen-fixation ability.

  8. Application of molecular markers in livestock improvement

    OpenAIRE

    Teneva A.; Petrović M.P.

    2010-01-01

    With recent developments in DNA technologies, a large number of genetic polymorphisms at DNA sequence level has been introduced over the last decades as named DNA-based markers. The discovery of new class of DNA profiling markers has facilitated the development of marker-based gene tags, mapbased cloning of livestock important genes, variability studies, phylogenetic analysis, synteny mapping, marker-assisted selection of favourable genotypes, etc. The most commonly used DNA-based markers hav...

  9. MtDNA COI-COII marker and drone congregation area: an efficient method to establish and monitor honeybee (Apis mellifera L.) conservation centres.

    Science.gov (United States)

    Bertrand, Bénédicte; Alburaki, Mohamed; Legout, Hélène; Moulin, Sibyle; Mougel, Florence; Garnery, Lionel

    2015-05-01

    Honeybee subspecies have been affected by human activities in Europe over the past few decades. One such example is the importation of nonlocal subspecies of bees which has had an adverse impact on the geographical repartition and subsequently on the genetic diversity of the black honeybee Apis mellifera mellifera. To restore the original diversity of this local honeybee subspecies, different conservation centres were set up in Europe. In this study, we established a black honeybee conservation centre Conservatoire de l'Abeille Noire d'Ile de France (CANIF) in the region of Ile-de-France, France. CANIF's honeybee colonies were intensively studied over a 3-year period. This study included a drone congregation area (DCA) located in the conservation centre. MtDNA COI-COII marker was used to evaluate the genetic diversity of CANIF's honeybee populations and the drones found and collected from the DCA. The same marker (mtDNA) was used to estimate the interactions and the haplotype frequency between CANIF's honeybee populations and 10 surrounding honeybee apiaries located outside of the CANIF. Our results indicate that the colonies of the conservation centre and the drones of the DCA show similar stable profiles compared to the surrounding populations with lower level of introgression. The mtDNA marker used on both DCA and colonies of the conservation centre seems to be an efficient approach to monitor and maintain the genetic diversity of the protected honeybee populations. PMID:25335970

  10. Control of origin of sesame oil from various countries by stable isotope analysis and DNA based markers--a pilot study.

    Directory of Open Access Journals (Sweden)

    Micha Horacek

    Full Text Available The indication of origin of sesame seeds and sesame oil is one of the important factors influencing its price, as it is produced in many regions worldwide and certain provenances are especially sought after. We joined stable carbon and hydrogen isotope analysis with DNA based molecular marker analysis to study their combined potential for the discrimination of different origins of sesame seeds. For the stable carbon and hydrogen isotope data a positive correlation between both isotope parameters was observed, indicating a dominant combined influence of climate and water availability. This enabled discrimination between sesame samples from tropical and subtropical/moderate climatic provenances. Carbon isotope values also showed differences between oil from black and white sesame seeds from identical locations, indicating higher water use efficiency of plants producing black seeds. DNA based markers gave independent evidence for geographic variation as well as provided information on the genetic relatedness of the investigated samples. Depending on the differences in ambient environmental conditions and in the genotypic fingerprint, a combination of both analytical methods is a very powerful tool to assess the declared geographic origin. To our knowledge this is the first paper on food authenticity combining the stable isotope analysis of bio-elements with DNA based markers and their combined statistical analysis.

  11. DETECTION OF PORK CONTAMINATION IN FRESH AND COOKED BEEF USING GENETIC MARKER MITOCHONDRIAL-DNA CYTOCHROME B BY DUPLEX-PCR

    Directory of Open Access Journals (Sweden)

    A. Ni’mah

    2016-03-01

    Full Text Available By mixing with pork, beef adulteration is frequently found in the traditional  market that very disturbing Moeslem community in Indonesia. This study was conducted to detect pork contamination in fresh and cooked beef using genetic marker mitochondrial DNA cytochrome b (mt-DNA Cyt b by duplex-PCR. A total of twelve samples was used in this study consisting six fresh meat samples and six cooked meat samples, respectively. Those beef and pork were bought from animal slaughterhouse and a supermarket in Surakarta. Cooked samples were prepared by boiling the meats in hot water at 100oC for 30 minutes. We designed pork contamination in beef in the level of 0, 1, 5, 10, 25%, respectively. The DNA genome was extracted and polymerase chain reaction (PCR was performed using species specific primer to isolate mt-DNA Cyt b gene from the samples. The results showed that the DNA genome was successfully extracted from pork, beef, and contaminated meat samples. In addition, visualization of duplex-PCR on 1.5% agarose gel was able to detect pork contamination in both fresh and cooked beef up to very small proportion (1%. The existence of pork in beef was indicated with the presence of specific 398 bp DNA band. It can be concluded, duplex-PCR of mt-DNA Cyt b gene was very sensitive in detection of pork contamination in fresh and cooked beef.

  12. A new technique for the quantitative assessment of 8-oxoguanine in nuclear DNA as a marker of oxidative stress. Application to dystrophin-deficient DMD skeletal muscles.

    Science.gov (United States)

    Nakae, Yoshiko; Stoward, Peter J; Bespalov, Ivan A; Melamede, Robert J; Wallace, Susan S

    2005-09-01

    This is the first report on the development of an immunohistochemical technique, combined with quantitative image analysis, for the assessment of oxidative stress quantitatively in nuclear DNA in situ, and its application to measure DNA damage in Duchenne muscular dystrophic (DMD) muscles. Three sequential staining procedures for cell nuclei, a cell marker, and a product of oxidative DNA damage, 8-oxoguanine (8-oxoG), were performed. First, the nuclei in muscle sections were stained with Neutral Red followed by the capture of their images with an image analysis system used for absorbance measurements. Second, the same sections were then immunostained for laminin in basement membranes as the cell marker. Next, the sections were treated with 2 N HCl to remove the bound Neutral Red and to denature tissue DNA. Third, the sections were immunostained for 8-oxoG in DNA, using diaminobenzidine (DAB) to reveal the antibody complex. This was followed by capture of the images of the immunostained sections as previously. The absorbances at 451.2 nm of bound Neutral Red and DAB polymer oxides, the final product of 8-oxoG immunostaining, were measured in the same myonuclei in the sections. Analysis of these absorbances permitted indices of the 8-oxoG content, independent of the nuclear densities, to be determined in nuclear DNA in single myofibres and myosatellite cells surrounded by basement membranes. We found that the mean index for the myonuclei in biceps brachii muscles of 2- to 7-year-old patients was 14% higher than that in age-matched normal controls. This finding of the increased oxidative stress in the myonuclei in young DMD muscles agrees with the previous reports of increased oxidative stress in the cytoplasm in the DMD myofibres and myosatellite cells. The present technique for the quantitative assessment of oxidative stress in nuclear DNA in situ is applicable not only in biomedical research but also in the development of effective drugs for degenerative diseases

  13. The results of the lipids peroxidation products on the DNA bases as biological markers of the oxidative stress

    International Nuclear Information System (INIS)

    Different ways of DNA damages have been studied, among these ones the direct way of DNA damages formation by the reactive oxygen species (R.O.S.). This way leads to the formation of oxidative DNA damages. In 1990, works have suggested an indirect way of DNA damages formation, the lipids peroxidation. Instead of oxidizing directly DNA, the R.O.S. oxide the lipids present in the cells and their membranes; The products coming from this degradation are able to provoke DNA damages. This way has not been studied very much. The work of this thesis is axed on this DNA theme and lipids peroxidation. In the first chapter, we begin by presenting DNA and the direct way of oxidative damages formation by the R.O.S.Then, we speak about the cell lipids suffering oxidation reactions and the different ways of lipids oxidation. Then, we present how the lipid peroxidation is a source of damages for DNA. (N.C.)

  14. Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.).

    Science.gov (United States)

    Daspute, Abhijit; Fakrudin, B

    2015-03-01

    Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7414) and a repulsion phase marker (IABTPPN7983) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7983, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7414 did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7414 (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F2 population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea. PMID:25774108

  15. Phylogeography of the common vampire bat (Desmodus rotundus: Marked population structure, Neotropical Pleistocene vicariance and incongruence between nuclear and mtDNA markers

    Directory of Open Access Journals (Sweden)

    Morgante João S

    2009-12-01

    Full Text Available Abstract Background The common vampire bat Desmodus rotundus is an excellent model organism for studying ecological vicariance in the Neotropics due to its broad geographic range and its preference for forested areas as roosting sites. With the objective of testing for Pleistocene ecological vicariance, we sequenced a mitocondrial DNA (mtDNA marker and two nuclear markers (RAG2 and DRB to try to understand how Pleistocene glaciations affected the distribution of intraspecific lineages in this bat. Results Five reciprocally monophyletic clades were evident in the mitochondrial gene tree, and in most cases with high bootstrap support: Central America (CA, Amazon and Cerrado (AMC, Pantanal (PAN, Northern Atlantic Forest (NAF and Southern Atlantic Forest (SAF. The Atlantic forest clades formed a monophyletic clade with high bootstrap support, creating an east/west division for this species in South America. On the one hand, all coalescent and non-coalescent estimates point to a Pleistocene time of divergence between the clades. On the other hand, the nuclear markers showed extensive sharing of haplotypes between distant localities, a result compatible with male-biased gene flow. In order to test if the disparity between the mitochondrial and nuclear markers was due to the difference in mutation rate and effective size, we performed a coalescent simulation to examine the feasibility that, given the time of separation between the observed lineages, even with a gene flow rate close to zero, there would not be reciprocal monophyly for a neutral nuclear marker. We used the observed values of theta and an estimated mutation rate for the nuclear marker gene to perform 1000 iterations of the simulation. The results of this simulation were inconclusive: the number of iterations with and without reciprocal monophyly of one or more clades are similar. Conclusions We therefore conclude that the pattern exhibited by the common vampire bat, with marked

  16. A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta

    Directory of Open Access Journals (Sweden)

    Coupland George

    2005-08-01

    Full Text Available Abstract Background Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have not been tested for simultaneous RNA isolation for RT-PCR applications. In addition, traditional map-based cloning technologies often use ill-proportioned marker regions even when working with the model plant Arabidopsis thaliana, where the availability of the full genome sequence can now be exploited for the creation of a high-density marker systems. Results We designed a high-density polymorphic marker set between two frequently used ecotypes. This new polymorphic marker set allows size separation of PCR products on agarose gels and provides an initial resolution of 10 cM in linkage mapping experiments, facilitated by a rapid plant nucleic acid extraction protocol using minimal amounts of A. thaliana tissue. Using this extraction protocol, we have also characterized segregating T-DNA insertion mutations. In addition, we have shown that our rapid nucleic acid extraction protocol can also be used for monitoring transcript levels by RT-PCR amplification. Finally we have demonstrated that our nucleic acid isolation method is also suitable for other plant species, such as tobacco and barley. Conclusion To facilitate high-throughput linkage mapping and other genomic applications, our nucleic acid isolation protocol yields sufficient quality of DNA and RNA templates for PCR and RT-PCR reactions, respectively. This new technique requires considerably less time compared to other purification methods, and in combination with a new polymorphic PCR marker set dramatically reduces the workload required for linkage mapping of mutations in A. thaliana utilizing crosses between Col-0 and Landsberg erecta (Ler ecotypes.

  17. The DNA-instability test as a specific marker of malignancy and its application to detect cancer clones in borderline malignancy

    Directory of Open Access Journals (Sweden)

    M Fukuda

    2009-06-01

    Full Text Available Recent progress in cytogenetic and biochemical mutator assay technologies has enabled us to detect single gene alterations and gross chromosomal rearrangements, and it became clear that all cancer cells are genetically unstable. In order to detect the genome-wide instability of cancer cells, a new simple method, the DNA-instability test, was developed. The methods to detect genomic instability so far reported have only demonstrated the presence of qualitative and quantitative alterations in certain specific genomic loci. In contrast to these commonly used methods to reveal the genomic instability at certain specific DNA regions, the newly introduced DNA-instability test revealed the presence of physical DNA-instability in the entire DNA molecule of a cancer cell nucleus as revealed by increased liability to denature upon HCl hydrolysis or formamide exposure. When this test was applied to borderline malignancies, cancer clones were detected in all cases at an early-stage of cancer progression. We proposed a new concept of “procancer” clones to define those cancer clones with “functional atypia” showing positivities for various cancer markers, as well as DNA-instability testing, but showing no remarkable ordinary “morphological atypia” which is commonly used as the basis of histopathological diagnosis of malignancy.

  18. Postglacial recolonization patterns and genetic relationships among whitefish ( Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons; Berg, Søren

    1999-01-01

    of mitochondrial DNA (mtDNA) segments, The endangered North Sea houting (classified as C. oxyrhynchus) differs morphologically and physiologically from other Danish whitefish (C. lavaretus). However, limited divergence of North Sea houting was observed both at the level of mtDNA and microsatellites...

  19. Streptococcus pneumoniae DNA Load in Blood as a Marker of Infection in Patients with Community-Acquired Pneumonia

    NARCIS (Netherlands)

    Peters, R.P.H.; Boer, de R.F.; Schuurman, T.; Gierveld, S.; Kooistra-Smid, M.; Agtmael, van M.A.; Vandenbroucke-Grauls, C.M.J.E.; Persoons, M.C.J.; Savelkoul, P.H.M.

    2009-01-01

    Direct detection of Streptococcus pneumoniae DNA in blood adds to culture results in the etiological diagnosis of patients with community-acquired pneumonia (CAP). Quantification of the amount of DNA, the bacterial DNA load (BDL), provides a measurement of DNAemia that may increase the understanding

  20. Effects of Regular Treadmill Exercise on a DNA Oxidative-Damage Marker and Total Antioxidant Capacity in Rat Hippocampal Tissue

    Science.gov (United States)

    Mahjoub, Soleiman; Ghadi, Arezoo; Pourbagher, Roghayeh; Hajian-Tilaki, Karimollah

    2016-01-01

    Background and Purpose Regular exercise can result in changes in the levels of oxidative stress in the hippocampus; however, little attention has been paid to physical-activity-induced neuronal protection to exposure to lead compounds. This study investigated the effects of regular treadmill exercise on a DNA oxidative-damage marker [8-hydroxy-2'-deoxyguanosine (8-OHdG)] and the total antioxidant capacity (TAC) of hippocampal tissue in lead-acetate exposed rats. Methods This study investigated the effects of 8 weeks of regular treadmill exercise on 8-OHdG and the TAC of hippocampal tissue in lead-acetate-exposed rats. Wistar rats were randomly divided into four groups: baseline, sham (control), lead, and exercise+lead. The exercise program involved running on a treadmill with increasing intensity five times a week for 8 weeks. Animals in the lead and exercise+lead groups received lead acetate at 20 mg/kg body weight intraperitoneally three times weekly for 8 weeks. Animals in the sham group received solvent (ethyl oleate) at 30 mg/kg body weight three times weekly for 8 weeks. TAC and 8-OHdG were measured by spectrophotometric and ELISA techniques, respectively. Data were analyzed by ANOVA and Tukey's post-hoc test with a significance cutoff of p≤0.05. Results The level of 8-OHdG and the TAC were significantly higher and lower, respectively, in the lead group than in the baseline and sham groups (p<0.01). However, the 8-OHdG level and TAC value in hippocampal tissue were significantly decreased and increased, respectively, in the exercise+lead group relative to the lead group (p<0.05). Conclusions The TAC of hippocampal tissue may be directly associated with neural protection mechanisms of exercise following lead acetate injection, and the beneficial effects of regular exercise in preventing hippocampal neuronal damage could be due to decreased hippocampal oxidative stress such as reflected by a lower 8-OHdG level and increased TAC.

  1. Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States.

    Science.gov (United States)

    Farrington, Heather L; Edwards, Christine E; Guan, Xin; Carr, Matthew R; Baerwaldt, Kelly; Lance, Richard F

    2015-01-01

    Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.

  2. Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix in environmental water samples from the United States.

    Directory of Open Access Journals (Sweden)

    Heather L Farrington

    Full Text Available Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA, genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR and quantitative (qPCR markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.

  3. Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States.

    Science.gov (United States)

    Farrington, Heather L; Edwards, Christine E; Guan, Xin; Carr, Matthew R; Baerwaldt, Kelly; Lance, Richard F

    2015-01-01

    Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species. PMID:25706532

  4. Inferring Genotype of DNA Molecular Marker by Bayesian Theorem%应用贝叶斯理论推断DNA分子标记基因型

    Institute of Scientific and Technical Information of China (English)

    莫惠栋; 姜长鉴

    2002-01-01

    引入贝叶斯理论用以从DNA分子标记的表现型(电泳谱带)推断其基因型(DNA来源).结果表明,根据标记座位独立假定而确定的遗传信息不完全标记的基因型概率,与根据邻近的遗传信息完全标记的基因型和有关重组率算得的相应贝叶斯概率,通常都有很大的差异.所以在进行数量性状基因定位和标记辅助选择等工作之前,应当计算每一个体基因组上所有遗传信息不完全座位的有关基因型的贝叶斯概率.文中列出计算未知基因型的贝叶斯概率的详细过程,也讨论了贝叶斯概率的若干推广应用.%Bayesian theorem is applied to infer the DNA molecular marker genotype(DNA chain type) from its phenotype (electrophoresis band type). The results indicated that large differences often present in the genotype probability of a molecular marker with incomplete genetic information when it is obtained from the assumption of independence among markers as compared with that inferred from the genotypes of the flanking markers with the complete genetic information and the recombination fractions among them based on the Bayesian theorem. Therefore, before utilizing the marker information, such as in mapping quantitative trait loci (QTL), marker assisted selection (MAS) etc., Bayesian probability of the genotype for all markers with incomplete genetic information must be calculated over the whole genome for every individual. This study provides detailed procedure for the calculation of the Bayesian probability of the unknown genotype. Several extensions were also discussed for the application of the Bayesian theorem.

  5. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  6. Trisomy 8 Acute Myeloid Leukemia Analysis Reveals New Insights of DNA Methylome with Identification of HHEX as Potential Diagnostic Marker

    OpenAIRE

    Saied, Marwa H.; Jacek Marzec; Sabah Khalid; Paul Smith; Gael Molloy; Young, Bryan D

    2015-01-01

    Trisomy 8 acute myeloid leukemia (AML) is the commonest numerical aberration in AML. Here we present a global analysis of trisomy 8 AML using methylated DNA immunoprecipitation-sequencing (MeDIP-seq). The study is based on three diagnostic trisomy 8 AML and their parallel relapse status in addition to nine non-trisomic AML and four normal bone marrows (NBMs). In contrast to non-trisomic DNA samples, trisomy 8 AML showed a characteristic DNA methylation distribution pattern because an increase...

  7. DNA 分子遗传标记技术在仓储害虫中的研究与应用%The Research and Application of Dna Molecular Genetic Markers in Stored -Product Pests

    Institute of Scientific and Technical Information of China (English)

    伍袆; 李志红; 李燕羽; 张涛; 曹阳

    2015-01-01

    DNA molecular genetic markers provided a new technique and method for the research of important economic insects on molecular level.Stored -product pests played an important role in the agricultural economy.The research and analysis on genetic material of stored -product pests had revealed phylogenetic development,genetic structure and evolution mechanism from the essence which could afford a theoretical support for the integrated pest management strategy.The DNA molecular genetic markers had shorter history on applying in stored -product pests. The coleoptera and psocoptera pests were the main research objects in the previous study.In the paper,the current study and application of DNA molecular genetic markers in stored grain insect were summarized,including species i-dentification,phylogenetic relationships,population genetic variation and resistance.Also the application prospects of DNA molecular markers in stored -product pests were discussed in details.%DNA 分子遗传标记的产生和发展,为从分子水平研究重要经济昆虫提供了全新的技术和手段。仓储害虫在农业经济中占有重要地位,通过对仓储害虫遗传物质的研究和分析,能够从生命的本质上探索仓储害虫的系统发育、遗传结构和进化机制等问题,为害虫综合治理策略提供理论支持。在仓储害虫中,分子标记研究起步较晚,研究的重点主要是鞘翅目和啮虫目害虫。回顾、分析了 DNA 分子标记技术在仓储害虫中的研究与应用,包括仓储害虫种类鉴定、系统发育、种群遗传多样性及抗药性等,并对该技术的研究前景进行了展望。

  8. Biomarkers for Exposure to Ambient Air Pollution - Comparison of Carcinogen-DNA Adduct Levels with Other Exposure Markers and Markers for Oxidative Stress

    DEFF Research Database (Denmark)

    Autrup, Herman; Daneshvar, Bahram; Dragsted, Lars Ove;

    1999-01-01

    Human exposure to genotoxic compounds present in ambient air has been studied using selected biomarkers in nonsmoking Danish bus drivers and postal workers. A large interindividual variation in biomarker levels was observed. Significantly higher levels of bulky carcinogen-DNA adducts (75.42 adducts....../10(8) nucleotides) and of 2-amino-apidic semialdehyde (AAS) in plasma proteins (56.7 pmol/mg protein) were observed in bus drivers working in the central part of Copenhagen, Denmark. In contrast, significantly higher levels of AAS in hemoglobin (55.8 pmol/mg protein), malondialdehyde in plasma (0. 96...... nmol/ml plasma), and polycyclic aromatic hydrocarbon (PAH)-albumin adduct (3.38 fmol/ microg albumin) were observed in the suburban group. The biomarker levels in postal workers were similar to the levels in suburban bus drivers. In the combined group of bus drivers and postal workers, negative...

  9. Biomarkers for exposure to ambient air pollution--comparison of carcinogen-DNA adduct levels with other exposure markers and markers for oxidative stress

    DEFF Research Database (Denmark)

    Autrup, H; Daneshvar, B; Dragsted, L O;

    1999-01-01

    Human exposure to genotoxic compounds present in ambient air has been studied using selected biomarkers in nonsmoking Danish bus drivers and postal workers. A large interindividual variation in biomarker levels was observed. Significantly higher levels of bulky carcinogen-DNA adducts (75.42 adducts....../10(8) nucleotides) and of 2-amino-apidic semialdehyde (AAS) in plasma proteins (56.7 pmol/mg protein) were observed in bus drivers working in the central part of Copenhagen, Denmark. In contrast, significantly higher levels of AAS in hemoglobin (55.8 pmol/mg protein), malondialdehyde in plasma (0. 96...... nmol/ml plasma), and polycyclic aromatic hydrocarbon (PAH)-albumin adduct (3.38 fmol/ microg albumin) were observed in the suburban group. The biomarker levels in postal workers were similar to the levels in suburban bus drivers. In the combined group of bus drivers and postal workers, negative...

  10. Biomarkers for exposure to ambient air pollution - Comparison of carcinogen-DNA adduct levels with other exposure markers and markers for oxidative stress

    DEFF Research Database (Denmark)

    Autrup, Herman; Daneshvar, Bahram; Dragsted, Lars Ove;

    1999-01-01

    Human exposure to genotoxic compounds present in ambient air has been studied using selected biomarkers in nonsmoking Danish bus drivers and postal workers. A large interindividual variation in biomarker levels was observed. Significantly higher levels of bulky carcinogen-DNA adducts (75.42 adducts....../10(8) nucleotides) and of 2-amino-apidic semialdehyde (AAS) in plasma proteins (56.7 pmol/mg protein) were observed in bus drivers working in the central part of Copenhagen, Denmark. In contrast, significantly higher levels of AAS in hemoglobin (55.8 pmol/mg protein), malondialdehyde in plasma (0.......96 nmol/ml plasma), and polycyclic aromatic hydrocarbon (PAH)-albumin adduct (3.38 fmol/mu g albumin) were observed in the suburban group. The biomarker levels in postal workers were similar to the levels in suburban bus drivers. In the combined group of bus drivers and postal workers, negative...

  11. Development, characterisation, inheritance, and cross-species utility of American lobster (Homarus americanus) microsatellite and mtDNA PCR-RFLP markers.

    Science.gov (United States)

    Jones, Matthew W; O'Reilly, Patrick T; McPherson, Arran A; McParland, Tara L; Armstrong, Dawn E; Cox, Andrea J; Spence, Koren R; Kenchington, Ellen L; Taggart, Chris T; Bentzen, Paul

    2003-02-01

    Effective management of exploited species demands contemporary knowledge of population structure and mating patterns. Genetic markers can prove useful in providing this knowledge. Despite its commercial importance, genetic markers for American lobster (Homarus americanus) are limited. We developed 12 tetra- and 1 trinucleotide microsatellite loci for American lobster that exhibit little stuttering after PCR amplification. Gene diversity of these loci ranged from 0.516 to 0.929. A four-locus multiplex permits rapid genotyping of progeny in parentage experiments with a paternity exclusion probability over the four loci of 97.8%. We examined the loci for conformity to Hardy-Weinberg expectations (HWE) and linkage using individuals from one location and found that four loci deviated from HWE. We also tested inheritance and pairwise linkage using 48 embryos from each of two females. With the exception of two loci that were derived from the same clone and separated by 72 bp, no evidence of linkage was found. We, for the first time, demonstrate the occurrence of multiple paternity in American lobster. We also observed an apparent occurrence of dispermic androgenesis, possibly the first documentation of such an event within a species. Ten of the loci amplified in European lobster (Homarus gammarus), although two were monomorphic and one deviated significantly from HWE. We quantified mitochondrial DNA (mtDNA) sequence variation through the use of PCR amplification of two DNA fragments, followed by digestion with restriction enzymes; eight haplotypes were detected. One of the two fragments amplified in European lobster. Both sets of markers should prove useful for population discrimination purposes, and the microsatellites, in particular the four-locus multiplex, should prove highly amenable to rapidly addressing questions about mating patterns. PMID:12669797

  12. DNA Marker Transmission and Linkage Analysis in Populations Derived from a Sugarcane (Saccharum spp. x Erianthus arundinaceus Hybrid.

    Directory of Open Access Journals (Sweden)

    Jian-wen Chen

    Full Text Available Introgression of Erianthus arundinaceus has been the focus of several sugarcane breeding programs in the world, because the species has desirable traits such as high biomass production, vigour, ratooning ability and good resistance to environmental stresses and disease. In this study four genetic maps were constructed for two intergeneric populations. The first population (BC1 was generated from a cross between an Erianthus/Saccharum hybrid YC96-40 and a commercial sugarcane variety CP84-1198. The second population (BC2 was generated from a cross between YCE01-116, a progeny of the BC1 cross and NJ57-416, a commercial sugarcane cultivar. Markers across both populations were generated using 35 AFLP and 23 SSR primer pairs. A total of 756 and 728 polymorphic markers were scored in the BC1 and BC2 populations, respectively. In the BC1 population, a higher proportion of markers was derived from the Erianthus ancestor than those from the Saccharum ancestor Badila. In the BC2 population, both the number and proportion of markers derived from Erianthus were approximately half of those in the BC1 population. Linkage analysis led to the construction of 38, 57, 36 and 47 linkage groups (LGs for YC96-40, CP84-1198, YCE01-116, and NJ57-416, encompassing 116, 174, 97 and 159 markers (including single dose, double dose and bi-parental markers, respectively. These LGs could be further placed into four, five, five and six homology groups (HGs, respectively, based on information from multi-allelic SSR markers and repulsion phase linkages detected between LGs. Analysis of repulsion phase linkage indicated that Erianthus behaved like a true autopolyploid.

  13. Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

    Science.gov (United States)

    Huberman, Eliezer; Baccam, Mekhine J.

    2007-02-27

    The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

  14. Anti-dsDNA antibodies as a classification criterion and a diagnostic marker for systemic lupus erythematosus: critical remarks.

    Science.gov (United States)

    Rekvig, O P

    2015-01-01

    Antibodies to mammalian dsDNA have, for decades, been linked to systemic lupus erythematosus (SLE) and particularly to its most serious complication, lupus nephritis. This canonical view derives from studies on its strong association with disease. The dogma was particularly settled when the antibody was included in the classification criteria for SLE that developed during the 1970s, most prominently in the 1982 American College of Rheumatology (ACR), and recently in The Systemic Lupus International Collaborating Clinics (SLICC) classification criteria. There are several problems to be discussed before the anti-dsDNA antibody can be accepted without further distinction as a criterion to classify SLE. Old and contemporary knowledge make it clear that an anti-dsDNA antibody is not a unifying term. It embraces antibodies with a wide spectrum of fine molecular specificities, antibodies that are produced transiently in context of infections and persistently in the context of true autoimmunity, and also includes anti-dsDNA antibodies that have the potential to bind chromatin (accessible DNA structures) and not (specificity for DNA structures that are embedded in chromatin and therefore unaccessible for the antibodies). This critical review summarizes this knowledge and questions whether or not an anti-dsDNA antibody, as simply that, can be used to classify SLE.

  15. 乙肝血清标志物模式与HBV-DNA含量的关系探讨%Correlation between HBV serological markers and HBV-DNA

    Institute of Scientific and Technical Information of China (English)

    张海业; 孙溯荫; 韦兰

    2011-01-01

    Objective To analyze the correlation between the lovel of HBV semiogloat markers and HBV-DNA.Mothods Serum samples of 800 patients from Xinyi Pepole's Hospital clinic department suffering HBV were detected by ELISA and HBV-DNA were detected by FQ-PCR.then analyze the correlation between HBV serological markers and HBV-DNA.Results The HBV-DNA was detoeted in some HBV serological markerg groups and each group was different in the result.HBsAg positive.such as HBsAg,HBeAg and Anti-HBc positive samples has higher amount of copies of HBV-DNA;the low level of HBV-DNA copies were detected in the group of HBsAg.HBeAg or Anti-HBe,Anti-HBo lmsitive; and the HBV-DNA copies rate is 2.98%in the single HBsAg positive.Among 120 HBe Ag positive samples.there were 118 HBV-DNA positive,the positive rate of HBV-DNA was 98.33%and the level of HBeAg positive wail correlated to HBV-DNA(r=0.993).Conclusion Both the detection of HBeAg and HBV-DNA cab reflect the active level of duplicate of HBV-M.The HBV-DNA level showed all obvious correlation to the HBeAg contend in Bera.%目的 探讨不同的乙肝血清标志物(HBV-M)模式与HBV-DNA定量检测结果之间的关系.方法 选择800例经酶联免疫吸附试验(ELISA)检测HBsAg结果为阳性的血清样本,采用实时荧光定量PCR技术(FQ-PCR)检测其HBV-DNA含量;并根据患者HBV-M的不同模式进行分组统计,分析探讨HBV-M模式与HBV-DNA含量之间的关系.结果 不同HBV-M模式中HBV-DNA阳性检出率和含量存在明显差异.①"大三阳"组HBV-DNA含量以中、高拷贝为主;②"小三阳"组及HBsAg(+)&Anti-HBc(+)组HBV-DNA含量以中、低拷贝为主;③单纯HBsAg(+)组HBV-DNA的检出率仅为2.98%.④HBeAg(+)血样中HBV-DNA的阳性检出率高达98.33%(118/120),两者之间存在明显正相关(r=0.993).结论 HBV-M与HBV-DNA的检测都能反映HBV感染、传染性及体内复制的情况;HBeAg与HBV-DNA含量存在明显正相关.两者联合检测对乙肝的临床诊疗具有重要指导意义.

  16. Clinical evaluation of a new enzyme immunoassay for hepatitis B virus core-related antigen; a marker distinct from viral DNA for monitoring lamivudine treatment.

    Science.gov (United States)

    Rokuhara, A; Tanaka, E; Matsumoto, A; Kimura, T; Yamaura, T; Orii, K; Sun, X; Yagi, S; Maki, N; Kiyosawa, K

    2003-07-01

    We aimed to assess the clinical performance of a newly developed chemiluminescence enzyme immunoassay (CLEIA) for the detection of hepatitis B virus (HBV) core-related antigen (HBcrAg) in patients with chronic HBV infection. A total of 82 patients with chronic HBV infection and 167 HBV-negative controls were studied. HBcrAg was measured by CLEIA with monoclonal antibodies to hepatitis B e antigen (HBeAg) and hepatitis B core antigen (HBcAg), and HBV DNA was measured by transcription-mediated amplification assay (TMA) and in-house real-time detection polymerase chain reaction (RTD-PCR). The HBcrAg assay detected viremia in 189 of 216 samples (88%) collected from 72 patients whilst the TMA assay detected viremia in 178 of the 216 samples (82%) (P = 0.019). The HBcrAg concentration correlated linearly with the HBV DNA concentration (P HBcrAg assay was not affected by the absence of hepatitis B e antigen from the serum or the presence of precore mutations in the HBV genome. In patients without anti-viral drugs, changes in their serum HBcrAg concentration over time corresponded to their HBV DNA concentration. In six additional patients who were later treated with lamivudine, HBV DNA concentration declined more rapidly than their HBcrAg concentration. Three months after treatment commenced, the ratio of HBcrAg: HBV DNA had increased in all six patients (P = 0.031). The HBcrAg assay is a sensitive and useful test for the assessment of a patient's HBV load. When monitoring the anti-viral effect of lamivudine, HBcrAg provides a viral marker which is independent of HBV DNA.

  17. Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers

    OpenAIRE

    Soto-Calderón, Iván Darío; Clark Nicholas, Jonathan; Wildschutte Julia, Vera Halo; DiMattio, Kelly; Jensen-Seaman, Michael Ignatius; Anthony, Nicola Mary

    2014-01-01

    The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci i...

  18. Long Terminal Repeat Circular DNA as Markers of Active Viral Replication of Human T Lymphotropic Virus-1 in Vivo.

    Science.gov (United States)

    Fox, James M; Hilburn, Silva; Demontis, Maria-Antonietta; Brighty, David W; Rios Grassi, Maria Fernanda; Galvão-Castro, Bernardo; Taylor, Graham P; Martin, Fabiola

    2016-03-01

    Clonal expansion of human T-lymphotropic virus type-1 (HTLV-1) infected cells in vivo is well documented. Unlike human immunodeficiency virus type 1 (HIV-1), HTLV-1 plasma RNA is sparse. The contribution of the "mitotic" spread of HTLV-1 compared with infectious spread of the virus to HTLV-1 viral burden in established infection is uncertain. Since extrachromosomal long terminal repeat (LTR) DNA circles are indicators of viral replication in HIV-1 carriers with undetectable plasma HIV RNA, we hypothesised that HTLV-1 LTR circles could indicate reverse transcriptase (RT) usage and infectious activity. 1LTR and 2LTR DNA circles were measured in HTLV-1 cell lines and peripheral blood mononuclear cells (PBMC) of asymptomatic carriers (ACs) and patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) or adult T cell leukaemia/lymphoma (ATLL). 1LTR DNA circles were detected in 14/20 patients at a mean of 1.38/100 PBMC but did not differentiate disease status nor correlate with HTLV-1 DNA copies. 2LTR DNA circles were detected in 30/31 patients and at higher concentrations in patients with HTLV-1-associated diseases, independent of HTLV-1 DNA load. In an incident case the 2LTR DNA circle concentration increased 2.1 fold at the onset of HAM/TSP compared to baseline. Detectable and fluctuating levels of HTLV-1 DNA circles in patients indicate viral RT usage and virus replication. Our results indicate HTLV-1 viral replication capacity is maintained in chronic infection and may be associated with disease onset. PMID:26985903

  19. Novel Tetra-nucleotide Microsatellite DNA Markers for Assessing the Evolutionary Genetics and Demographics of Northern Snakehead (Channa argus) Invading North America

    Science.gov (United States)

    King, Timothy L.; Johnson, R.L.

    2011-01-01

    We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy-Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness

  20. Analysis of microsatellite markers D18S70 and d20S116 in DNA isolated from dentin: Use in forensic medicine

    Directory of Open Access Journals (Sweden)

    Puzović Dragana

    2009-01-01

    Full Text Available Introduction. Short tandem repeats and more specifically microsatellites represent a powerful tool in forensic medicine. In the past years, they have been extensively used in human identification and paternity testing. Objective The aim of the present study was to analyze two microsatellite markers in the Serbian population, i.e. to determine the number of alleles and the relevant forensic parameters. Methods. DNA was isolated from teeth samples using standard proteinase K digestion and phenol/chloroform alcohol extraction. PCR products were analyzed on polyacrilamide gels and visualized by AgNO3 staining. Forensic parameters were calculated using the Cervus software. Results. The loci D18S70 and D20S116 were analyzed on a sample of 70 unrelated, healthy adult individuals from Serbia. The number of alleles was determined and Hardy Weinberg equilibrium was confirmed for both loci. D18S70 and D20S116 demonstrated 6 and 8 alleles, respectively. The power of discrimination (PD and the power of exclusion (PE for the tested STR loci, D18S70 and D20S116 were 0.92 (PD, 0.41 (PE and 0.95 (PD, 0.480 (PE, respectively. Conclusion. According to the presented data, D18S70 and D20S116 are most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that these two microsatellites represent useful markers for individual identification and parentage analysis in the Serbian population.

  1. Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers

    OpenAIRE

    Lijuan Zhang; Hu Li; Shujuan Li; Aibing Zhang; Fei Kou; Huaizhu Xun; Pei Wang; Ying Wang; Fan Song; Jianxin Cui; Jinjie Cui; Gouge, Dawn H.; Wanzhi Cai

    2015-01-01

    Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populatio...

  2. Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

    International Nuclear Information System (INIS)

    DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development

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

    Directory of Open Access Journals (Sweden)

    Asma A. AL-Huqail

    2015-01-01

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

  4. Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

    Energy Technology Data Exchange (ETDEWEB)

    Boerkamp, Kim M., E-mail: K.M.Boerkamp@uu.nl; Rutteman, Gerard R. [Department of Clinical Science of Companion Animals, Faculty of Veterinary Medicine, UU, Yalelaan 104, 3584 CM, Utrecht (Netherlands); Kik, Marja J. L. [Department of Pathobiology, Faculty of Veterinary Medicine, UU, Yalelaan 1, 3508 TD, Utrecht (Netherlands); Kirpensteijn, Jolle [Department of Clinical Science of Companion Animals, Faculty of Veterinary Medicine, UU, Yalelaan 104, 3584 CM, Utrecht (Netherlands); Schulze, Christoph; Grinwis, Guy C. M. [Department of Pathobiology, Faculty of Veterinary Medicine, UU, Yalelaan 1, 3508 TD, Utrecht (Netherlands)

    2012-12-03

    DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development.

  5. Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

    Directory of Open Access Journals (Sweden)

    Christoph Schulze

    2012-12-01

    Full Text Available DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development.

  6. DNA Methylation and Methylation Polymorphism in Genetically Stable In vitro Regenerates of Jatropha curcas L. Using Methylation-Sensitive AFLP Markers.

    Science.gov (United States)

    Rathore, Mangal S; Jha, Bhavanath

    2016-03-01

    The present investigation aimed to evaluate the degree and pattern of DNA methylation using methylation-sensitive AFLP (MS-AFLP) markers in genetically stable in vitro regenerates of Jatropha curcas L.. The genetically stable in vitro regenerates were raised through direct organogenesis via enhanced axillary shoot bud proliferation (Protocol-1) and in vitro-derived leaf regeneration (Protocol-2). Ten selective combinations of MS-AFLP primers produced 462 and 477 MS-AFLP bands in Protocol-1 (P-1) and Protocol-2 (P-2) regenerates, respectively. In P-1 regenerates, 15.8-31.17 % DNA was found methylated with an average of 25.24 %. In P-2 regenerates, 15.93-32.7 % DNA was found methylated with an average of 24.11 %. Using MS-AFLP in P-1 and P-2 regenerates, 11.52-25.53 % and 13.33-25.47 % polymorphism in methylated DNA was reported, respectively. Compared to the mother plant, P-1 regenerates showed hyper-methylation while P-2 showed hypo-methylation. The results clearly indicated alternation in degree and pattern of DNA methylation; hence, epigenetic instability in the genetically stable in vitro regenerates of J. curcas, developed so far using two different regeneration systems and explants of two different origins. The homologous nucleotide fragments in genomes of P-1 and P-2 regenerates showing methylation re-patterning might be involved in immediate adaptive responses and developmental processes through differential regulation of transcriptome under in vitro conditions. PMID:26588922

  7. Statistical Methods for the Detection and Space-Time Monitoring of DNA Markers in the Pollen Cloud

    OpenAIRE

    Marchand, Philippe

    2013-01-01

    The analysis of pollen grains finds applications in fields as diverse as allergology, paleoecology, apiculture and forensics. In contrast with morphological identification methods that require the visual inspection of individual pollen grains, recently-developed genetic approaches have the potential to increase both the scale and resolution of pollen analyses. In the first part of this dissertation, I describe efficient experimental designs to determine the prevalence of a genetic marker in a...

  8. Molecular discrimination of six species of Bagrid catfishes from Indus river system using randomly amplified polymorphic DNA markers.

    Science.gov (United States)

    Saini, Archana; Dua, Anish; Mohindra, Vindhya; Lakra, W S

    2011-06-01

    Bagrid catfishes constitute a very important group of fishes having immense commercial importance in south-east countries. The phylogenetic relationships and genome specificity among six species of Bagrid catfishes (Mystus bleekeri, M. cavasius, M. vittatus, M. tengara, M. aor and M. seenghala) were investigated using RAPD markers as discriminating characters for the first time. 511 RAPD fragments were generated using ten decamer primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 92 and 2,863 bp, which were assigned to 155 RAPD loci. Clearly resolved and repeatable bands were scored for their presence or absence in a binary matrix. Different RAPD profiles were observed for all the six Mystus species. In the present study three group diagnostic, eleven group exclusive and 18 species-specific markers were generated. Thus six Mystus species can be successfully differentiated on the basis of these 18 species-specific RAPD markers. UPGMA dendrogram constructed on the basis of genetic distance formed two distinct clusters, M. seenghala and M. aor form one separate cluster from other four species i.e., M. tengara, M. cavasius, M. bleekeri and M. vittatus. The inferences drawn from the above study clearly showed their genetic distinctness from the other four Mystus species and supported their inclusion into a separate genus, Sperata. PMID:20127179

  9. Repetitive, Marker-Free, Site-Specific Integration as a Novel Tool for Multiple Chromosomal Integration of DNA

    DEFF Research Database (Denmark)

    Petersen, Kia Vest; Martinussen, Jan; Jensen, Peter Ruhdal;

    2013-01-01

    We present a tool for repetitive, marker-free, site-specific integration in Lactococcus lactis, in which a nonreplicating plasmid vector (pKV6) carrying a phage attachment site (attP) can be integrated into a bacterial attachment site (attB). The novelty of the tool described here is the inclusion...... of a minimal bacterial attachment site (attBmin), two mutated loxP sequences (lox66 and lox71) allowing for removal of undesirable vector elements (antibiotic resistance marker), and a counterselection marker (oroP) for selection of loxP recombination on the pKV6 vector. When transformed into L. lactis...... expressing the phage TP901-1 integrase, pKV6 integrates with high frequency into the chromosome, where it is flanked by attL and attR hybrid attachment sites. After expression of Cre recombinase from a plasmid that is not able to replicate in L. lactis, loxP recombinants can be selected for by using 5...

  10. Obtaining marker-free transgenic soybean plants with optimal frequency by constructing a three T-DNA binary vector

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Obtaining marker-free plants with high efficiency will benefit the environmental release of transgenic crops.To achieve this point,a binary vector with three T-DNAs was constructed using several mediate plasmids,in which one copy of BAR gene expression cassette and two copies of VIP1 gene expression cassette were included.EHA101 Agrobacterium strain harboring the final construct was applied to transform soybean cotyledon nodes.Through 2-3 months regeneration and selection with 3-5 mg·L-1 glufosinate,transgenic soybean plants were obtained at 0.83%-3.16%,and the co-transformation efficiency of both genes in the same individual reached up to 86.4%,based on the southern blot test.Using PCR analysis,southern blot and northern blot tests,as well as leaf painting of herbicide in T1 progenies,41 plants were eliminated of BAR gene with the frequency of 7.6%.Among the T1 populations tested,the loss of the alien genes happened in 22.7% lines,the silence of the BAR gene took place in 27.3% lines,and VIP1 gene silence existed in 37.1% marker-free plants.The results also suggested that the plasmid with three T-DNAs might be an ideal vector to generate marker-free genetically modified organisms.

  11. A novel method for the preparation of template DNA for PCR from beer to detect materials and to develop DNA markers to evaluate the quality of beer.

    Science.gov (United States)

    Nakamura, Sumiko; Tsushima, Ryosuke; Ohtsubo, Ken'ichi

    2013-01-01

    We developed a method for the preparation of template DNAs for polymerase chain reaction (PCR) from beer. We improved the method by (i) lyophilizing and pulverizing the beer to concentrate DNAs, (ii) decomposition of polysaccharides and proteins so as not to inhibit DNA extraction by the use of heat-resistant amylase and proteinase K, (iii) separation of template DNA by purification using 70% EtOH extraction and isopropyl alcohol precipitation, and (iv) the use of magnetic beads to purify DNA. We developed suitable 7 STS (sequence-tagged site) primers related to beer quality for PCR, and it proved possible to identify 16 dominant malting barley cultivars and 22 kinds of beers. To digitize the results of PCR, discriminative DNA bands were binarized as 0 (disappeared) or 1 (appeared) and subjected to multiple regression analysis. Estimation formulae for the quality of beer were developed using the above-mentioned independent variables based on the results of PCR against dependent variables related to the qualities of beer, including foam stability, bitterness, sourness and astringency. These equations showed multiple regression coefficients of 0.93, 0.82, 0.87, and 0.87 for calibration.

  12. DNA markers closely linked to nematode resistance genes in sugar beet (Beta vulgaris L.) mapped using chromosome additions and translocations originating from wild beets of the Procumbentes section.

    Science.gov (United States)

    Jung, C; Koch, R; Fischer, F; Brandes, A; Wricke, G; Herrmann, R G

    1992-03-01

    Genes conferring resistance to the beet cyst nematode (Heterodera schachtii Schm.) have been transferred to sugar beet (Beta vulgaris L.) from three wild species of the Procumbentes section using monosomic addition and translocation lines, because no meiotic recombination occurs between chromosomes of cultured and wild species. In the course of a project to isolate the nematode resistance genes by strategies of reverse genetics, probes were cloned from DNA of a fragmented B. procumbens chromosome carrying a resistance gene, which had been isolated by pulsed-field gel electrophoresis. One probe (pRK643) hybridized with a short dispersed repetitive DNA element, which was found only in wild beets, and thus may be used as a molecular marker for nematode resistance to progeneis of monosomic addition lines segregating resistant and susceptible individuals. Additional probes for the resistance gene region were obtained with a polymerase chain reaction (PCR)-based strategy using repetitive primers to amplify DNA located between repetitive elements. One of these probes established the existence of at least six different chromosomes from wild beet species, each conferring resistance independently of the others. A strict correlation between the length of the wild beet chromatin introduced in fragment addition and translocation lines and the repeat copy number has been used physically to map the region conferring resistance to a chromosome segment of 0.5-3 Mb.

  13. Presence of antibodies against a cell-surface protein, cross-reactive with DNA, in systemic lupus erythrematosus: a marker of the disease

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, L.; Lety, M.A.; Choquette, D.; Viard, J.P.; Jacob, F.; Louvard, D.; Bach, J.F.

    1987-05-01

    Antibodies against a cell-surface protein, cross-reactive with double-stranded DNA, were detected in the serum of 25 patients with active human systemic lupus erythematosus (SLE), defined on the basis of the revised American Rheumatism Association classification. Among these sera, two did not display anti-DNA antibodies, as shown by Farr assay, solid-phase radioimmunoassay, and Crithidia luciliae test. Five other SLE patients were consecutively studied in active and remission states. Antibodies against the protein were detected in the serum of the 5 SLE patients when they were in active phase but not in the serum of the same patients in inactive phase of the disease. The anti-protein antibodies were not found in the serum of 10 inactive SLE patients or in the sera of 10 normal human controls, 10 patients with rheumatoid arthritis, 5 patients with scleroderma, and 4 patients with primary sicca syndrome. Taken together, these results strongly suggest that antibodies against this cell-surface protein could provide a better diagnosis marker and activity index than anti-DNA antibodies in SLE.

  14. Hybridization and massive mtDNA unidirectional introgression between the closely related Neotropical toads Rhinella marina and R. schneideri inferred from mtDNA and nuclear markers

    Directory of Open Access Journals (Sweden)

    Schneider Horacio

    2011-09-01

    Full Text Available Abstract Background The classical perspective that interspecific hybridization in animals is rare has been changing due to a growing list of empirical examples showing the occurrence of gene flow between closely related species. Using sequence data from cyt b mitochondrial gene and three intron nuclear genes (RPL9, c-myc, and RPL3 we investigated patterns of nucleotide polymorphism and divergence between two closely related toad species R. marina and R. schneideri. By comparing levels of differentiation at nuclear and mtDNA levels we were able to describe patterns of introgression and infer the history of hybridization between these species. Results All nuclear loci are essentially concordant in revealing two well differentiated groups of haplotypes, corresponding to the morphologically-defined species R. marina and R. schneideri. Mitochondrial DNA analysis also revealed two well-differentiated groups of haplotypes but, in stark contrast with the nuclear genealogies, all R. schneideri sequences are clustered with sequences of R. marina from the right Amazon bank (RAB, while R. marina sequences from the left Amazon bank (LAB are monophyletic. An Isolation-with-Migration (IM analysis using nuclear data showed that R. marina and R. schneideri diverged at ≈ 1.69 Myr (early Pleistocene, while R. marina populations from LAB and RAB diverged at ≈ 0.33 Myr (middle Pleistocene. This time of divergence is not consistent with the split between LAB and RAB populations obtained with mtDNA data (≈ 1.59 Myr, which is notably similar to the estimate obtained with nuclear genes between R. marina and R. schneideri. Coalescent simulations of mtDNA phylogeny under the speciation history inferred from nuclear genes rejected the hypothesis of incomplete lineage sorting to explain the conflicting signal between mtDNA and nuclear-based phylogenies. Conclusions The cytonuclear discordance seems to reflect the occurrence of interspecific hybridization between these

  15. Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera.

    Directory of Open Access Journals (Sweden)

    Gianpiero Marconi

    Full Text Available Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone and salinity-sensitive (Toccata rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4 and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site

  16. DNA repair deficiency as a susceptibility marker for spontaneous lymphoma in golden retriever dogs: a case-control study.

    Directory of Open Access Journals (Sweden)

    Douglas H Thamm

    Full Text Available There is accumulating evidence that an individual's inability to accurately repair DNA damage in a timely fashion may in part dictate a predisposition to cancer. Dogs spontaneously develop lymphoproliferative diseases such as lymphoma, with the golden retriever (GR breed being at especially high risk. Mechanisms underlying such breed susceptibility are largely unknown; however, studies of heritable cancer predisposition in dogs may be much more straightforward than similar studies in humans, owing to a high degree of inbreeding and more limited genetic heterogeneity. Here, we conducted a pilot study with 21 GR with lymphoma, 20 age-matched healthy GR and 20 age-matched healthy mixed-breed dogs (MBD to evaluate DNA repair capability following exposure to either ionizing radiation (IR or the chemical mutagen bleomycin. Inter-individual variation in DNA repair capacity was evaluated in stimulated canine lymphoctyes exposed in vitro utilizing the G2 chromosomal radiosensitivity assay to quantify clastogen-induced chromatid-type aberrations (gaps and breaks. Golden retrievers with lymphoma demonstrated elevated sensitivity to induction of chromosome damage following either challenge compared to either healthy GR or MBD at multiple doses and time points. Using the 75(th percentile of chromatid breaks per 1,000 chromosomes in the MBD population at 4 hours post 1.0 Gy IR exposure as a benchmark to compare cases and controls, GR with lymphoma were more likely than healthy GR to be classified as "sensitive" (odds ratio = 21.2, 95% confidence interval 2.3-195.8. Furthermore, our preliminary findings imply individual (rather than breed susceptibility, and suggest that deficiencies in heritable factors related to DNA repair capabilities may be involved in the development of canine lymphoma. These studies set the stage for larger confirmatory studies, as well as candidate-based approaches to probe specific genetic susceptibility factors.

  17. Targeted Sequencing for Discovery and Validation of DNA Methylation Markers of Colon Cancer Metastasis — EDRN Public Portal

    Science.gov (United States)

    Colon cancer is the second leading cause of cancer death in the United States. A key issue in treating colon cancer patients is inability to accurately predict tumors that have metastatic potential and require adjuvant chemotherapy. This project will test the model that tumor metastases arise from intra-tumor heterogeneity generated by DNA methylation events, and that detecting these events can provide a predictve signature of tumors with poor outcome

  18. Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation

    Science.gov (United States)

    Jumpathong, Watthanachai; Chan, Wan; Taghizadeh, Koli; Babu, I. Ramesh; Dedon, Peter C.

    2015-01-01

    Although mechanistically linked to disease, cellular molecules damaged by endogenous processes have not emerged as significant biomarkers of inflammation and disease risk, due in part to poor understanding of their pharmacokinetic fate from tissue to excretion. Here, we use systematic metabolite profiling to define the fate of a common DNA oxidation product, base propenals, to discover such a biomarker. Based on known chemical reactivity and metabolism in liver cell extracts, 15 candidate metabolites were identified for liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) quantification in urine and bile of rats treated with thymine propenal (Tp). Analysis of urine revealed three metabolites (6% of Tp dose): thymine propenoate and two mercapturate derivatives of glutathione conjugates. Bile contained an additional four metabolites (22% of Tp dose): cysteinylglycine and cysteine derivatives of glutathione adducts. A bis-mercapturate was observed in urine of untreated rats and increased approximately three- to fourfold following CCl4-induced oxidative stress or treatment with the DNA-cleaving antitumor agent, bleomycin. Systematic metabolite profiling thus provides evidence for a metabolized DNA damage product as a candidate biomarker of inflammation and oxidative stress in humans. PMID:26283391

  19. Identification of Perkinsus-like parasite in Manila clam, Ruditapes philippinarum using DNA molecular marker at ITS region

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Genomic DNA was extracted from hypnospores of Perkinsus-like parasite of Manila clam Ruditapes philippinarum collected at the fishing grounds in Huanghai Sea coast Shicheng Island and East China Sea coast Ningbo, China. The internal transcribed spacer(ITS)in rDNA was PCR-amplified, cloned, sequenced, and compared with that of five Perkinsus species in GenBank. The fragment amplified from DNA of parasite of either Shicheng Island or Ningbo contained 649 bp, including partial ssrRNA(51 bp) and ITS(+5.8 S)(598 bp) regions. The ITS(+5.8S) sequences of Perkinsus-like parasite of both Shicheng Island and Ningbo were all 99% identical to those ofPerkinsus atlanticus,and were not more than 95% identical to those of other four Perkinsus species including P. marinus, P.andrewsi, P. qugwadi and P. medierraneus.The ITS (+5.8S) sequence of Perkinsus-like parasite of Shicheng Island was 99% identical to that of Ningbo. These facts about nucleotide sequences suggested that the Perkinsus-like parasite in Manila clam, Ruditapes philippinarum collected from either the Huanghai Sea coast or the East China Sea coast was P. atlanticus, and might reflect P. atlanticus strains of distinct geographic distribution.

  20. Construction of full-length cDNA library and development of EST-derived simple sequence repeat (EST-SSR) markers in Senecio scandens.

    Science.gov (United States)

    Qian, Gang; Ping, Junjiao; Lu, Jian; Zhang, Zhen; Wang, Lei; Xu, Delin

    2014-12-01

    Senecio scandens Buch.-Ham. ex D. Don (Compositae) is a crucial source of Chinese traditional medicine with antibacterial properties. We constructed a cDNA library and obtained expressed sequence tags (ESTs) to show the distribution of gene ontology annotations for mRNAs, using an individual plant with superior antibacterial characteristics. Analysis of comparative genomics indicates that the putative uncharacterized proteins (21.07%) might be derived from "molecular function unknown" clones or rare transcripts. Furthermore, the Compositae had high cross-species transferability of EST-derived simple sequence repeats (EST-SSR), based on valid amplifications of 206 primer pairs developed from the newly assembled expressed sequence tag sequences in Artemisia annua L. Among those EST-SSR markers, 52 primers showed polymorphic amplifications between individuals with contrasting diverse antibacterial traits. Our sequence data and molecular markers will be cost-effective tools for further studies such as genome annotation, molecular breeding, and novel transcript profiles within Compositae species. PMID:25007751

  1. Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago

    Directory of Open Access Journals (Sweden)

    Sávio P. Reis

    2008-01-01

    Full Text Available In this study, 15 microsatellite DNA loci used in comparative tests by the International Society for Animal Genetics were applied to the evaluation of genetic diversity and management, and the efficiency of paternity testing in Marajoara horses and Puruca ponies from the Marajó Archipelago. Based on the genotyping of 93 animals, mean allelic diversity was estimated as 9.14 and 7.00 for the Marajoara and Puruca breeds, respectively. While these values are similar to those recorded in most European breeds, mean levels of heterozygosity were much lower (Marajoara 49%, Puruca 40%, probably as a result of high levels of inbreeding in the Marajó populations. The mean informative polymorphic content of this 15-marker system was over 50% in both breeds, and was slightly higher in the Marajoara horses. The discriminative power and exclusion probabilities derived from this system were over 99% for both populations, emphasizing the efficacy of these markers for paternity testing and genetic management in the two breeds.

  2. Development and validation of DNA markers linked to Sdvy-1, a common bean gene conferring resistance to the yellowing strain of Soybean dwarf virus.

    Science.gov (United States)

    Yamashita, Yoko; Takeuchi, Toru; Okuyama, Masataka; Sasaki, Jun; Onodera, Kakumasa; Sato, Mikako; Souma, Chihiro; Ebe, Shigehiko

    2014-12-01

    The yellowing strain of Soybean dwarf virus (SbDV-YS) causes yellowing and yield loss in common bean (Phaseolus vulgaris). The most effective control is achieved through breeding for resistance. An indeterminate climbing cultivar with a white seed coat, 'Oofuku', is resistant to SbDV-YS in inoculation tests. We crossed 'Oofuku' with an elite cultivar, 'Taisho-Kintoki', which is SbDV-YS-susceptible, determinate dwarf with a red-purple seed coat, and performed amplified-fragment-length polymorphism analysis of F3 lines. From nucleotide sequences of the resistant-specific fragments and their flanking regions, we developed five DNA markers, of which DV86, DV386, and DV398 were closely linked to Sdvy-1, a resistance gene. Using the markers, we developed 'Toiku-B79' and 'Toiku-B80', the near-isogenic lines (NILs) incorporating Sdvy-1 in the background of 'Taisho-Kintoki'. The NILs had similar growth habit, maturity date and seed shape to those of 'Taisho-Kintoki'. The quality of boiled beans was also similar, except that the NILs had more seed coat cracking than 'Taisho-Kintoki'. The NILs showed no SbDV-YS infection in inoculation tests. We suggest that Sdvy-1 is a useful source of SbDV-YS resistance in common bean.

  3. Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers.

    Science.gov (United States)

    Zhang, Lijuan; Li, Hu; Li, Shujuan; Zhang, Aibing; Kou, Fei; Xun, Huaizhu; Wang, Pei; Wang, Ying; Song, Fan; Cui, Jianxin; Cui, Jinjie; Gouge, Dawn H; Cai, Wanzhi

    2015-01-01

    Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populations from central China and peripheral China regions. Analysis of molecular variance showed a high level of geographical differentiation at different hierarchical levels. Isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among A. suturalis populations, which suggested gene flow is not restricted by distance. In seven peripheral populations, the high levels of genetic differentiation and the small Nem values implied that geographic barriers were more likely restrict gene flow. Neutrality tests and the Bayesian skyline plot suggested population expansion likely happened during the cooling transition between Last Interglacial and Last Glacial Maximum. All lines of evidence suggest that physical barriers, Pleistocene climatic oscillations and geographical heterogeneity have affected the population structure and distribution of this insect in China. PMID:26388034

  4. High-resolution melt-curve analysis of random-amplified-polymorphic-DNA markers, for the characterisation of pathogenic Leptospira

    DEFF Research Database (Denmark)

    Tulsiani, Suhella; Craig, S B; Graham, G C;

    2010-01-01

    A new test for pathogenic Leptospira isolates, based on RAPD-PCR and high-resolution melt (HRM) analysis (which measures the melting temperature of amplicons in real time, using a fluorescent DNA-binding dye), has recently been developed. A characteristic profile of the amplicons can be used...... typed against 13 previously published RAPD primers, using a real-time cycler (the Corbett Life Science RotorGene 6000) and the optimised reagents from a commercial kit (Quantace SensiMix). RAPD-HRM at specific temperatures generated defining amplicon melt profiles for each of the tested serovars...

  5. Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers.

    Science.gov (United States)

    Ho, Adeljean L F C; Pruett, Christin L; Lin, Junda

    2016-08-01

    Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes. A divergence-dating analysis supported the hypothesis of the genus Poecilia dispersing into Central America in the early Pliocene (ancestors of Psychropoecilia+Allopoecilia+Mollienesia: 7.3-2.0Mya) from predominantly South America. Subsequently, one lineage (subgenus Allopoecilia: 5.1-1.3Mya) expanded deeper into South America from Lower-Central America, and one lineage expanded from Nuclear-Central America into South America (subgenus Mollienesia: 0.71-0.14Mya). The subgenus Mollienesia diverged into three monophyletic groups that can be identified by nuptial male dorsal fin morphology and inner jaw dentition. A subclade of the unicuspid short-fins (subgenus Mollienesia) was the lineage that expanded into South America during the middle Pleistocene. Species in this subclade are now distributed across northern South America, where they are partially sympatric with Allopoecilia. However the P. (A.) caucana complex was not monophyletic, with P. (A.) wandae clustering in the Mollienesia subclade that expanded into South America. It is apparent that characters (body size, scale count, pigmentation, and gonopodium morphology) used to define the P. (A

  6. Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers

    Directory of Open Access Journals (Sweden)

    Mariën J

    2008-03-01

    Full Text Available Abstract Background In recent years, several new hypotheses on phylogenetic relations among arthropods have been proposed on the basis of DNA sequences. One of the challenged hypotheses is the monophyly of hexapods. This discussion originated from analyses based on mitochondrial DNA datasets that, due to an unusual positioning of Collembola, suggested that the hexapod body plan evolved at least twice. Here, we re-evaluate the position of Collembola using ribosomal protein gene sequences. Results In total 48 ribosomal proteins were obtained for the collembolan Folsomia candida. These 48 sequences were aligned with sequence data on 35 other ecdysozoans. Each ribosomal protein gene was available for 25% to 86% of the taxa. However, the total sequence information was unequally distributed over the taxa and ranged between 4% and 100%. A concatenated dataset was constructed (5034 inferred amino acids in length, of which ~66% of the positions were filled. Phylogenetic tree reconstructions, using Maximum Likelihood, Maximum Parsimony, and Bayesian methods, resulted in a topology that supports monophyly of Hexapoda. Conclusion Although ribosomal proteins in general may not evolve independently, they once more appear highly valuable for phylogenetic reconstruction. Our analyses clearly suggest that Hexapoda is monophyletic. This underpins the inconsistency between nuclear and mitochondrial datasets when analyzing pancrustacean relationships. Caution is needed when applying mitochondrial markers in deep phylogeny.

  7. Hybrid microarray based on double biomolecular markers of DNA and carbohydrate for simultaneous genotypic and phenotypic detection of cholera toxin-producing Vibrio cholerae.

    Science.gov (United States)

    Shin, Hwa Hui; Seo, Jeong Hyun; Kim, Chang Sup; Hwang, Byeong Hee; Cha, Hyung Joon

    2016-05-15

    Life-threatening diarrheal cholera is usually caused by water or food contaminated with cholera toxin-producing Vibrio cholerae. For the prevention and surveillance of cholera, it is crucial to rapidly and precisely detect and identify the etiological causes, such as V. cholerae and/or its toxin. In the present work, we propose the use of a hybrid double biomolecular marker (DBM) microarray containing 16S rRNA-based DNA capture probe to genotypically identify V. cholerae and GM1 pentasaccharide capture probe to phenotypically detect cholera toxin. We employed a simple sample preparation method to directly obtain genomic DNA and secreted cholera toxin as target materials from bacterial cells. By utilizing the constructed DBM microarray and prepared samples, V. cholerae and cholera toxin were detected successfully, selectively, and simultaneously; the DBM microarray was able to analyze the pathogenicity of the identified V. cholerae regardless of whether the bacteria produces toxin. Therefore, our proposed DBM microarray is a new effective platform for identifying bacteria and analyzing bacterial pathogenicity simultaneously. PMID:26735874

  8. Population distribution of 45S and 5S rDNA in golden mahseer, Tor putitora: population-specific FISH marker

    Indian Academy of Sciences (India)

    Mamta Singh; Ravindra Kumar; N. S. Nagpure; Basdeo Kushwaha; Indra Mani; U. K. Chauhan; W. S. Lakra

    2009-12-01

    Chromosomal locations of major 45S and minor 5S ribosomal DNAs (rDNAs) and organization of 5S rRNA genes were analysed in five different populations of golden mahseers (Tor putitora) using fluorescence in situ hybridization (FISH) and Southern blot hybridization. All five populations of T. putitora ($2n = 100$) showed a similar type of macro-karyotype composed of 12 metacentric, 22 submetacentric, 14 subtelocentric and 52 telocentric chromosomes. Analysis of active nucleolar organizer regions (NORs) by silver staining did not show any differences in number and chromosomal position in different populations. But FISH data showed significant difference between the populations, four of the five populations showed six 18S (three pairs) and two 5S (one pair) signals with positional polymorphism, while one population showed eight 18S and four 5S signals, respectively. Southern blot data confirms that 5S rDNA clusters present on two different chromosome pairs in Kosi river population contain non-transcribed spacers (NTS) of same length. In the present study, simultaneous localization of 45S and 5S rDNA by in situ hybridization helped us to develop the discrete population-specific markers in different geographically isolated populations of T. putitora.

  9. Molecular differentiation of the Old World Culicoides imicola species complex (Diptera, Ceratopogonidae), inferred using random amplified polymorphic DNA markers.

    Science.gov (United States)

    Sebastiani, F; Meiswinkel, R; Gomulski, L M; Guglielmino, C R; Mellor, P S; Malacrida, A R; Gasperi, G

    2001-07-01

    Samples of seven of the 10 morphological species of midges of the Culicoides imicola complex were considered. The importance of this species complex is connected to its vectorial capacity for African horse sickness virus (AHSV) and bluetongue virus (BTV). Consequently, the risk of transmission may vary dramatically, depending upon the particular cryptic species present in a given area. The species complex is confined to the Old World and our samples were collected in Southern Africa, Madagascar and the Ivory Coast. Genomic DNA of 350 randomly sampled individual midges from 19 populations was amplified using four 20-mer primers by the random amplified polymorphic DNA (RAPD) technique. One hundred and ninety-six interpretable polymorphic bands were obtained. Species-specific RAPD profiles were defined and for five species diagnostic RAPD fragments were identified. A high degree of polymorphism was detected in the species complex, most of which was observed within populations (from 64 to 76%). Principal coordinate analysis (PCO) and cluster analysis provided an estimate of the degree of variation between and within populations and species. There was substantial concordance between the taxonomies derived from morphological and molecular data. The amount and the different distributions of genetic (RAPD) variation among the taxa can be associated to their life histories, i.e. the abundance and distribution of the larval breeding sites and their seasonality.

  10. First assessment on the molecular phylogeny of Anatololacerta (Squamata, Lacertidae) distributed in Southern Anatolia: insights from mtDNA and nDNA markers.

    Science.gov (United States)

    Candan, Kamil; Kankılıç, Tolga; Güçlü, Özgür; Kumlutaş, Yusuf; Durmuş, Salih Hakan; Lymberakis, Petros; Poulakakis, Nikos; Ilgaz, Çetin

    2016-05-01

    The genus Anatololacerta (Lacertidae) occurs mainly in Anatolia (western and southern Turkey) and on the Aegean islands Samos, Ikaria, and Rhodos. Although its taxonomy has long been debated and is currently nascent, three morphological species have been attributed to this genus: Anatololacerta anatolica, Anatololacerta oertzeni, and Anatololacerta danfordi. Here, we investigated the evolutionary history of A. oertzeni and Anatololacerta danfordi based on both mitochondrial and nuclear markers (16S rRNA and cmos). In total, 34 Anatololacerta specimens were analyzed using maximum likelihood (ML) and Bayesian inference (BI) methods. Our results supported the presence of four well-supported lineages: two belongs to A. oertzeni and two to A. danfordi. The temporal diversification of these lineages probably started with the divergence of the first A. oertzeni lineage from western Antalya at 7.9 Mya. The other two major splits may have occurred in early Pliocene (4.4 Mya: the divergence of the second A. oertzeni from A. danfordi) and in late Pliocene (2.7 Mya: the divergence of the two lineages of A. danfordi). The phylogeographical scenario suggests that the major diversification events (from late Miocene to late Pliocene) could be related with climatic oscillations (such as the late Miocene aridification and the Messinian Salinity Crisis) and tectonic movements (such as the uplift of the central Taurus mountain). PMID:25489775

  11. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  12. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  13. cDNA sequence of the horse (Equus caballus) LAMA3 gene and characterization of two intronic SNP markers.

    Science.gov (United States)

    Milenkovic, Dragan; Mata, Xavier; Chadi, Sead; Guérin, Gérard

    2005-12-01

    Laminins are large heterotrimeric basement membrane glycoproteins composed of alpha, beta and gamma chains. The Laminin 5 isoform has an alpha3beta3gamma2 composition and is essential for the adhesion of basal keratinocytes to the underlying epithelial basement membrane where it is mainly located. Mutations in the genes coding for the 3 chains have been associated with a severe skin blistering disease, Herlitz's junctional epidermolysis bullosa (JEB), observed in different species as man, dog, cat and horse. In this study, we report the sequence of the 5.2 kb horse laminin alpha 3 cDNA (LAMA3) as well as the detection of two intronic SNPs. These data will be useful to further identify causal mutations for the disease in this gene. PMID:16287627

  14. Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers.

    Science.gov (United States)

    Hagelberg, E; Kayser, M; Nagy, M; Roewer, L; Zimdahl, H; Krawczak, M; Lió, P; Schiefenhövel, W

    1999-01-29

    Present-day Pacific islanders are thought to be the descendants of Neolithic agriculturalists who expanded from island South-east Asia several thousand years ago. They speak languages belonging to the Austronesian language family, spoken today in an area spanning half of the circumference of the world, from Madagascar to Easter Island, and from Taiwan to New Zealand. To investigate the genetic affinities of the Austronesian-speaking peoples, we analysed mitochondrial DNA, HLA and Y-chromosome polymorphisms in individuals from eight geographical locations in Asia and the Pacific (China, Taiwan, Java, New Guinea highlands, New Guinea coast, Trobriand Islands, New Britain and Western Samoa). Our results show that the demographic expansion of the Austronesians has left a genetic footprint. However, there is no simple correlation between languages and genes in the Pacific.

  15. Mapping of DNA sex-specific markers and genes related to sex differentiation in turbot (Scophthalmus maximus).

    Science.gov (United States)

    Viñas, Ana; Taboada, Xoana; Vale, Luis; Robledo, Diego; Hermida, Miguel; Vera, Manel; Martínez, Paulino

    2012-10-01

    Production of all-female populations in turbot can increase farmer's benefits since sexual dimorphism in growth in this species is among the highest within marine fish, turbot females reaching commercial size 3-6 months earlier than males. Puberty in males occurs earlier than in females, which additionally slows their growth. Thus, elucidating the mechanisms of sex determination and gonad differentiation is a relevant goal for turbot production. A ZZ/ZW sex determination mechanism has been suggested for this species, and four sex-related quantitative trait loci (QTL) were detected, the major one located in linkage group (LG) 5 and the three minor ones in LG6, LG8, and LG21. In the present work, we carried out a linkage analysis for several sex-related markers: (1) three anonymous sex-associated RAPD and (2) several candidate genes related to sex determination and gonad differentiation in other species (Sox3, Sox6, Sox8, Sox9, Sox17, Sox19, Amh, Dmrta2, Cyp19a, Cyp19b). We focused our attention on their co-localization with the major and minor sex-related QTL trying to approach to the master sex-determining gene of this species. Previously described growth-related QTL were also considered since the association observed between growth and sex determination in fish. Amh, Dmrta2, and one RAPD were located in LG5, while Sox9 and Sox17 (LG21), Cyp19b (LG6), and a second RAPD (LG8) co-mapped with suggestive sex-related QTL, thus supporting further analyses on these genes to elucidate the genetic basis of this relevant trait for turbot farming. PMID:22552957

  16. POPULAR MOLECULAR MARKERS IN BACTERIA

    OpenAIRE

    Weilong, Liu; Lv, Li; MD. ASADUZZAMAN KHAN AND FEIZHOU ZHU

    2012-01-01

    Molecular markers are defined as the fragments of DNA sequence associated with a genome, which are used to identify a particular DNA sequence. Nowadays, with the explosive growth of genetic research and bacterial classification, molecular marker is an important tool to identify bacterial species. Taking account to its significant roles in clinic, medicine and food industry, in this review article, we summarize the traditional research and new development about molecular markers (also called g...

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

    Institute of Scientific and Technical Information of China (English)

    LI Qi; KIJIMA Akihiro

    2006-01-01

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

  18. Genetic variability in four Alouatta species measured by means of nine DNA microsatellite markers: genetic structure and recent bottlenecks.

    Science.gov (United States)

    Ruiz-Garcia, M; Escobar-Armel, P; Alvarez, D; Mudry, M; Ascunce, M; Gutierrez-Espeleta, G; Shostell, J M

    2007-01-01

    We used microsatellite DNA to study the population genetics of 4 Alouatta species from Central and South America. Our main findings include the following: (1) A. seniculus had the highest level of microsatellite variability while A. caraya and A. palliata had the lowest mean number of alleles per locus and the lowest expected heterozygosity, respectively; (2) the samples of A. seniculus and A. palliata came from different regions and were not in Hardy-Weinberg equilibrium (HWE) which may indicate a Wahlund effect and differentiated gene pools -- in contrast, A. macconnelli and A. caraya were in HWE; (3) the microsatellite genetic heterogeneity of the 4 Alouatta species was similar to the karyotype divergence found among these Alouatta species; the species pair with the lowest level of heterogeneity (genetic differentiation) was A. seniculus/A. caraya, while the Central American species, A. palliata, was highly differentiated from the other 3 South American species; (4) we recommend the establishment of a conservation plan to help protect A. caraya because the Cornuet and Luikart procedure demonstrated a recent bottleneck for this species. PMID:17303937

  19. The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae.

    Science.gov (United States)

    Kårehed, Jesper; Groeninckx, Inge; Dessein, Steven; Motley, Timothy J; Bremer, Birgitta

    2008-12-01

    The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as "true"). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron. We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species. PMID:18950720

  20. DNA topoisomerase II-alpha as a proliferation marker in astrocytic neoplasms of the central nervous system: correlation with MIB1 expression and patient survival.

    Science.gov (United States)

    Holden, J A; Townsend, J J

    1999-12-01

    DNA topoisomerase II-alpha (topo II-alpha) is the target of a variety of clinically used anticancer drugs such as etoposide, teniposide, and doxorubicin. The enzyme has also been used as a cell proliferation marker. Because proliferation measurements in central nervous system (CNS) astrocytic neoplasms have been shown to have prognostic importance and because drugs targeting topo II-alpha may be useful in treating these tumors, we determined topo II-alpha expression in 26 patients with CNS astrocytomas. In these tumors, topo II-alpha expression correlated well with the known proliferation marker, MIB1 (correlation coefficient = 0.94). Topo II-alpha expression also correlated with the histologic classification of the tumor. Grade 1 lesions had an average topo II-alpha index of 2.1 (range, 0 to 3.4); grade 2 lesions, 4.0 (range, 0 to 11.4); grade 3 lesions, 17.3 (range, 3.8 to 69.8); and grade 4 lesions (glioblastoma multiforme), 39.5 (range, 14.8 to 84.0). The average topo II-alpha and MIB1 index of patients alive two years after diagnosis was 8.8 (range, 0 to 45.6) and 11.8 (range, 0.2 to 44.0), respectively. In contrast, the average topo II-alpha and MIB1 index of 30.5 (range, 2.8 to 69.8) and 33.8 (range, 2.2 to 84.6), respectively, was observed in tumors from patients who were dead from disease by two years. The topo II-alpha index between patients alive and dead at two years was statistically different at the 95% confidence level. The MIB1 differences between these two groups of patients was not found to be statistically different. PMID:10619260

  1. TP53 mutations, human papilloma virus DNA and inflammation markers in esophageal squamous cell carcinoma from the Rift Valley, a high-incidence area in Kenya

    Directory of Open Access Journals (Sweden)

    Martel-Planche Ghislaine

    2011-10-01

    Full Text Available Abstract Background Squamous Cell Carcinoma of Esophagus is one of the most common malignancies in both men and women in eastern and south-eastern Africa. In Kenya, clinical observations suggest that this cancer is frequent in the Rift Valley area. However, so far, there has been no report on the molecular characteristics of esophageal squamous cell carcinoma (ESCC in this area. Results We have analyzed TP53 mutations, the presence of human papilloma virus (HPV DNA and expression of inflammation markers Cyclooxygenase 2 (Cox-2 and Nitrotyrosine (NTyR in 28 cases (13 males and 15 females of archived ESCC tissues collected at the Moi Teaching and Referral Hospital in Eldoret, Kenya. Eleven mutations were detected in TP53 exons 5 to 8 (39%. All ESCC samples were negative for HPV 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73 and 82. Immunohistochemical analysis of Cox-2 and NTyR showed a low proportion of positive cases (17.4% and 39.1%, respectively. No association between the above markers and suspected risk factors (alcohol or tobacco use, hot tea drinking, use of charcoal for cooking was found. Conclusion Our findings suggest that mechanisms of esophageal carcinogenesis in eastern Africa might be different from other parts of the world. Low prevalence of TP53 mutation compared with other intermediate or high incidence areas of the world highlights this hypothesis. Our data did not support a possible ole of HPV in this series of cases. Further studies are needed to assess and compare the molecular patterns of ESCC from Kenya with those of high-incidence areas such as China or Central Asia.

  2. Examination of DNA methylation status of the ELOVL2 marker may be useful for human age prediction in forensic science.

    Science.gov (United States)

    Zbieć-Piekarska, Renata; Spólnicka, Magdalena; Kupiec, Tomasz; Makowska, Żanetta; Spas, Anna; Parys-Proszek, Agnieszka; Kucharczyk, Krzysztof; Płoski, Rafał; Branicki, Wojciech

    2015-01-01

    Age estimation in forensic investigations may complement the prediction of externally visible characteristics and the inference of biogeographical ancestry, thus allowing a better description of an unknown individual. Multiple CpG sites that show linear correlation between age and degree of DNA methylation have been identified in the human genome, providing a selection of candidates for age prediction. In this study, we optimized an assay based on bisulfite conversion and pyrosequencing of 7 CpG sites located in the ELOVL2 gene. Examination of 303 blood samples collected from individuals aged 2-75 years allowed selection of the most informative site, explaining 83% of variation in age. The final linear regression model included two CpG sites in ELOVL2 and enabled age prediction with R(2)=0.859, prediction error=6.85 and mean absolute deviation MAD=5.03. Examination of a testing set of 124 blood samples (MAD=5.75) showed that 68.5% of samples were correctly predicted, assuming that chronological and predicted ages matched ± 7 years. It was found that the ELOVL2 methylation status in bloodstains had not changed significantly after 4 weeks of storage in room temperature conditions. Analysis of 45 bloodstains deposited on tissue paper after 5, 10 and 15 years of storage in room conditions indicated that although a gradual decrease of positive PCR results was observed, the general age prediction success rate remained similar and equaled 60-78%. The obtained results show that the ELOVL2 locus provides a very good source of information about human chronological age based on analysis of blood, including bloodstains, and it may constitute a powerful and reliable predictor in future forensic age estimation models.

  3. Application of cpDNA Marker Technique in Parents Selection and Combination of Potato Breeding%cpDNA标记在马铃薯杂交亲本选配中的应用

    Institute of Scientific and Technical Information of China (English)

    胡祚; 郝大海; 段晓艳; 王兆富; 李周; 苏跃; 冯泽蔚; 李灿辉

    2011-01-01

    Parents selection and combination is the initiate and important step to potato breeding program. U-sing chloroplast DNA ( cpDNA) marker technique, the author detected cytoplast genetic background of the parents and 380 clones derived from hybrid true potato seeds of two cross combinations (Shepody x CIP 004 n = 187 and PB 06 x CIP 004 n = 193 ) . Results showed that Shepody harbored T-type markers of cpDNA which was subjected to the Tuberosum subspecies of Solarium tuberosum L. , but both PB 06 and CIP 004 had A-type markers of cpDNA which belonged to the Andigena subspecies of Solarium tuberosum L.. All clones tested could also be divided into two groups which separately shared the same cpDNA markers with female parents, and the averaged growth period of each group tended to female parents, respectively. The aboved results demonstrated that there was a great potential for cpDNA marker technique in parents selection and combination of potato breeding program.%亲本选配是马铃薯杂交育种工作的重点和难点.利用叶绿体DNA(cpDNA)标记方法,对两个马铃薯杂交组合(Shepody×CIP 004和PB 06×CIP 004)的亲本、及其杂交实生种子后代群体的细胞质遗传背景进行了分析.结果显示:Shepody拥有T-型cpDNA标记,属于普通栽培亚种(Solanium tuberosum ssp.tuberosum);CIP004和PB06拥有A-型cpDNA标记,均属于安第斯栽培亚种(Solanium tuberosum ssp.andigena);在cpDNA两个标记位点(H1和H2)上,2个杂交组合实生种子后代群体的细胞质遗传背景分别与其母本完全一致,平均生育期分别与其母本接近.上述结果表明,cpDNA标记技术在马铃薯杂交亲本选配和早世代选育中具有重要的应用价值.

  4. A New Classification of Ficus Subsection Urostigma (Moraceae Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS, Morphology and Leaf Anatomy.

    Directory of Open Access Journals (Sweden)

    Bhanumas Chantarasuwan

    Full Text Available Ficus subsection Urostigma as currently circumscribed contains 27 species, distributed in Africa, Asia, Australia and the Pacific, and is of key importance to understand the origin and evolution of Ficus and the fig-wasp mutualism. The species of subsection Urostigma are very variable in morphological characters and exhibit a wide range of often partly overlapping distributions, which makes identification often difficult. The systematic classification within and between this subsection and others is problematic, e.g., it is still unclear where to classify F. amplissima and F. rumphii. To clarify the circumscription of subsection Urostigma, a phylogenetic reconstruction based on four nuclear DNA markers (ITS, ETS, G3pdh, and ncpGS combined with morphology and leaf anatomy is conducted. The phylogenetic tree based on the combined datasets shows that F. madagascariensis, a Madagascan species, is sister to the remainder of subsect. Urostigma. Ficus amplissima and F. rumphii, formerly constituting sect. Leucogyne, appear to be imbedded in subsect. Conosycea. The result of the phylogenetic analysis necessitates nomenclatural adjustments. A new classification of Ficus subsection Urostigma is presented along with the morphological and leaf anatomical apomorphies typical for the clades. Two new species are described ─ one in subsect. Urostigma, the other in Conosycea. One variety is raised to species level.

  5. A New Classification of Ficus Subsection Urostigma (Moraceae) Based on Four Nuclear DNA Markers (ITS, ETS, G3pdh, and ncpGS), Morphology and Leaf Anatomy.

    Science.gov (United States)

    Chantarasuwan, Bhanumas; Berg, Cornelis C; Kjellberg, Finn; Rønsted, Nina; Garcia, Marjorie; Baider, Claudia; van Welzen, Peter C

    2015-01-01

    Ficus subsection Urostigma as currently circumscribed contains 27 species, distributed in Africa, Asia, Australia and the Pacific, and is of key importance to understand the origin and evolution of Ficus and the fig-wasp mutualism. The species of subsection Urostigma are very variable in morphological characters and exhibit a wide range of often partly overlapping distributions, which makes identification often difficult. The systematic classification within and between this subsection and others is problematic, e.g., it is still unclear where to classify F. amplissima and F. rumphii. To clarify the circumscription of subsection Urostigma, a phylogenetic reconstruction based on four nuclear DNA markers (ITS, ETS, G3pdh, and ncpGS) combined with morphology and leaf anatomy is conducted. The phylogenetic tree based on the combined datasets shows that F. madagascariensis, a Madagascan species, is sister to the remainder of subsect. Urostigma. Ficus amplissima and F. rumphii, formerly constituting sect. Leucogyne, appear to be imbedded in subsect. Conosycea. The result of the phylogenetic analysis necessitates nomenclatural adjustments. A new classification of Ficus subsection Urostigma is presented along with the morphological and leaf anatomical apomorphies typical for the clades. Two new species are described ─ one in subsect. Urostigma, the other in Conosycea. One variety is raised to species level.

  6. Complete sequence of HLA-B27 cDNA identified through the characterization of structural markers unique to the HLA-A, -B, and -C allelic series

    Energy Technology Data Exchange (ETDEWEB)

    Szoets, H.; Reithmueller, G.; Weiss, E.; Meo, T.

    1986-03-01

    Antigen HLA-B27 is a high-risk genetic factor with respect to a group of rheumatoid disorders, especially ankylosing spondylitis. A cDNA library was constructed from an autozygous B-cell line expressing HLA-B27, HLA-Cw1, and the previously cloned HLA-A2 antigen. Clones detected with an HLA probe were isolated and sorted into homology groups by differential hybridization and restriction maps. Nucleotide sequencing allowed the unambiguous assignment of cDNAs to HLA-A, -B, and -C loci. The HLA-B27 mRNA has the structure features and the codon variability typical of an HLA class I transcript but it specifies two uncommon amino acid replacements: a cysteine in position 67 and a serine in position 131. The latter substitution may have functional consequences, because it occurs in a conserved region and at a position invariably occupied by a species-specific arginine in humans and lysine in mice. The availability of the complete sequence of HLA-B27 and of the partial sequence of HLA-Cw1 allows the recognition of locus-specific sequence markers, particularly, but not exclusively, in the transmembrane and cytoplasmic domains.

  7. DNA分子标记在果树种质资源遗传多样性研究中的应用%Application of DNA Molecular Markers in Genetic Diversity Study of Fruit Tree Germplasm Resources

    Institute of Scientific and Technical Information of China (English)

    周蓓蓓; 朱海军; 生静雅; 刘广勤

    2011-01-01

    简要介绍了DNA分子标记的主要类型、原理及特点,重点综述了RFLP、RAPD、AFLP、SSR、EST - SSR和SNP标记技术在果树种质资源遗传多样性研究中的应用现状.%This article briefly introduces the main type, principle and characteristics of DNA molecular marker techniques, and emphatically summarizes the application status of RFLP, RAPD, AFLP, SSR, EST -SSR and SNP marker techniques in the genetic diversity study of fruit tree germplasm resources.

  8. Marker development

    Energy Technology Data Exchange (ETDEWEB)

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  9. Development of SCAR marker specific to non-toxic Jatropha curcas L. and designing a novel multiplexing PCR along with nrDNA ITS primers to circumvent the false negative detection

    KAUST Repository

    Mastan, Shaik G.

    2011-05-10

    Jatropha curcas L., a multipurpose shrub, has acquired significant economic importance for its seed oil which can be converted to biodiesel an emerging alternative to petro-diesel. In addition to the commercial value, it is also having medicinal and even high nutritional value to use as animal fodder which is limited due to the toxicity. Development of molecular marker will enable to differentiate non-toxic from toxic variety of J. curcas in a mixed population and also for quality control since the toxic components of J. curcas has deleterious effect on animals. In the present study, the efforts were made to generate the specific SCAR marker for toxic and/or non-toxic J. curcas from RAPD markers. Among the markers specific for toxic and non-toxic varieties, four were selected, purified, cloned, sequenced, and designed primers out of which one set of primers NT-JC/SCAR I/OPQ15-F and R could able to discriminate the non-toxic with toxic Jatropha by giving expected 430 bp size amplification in non-toxic variety. Furthermore, novel multiplex PCR was designed using the nrDNA ITS primers to overcome the false negatives. Present work also demonstrates utility of the conserved regions of nrDNA coding genes in ruling out the artifacts in PCR-like false negatives frequently occur in SCAR due to various reasons. The specific SCAR markers generated in the present investigation will help to distinguish non-toxic from toxic varieties of J. curcas or vice versa, and isolated marker along with designed multiplex protocol has applications in quality control for selective cultivation of non-toxic variety and will also assist in breeding and molecular mapping studies. © 2011 Springer Science+Business Media, LLC.

  10. Tumor Markers

    Science.gov (United States)

    ... guidelines on a variety of topics, including tumor markers for breast cancer, colorectal cancer, lung cancer, and others. The ... of recurrence 70-Gene signature (Mammaprint®) Cancer type: Breast ... Can tumor markers be used in cancer screening? Because tumor markers ...

  11. Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.

    Science.gov (United States)

    Ray, Soham; Bose, Lotan K; Ray, Joshitha; Ngangkham, Umakanta; Katara, Jawahar L; Samantaray, Sanghamitra; Behera, Lambodar; Anumalla, Mahender; Singh, Onkar N; Chen, Meingsheng; Wing, Rod A; Mohapatra, Trilochan

    2016-08-01

    African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa. PMID:27299359

  12. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences.

    Science.gov (United States)

    Wambulwa, Moses C; Meegahakumbura, Muditha K; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents

  13. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences.

    Science.gov (United States)

    Wambulwa, Moses C; Meegahakumbura, Muditha K; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents

  14. Application of DNA Molecular Markers in Chinese Medicinal Materia Identification and its Development Trends%DNA分子标记在中药鉴定中的应用及发展趋势分析

    Institute of Scientific and Technical Information of China (English)

    李力; 徐永莉; 张月云; 赵成坚

    2009-01-01

    目的 对DNA分子遗传标记技术在中药材鉴定领域的应用作一综述.方法 通过查阅20世纪90年代以来发表的文献进行归纳分析.结果 DNA分子遗传标记技术具有微量、快速、特异性强、准确可靠、对样本要求较低的特点;使用较多的方法 主要有RAPD、ISSR、ITS标记以及rRNA基因序列分析技术.同时,DNA分子标记技术也存在着使用局限、对实验硬件和从业人员的技术要求高、成本较高、技术复杂度高、对不同部位入药的药材仍然难以区分以及无法用于成药、复方、提取液鉴定等弱点.结论 DNA分子遗传标记作为中药材鉴定的方法 还有待发展和完善.%Objective The paper summarizes the researches of application of DNA molecular markers in Chinese medicinal mate-ria. Methods Induction and analysis were used by referring to literature released since 1990s . Results DNA Marker Technologies have characteristics of trace,rapid,peculiarity, accuracy and credibility, lower requirements for the sample. Random amplified polymorphic DNA (RAPD) , inter - simple sequence repeat (ISSR) , interial transcribed spaoers (ITS) and rRNA gene sequencing technology are often used. However, DNA Marker Technologies have some disadvantages that employees are required special skills,the cost is high and the technique is complicated,while it is difficult to distinguish different parts of Chinese medicinal materia used medicinally and identify patent medicine, Chinese medicine complex prescription and the extract of Chinese medicinal materia. Conclusion The methods of Chinese medicinal materia identification by DNA molecular markers need to develop and improve.

  15. Correlation study of serum markers and HBV-DNA levels in hepatitis B patients%乙型肝炎患者血清标志物与HBV-DNA含量的相关性研究

    Institute of Scientific and Technical Information of China (English)

    赵卫; 周盛杰

    2013-01-01

    Objective To investigate the correlation of serum markers and HBV-DNA levels in hepatitis B patients and its clinical significance. Methods Two hundred and fifty-eight hepatitis B patients was detected for serum markers by ELISA and HBV-DNA levels by quantitative fluorescent polymerase chain reaction (QF-PCR).The correlation between serum markers and HBV-DNA levels were investigated. Results In HBsAg+/HBeAg+ group and HBsAg+/ HBeAg+/anti-HBc+ group, the positive rate of HBV-DNA and the levels of HBV-DNA were the highest. For the five infection modes of HBsAg7anti-HBe7anti-HBc+, HBsAg+/HBc+, anti-HBs+/anti-HBe+/ anti-HBc+, anti-HBe+/anti-HBc+, an-ti-HBs+, the HBV-DNA positive rates were 62.96%, 52.94%, 37.50%, 27.27%, 4.35%, respectively. Conclusion There is a correlation between the positive rate of HBV-DNA and the serum markers in hepatitis B patients. The detection serum markers combined with the quantitative detection of HBV-DNA can accurately reflect the extent of virus replication and infection intensity, which is of great significance for the early diagnosis, treatment and prognosis of hepatitis B.%目的 探讨乙型肝炎患者血清标志物与HBV-DNA定量检测之间的关系及其临床意义.方法 选择258例经我院确诊的乙肝患者,采用酶联免疫吸附试验法检测患者体内血清标志物,采用荧光定量聚合酶链反应检测HBV-DNA含量,比较血清标志物与HBV-DNA检测量之间的关系.结果 HBsAg+/HBeAg+组与HBsAg+/HBeAg+/抗-HBc+组HBV-DNA阳性检出率与含量最高;HBsAg+/抗-HBe+/抗-HBc+、HBsAg+/HBc+、抗-HBs+抗HBe+/抗-HBc+、抗-HBe+/抗-HBc+、抗-HBs+5种感染模式下HBV-DNA阳性检测率分别为62.96%、52.94%、37.50%、27.27%、4.35%.结论 乙肝患者血清HBV-DNA阳性率与血清标志物存在相关性;同时进行血清标志物的检测与HBV-DNA定量检测能较准确直接地反应病毒复制程度及传染强度,对于早期诊断、治疗及预后判断具有指导意义.

  16. 乙型肝炎病毒核酸载量与血清学标志物相关性的研究%Relativity analysis between hepatitis B virus DNA and serological markers

    Institute of Scientific and Technical Information of China (English)

    周诚; 黄维金; 吴星; 辜文洁; 蓝海云; 梁争论; 李河民

    2009-01-01

    目的 分析HBV DNA载量与血清学标志物的相关性.方法 应用乙型肝炎病毒核酸试剂定量检测468份献血员样本HBV DNA含量,并分别定性或定量检测HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc及抗-HBc IgM血清学标志物,计算不同病毒核酸水平样本中5个乙肝血清学标志物阳性率及HBsAg、抗-HBs水平的分布情况. 结果 HBV DNA阴性样本中HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc阳性率分别为12.8%、39.8%、0、21.1%、49.6%,而HBVDNA阳性样本中HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc血清学标志物阳性率分别为91.3%、0.7%、20.9%、65.0%、88.6%,血清学指标在不同HBVDNA水平的阳性率差异具有统计学意义(X2=197.4,P<0.01).HBVDNA载量与HBsAg水平成正相关性,与抗-HBs水平成负相关性. 结论低水平的HBsAg在不同HBV DNA载量水平的样本均有分布,HBsAg检测能力需要进一步提高,另外在我国人群中存在低乙型肝炎病毒核酸水平携带者,乙型肝炎病毒核酸可以弥补血清学检测试剂的不足.%Objective To study the relationship between the copies of HBV and serologic makers. Mothods Detect HBV DNA and serum HBsAg, Anti-HBs, anti-HBc, HBeAg, anti-HBe and anti-HBc IgM of 468 samples. To c, omtpare the positive rate of different serum markers in different HBV DNA levels, and analyses the relationship between HBV DNA levels and quantitative HBsAg, anti-HBs levels. Results In HBV DNA-negative samples, the positive rote of HBsAg, anti-HBs, anti-HBc, HBeAg, anti-HBe is 12.8%, 11.3%, 0, 21.1%, 49.6% separately. In HBV DNA-positive samples, that is 9t.3%,0.7% ,20.9% ,65.0% ,88.6%. There are obviously significant difference among serological markers in different HBV DNA levels (χ2=197.4, P<0.01). The results show the positive correlation between HBV DNA levels and quantitative HBsAg and the negative correlation between HBV DNA levels and quantitative anti-HBs. The positive rate of HBeAg(χ2=39.6, P<0.01), anti-HBe(χ2

  17. Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers

    NARCIS (Netherlands)

    K.T.C.A. Peijnenburg; C.Y. Fauvelot; J.A.J. Breeuwer; S.B.J. Menken

    2006-01-01

    Abstract Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic,

  18. 微卫星DNA多态性分析在常用近交系小鼠遗传监测中的应用研究%Microsatellite DNA Polymorphisms in Inbred Strain Mice and Selection as Genetic Monitoring Markers

    Institute of Scientific and Technical Information of China (English)

    欧阳兆和; 陈振文; 李瑞生; 战大伟

    2003-01-01

    The aim of genetic monitoring is to checking the genetic contamination within inbred starains, which insures that the strains according with the require of colony . At present the methods based on allozyme biochemistry are the National Standard instructed. methods that using microsatellite DNA would be more useful for genetic monitoring than methods based on allozyme biochemistry because the genome itself is being tested rather than a protein product and a larger portion of the genome can be sampled, and easy to distinguish. methods that using microsatellite DNA had abundant microsatellite loci(over 7300, before 1999) can be identified. Applying enough microsatellite loci will present abundant straps and well polymorphism, which can reflection inherit and variation of roundly genene. In addition, this novel approach allows the rapid, sensitive, convenientand accuracy, even individual identificaton. So we should select microsatellite DNA which is polymorphisms as genetic monitoring markers to determining the strains' origin and genetic background of inbred mice.Untill now Only feasibility has been reported, and in which microsatellite DNA loci have not enough polymorphisms to distinguish genetic differences. Articles on standards and practicality have not been founded in our country. With the optimization of components of reaction buffer and amplificaton parameter, PCR for amplification microsatellite DNA was finally set up. Using the techniques microsatellite DNA can amplified efficaciously. The final concentrations of Mg2+ was 1 . 5-3.0 mmol/L, annealing temperature was 50 ℃-65 ℃. The condition for the PCR amplify were , 94 ℃ for 3min, 30cycles of 94℃ for 30s, 50℃-65℃ for 30s,72℃ for 1min,finally at 72℃ for 1min,then store at 4℃.

  19. De novo DNA sequence driven bulk segregant analysis can pinpoint candicate loci for Total Glycoalkaloid (TGA) content in potato without prior knowledge of molecular markers

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Petersen, Annabeth Høgh;

    Potato breeding is a slow and costly affair, primarily done as a classical "mate and phenotype" approach using relatively small populations. In contrast, Marker Assisted Selection (MAS) allows cost-effective screening of much larger effective populations sizes because most of the offspring...

  20. O6-methylguanine-DNA methyltransferase as a prognostic and predictive marker for basal-like breast cancer treated with cyclophosphamide-based chemotherapy

    OpenAIRE

    ISONO, SAYURI; FUJISHIMA, MAKOTO; AZUMI, TATSUYA; HASHIMOTO, YUKIHIKO; Komoike, Yoshifumi; YUKAWA, MASAO; WATATANI, MASAHIRO

    2014-01-01

    The O6-methylguanine-DNA methyltransferase (MGMT) protein protects cells from alkylating agents by removing alkyl groups from the O6-position of guanine. However, its effect on DNA damage induced by cyclophosphamide (CPM) is unclear. The present study investigated whether MGMT expression was correlated with prognosis in patients with breast cancer that was managed according to a common therapeutic protocol or treated with CPM-based chemotherapy. The intrinsic subtypes and MGMT protein express...

  1. Prospective analysis of DNA damage and repair markers of lung cancer risk from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial

    OpenAIRE

    Sigurdson, Alice J.; Jones, Irene M.; Wei, Qingyi; Wu, Xifeng; Spitz, Margaret R; Stram, Douglas A.; Gross, Myron D.; Huang, Wen-Yi; Wang, Li-E; Gu, Jian; Thomas, Cynthia B.; Reding, Douglas J.; Hayes, Richard B; Caporaso, Neil E.

    2010-01-01

    Mutagen challenge and DNA repair assays have been used in case–control studies for nearly three decades to assess human cancer risk. The findings still engender controversy because blood was drawn after cancer diagnosis so the results may be biased, a type called ‘reverse causation’. We therefore used Epstein–Barr virus-transformed lymphoblastoid cell lines established from prospectively collected peripheral blood samples to evaluate lung cancer risk in relation to three DNA repair assays: al...

  2. Construction of a DNA library representing 15q11-13 by subtraction of two flow sorted marker chromosome-specific libraries

    Energy Technology Data Exchange (ETDEWEB)

    Blennow, E.; Werelius, B.; Nordenskjoeld, M. [Karolinska Hospital, Stockholm (Sweden)] [and others

    1994-09-01

    Constitutional extra {open_quotes}marker chromosomes{close_quotes} are found in {approx}0.5/1000 of newborns. Of these, 50% are inverted duplications of the pericentromeric region of chromosome 15, including two variants; (1) inv dup(15)(pter{yields}q11:q11{yields}pter) and (2) inv dup(15) (pter{yields}q12-13::q12-13{yields}pter). Variant (1) is found in phenotypically normal individuals, whereas variant (2) will produce a typical clinical picture including mental retardation, autism, hyperactivity and discrete dysmorphic features. Fluorescence in situ hybridization (FISH) using single copy probes from the Prader-Willi region confirms these observations as well as chromosome painting using a flow-sorted marker chromosome-specific library from a variant (1) marker, hybridized to the chromosomes of a patient with a variant (2) marker chromosome. Followingly, a flow-sorted biotinylated variant (1) library was subtracted from a non-labeled variant (2) library using magnetic beads and subsequent amplification by degenerate oligonucleotide-primed PCR (DOP-PCR). The successful result was demonstrated by using the amplified material for chromosome painting on chromosome slides from variant (1) and variant (2) patients. We have constructed a library from 15q11-13. This region contains genes producing a specific abnormal phenotype when found in a tri- or tetrasomic state. The region also contains the genes responsible for the Prader-Willi and Angelman syndromes when the paternal/maternal copy is missing, respectively. It is therefore a region where parental imprinting plays an important role. The isolated library may be used to isolate single copy clones which will allow further investigations of this region.

  3. The Use of DNA Microsatellite Markers for Genetic Diversity Identifi cation of Soybean (Glycine max (L Meriil. as a Supplementary Method in Reference Collections Management

    Directory of Open Access Journals (Sweden)

    Nina Agusti Widaningsih

    2016-02-01

    Full Text Available Large number of new soybean varieties are mostly derived from crosses of elite genotypes resulted ina narrowing of both the genetic diversity and the phylogenetic relationship between soybean varieties. Thus,discrimination among soybean varieties is becoming more diffi cult, especially when morphological traits wereapplied. In Plant Variety Protection (PVP system, new varieties of soybeans including granted PVP right, localand breeding varieties registered in PVP offi ce were frequently increased, implicate on increasingly the numberof soybean varieties collections. To assist the management of varieties collections, a standard fi ngerprinting datais further needed. In comparison to the management of plant collection in the fi eld, molecular marker systemswhich are rapid, reliable, informative and relatively simple are continually sought for practical applications ingermplasm conservation, management and enhancement. This study aimed to identify the genetic diversity andphylogenetic relationship of soybean varieties that have earned PVP Right as well as local varieties and breedingvarieties registered in the PVP offi ce using microsatellite or simple sequence repeats (SSR markers.This study was conducted in Molecular Biology laboratory, Indonesian Center for Agricultural Biotechnologyand Genetic Resources Research and Development (ICABIOGRAD Bogor, from February to May 2013. The datawere analyzed using the genetic analysis package NTSYSpc 2.02i and PowerMarker V3.25. The result showed arelatively narrow genetic diversity among 45 varieties of soybean analyzed in present study which were indicatedby the small number of genotypes and total number of alleles (NA, and the low value of gene diversity and PICvalues (<0.75. Cluster analysis showed that the grouping varieties are not related to morphological characters butrelated to phylogeny relationship between varieties. Despite the group of varieties were not clustered in accordancewith morphological

  4. Chromosomal localization of 5S rDNA in Chinese shrimp (Fenneropenaeus chinensis):a chromosome-specific marker for chromosome identification

    Institute of Scientific and Technical Information of China (English)

    郇聘; 张晓军; 李富花; 赵翠; 张成松; 相建海

    2010-01-01

    Chinese shrimp(Fenneropenaeus chinensis)is an economically important aquaculture species in China.However,cytogenetic and genomic data is limited in the organism partly because the chromosomes are difficult to isolate and analyze.In this study,fluorescence in-situ hybridization(FISH) was used to identify the chromosomes of F.chinensis.The 5S ribosomal RNA gene(rDNA)of F. chinensis was isolated,cloned and then used as a hybridization probe.The results show that the 5S rDNA was located on one pair of homologo...

  5. 云杉属树种天然群体DNA标记的国外研究进展%Advances in Foreign Researches on DNA Markers in Spruce Natural Groups

    Institute of Scientific and Technical Information of China (English)

    罗建勋; 董昕; 辜云杰

    2012-01-01

    本文综述了自21世纪初以来DNA标记技术在国外云杉属树种中的应用情况,涉及到的树种以挪威云杉为主,多至十几种,标记种类主要包括AFLP、RAPD、RFLP、SSR、ISSR、STS、EST、VNTR和SNPs等。另外,对几种群体遗传参数进行比较分析,表明云杉天然群体遗传变异丰富,其中利用ISSR检测到白云杉天然群体多态位点百分率可达90%,利用RAPD检测到挪威云杉群体总遗传变异高至0.941;群体间存在遗传分化,产生了适应环境的变异,除一个利用mtVNTR研究所得结果外,其他研究均表明,云杉群体间遗传分化程度并不是很高,云杉群体变异主要表现为群体内变异。同时,对DNA标记在云杉属种质资源保存及遗传改良方面的前景进行了展望。%This paper deals with the application of DNA markers in spruce during the first 10 years of 21st Century.The species of spruce referred to more than 10 species,in which Norway Spruce was main.The DNA markers included AFLP,RAPD,RFLP,SSR,ISSR,STS,EST,VNTR and SNPs,etc.Moreover,several group genetic parameters were compared and analyzed.The results have shown that the genetic variation of spruce natural groups is rich.Polymorphic loci percentage of white spruce is up to 90% by ISSR.Total genetic diversity is up to 0.941 in Norway spruce detected by RAPD.The genetic differentiation between groups displays that a new variation fit for environment changing has occurred.All the results except one with mtVNTR indicate that the level of genetic differentiation among groups is low and main variation lies in inter-group.Meanwhile,this review also forecasts the application of DNA markers in the field of germ plasm resource conservation and genetic improvement.

  6. Phenotypic assortment in Tetrahymena thermophila: assortment kinetics of antibiotic-resistance markers, tsA, death, and the highly amplified rDNA locus.

    Science.gov (United States)

    Merriam, E V; Bruns, P J

    1988-10-01

    Phenotypic assortment in Tetrahymena thermophila results from random distribution of alleles during amitotic division of the macronucleus. The rate of assortment is dependent on input ratio and the number of assorting units. The assortment of the antibiotic resistance markers Chx, Mpr and gal was determined and is consistent for each with the model of 45 assorting chromosomes. The gene tsA (previously ts-1) shows normal assortment, in contrast to previous reports. A mutation in the highly amplified ribosomal locus (rdnA2) assorts as if present at only 45 copies. Death of clones occurred at a rate consistent with assortment for a single gene.

  7. 乙型肝炎血清标志物和HBV-DNA载量相关性分析%Study on the correlation between serum markers of hepatitis B and HBV-DNA

    Institute of Scientific and Technical Information of China (English)

    罗慧琴; 王志刚; 李玲; 刘付芹

    2013-01-01

    目的 探讨乙肝血清标志物与病毒DNA水平之间的相关性.方法 采用实时荧光定量PCR对874例HBV感染者血清中HBV-DNA含量进行检测,同时运用ELISA法检测HBV血清标志物,并统计分析患者乙型肝炎血清标志物、病毒DNA之间的相关性及分布特点.结果 在受检的874例标本中,男性533例,阳性率58.16% (310/533);女性341例,阳性率50.44%(172/341),男性和女性阳性率比较差异有统计学意义(X2=5.01,P<0.05),男性和女性HBV-DNA水平差异无统计学意义(t =0.117,P=0.907).乙肝总阳性率和HBV-DNA水平均随年龄的增长呈下降趋势,不同年龄组间比较差异有统计学意义.同一年龄段的大三阳与小三阳、两头阳和三抗阳之间比较差异有统计学意义;其中男性和女性HBV-DNA水平随年龄增长均呈下降趋势,差异有统计学意义.≤20岁以下人群HBV-DNA阳性率最高达82.86%.结论 HBV-DNA阳性率和HBV-DNA水平都随年龄增长呈下降趋势,其中≤20岁年龄段HBV-DNA阳性率最高达82.86%;男性HBV-DNA的阳性率高于女性.%Objective To investigate the correlation between HBV serum markers and HBV DNA levels.Methods HBV-DNA and serum markers in 874 cases of HBV infected persons were detected by real-time fluorescence quantitative PCR and ELISA,respectively.SPSS 16.0 was used to analyze the correlation and distribution characteristics.Results In 874 cases,533 positive cases were male,the positive rate was 58.16% (310/533).341 positive cases were female,the positive rate was 50.44% (172/341).There was statistical difference (x2 =5.01,P <0.05) comparing male with female.But there was no statistical difference (t =0.117,P =0.907) in HBV-DNA level between male and female.The total positive rate and HBV-DNA level showed descending tendency with age,and there were statistical differences among different age groups.When comparing big 3 this world,small 3 this world,two head positive and three antibody positive

  8. Bone Markers

    Science.gov (United States)

    ... bone turnover: C-telopeptide (C-terminal telopeptide of type 1 collagen (CTx)) – a marker for bone resorption. It is ... resorption include: N-telopeptide (N-terminal telopeptide of type 1 collagen (NTx)) – a peptide fragment from the amino terminal ...

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

    OpenAIRE

    Helmi, A.

    2011-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  11. Middle-Upper Pleistocene climate changes shaped the divergence and demography of Cycas guizhouensis (Cycadaceae): Evidence from DNA sequences and microsatellite markers.

    Science.gov (United States)

    Feng, Xiuyan; Zheng, Ying; Gong, Xun

    2016-01-01

    Climatic oscillations in the Pleistocene have had profound effects on the demography and genetic diversity of many extant species. Cycas guizhouensis Lan &R.F. Zou is an endemic and endangered species in Southwest China that is primarily distributed along the valleys of the Nanpan River. In this study, we used four chloroplast DNAs (cpDNA), three nuclear genes (nDNA) and 13 microsatellite (SSR) loci to investigate the genetic structure, divergence time and demographic history of 11 populations of C. guizhouensis. High genetic diversity and high levels of genetic differentiation among the populations were observed. Two evolutionary units were revealed based on network and Structure analysis. The divergence time estimations suggested that haplotypes of C. guizhouensis were diverged during the Middle-Upper Pleistocene. Additionally, the demographic histories deduced from different DNA sequences were discordant, but overall indicated that C. guizhouensis had experienced a recent population expansion during the post-glacial period. Microsatellite data revealed that there was a contraction in effective population size in the past. These genetic features allow conservation measures to be taken to ensure the protection of this endangered species from extinction. PMID:27270859

  12. Possible repetitive DNA markers for Eusorghum and Parasorghum and their potential use in examining phylogenetic hypotheses on the origin of Sorghum species.

    Science.gov (United States)

    Hoang-Tang; Dube, S K; Liang, G H; Kung, S D

    1991-04-01

    Genomic structures of two major species in section Eusorghum (Sorghum), Sorghum bicolor and Sorghum halepense, and their phylogenetic relationships with a species in section Parasorghum, Sorghum versicolor, were studied by using cloned repetitive DNA sequences from the three species. Of the five repetitive DNA clones isolated from S. bicolor and S. halepense, four produced qualitatively similar hybridization patterns with detectable variations in copy numbers of some of the restriction fragments on the Southern blots of the two genomic DNAs. One clone was shown to be diagnostic for S. halepense. Molecular analysis at the DNA level indicates that S. bicolor and S. halepense have similar but not identical genomes, consonant with differences in karyotypes, meiotic chromosome behaviors, morphology, and physiology of the species. In addition to five repetitive clones isolated from S. bicolor and S. halepense, eight more sequences were cloned from S. versicolor. Nine clones were found to be specific for either S. bicolor and S. halepense or S. versicolor. The remaining four had a moderate to strong homology with sequences present in all Sorghum species studied. We speculate that the genome in the common ancestor of Sorghum has differentiated to give rise to genomes of at least three major chromosome sizes; large, medium, and small, as seen at present. Amplifications, eliminations, rearrangements, and new syntheses of repetitive sequences may have been involved in genome differentiation of these species. The results also suggest that the S. versicolor genome has strongly diverged from the genomes of the two species in section Eusorghum.

  13. Molecular analysis of RAPD DNA based markers: their potential use for the detection of genetic variability in jojoba (Simmondsia chinensis L Schneider).

    Science.gov (United States)

    Amarger, V; Mercier, L

    1995-01-01

    We have applied the recently developed technique of random amplified polymorphic DNA (RAPD) for the discrimination between two jojoba clones at the genomic level. Among a set of 30 primers tested, a simple reproducible pattern with three distinct fragments for clone D and two distinct fragments for clone E was obtained with primer OPB08. Since RAPD products are the results of arbitrarily priming events and because a given primer can amplify a number of non-homologous sequences, we wondered whether or not RAPD bands, even those of similar size, were derived from different loci in the two clones. To answer this question, two complementary approaches were used: i) cloning and sequencing of the amplification products from clone E; and ii) complementary Southern analysis of RAPD gels using cloned or amplified fragments (directly recovered from agarose gels) as RFLP probes. The data reported here show that the RAPD reaction generates multiple amplified fragments. Some fragments, although resolved as a single band on agarose gels, contain different DNA species of the same size. Furthermore, it appears that the cloned RAPD products of known sequence that do not target repetitive DNA can be used as hybridization probes in RFLP to detect a polymorphism among individuals.

  14. Combination of 768-well microplate array diagonal gel electrophoresis with duplex PCR of X and Y chromosome markers for quality control of epidemiological DNA banks.

    Science.gov (United States)

    Huang, Shuwen; Chen, Xiao-he; Day, Ian N M

    2006-08-01

    Large DNA banks for human epidemiological studies have become an increasingly important research tool. The power of genotype-phenotype studies is dependent both on the quality of phenotyping and of genotyping and of correct linking of phenotypes to genotypes. Samples must be tracked through numerous steps between subject or patient and post-genotypic data. Only one phenotype, sex, has a perfect and binary correlation with genotype. In mixed sex studies, it may be advantageous for purposes of quality control to keep sexes mixed during the steps from acquisition to DNA bank, in order to be able to check later for sample swaps. We have designed a duplex PCR combining an amplicon from MAOA marking the X chromosome and an amplicon from DDX3Y marking the Y chromosome. We combined this with a simple economical palmtop sized 768-well microplate compatible electrophoresis system developed in-house for examination of duplex PCR products. We applied this quality control test in the validation of two DNA banks.

  15. Molecular Diversity of Antagonistic Streptomyces spp. against Botrytis allii, the agent of onion gray mold using Random Amplified Polymorphic DNA (RAPD Markers

    Directory of Open Access Journals (Sweden)

    M. Jorjandi

    2014-08-01

    Full Text Available As an aim in sustainable agriculture, biological control of plant diseases has received intensive attention mainly as a response to public concern about the use of chemical fungicides in the environment. Soil Actinomycetes particularly Streptomyces spp. enhance soil fertility and have antagonistic activity against wide range of plant pathogens. To investigate for biocontrol means against the pathogen, 30 isolates of Actinomycetes have been isolated from agricultural soils of Kerman province of Iran and assayed for antagonistic activity against Botrytis allii, the agent of onion gray mold. RAPD DNA analysis has been used to determine the relatedness of active and non-active isolates based on their RAPD-PCR fingerprints. PCR amplifiable DNA samples have been isolated using the CTAB method and amplified fragments have been obtained from 5 random 10-mer primers. Different DNA fingerprinting patterns have been obtained for all of the isolates. Electrophoretic and cluster analysis of the amplification products has revealed incidence of polymorphism among the isolates. A total of 138 bands, ranging in size from 150-2800 bp, have been amplified from primers which 63.7% of the observed bands have been polymorphic. Genetic distances among different varieties have been analyzed with a UPGMA (Unweighted pair-group method, arithmetic average-derived dendrogram. Resulting dendrogram has showed from 0.65 to 0.91 similarities among varieties and divided the isolates into five major groups. Isolates which haven’t had any antagonistic activity against B. allii have been separated into a group and other isolates classified into four groups. The results indicate that RAPD is an efficient method for discriminating and studying genetic diversity of Streptomyces isolates.

  16. Confirmation of Clematis hybrids using molecular markers

    Science.gov (United States)

    The hybrid origin of two progeny from reciprocal crosses of Clematis tubulosa and C. brevicaudata was investigated using molecular markers generated by randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and single nucleotide polymorphisms (SNPs). Morphologi...

  17. Investigating the prehistory of Tungusic peoples of Siberia and the Amur-Ussuri region with complete mtDNA genome sequences and Y-chromosomal markers.

    Directory of Open Access Journals (Sweden)

    Ana T Duggan

    Full Text Available Evenks and Evens, Tungusic-speaking reindeer herders and hunter-gatherers, are spread over a wide area of northern Asia, whereas their linguistic relatives the Udegey, sedentary fishermen and hunter-gatherers, are settled to the south of the lower Amur River. The prehistory and relationships of these Tungusic peoples are as yet poorly investigated, especially with respect to their interactions with neighbouring populations. In this study, we analyse over 500 complete mtDNA genome sequences from nine different Evenk and even subgroups as well as their geographic neighbours from Siberia and their linguistic relatives the Udegey from the Amur-Ussuri region in order to investigate the prehistory of the Tungusic populations. These data are supplemented with analyses of Y-chromosomal haplogroups and STR haplotypes in the Evenks, Evens, and neighbouring Siberian populations. We demonstrate that whereas the North Tungusic Evenks and Evens show evidence of shared ancestry both in the maternal and in the paternal line, this signal has been attenuated by genetic drift and differential gene flow with neighbouring populations, with isolation by distance further shaping the maternal genepool of the Evens. The Udegey, in contrast, appear quite divergent from their linguistic relatives in the maternal line, with a mtDNA haplogroup composition characteristic of populations of the Amur-Ussuri region. Nevertheless, they show affinities with the Evenks, indicating that they might be the result of admixture between local Amur-Ussuri populations and Tungusic populations from the north.

  18. Investigation of the relationship between serological markers of hepatitis B virus infection and HBV-DNA%乙型肝炎病毒感染血清学标志物与HBV-DNA的关系探讨

    Institute of Scientific and Technical Information of China (English)

    黄洁; 吴建华

    2014-01-01

    Objective To investigate the relationship between serum hepatitis B virus markers (HBV-M ) and HBV-DNA . Methods Enhanced chemiluminescence enzyme immunoassay (ECLIA ) and real-time fluorescent quantitative polymerase chain re-action(FQ-PCR) were employed to detect HBV-M and HBV-DNA in 262 serum samples ,respectively .HBV surface antigen(HB-sAg) ,anti-HBV surface antibody(HBsAb) ,HBV e antigen(HBeAg) ,anti-HBV e antibody(HBeAb) ,anti-HBV core antibody(HB-cAb) were included in HBV-M .Results Compared the positive rates of HBV-DNA ,HBsAg ,HBeAb in HBeAg-negative patients with those in HBeAg-positive patients ,the differences were statistically significant (P< 0 .01) .29(36 .7% ) patients with HBV-DNA logarithm value not less than 5 were found in HBeAg-negative patients .Differences of HBeAg ,HBeAb positive rates among patients with different ages were statistically significant (P<0 .01) .25 patients with HBsAg less than 250 IU/mL were found in HBV-DNA-positive patients ,12(48 .0% ) of which showed HBV-DNA logarithm value not less than 5 .HBV-DNA logarithm value of HBV-DNA-positive patients was positively correlated to HBeAg and HBeAb (r= 0 .542 ,0 .607 ,P< 0 .01) .Conclusion Com-bined detection of HBV-M and HBV-DNA contributes to estimating the HBV infection .%目的:探讨血清乙型肝炎病毒标志物(HBV-M )与 HBV-DNA之间的关系。方法分别采用增强化学发光酶联免疫分析(ECLIA )技术及实时荧光定量聚合酶链反应(FQ-PCR)对262例血清进行 HBV-M、HBV-DNA检测,HBV-M 包括 HBV表面抗原(HBsAg)、抗HBV表面抗体(HBsAb)、HBV e抗原(HBeAg)、抗 HBV e抗体(HBeAb)、抗 HBV核心抗体(HBcAb)。结果 HBeAg 阴性患者的 HBV-DNA、HBsAg、HBeAb阳性率与 HBeAg 阳性患者比较,差异均有统计学意义( P<0.01)。HBeAg阴性患者 HBV-DNA对数值不低于5的有29例(36.7%)。不同年龄患者 HBeAg、HBeAb阳性率的差异有统计学意义(P<0.01

  19. Marcadores virológicos no convencionales en pacientes infectados con el virus de la inmunodeficiencia humana: ADN HIV-T, ADN HIV- 2LTR y ARN de HIV Non conventional virological markers in HIV-infected patients: T-HIV DNA, 2LTR-HIV DNA and HIV RNA

    Directory of Open Access Journals (Sweden)

    Rosana Gariglio

    2004-10-01

    study, we analyzed the presence of total HIV DNA (T-HIV DNA, non-integrated DNA with 2LTR (2LTR-HIV DNA and HIV RNA in a group of 55 HIV-positive subjects from Rosario City, with different clinical stages, with and without HAART. All markers were evaluated by PCR assays optimized in our laboratory that included colorimetric detection in microplate. HIV RNA clinical sensitivity was compared with a reference test, bDNA, resulting in 74% and 64% respectively, with an 85% of agreement. Thus, our HIV RNA assay could be used to monitor patients under HAART and at risk of infection. The 2LTR-HIV DNA was 54% positive although it was absent in patients with high VL. This marker was considered a labile product therefore its presence was associated with recent infection. However, current evidences question its stability. Thus, its clinical significance should be reconsidered. The absence of 2LTR-HIV DNA in patients with detectable VL may relate to the heterogeneity of the sequence used for its detection. T-HIV DNA was present in 100% of the samples and could be a relevant remission marker when therapies that effectively eradicate the infection became available.

  20. Nuclear rDNA pseudogenes in Chagas disease vectors: evolutionary implications of a new 5.8S+ITS-2 paralogous sequence marker in triatomines of North, Central and northern South America.

    Science.gov (United States)

    Bargues, M Dolores; Zuriaga, M Angeles; Mas-Coma, Santiago

    2014-01-01

    A pseudogene, paralogous to rDNA 5.8S and ITS-2, is described in Meccus dimidiata dimidiata, M. d. capitata, M. d. maculippenis, M. d. hegneri, M. sp. aff. dimidiata, M. p. phyllosoma, M. p. longipennis, M. p. pallidipennis, M. p. picturata, M. p. mazzottii, Triatoma mexicana, Triatoma nitida and Triatoma sanguisuga, covering North America, Central America and northern South America. Such a nuclear rDNA pseudogene is very rare. In the 5.8S gene, criteria for pseudogene identification included length variability, lower GC content, mutations regarding the functional uniform sequence, and relatively high base substitutions in evolutionary conserved sites. At ITS-2 level, criteria were the shorter sequence and large proportion of insertions and deletions (indels). Pseudogenic 5.8S and ITS-2 secondary structures were different from the functional foldings, different one another, showing less negative values for minimum free energy (mfe) and centroid predictions, and lower fit between mfe, partition function, and centroid structures. A complete characterization indicated a processed pseudogenic unit of the ghost type, escaping from rDNA concerted evolution and with functionality subject to constraints instead of evolving free by neutral drift. Despite a high indel number, low mutation number and an evolutionary rate similar to the functional ITS-2, that pseudogene distinguishes different taxa and furnishes coherent phylogenetic topologies with resolution similar to the functional ITS-2. The discovery of a pseudogene in many phylogenetically related species is unique in animals and allowed for an estimation of its palaeobiogeographical origin based on molecular clock data, inheritance pathways, evolutionary rate and pattern, and geographical spread. Additional to the technical risk to be considered henceforth, this relict pseudogene, designated as "ps(5.8S+ITS-2)", proves to be a valuable marker for specimen classification, phylogenetic analyses, and systematic

  1. Rab11 and Lysotracker Markers Reveal Correlation between Endosomal Pathways and Transfection Efficiency of Surface-Functionalized Cationic Liposome-DNA Nanoparticles.

    Science.gov (United States)

    Majzoub, Ramsey N; Wonder, Emily; Ewert, Kai K; Kotamraju, Venkata Ramana; Teesalu, Tambet; Safinya, Cyrus R

    2016-07-01

    Cationic liposomes (CLs) are widely studied as carriers of DNA and short-interfering RNA for gene delivery and silencing, and related clinical trials are ongoing. Optimization of transfection efficiency (TE) requires understanding of CL-nucleic acid nanoparticle (NP) interactions with cells, NP endosomal pathways, endosomal escape, and events leading to release of active nucleic acid from the lipid carrier. Here, we studied endosomal pathways and TE of surface-functionalized CL-DNA NPs in PC-3 prostate cancer cells displaying overexpressed integrin and neuropilin-1 receptors. The NPs contained RGD-PEG-lipid or RPARPAR-PEG-lipid, targeting integrin, and neuropilin-1 receptors, respectively, or control PEG-lipid. Fluorescence colocalization using Rab11-GFP and Lysotracker enabled simultaneous colocalization of NPs with recycling endosome (Rab11) and late endosome/lysosome (Rab7/Lysotracker) pathways at increasing mole fractions of pentavalent MVL5 (+5 e) at low (10 mol %), high (50 mol %), and very high (70 mol %) membrane charge density (σM). For these cationic NPs (lipid/DNA molar charge ratio, ρchg = 5), the influence of membrane charge density on pathway selection and transfection efficiency is similar for both peptide-PEG NPs, although, quantitatively, the effect is larger for RGD-PEG compared to RPARPAR-PEG NPs. At low σM, peptide-PEG NPs show preference for the recycling endosome over the late endosome/lysosome pathway. Increases in σM, from low to high, lead to decreases in colocalization with recycling endosomes and simultaneous increases in colocalization with the late endosome/lysosome pathway. Combining colocalization and functional TE data at low and high σM shows that higher TE correlates with a larger fraction of NPs colocalized with the late endosome/lysosome pathway while lower TE correlates with a larger fraction of NPs colocalized with the Rab11 recycling pathway. The findings lead to a hypothesis that increases in σM, leading to enhanced

  2. Comparison of two methods for measuring γ-H2AX nuclear fluorescence as a marker of DNA damage in cultured human cells: applications for microbeam radiation therapy

    International Nuclear Information System (INIS)

    Microbeam radiation therapy (MRT) delivers single fractions of very high doses of synchrotron x-rays using arrays of microbeams. In animal experiments, MRT has achieved higher tumour control and less normal tissue toxicity compared to single-fraction broad beam irradiations of much lower dose. The mechanism behind the normal tissue sparing of MRT has yet to be fully explained. An accurate method for evaluating DNA damage, such as the γ-H2AX immunofluorescence assay, will be important for understanding the role of cellular communication in the radiobiological response of normal and cancerous cell types to MRT. We compare two methods of quantifying γ-H2AX nuclear fluorescence for uniformly irradiated cell cultures: manual counting of γ-H2AX foci by eye, and an automated, MATLAB-based fluorescence intensity measurement. We also demonstrate the automated analysis of cell cultures irradiated with an array of microbeams. In addition to offering a relatively high dynamic range of γ-H2AX signal versus irradiation dose ( > 10 Gy), our automated method provides speed, robustness, and objectivity when examining a series of images. Our in-house analysis facilitates the automated extraction of the spatial distribution of the γ-H2AX intensity with respect to the microbeam array — for example, the intensities in the peak (high dose area) and valley (area between two microbeams) regions. The automated analysis is particularly beneficial when processing a large number of samples, as is needed to systematically study the relationship between the numerous dosimetric and geometric parameters involved with MRT (e.g., microbeam width, microbeam spacing, microbeam array dimensions, peak dose, valley dose, and geometric arrangement of multiple arrays) and the resulting DNA damage.

  3. Prospective analysis of DNA damage and repair markers of lung cancer risk from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial.

    Science.gov (United States)

    Sigurdson, Alice J; Jones, Irene M; Wei, Qingyi; Wu, Xifeng; Spitz, Margaret R; Stram, Douglas A; Gross, Myron D; Huang, Wen-Yi; Wang, Li-E; Gu, Jian; Thomas, Cynthia B; Reding, Douglas J; Hayes, Richard B; Caporaso, Neil E

    2011-01-01

    Mutagen challenge and DNA repair assays have been used in case-control studies for nearly three decades to assess human cancer risk. The findings still engender controversy because blood was drawn after cancer diagnosis so the results may be biased, a type called 'reverse causation'. We therefore used Epstein-Barr virus-transformed lymphoblastoid cell lines established from prospectively collected peripheral blood samples to evaluate lung cancer risk in relation to three DNA repair assays: alkaline Comet assay, host cell reactivation (HCR) assay with the mutagen benzo[a]pyrene diol epoxide and the bleomycin mutagen sensitivity assay. Cases (n = 117) were diagnosed with lung cancer between 0.3 and 6 years after blood collection and controls (n = 117) were frequency matched on calendar year and age at blood collection, gender and smoking history; all races were included. Case and control status was unknown to laboratory investigators. In unconditional logistic regression analyses, statistically significantly increased lung cancer odds ratios (OR(adjusted)) were observed for bleomycin mutagen sensitivity as quartiles of chromatid breaks/cell [relative to the lowest quartile, OR = 1.2, 95% confidence interval (CI): 0.5-2.5; OR = 1.4, 95% CI: 0.7-3.1; OR = 2.1, 95% CI: 1.0-4.4, respectively, P(trend) = 0.04]. The magnitude of the association between the bleomycin assay and lung cancer risk was modest compared with those reported in previous lung cancer studies but was strengthened when we included only incident cases diagnosed more than a year after blood collection (P(trend) = 0.02), supporting the notion the assay may be a measure of cancer susceptibility. The Comet and HCR assays were unrelated to lung cancer risk. PMID:20929901

  4. Prenatal Screening Using Maternal Markers

    Directory of Open Access Journals (Sweden)

    Howard Cuckle

    2014-05-01

    Full Text Available Maternal markers are widely used to screen for fetal neural tube defects (NTDs, chromosomal abnormalities and cardiac defects. Some are beginning to broaden prenatal screening to include pregnancy complications such as pre-eclampsia. The methods initially developed for NTDs using a single marker have since been built upon to develop high performance multi-maker tests for chromosomal abnormalities. Although cell-free DNA testing is still too expensive to be considered for routine application in public health settings, it can be cost-effective when used in combination with existing multi-maker marker tests. The established screening methods can be readily applied in the first trimester to identify pregnancies at high risk of pre-eclampsia and offer prevention though aspirin treatment. Prenatal screening for fragile X syndrome might be adopted more widely if the test was to be framed as a form of maternal marker screening.

  5. Molecular Markers: an Introduction and Applications

    Directory of Open Access Journals (Sweden)

    Firas Rashad Al-Samarai

    2015-09-01

    Full Text Available The dramatic development of molecular genetics has laid the groundwork for genomics. It has introduced new generations of molecular markers for use in the genetic improvement of farm animals. These markers provide more accurate genetic information and better understanding of the animal genetic resources. Scientists, unfamiliar with the different molecular techniques tend to get lost as each has its own advantages and disadvantages. This review represents a trail to shade alight on the different types of molecular markers by introducing a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review could be helpful to better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.

  6. Analyzsis of population genetic structure of laboratory orange tabby cat by microsatellite DNA markers%微卫星DNA标记技术对试验用虎皮猫群体遗传结构的分析

    Institute of Scientific and Technical Information of China (English)

    衣帅; 谢姗珊; 刘继峰; 杜小燕; 齐飞虎; 李益琛; 任文陟; 刘殿峰; 陈振文

    2013-01-01

    用筛选优化出的24个具有丰富多态性的微卫星位点对华北制药厂的34只虎皮猫基因组DNA进行PCR扩增,对扩增产物进行琼脂糖凝胶电泳和STR扫描,运用popgene3.2软件对试验用虎皮猫群体进行群体遗传结构分析.结果显示,虎皮猫群体平均观测等位基因数为4.083 3,平均有效等位基因数为2.632 3,平均有效杂合度为0.610 8,平均香隆指数为1.078 6.结果表明,微卫星DNA标记技术适于猫群体遗传结构分析;该试验用虎皮猫群体符合封闭群的遗传特性.%To evaluate the genetic structure of the laboratory orange tabby cat population. Twenty four refined polymorphic microsatellite loci were applied to amplify the genomic DNA from 34 orange tabby cats in Huabei Pharmaceutical factory by PCR. The PCR products were analyze by agarose gel electrophoresis,and short tandem repeat(STR) scanning. Software popgene 3. 2 was used to analyze the genetic structure. For the orange tabby cat population, the observed average number of alleles is 4. 083 3;the average effective number of alleles is 2. 632 3; the mean effective heterozygosity is 0. 610 8;the mean Shannon's information index is 1. 078 6. The microsatellite DNA markers are suitable for analyzing the genetic structure of cats and the laboratory orange tabby cat population has the characters of closed colony.

  7. Mitochondrial DNA in Sensitive Forensic Analysis

    OpenAIRE

    Nilsson, Martina

    2007-01-01

    Genetic profiling is commonly performed on the autosomes using multiple DNA markers. Although routine forensic DNA analysis is robust and based on reliable technologies, samples with degraded or limited amounts of DNA often fail. In these cases, the analysis of mitochondrial DNA (mtDNA) can be very valuable due to the high copy number per cell. This thesis describes evaluation and modifications of existing technologies that are useful in forensic DNA typing, mainly focusing on mtDNA. DNA quan...

  8. Study on the genetic diversity of Lentinula edodes 135 and 9015 by random amplified polymorphic DNA(RAPD) markers%香菇135和9015品种遗传多样性的RAPD分子标记研究

    Institute of Scientific and Technical Information of China (English)

    叶长文; 谭海芹; 吴应森; 吴敏; 朱旭芬

    2013-01-01

    通过抗逆性较差的香菇135品种和自然变异抗性新菌株庆元9015品种的RAPD研究,寻找两者间有差异的基因,并对其进行克隆和测序.GenBank查询结果表明,这些片段可能的部分开放阅读框(ORF)与多种生物的水解酶或者信息素受体的部分氨基酸序列有较高的同源性.这些片段可以作为两者间的特异分子标记.%Random amplified polymorphic DNA(RAPD)was used to study the differencial genes between the Lentinula edodes (Qingyuan) strain 135 with poor resistance and strain 9015 (a new strain by natural variation). Several differencial genes were obtained, and then cloned and sequenced. The results in GenBank revealed that the partially possible Open Reading Frames (ORF) of these fragments had higher homology with some hydrolases and pheromone precursor receptor genes of several kinds of organisms. And we presume these genes fragments could be as the specific molecular markers for specifying Lentinula edodes 135 and 9015.

  9. Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...ed papers. Data file File name: pgdbj_dna_marker_linkage_map_plant_marker_list.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgd...bj-dna-marker-linkage-map/LATEST/pgdbj_dna_marker_linkage_map_plant_marker_list.zip F...ile size: 1.6 MB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/pgd...About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Marker list - PGD

  10. Routine DNA testing

    Science.gov (United States)

    Routine DNA testing. It’s done once you’ve Marker-Assisted Breeding Pipelined promising Qantitative Trait Loci within your own breeding program and thereby established the performance-predictive power of each DNA test for your germplasm under your conditions. By then you are ready to screen your par...

  11. DNA分子标记技术在真菌系统学研究中的应用及影响%DNA molecular marker techniques: application to and influence on fungal systematics

    Institute of Scientific and Technical Information of China (English)

    余知和; 曾昭清

    2013-01-01

    DNA分子标记技术为真菌系统进化研究提供了许多新的方法,真菌分子系统学已成为一门成熟的学科.简述了真菌分子系统学的发展简史和代表性的研究方法以及对真菌系统学的主要贡献,包括将广义的真菌划分为3个类群,粘菌和卵菌不再属于真菌界成员.真菌生命之树项目的研究结果对真菌界高阶分类系统作出重大调整,将先前的4个门(壶菌门、接合菌门、子囊菌门和担子菌门)变为7个门(微孢子虫门、壶菌门、新丽鞭毛菌门、芽枝霉门、球囊菌门、子囊菌门和担子菌门)和4个亚门,并对真菌各类群概念作出修订.此外,DNA分子标记技术对真菌种概念的认识、有性型-无性型关联及分子生态学等研究领域产生了重要影响.%DNA molecular markers technique has been introduced as new approaches to study fungal phylogeny and evolution. Nowadays, fungal molecular systematics is a mature discipline, and the history of development and representative research approaches of fungal molecular systematics and the main attributions of these approaches to fungal systematics are discussed in this paper. The organisms studied by mycologists, fungi, are divided into three different groups. The slime moulds and oomycetes do not belong to the Kingdom of Fungi. The recent milestone is the AFTOL (Assembling the Fungal Tree of Life) project, in which a higher-level phylogenetic classification of the Fungi is proposed. The kingdom Fungi traditionally consisted of Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota, but more recent classifications of the fungal kingdom now include Ascomycota, Basidiomycota, Chytridiomycota, Blastocladiomycota, Neocallimastigomycota, Glomeromycota, Microsporidia and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina and Zoopagomycotina. The concept of the different taxa in fungi has also been revised. Furthermore, the

  12. Forensic DNA profiling and database.

    Science.gov (United States)

    Panneerchelvam, S; Norazmi, M N

    2003-07-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  13. Forensic DNA Profiling and Database

    OpenAIRE

    Panneerchelvam, S.; Norazmi, M. N.

    2003-01-01

    The incredible power of DNA technology as an identification tool had brought a tremendous change in crimnal justice . DNA data base is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. This article discusses the essential steps in compilation of COmbined DNA Index System (CODIS) on validated polymerase chain amplified STRs and their use in crime detection.

  14. Review of the Methods for Developing SSR Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xue; CHANG Wei; HAN Yingpeng; LI Wenbin

    2008-01-01

    Microsatellite marker (or Simple Sequence Repeate,SSR) is a marker technology based on DNA molecular length polymorphism.It is also one of the most commonly used molecular markers.Traditional SSR marker development methods are relatively time-consuming and mostly relying on the known genome sequence information while recently developed methods of SSR marker based on RAPD,ISSR-PCR SSR,the use of hybrid options, sequence tag SSR library access and screening EST-SSR have been widely used.This paper gave an overview of the methods mentioned above for the development of SSR markers.

  15. The results of the lipids peroxidation products on the DNA bases as biological markers of the oxidative stress; Les adduits des produits de la peroxydation lipidique sur les bases de l'ADN comme biomarqueurs du stress oxydant

    Energy Technology Data Exchange (ETDEWEB)

    Falletti, O

    2007-10-15

    Different ways of DNA damages have been studied, among these ones the direct way of DNA damages formation by the reactive oxygen species (R.O.S.). This way leads to the formation of oxidative DNA damages. In 1990, works have suggested an indirect way of DNA damages formation, the lipids peroxidation. Instead of oxidizing directly DNA, the R.O.S. oxide the lipids present in the cells and their membranes; The products coming from this degradation are able to provoke DNA damages. This way has not been studied very much. The work of this thesis is axed on this DNA theme and lipids peroxidation. In the first chapter, we begin by presenting DNA and the direct way of oxidative damages formation by the R.O.S.Then, we speak about the cell lipids suffering oxidation reactions and the different ways of lipids oxidation. Then, we present how the lipid peroxidation is a source of damages for DNA. (N.C.)

  16. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm (Camellia sinensis (L. O. Kuntze Based on nSSR Markers and cpDNA Sequences

    Directory of Open Access Journals (Sweden)

    Lianming Gao

    2016-08-01

    Full Text Available Africa is one of the key centres of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships and breeding patterns of tea accessions collected from eight countries in Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica respectively, as well as an admixed mosaic group whose individuals were defined as hybrids of F2 and BC generation with high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centres corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA and East Africa (Tea Research Foundation of Kenya, TRFK. Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centres, TRFCA and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study

  17. Identification of Pheretima aspergillum by CO Ⅰ and 16S rRNA with DNA Molecular Marker Methods%基于COⅠ与16S rRNA基因对广地龙的DNA分子鉴定研究

    Institute of Scientific and Technical Information of China (English)

    韦健红; 李薇; 吴文如; 喻良文

    2012-01-01

    OBJECTIVE: To establish a rapid, accurate and standardized DNA molecular marker method for the identification of Pheretima aspergillum. METHODS: The CO Ⅰ and 16S rRNA gene sequences of P. aspergillum from 5 different populations were determined using CodonCode Aligner sequence assembly. In addition, the CO Ⅰ and 16S rRNA gene sequences of P. aspergillum were downloaded from GenBank, and intraspecific and interspecific K2P genetic distance between P. aspergillum and counterfeit were calculated with MEGA 4.1 to construct NJ and MP phylogenetic tree. RESULTS: The variation sites and information sites of CO Ⅰ were higher than those of 16S rRNA. There were no insertions and deletions of CO Ⅰ , and there were 4 insertions and deletions of 16S rRNA. The interspecific genetic distances of CO Ⅰ and 16S rRNA sequences were significantly greater than intraspecific ones, and CO Ⅰ and 16S rRNA gene can be identified from the other earthworm species. CONCLUSION: The CO I and 16S rRNA gene can provide reference for the identification of the animal Chinese medicine at the molecular level, and accumulate information for DNA barcode of animal Chinese medicine.%目的:建立一种快速、准确和标准化的广地龙DNA分子标记鉴别方法.方法:测定了5个不同居群广地龙的线粒体细胞色素酶亚单位(CO)Ⅰ和16S rRNA基因序列,采用CodonCode Aligner进行序列拼接,通过下载GenBank地龙原动物的CO Ⅰ与16S rRNA序列,采用MEGA 4.1计算广地龙及其伪品地龙的种内、种间的K2P遗传距离,并基于K2P模型构建NJ和MP树.结果:COⅠ变异位点、信息位点均高于16S rRNA,CO Ⅰ基因无插入和缺失,16S rRNA存在4个插入和缺失.CO Ⅰ和16S rRNA序列种间遗传距离均明显大于种内,CO Ⅰ和16S rRNA基因均能将广地龙从其他地龙或蚯蚓物种鉴别开来.结论:获得的广地龙CO Ⅰ和16S rRNA序列可为动物性中药材地龙的分子水平鉴定提供参考,为动物性中药材DNA条

  18. The application of combination detection of hepatitis B serological markers quantifi-cation and HBV DNA quantification in the diagnosis of hepatitis B virus infection%乙肝血清学标志物定量和HBV DNA定量联合检测在乙肝病毒感染诊断中的应用

    Institute of Scientific and Technical Information of China (English)

    吴洪秋; 张永良; 黄坚尧; 张汉运

    2016-01-01

    Objective To analyze the application value of combination detection in the diagnosis of hepatitis B virus ( HBV) infection by the quantitative detection of serological markers and HBV DNA of hepatitis B patients. Methods The serum samples of 120 hepatitis B patients from Jun. 2013 to Jun. 2015 were collected, and the ELISA qualitative test and RT-PCR were used to detect the contents of HBV serological markers ( HBsAg, anti-HBs, HBeAg, anti-HBe, anti-HBc) and HBV DNA. Results The HBV DNA positive rate was 96. 15% in Ⅰ group; the HBV DNA positive rate was 48. 08% in Ⅱ group;the HBV DNA positive rate was 4. 76% inⅢgroup. The quantitative HBV DNA inⅠgroup was significantly higher than that in Ⅱ and Ⅲ groups ( P0. 05). Conclusion The combination detection of HBV serological markers and HBV DNA quantification plays a complementary role in the diagnosis of HBV infection, and has a more accurate diagnosis as well as can provide a more effective reference.%目的:分析乙肝患者的血清标志物和乙肝病毒( HBV) DNA联合检测在HBV感染诊断中的应用价值。方法以2013年6月-2015年6月在珠海市妇幼保健院就诊的120例乙肝患者血清样本作为研究资料,分别采用ELISA定性试验和实时荧光定量PCR( RT-PCR)检测HBV血清标志物( HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc)和HBV DNA含量。结果Ⅰ组HBV DNA阳性率为96.15%;Ⅱ组HBV DNA阳性率为48.08%;Ⅲ组HBV DNA阳性率为4.76%。Ⅰ组HBV DNA定量显著高于Ⅱ、Ⅲ两组( P0.05)。结论乙肝血清标志物定量与HBV DNA定量联合检测在诊断HBV感染过程中起互相补充的作用,诊断结果更加准确,可提供更有效的参考依据。

  19. 银鲫种系细胞标记分子Vasa: cDNA克隆及其抗体制备%Gibel carp germ cell marker Vasa: cDNA cloning and its antibody preparation

    Institute of Scientific and Technical Information of China (English)

    徐红艳; 彭金霞; 桂建芳; 洪云汉

    2005-01-01

    种系细胞始自胚胎发育早期, 是动物生殖及生殖工程的基础.为研究鱼类的种系细胞提供标记分子, 我们克隆并鉴定了银鲫的vasa cDNA 即Cagvasa.Cagvasa cDNA全长2 771 碱基(nt), 编码的蛋白为银鲫Vasa即CagVasa, 全长701 个氨基酸(aa).CagVasa蛋白与已知Vasa蛋白的结构特征一致:在N端有14个RGG重复序列, 在C端Vasa所特有的8个功能域俱全.银鲫Vasa与鲤鱼、斑马鱼、陆生脊椎动物和果蝇的Vasa蛋白分别有95%, 89%, 61%-66%和50%的同源性.卵巢切片的RNA原位杂交揭示, Cagvasa 限于种系细胞, 且表达水平呈现出低-高-低的动态变化:即两头低 (卵原细胞跟Ⅳ期成熟卵子), 中间高(Ⅱ-Ⅲ期卵子).为分析鱼类种系细胞提供手段, 我们用310-aa 的N端序列产生细菌的重组蛋白来免疫大白兔, 获得了抗Vasa的多克隆抗体αVasa.Western免疫印迹表明, αVasa特异性地识别一个鱼类性腺的蛋白,该蛋白的分子量为75 kD, 仅见于银鲫的性腺和卵子.卵巢切片的组织免疫荧光共聚焦显微分析表明, 抗体αVasa只对种系细胞染色:卵原细胞着色最深, 卵母细胞和早期的卵子都浓染, 成熟卵则浅染.类似情况亦见之于精子发生早期阶段的雄性种系细胞.卵巢和精巢的体细胞则不着色.因此, Cagvasa编码的当是Vasa同源蛋白, 为银鲫种系细胞的第一个标记分子.我们的研究表明, 抗体αVasa染色灵敏度高, 特异性好, 当是鉴别银鲫及其它鲤科鱼类的种系细胞的有效手段%The basis for animal reproduction and reproductive biotechnology is germ cells that are segregated from the somatic lineage early in embryonic development and produce sperm and eggs for germline transmission between generations. To provide a germ cell marker, we cloned and characterized Cagvasa, a vasa homolog from the gibel carp Carassius auratus gibelio. The Cagvasa cDNA is 2 771 nt (nucleotide) and encodes a 701-aa(amino acid) protein

  20. Fingerprints for two grain amaranthus varieties KBGA1 and Suvarna using RAPD and legume based SSR markers

    OpenAIRE

    Meera N., Lohithaswa HC, Niranjana Murthy and Shailaja Hittalmani

    2014-01-01

    Genotype specific fingerprints were detected in two grain amaranthus varieties KBGA1 and Suvarna using SSR and RAPD markers. In this study 41 Pigeon Pea SSR markers and 6 RAPD markers were used to generate DNA fingerprints for the two varieties of grain amaranthus. Analysis of polymorphic fragments generated from SSR and RAPD markers revealed the genetic variation between grain amaranthus varieties KBGA1 and Suvarna. The results indicate that DNA markers are appropriate tools for assessing ge...

  1. Ceramic subsurface marker prototypes

    Energy Technology Data Exchange (ETDEWEB)

    Lukens, C.E. [Rockwell International Corp., Richland, WA (United States). Rockwell Hanford Operations

    1985-05-02

    The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

  2. Biologic markers in risk assessment for environmental carcinogens

    OpenAIRE

    Perera, F.; Mayer, J.; Santella, R. M.; Brenner, D; Jeffrey, A.; Latriano, L; Smith, S.; Warburton, D; Young, T. L.; Tsai, W. Y.; Hemminki, K; Brandt-Rauf, P

    1991-01-01

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers h...

  3. Generation and application of SSR markers in avocado

    International Nuclear Information System (INIS)

    Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author)

  4. Heterosis, marker mutational processes and population inbreeding history.

    OpenAIRE

    Tsitrone, A; Rousset, F.; David, P.

    2001-01-01

    Genotype-fitness correlations (GFC) have previously been studied using allozyme markers and have often focused on short-term processes such as recent inbreeding. Thus, models of GFC usually neglect marker mutation and only use heterozygosity as a genotypic index. Recently, GFC have also been reported (i) with DNA markers such as microsatellites, characterized by high mutation rates and specific mutational processes and (ii) using new individual genotypic indices assumed to be more precise tha...

  5. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

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

  6. MARKER ASSISTED SELECTION IN DISEASE RESISTANCE BREEDING

    Directory of Open Access Journals (Sweden)

    Narasimhulu Ragimekula

    2013-08-01

    Full Text Available Feeding ever-increasing population is the main challenge faced by the agricultural scientists and to meet this plant breeders have to put continuous efforts to develop new crop varieties on fast track basis. DNA based polymorphism, commonly known as DNA markers can be used for genetic improvement through selection for favourable traits such as disease resistance. Molecular markers are becoming an essential component in backcross breeding programs for tracking the resistance genes in gene pyramiding. Marker assisted selection (MAS, is expected to increase genetic response by affecting efficiency and accuracy of selection. Even though marker-assisted selection now plays a prominent role in the field of plant breeding, examples of successful, practical outcomes are rare. MAS, with few exceptions, has not yet delivered its expected benefits in commercial breeding. It is clear that DNA markers hold great promise, but realizing that promise remains elusive. The economic and biological constraints such as a low return of investment in small-grain cereal breeding, lack of diagnostic markers, and the prevalence of QTL-background effects hinder the broad implementation of MAS. Until complex traits can be fully dissected, the application of MAS will be limited to genes of moderate-to-large effect and to applications that do not endanger the response to conventional selection. Till then, observable phenotype will remain an important component of genetic improvement programmes, because it takes in to account the collective effect of all genes. In future, chip-based, high-throughput genotyping platforms and the introduction of genomic selection will reduce the current problems of integrating MAS in practical breeding programs and open new avenues for a molecular-based resistance breeding.

  7. Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...d 1 README README_e.html - 2 Registered plant list pgdbj_dna_marker_linkage_map_plant_species_list_en.zip (2...0.0 KB) Simple search and download 3 Marker list pgdbj_dna_marker_linkage_map_pla...nt_marker_list.zip (1.6 MB) Simple search and download 4 QTL list pgdbj_dna_marker_linkage_map_plant_qtl_lis...t.zip (22.6 KB) Simple search and download 5 Plant DB link pgdbj_dna_marker_linkage_map_plant_db_link_en.zip

  8. Embryonic Stem Cell Markers

    OpenAIRE

    Lan Ma; Liang Li; Wenxiu Zhao; Xiang Ji; Fangfang Zhang

    2012-01-01

    Embryonic stem cell (ESC) markers are molecules specifically expressed in ES cells. Understanding of the functions of these markers is critical for characterization and elucidation for the mechanism of ESC pluripotent maintenance and self-renewal, therefore helping to accelerate the clinical application of ES cells. Unfortunately, different cell types can share single or sometimes multiple markers; thus the main obstacle in the clinical application of ESC is to purify ES cells from other type...

  9. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...e, which includes databases of DNA markers, QTLs, and information of organisms. Data file File name: pgd...bj_dna_marker_linkage_map_plant_db_link_en.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgd...bj-dna-marker-linkage-map/LATEST/pgdbj_dna_marker_linkage_map_plant_db_link_en.zip File size: 36.3... KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_dna_marker

  10. DNA-Based Kinship Analysis

    OpenAIRE

    Maguire, Christopher; Woodward, Michael

    2008-01-01

    Relatedness between individuals and groups can be investigated using DNA markers. A child’s DNA profile is a combination of alleles passed down from the father and mother. This means that relationships can be investigated between alleged family members. DNA profiling is commonly used to test for potential paternity, parentage and sibship (whether people are related as brothers or sisters) relationships. In many forensic cases more complex relationships have to be considered.

  11. 与大豆田间老化抗性连锁的分子标记的发掘及辅助选择应用研究%Developing DNA Markers for Assisting Selection of Field Weathering Resistance in Soybean

    Institute of Scientific and Technical Information of China (English)

    叶昌荣; Prapa Sripichitt; Vipa Hongtrakul; Sunanta Juntakool; Arom Sripichitt; Shu Fu-kai

    2007-01-01

    this study is to identify DNA markers linked to the field weathering resistant genes,and to develop markers for assisting selection in breeding program.The field weathering resistance of soybean variety Chiangmai 60(susceptible),GC10981 (resistant)and 139 F2 progenies derived from the cross of CM60/GC10981 was tested by modified incubator weathering and the controlled deterioration treatment.The seeds germination and viability of F2 progenies showed normal distribution under both treatments.It hinted that the field weathering resistance was controlled by polygene.According to the seeds germination and viability of the F2 progenies,six extremely resistant plants and seven extremely susceptible plants were pooled for bulk segregant analysis by AFLP markers.Five field weathering resistance linked polymorphism were identified from 2162 AFLP markers.The 5 DNA fragments were cloned and sequenced.PCR primers were designed from the sequences to amplify the related DNA fragment from the genomic DNA of F2 progenies.It was found that marker Eaag/Mcac-233 and Eact/Mctt-157 were in the same linkage group with a genetic distance of 25.8 cM.A major QTL controlling the field weathering resistance was identified between these two markers.The QTL located at 14 cM from marker Eaag/Mcac-233 and explained 29.7% of the Cariation in field weathering resistance.These two DNA markers have been used for assisting selection in breeding program as an attempt.Seven F2 progenies were selected and backcrossed to CM60 using the developed markers in combination with field weathering resistance characters.The germination and viability of 18 BC1F1 progenies(41.9%)were higher than the mean of CM60 and GC10981 by controlled deterioration test.It is potentially possible to use these markers for assisting selection in breeding programs that focus on seed quality in the tropics.

  12. Identification of a RAPD marker linked to a blast resistance gene in Oryza sativa L.

    Institute of Scientific and Technical Information of China (English)

    LUJun; ZHUANGJieyun; LINHongxuan; ZHENGKangle

    1994-01-01

    Marker-aided selection has received more attention in recent years. This relies on the exploitation of close linkage between molecular markers and target gene(s). We report here a randomly amplified polymorphic DNA (RAID) marker tightly linked to the blast resistance gene Pi-11(t) derived from Hongjiaozhan, which confers the resistante to race ZBI of Pyricularia oryzae Car.

  13. Biological (molecular and cellular) markers of toxicity

    Energy Technology Data Exchange (ETDEWEB)

    Shugart, L.R.; D' Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

    1991-12-15

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

  14. Biological (molecular and cellular) markers of toxicity

    International Nuclear Information System (INIS)

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO6-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O6-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP

  15. Uniparental genetic markers in South Amerindians

    Directory of Open Access Journals (Sweden)

    Rafael Bisso-Machado

    2012-01-01

    Full Text Available A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.

  16. Genetic confirmation of mungbean (Vigna radiata) and mashbean (Vigna mungo) interspecific recombinants using molecular markers

    OpenAIRE

    Ghulam eAbbas; Amjad eHameed; Muhammad eRizwan; Muhammad eAhsan; Muhammad Jawad eAsghar; Nayyer eIqbal

    2015-01-01

    The present study was conducted with the aim to investigate recombination between mungbean (female) and mashbean (male) interspecific crosses using molecular markers i.e., URP (Universal Rice Primers), RAPD (Random Amplified Polymorphic DNA) and SSR (Simple Sequence Repeats). As a first step parental screening was performed and polymorphic markers differentiating parent genotypes were identified. Recombinations were then confirmed through polymorphic DNA markers in many of the hybrids. The N...

  17. Prevalence of Serologic Hepatitis B Markers in Blood Donors From Puebla, Mexico: The Association of Relatively High Levels of Anti-Core Antibodies With the Detection of Surface Antigen and Genomic DNA

    Directory of Open Access Journals (Sweden)

    Sosa-Jurado

    2016-06-01

    Full Text Available Background The hepatitis B virus (HBV causes chronic hepatitis, hepatic cirrhosis, and hepatocellular carcinoma. Surface antigen (HBsAg detection is a definitive test that can confirm HBV infection, while the presence of antibodies against the core protein (anti-HBc suggests either a previous or ongoing infection or occult hepatitis B infection (OBI. Objectives The aim of the present study was to determine the prevalence of anti-HBc and HBsAg in blood donors. Further, the study aimed to estimate the anti-HBc level at which HBV DNA is detected in putative OBI cases, as well as to search for mutations in the “a” determinant associated with the non-detection of HBsAg in serum. Patients and Methods We conducted a cross-sectional study from 2003–2009. The study included 120,552 blood donors from the state of Puebla, Mexico. Different commercial systems based on microparticles (enzymatic (MEIA or chemiluminescent (CMIA were used to determine the HBsAg and anti-HBc levels. For the detection of HBV DNA, a nested polymerase chain reaction (nested PCR was used and the genotypes were determined using Sanger sequencing. Results Of the 120,552 blood donors, 1437 (1.19%, 95% CI: 1.12 - 1.26 were reactive to anti-HBc, while 82 (0.066%, 95% CI: 0.053 - 0.079 were reactive to HBsAg. Some 156 plasma samples collected in 2009 from anti-HBc-positive/HBsAg-negative blood donors were submitted for HBV DNA detection in a search for probable OBI. Viral DNA was detected in 27/156 (17.3%, 95% CI: 11.5 - 23.1. Our results show an association between HBV DNA or HBsAg and anti-HBc S/CO levels ≥ 4.0. All DNA samples were identified as genotype H and some “a” determinant mutations were identified, although none corresponded to mutations previously reported to hinder the detection of HBsAg by commercial immunoassays. Conclusions We observed that as the anti-HBc levels increase, there is a higher prevalence of the viral protein HBsAg in blood donors. Samples testing

  18. [Genetic virulence markers of opportunistic bacteria].

    Science.gov (United States)

    Bondarenko, V M

    2011-01-01

    The analysis of opportunistic bacteria phenotypic and genetic virulence markers indicates that pathogenicity formation is based on a structural modification of bacterial DNA which is linked with migration of interbacterial pathogenicity "islands" genetic determinants. Structural organization features of these mobile genetic elements determine high expression probability, and PCR detection of pathogenicity "islands" determinants that control adhesins, invasins, cytotoxic and cytolitic toxines synthesis may indicate etiopathogenetic significance of clinical isolates.

  19. Embryonic Stem Cell Markers

    Directory of Open Access Journals (Sweden)

    Lan Ma

    2012-05-01

    Full Text Available Embryonic stem cell (ESC markers are molecules specifically expressed in ES cells. Understanding of the functions of these markers is critical for characterization and elucidation for the mechanism of ESC pluripotent maintenance and self-renewal, therefore helping to accelerate the clinical application of ES cells. Unfortunately, different cell types can share single or sometimes multiple markers; thus the main obstacle in the clinical application of ESC is to purify ES cells from other types of cells, especially tumor cells. Currently, the marker-based flow cytometry (FCM technique and magnetic cell sorting (MACS are the most effective cell isolating methods, and a detailed maker list will help to initially identify, as well as isolate ESCs using these methods. In the current review, we discuss a wide range of cell surface and generic molecular markers that are indicative of the undifferentiated ESCs. Other types of molecules, such as lectins and peptides, which bind to ESC via affinity and specificity, are also summarized. In addition, we review several markers that overlap with tumor stem cells (TSCs, which suggest that uncertainty still exists regarding the benefits of using these markers alone or in various combinations when identifying and isolating cells.

  20. Correlation between Serum Markers of Hepatitis B Virus and DNA HBV%乙肝病毒血清标志物与HBV DNA的相关性研究

    Institute of Scientific and Technical Information of China (English)

    张智贤; 何秋莹; 温英梦; 曾华

    2015-01-01

    目的探讨乙型肝炎血清标志物(HBsAg、抗HBs、HBeAg、抗HBe、抗HBc)与乙肝病毒基因(HBV DNA)的相关性和临床意义。方法回顾性分析553例乙肝患者的HBV DNA定量及乙肝两对半定量结果,计算不同乙肝血清学标志物组合模式中HBV DNA阳性率及分布情况,分析乙型肝炎血清标志物与HBV DNA相关性。结果6组血清学模式对应的HBV DNA阳性率在9.5~80.0%不等,以HBsAg(+)HBeAg(+)抗HBc(±)组对应的DNA阳性率及DNA拷贝数为最高。 HBsAg、抗HBs、HBeAg、抗HBe、HBcAg与HBV DNA对数spearman结果分别为r=0.009,>0.05;r=-0.155,>0.05;r=0.541,0.05。结论 HBeAg含量与HBV DNA含量存在正相关(<0.05),抗HBe含量与HBV DNA含量存在负相关(<0.05)。联合检测乙肝血清学标志物定量和HBV DNA定量,可以为乙型肝炎的诊断、治疗及疗效评价提供一个更准确的依据。%Objective To detect and investigate the cor elation and clinical significance of HBV DNA and HBV M in Hepatitis B patients. Methods The test results of the quantity of HBV DNA and HBV M in 553 hepatitis B patients were analyzed retrospectively, and the the correlation between HBV DNA and HBV M was analyzed. Results Al the 6 models held HBV DNA positive rates ranging from 9.5%to 80.0%and 80.0%for the model of positive HBsAg(+)HBeAg(+) Anti-HBc(±). There was statistical significance among the spearman's rank cor elation coef icient between HBV DNA and HBeAg (r=0.541,<0.05) as wel as HBV DNA and Anti-HBe (r=-0.493,<0.05). Conclusion HBV DNA was positively cor elated with HBeAg and negatively cor elated with Anti-HBe statistical y. Combined detection of HBV DNA and HBV M can ef ectively monitor HBV replication,it has important value in monitoring curative ef ect and judging prognosis.

  1. Evaluation of molecular markers linked to fragrance and genetic diversity in Indian aromatic rice

    OpenAIRE

    RAI, VED PRAKASH; Singh, Anil Kumar; JAISWAL, HEMANT KUMAR; Singh, Sheo Pratap; SINGH, RAVI PRATAP; WAZA, SHOWKAT AHMAD

    2015-01-01

    DNA-based markers have the potential to improve the efficiency and precision of breeding programs based on marker-assisted selection. In the present study we evaluated the predictive abilities of previously reported PCR-based simple sequence repeat and functional markers related to fragrance in a set of 24 rice genotypes, including traditional basmatis, evolved basmatis, and aromatic indigenous landraces. High-resolution melting analysis with 3 markers was also performed to detect the presenc...

  2. Epigenetic Markers of Renal Function in African Americans

    Directory of Open Access Journals (Sweden)

    Samantha M. Bomotti

    2013-01-01

    Full Text Available Chronic kidney disease (CKD is an increasing concern in the United States due to its rapidly rising prevalence, particularly among African Americans. Epigenetic DNA methylation markers are becoming important biomarkers of chronic diseases such as CKD. To better understand how these methylation markers play a role in kidney function, we measured 26,428 DNA methylation sites in 972 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA study. We then evaluated (1 whether epigenetic markers are associated with estimated glomerular filtration rate (eGFR, (2 whether the significantly associated markers are also associated with traditional risk factors and/or novel biomarkers for eGFR, and (3 how much additional variation in eGFR is explained by epigenetic markers beyond established risk factors and biomarkers. The majority of methylation markers most significantly associated with eGFR (24 out of the top 30 appeared to function, at least in part, through pathways related to aging, inflammation, or cholesterol. However, six epigenetic markers were still able to significantly predict eGFR after adjustment for other risk factors. This work shows that epigenetic markers may offer valuable new insight into the complex pathophysiology of CKD in African Americans.

  3. Characterization of the standard and recommended CODIS markers.

    Science.gov (United States)

    Katsanis, Sara H; Wagner, Jennifer K

    2013-01-01

    As U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light of scientific advances, reveal biomedically relevant information. While CODIS loci were selected largely because they lack phenotypic associations, how this criterion was assessed is unclear. To clarify their phenotypic relevance, we describe the standard and recommended CODIS markers within the context of what is known currently about the genome. We characterize the genomic regions and phenotypic associations of the 24 standard and suggested CODIS markers. None of the markers are within exons, although 12 are intragenic. No CODIS genotypes are associated with known phenotypes. This study provides clarification of the genomic significance of the key identification markers and supports--independent of the forensic scientific community--that the CODIS profiles provide identification but not sensitive or biomedically relevant information.

  4. Recombinogenic engineering of conjugative plasmids with fluorescent marker cassettes

    DEFF Research Database (Denmark)

    Reisner, A.; Molin, Søren; Zechner, E.L.

    2002-01-01

    An efficient approach for the insertion of fluorescent marker genes with sequence specificity into conjugative plasmids in Escherichia coli is described. For this purpose, homologous recombination of linear double-stranded targeting DNA was mediated by the bacteriophage lambda recombination...... functions using very short regions of homology. Initial manipulation of the IncFII target plasmids R1 and R1drd19 indicated that the linear targeting DNA should be devoid of all extraneous homologies to. the target molecule for optimal insertion specificity. Indeed, a simple recombination assay proved...... resistance genes and fluorescent markers. The choice of 5' non-homologous extensions in primer pairs used for amplifying the marker cassettes determines the site specificity of the targeting DNA. This methodology is applicable to the modification of all plasmids that replicate in E coli and is not restricted...

  5. Markers of immunity and bacterial translocation in cirrhosis

    DEFF Research Database (Denmark)

    Mortensen, Christian

    2015-01-01

    complications. The optimal surrogate marker of BT in patients with cirrhosis, however, is a matter of controversy. In the first study, we investigated the relationship between markers of inflammation, haemodynamics and prognosis in 45 patients and 12 controls. We found high-sensitive C-reactive protein......, in 38 patients with ascites, we found no association between bDNA and immunity, in contrast to some previous findings. In the final paper, exploring one possible translocation route, we hypothesized a difference in bDNA levels between the blood from the veins draining the gut on one hand and the liver...... on the other. Collecting samples during the insertion of a shunt between the two vessels in 28 patients, our finding did not suggest marked differences in bDNA, but conversely to expectations, suggested marked hepatic production of two markers of inflammation. The main results of the present thesis support...

  6. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers

    Science.gov (United States)

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J.; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program. PMID:26697053

  7. Genetic confirmation of mungbean (Vigna radiata and mashbean (Vigna mungo interspecific recombinants using molecular markers

    Directory of Open Access Journals (Sweden)

    Ghulam eAbbas

    2015-12-01

    Full Text Available The present study was conducted with the aim to investigate recombination between mungbean (female and mashbean (male interspecific crosses using molecular markers i.e., URP (Universal Rice Primers, RAPD (Random Amplified Polymorphic DNA and SSR (Simple Sequence Repeats. As a first step parental screening was performed and polymorphic markers differentiating parent genotypes were identified. Recombinations were then confirmed through polymorphic DNA markers in many of the hybrids. The NM 2006 × Mash 88 was found to be most successful interspecific cross as many of true recombinants, confirmed by molecular markers, belonged to this cross combination. The SSR markers were more efficient in detecting genetic variability and recombinations with reference to specific chromosomes and particular loci, while SSR (RIS and RAPD identified variability dispersed throughout the genome. The DNA based marker assisted approach provided evidence for genetic confirmation of mungbean and mashbean interspecific recombinants and escalated the authenticity of selection in mungbean improvement programme.

  8. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers.

    Science.gov (United States)

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program.

  9. Cleaving DNA with DNA

    Science.gov (United States)

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

    1998-03-01

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

  10. Molecular markers for use in plant molecular breeding and germplasm evaluation

    International Nuclear Information System (INIS)

    A number of molecular marker technologies exist, each with different advantages and disadvantages. When available, genome sequence allows for the development of greater numbers and higher quality molecular markers. When genome sequence is limited in the organism of interest, related species may serve as sources of molecular markers. Some molecular marker technologies combine the discovery and assay of DNA sequence variations, and therefore can be used in species without the need for prior sequence information and up-front investment in marker development. As a prerequisite for marker-assisted selection (MAS), there must be a known association between genetic markers and genes affecting the phenotype to be modified. Comparative databases can facilitate the transfer of knowledge of genetic marker-phenotype association across species so that discoveries in one species may be applied to many others. Further genomics research and reductions in the costs associated with molecular markers will continue to provide new opportunities to employ MAS. (author)

  11. Tumour markers in urology

    International Nuclear Information System (INIS)

    The same applies essentially also for the bladder carcinomas: There is no reliable marker for these cancers which would be useful for clinical purposes. TPA has proven to be too non-specific in malignoma-detection and therefore hardly facilitates clinical decision-making in individual cases. The CEA is not sensitive enough to be recommendable for routine application. However, in advanced stages a CEA examination may be useful if applied within the scope of therapeutic efforts made to evaluate efficacy. In cases of carcinomas of the prostate the sour prostate-specific phosphatase (SPP) and, more recently, especially the prostate-specific antigen (PSA) have proven in follow-up and therapy monitoring, whereby the PSA is superior to the SPP. Nevertheless, both these markers should be employed in therapy monitoring because differences in behaviour will be observed when the desired treatment effect is only achieved in one of the two markers producing tumour cell clonuses. Both markers, but especially the PSA, are quite reliably in agreement with the result of the introduced chemo-/hormone therapy, whereby an increase may be a sure indicator of relapse several months previous to clinical symptoms, imaging procedures, so-called routine laboratory results and subjective complaints. However, none of the 2 markers is appropriate for the purposes of screening or early diagnosis of carcinomas of the prostate. (orig.)

  12. Maternal Serum Screening Markers and Adverse Outcome: A New Perspective

    Directory of Open Access Journals (Sweden)

    David Krantz

    2014-07-01

    Full Text Available There have been a number of studies evaluating the association of aneuploidy serum markers with adverse pregnancy outcome. More recently, the development of potential treatments for these adverse outcomes as well as the introduction of cell-free fetal DNA (cffDNA screening for aneuploidy necessitates a re-evaluation of the benefit of serum markers in the identification of adverse outcomes. Analysis of the literature indicates that the serum markers tend to perform better in identifying pregnancies at risk for the more severe but less frequent form of individual pregnancy complications rather than the more frequent but milder forms of the condition. As a result, studies which evaluate the association of biomarkers with a broad definition of a given condition may underestimate the ability of such markers to identify pregnancies that are destined to develop the more severe form of the condition. Consideration of general population screening using cffDNA solely must be weighed against the fact that traditional screening using serum markers enables detection of severe pregnancy complications, not detectable with cffDNA, of which many may be amenable to treatment options.

  13. Isolation, Sequencing and Identification of Two Pig Novel Molecular Markers Using DNA Differential Display Technique and Their Trait Analysis%用DNA差异显示技术分离、测序和鉴定猪的两个新分子标记及其与性状的关联分析

    Institute of Scientific and Technical Information of China (English)

    刘永刚; 熊远著; 邓昌炎; 雷明刚; 左波; 李家连; 蒋思文; 李凤娥; 郑嵘

    2005-01-01

    In order to find more candidate genes or DNA molecular markers which are correlated with the traits, we used DNA differential display technique to scan the whole genome of F2 pig population based on Large White xMeishan, and two molecular markers were found to be significantly correlated with the traits. Marker 1 was associated with: estimated backfat thickness at last rib (P< 0.01), estimated backfat thickness at last 3~4th rib(P< 0.01), estimated lean meat percentage (P< 0.01), bone weight (P < 0.05),bone percentage (P < 0.05), fat meat weight (P < 0.05), fat meat percentage (P < 0.05), ratio of lean meat to fat meat (P < 0.05), backfat thickness at shoulder (P < 0.05), backfat thickness at 6-7th thorax (P < 0.01), and marker 2 was associated with: longissimus dorsi pH (P< 0.05), drip loss rate (P < 0.05), water holding capacity (P < 0.05), meat color score oflongissimus dorsi (P < 0.05), water moisture of longissimus dorsi (P < 0.05), rib numbers (P < 0.05), bone percentage (P < 0.05), backfat thickness at thorax-waist (P < 0.05),gaster net weight (P < 0.01). The two markers were then isolated, sequenced and identified. BLAST analysis revealed that the two markers were not homologous to any of the known porcine genes from GenBank and subsequenfiy submitted to GenBank database(Accession number: CN605659 and AY626262). The method used in this study provides an additional useful tool in the investigation of candidate genes or DNA molecular markers, which were correlated with the traits.%为了寻找更多的和性状关联的猪候选基因或分子标记,用DNA差异显示技术扫描140头大白×梅山F2猪的DNA,发现了2个与猪的性状具有显著关联的分子标记,并对这2个分子标记进行测序和鉴定.标记1与最后肋骨处估测背膘厚(P<0.01)、倒数三四肋骨处估测背膘厚(P<0.01)、估测瘦肉率(P<0.01)、骨重(P<0.05)、骨率(P<0.05)、肥肉重(P<0.05)、肥肉率(P<0

  14. DNA mini-barcodes.

    Science.gov (United States)

    Hajibabaei, Mehrdad; McKenna, Charly

    2012-01-01

    Conventional DNA barcoding uses an approximately 650 bp DNA barcode of the mitochondrial gene COI for species identification in animal groups. Similar size fragments from chloroplast genes have been proposed as barcode markers for plants. While PCR amplification and sequencing of a 650 bp fragment is consistent in freshly collected and well-preserved specimens, it is difficult to obtain a full-length barcode in older museum specimens and samples which have been preserved in formalin or similar DNA-unfriendly preservatives. A comparable issue may prevent effective DNA-based authentication and testing in processed biological materials, such as food products, pharmaceuticals, and nutraceuticals. In these cases, shorter DNA sequences-mini-barcodes-have been robustly recovered and shown to be effective in identifying majority of specimens to a species level. Furthermore, short DNA regions can be utilized via high-throughput sequencing platforms providing an inexpensive and comprehensive means of large-scale species identification. These properties of mini-barcodes, coupled with the availability of standardized and universal primers make mini-barcodes a feasible option for DNA barcode analysis in museum samples and applied diagnostic and environmental biodiversity analysis.

  15. Development and validation of new SSR markers from expressed regions in the garlic genome

    Directory of Open Access Journals (Sweden)

    Meryem Ipek

    2015-02-01

    Full Text Available Only a limited number of simple sequence repeat (SSR markers is available for the genome of garlic (Allium sativum L. despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

  16. 玉米胚乳DNA的快速提取方法及其在wx基因分子标记辅助选择中的应用%A Rapid DNA Extraction Protocol from Endosperm and Its Applications in Marker-assisted Selection for wx Gene in Maize

    Institute of Scientific and Technical Information of China (English)

    彭勃; 赵晓雷; 付从贵; 张巧云; 王奕

    2014-01-01

    Extracting genomic DNA is one of the bottleneck steps for molecular breeding. In this study, a high throughput and rapid genomic DNA extraction protocol for maize, named as sucrose prep method, were developed. According to this method, 20~30 mg of endosperm cut from seed were suffered by 3 steps, i.e. grinding, heating and instantaneously centrifuging in batch, and then the genomic DNA template with robust PCR products were obtained. In addition, there are no significant difference for germination rates between endosperm sampled seeds and non-sampled control. Three genotypes with W xW x, W xwx and wxwx identified by genotyping endosperm DNA were in completely accordance with the corresponding phenotypes in 190 F2 individuals. Therefore, endosperm DNA extracted through the Sucrose prep method was a simple, rapid and low cost method, and especially suitable for the application in high throughput marker-assisted selection.%模板DNA的制备是制约分子育种效率的瓶颈步骤之一。本研究介绍一种高通量快速的玉米基因组DNA提取方法,即蔗糖提取液法。该方法切取20~30 mg玉米种子胚乳,通过批量化研磨、加热和瞬时离心3个步骤,即可获得稳健PCR扩增的模板DNA,并且在光温培养箱条件下切取部分胚乳的剩余种子与对照完整种子发芽率无显著差异。通过蔗糖提取液法提取192粒F2种子胚乳DNA,鉴定W xW x、W xwx和wxwx 3种基因型与表型鉴定结果相一致。蔗糖提取液法提取胚乳DNA简单、快速、成本低廉,可有效用于高通量分子标记辅助选择。

  17. Biologic markers in risk assessment for environmental carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Perera, F.; Mayer, J.; Santella, R.M.; Brenner, D.; Jeffrey, A.; Latriano, L.; Smith, S.; Warburton, D.; Young, T.L.; Tsai, W.Y.; Brandt-Rauf, P. (Columbia Univ. School of Public Health, New York, NY (United States)); Hemminki, K. (Finnish School of Occupational Health, Helsinki (Finland))

    1991-01-01

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers have, however, already provided valuable insights into the magnitude of interindividual variation in response to carcinogenic exposures, with major implications for risk assessment.

  18. Marker chromosome 21 identified by microdissection and FISH

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Y.; Palmer, C.G. [Indiana Univ. School of Medicine, Indianapolis, IN (United States); Rubinstein, J. [Univ. Affiliated Cincinnati Center for Developmental Disorders, OH (United States)] [and others

    1995-03-27

    A child without Down`s syndrome but with developmental delay, short stature, and autistic behavior was found to be mosaic 46,XX/47,XX,+mar(21) de novo. The marker was a small ring or dot-like chromosome. Microdissection of the marker was performed. The dissected fragments were biotinylated with sequence-independent PCR as a probe pool for fluorescence in situ hybridization (FISH). FISH results suggested an acrocentric origin of the marker. Subsequent FISH with {alpha}-satellite DNA probes for acrocentric chromosomes and chromosome-specific 21 and 22 painting probes confirmed its origin from chromosome 21. 14 refs., 3 figs.

  19. Biologic markers in risk assessment for environmental carcinogens

    International Nuclear Information System (INIS)

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers have, however, already provided valuable insights into the magnitude of interindividual variation in response to carcinogenic exposures, with major implications for risk assessment

  20. Characterization of fluorescent eye markers for mammalian transgenic studies.

    Directory of Open Access Journals (Sweden)

    Jonathan C Cornett

    Full Text Available Genotyping mice by DNA based methods is both laborious and costly. As an alternative, we systematically examined fluorescent proteins expressed in the lens as transgenic markers for mice. A set of eye markers has been selected such that double and triple transgenic animals can be visually identified and that fluorescence intensity in the eyes can be used to distinguish heterozygous from homozygous mice. Taken together, these eye markers dramatically reduce the time and cost of genotyping transgenics and empower analysis of genetic interaction.

  1. RAPD markers related to sex locus in Populus tomentosa

    Institute of Scientific and Technical Information of China (English)

    Wanwei HOU; Junfeng FAN; Feimei ZHOU; Shufang ZHAO

    2009-01-01

    By using the methods of random amplified polymorphic DNA (RAPD) and bulked segregate analysis (BSA), we identified markers that are linked to the sex determination in the dioecious Populus tomentosa. Male and female bulks were created through rough mixing equal amounts of its five individual DNA. A total of 88 primers were screened. Twelve primers produced clear patterns with at least one band that appeared to be polymorphic between the two bulks. Subsequently, five male and female individuals were analyzed with those 12 primers, and only S60 (ACCCGGTCAC) could generate a common 1800bp DNA fragment in all five male individuals and male pool but not in any female individuals. It can be concluded that the gender of P. tomentosa is most likely connected to the S60-1800bp DNA fragment and RAPD markers. S60, therefore, can be used for selecting the gender of P. tomentosa.

  2. 不同临床类型乙型肝炎患者HBV血清标志物与HBV DNA含量关系的研究%Study on the Relationship between Hepatitis B Virus Serum Markers and Content of HBV-DNA in Patients with Hepatitis B of Various Clinical Types

    Institute of Scientific and Technical Information of China (English)

    李生; 陈钦艳

    2012-01-01

    目的 探讨不同临床类型乙型肝炎患者HBV血清标志物及HBV DNA含量关系,为乙肝防治提供依据.方法 306例乙肝患者中,慢性肝炎104例、肝硬化126例、肝癌76例,采用酶联免疫吸附试验(ELISA)法检测血清HBV标志物(HBsAg、抗-HBs、HBeAg、抗-HBe、抗-HBc),用荧光定量PCR(FQ-PCR)检测HBV DNA,分析两者的关系.结果 306例患者小三阳(HBsAg阳性、抗-HBe阳性、抗-HBc阳性)检出率为47.06%(144/306),大三阳(HBsAg阳性、HBeAg阳性、抗-HBc阳性)检出率为20.26%(62/306);慢性肝炎组大三阳检出率、HBV DNA含量均高于肝硬化组、肝癌组(P均<0.01);慢性肝炎组小三阳检出率均低于肝硬化组、肝癌组(P均<0.01).62例大三阳组患者HBV DNA含量高于144例小三阳组患者(P<0.05).结论 慢性肝炎患者HBV血清标志物以大三阳表现为主,肝硬化、肝癌患者以小三阳表现为主,慢性肝炎患者HBV DNA含量高于肝硬化、肝癌患者,HBV血清标志物及HBV DNA联合检测对乙型肝炎患者的临床诊断及治疗具有重要意义.%Objective To explore the relationship between hepatitis B virus( HBV ) serum markers and content of HBV-DNA in patients with hepatitis B of various clinical types, and to provide evidence for prevention and treatment of hepatitis B. Methods Three hundred and six patients with hepatitis B were enrolled in the study, which including 104 cases of chronic hepatitis B, 126 cases of liver cirrhosis and 76 cases of liver cancer. HBV serum markers( HBsAg, anti-HBs,HBeAg,anti-HBe,anti-HBc ) were measured by enzyme immunoassay( FLISA ) and the content of HBV-DNA was detected by fluorescence quantitative PCB( FQ-PCR),and their relationship was analyzed. Results Of 306 cases,patients with positive HBsAg,positive anti-HBe and positive anti-HBc accounted for 47. 06%( 144/306 ) while patients with positive HBsAg,positive HBeAg and positive anti-HBc accounted for 20.26%( 62/306 ). The detection rate of patients

  3. Discharge of lead contamination by natural compounds pectin and chitin:biochemical analysis of DNA, RNA, DNase, RNase and GOT in albino rat as an early bio-marker of lead-toxicity

    Institute of Scientific and Technical Information of China (English)

    Abd El-Moneim MR Afify; Hossam S El-Beltagi

    2011-01-01

    Objective:To study the effect of different concentrations of lead in drinking water on nucleic acid contents, nuclease activities and glutamic-oxalacetic transaminease (GOT) in different tissues and reduce toxic effects of lead on environment especially human and rats by using pectin and chitin natural compounds in rat diets. Methods:Male albino rats were divided into eight groups. Groups 1, 4, 5 and 6 were fed on synthetic diet and given deionized water containing 0, 150, 250 and 1 500 μg lead/mL. Groups 2 and 3 were fed on synthetic diet containing 2%apple pectin or 2%grasp shell chitin and served as positive control. Groups 7 and 8 were fed on synthetic diet containing 2%pectin or 2%chitin and drinking water containing 250 μg lead/mL. At the end of the experimental period, animals (6 week) were killed by decapitation. All organs of each rat were dissected out and chilled for determination of DNA, RNA, DNase, RNase and GOT. Results:The data showed that higher lead concentration increased the activity of GOT in all organs. The concentrations of both DNA and RNA were increased with decreasing the activities of DNase and RNase. Adding 2%pectin or chitin with lead concentration 250 μg/mL showed discharge of lead, maintained the amount of nucleic acids and activated the related decomposition enzymes. Conclusions: Pectin or chitin natural compounds have the ability to chelate to lead and subsequently work as active natural compounds to discharge lead contamination.

  4. Microarray-Based Analysis of Methylation Status of CpGs in Placental DNA and Maternal Blood DNA – Potential New Epigenetic Biomarkers for Cell Free Fetal DNA-Based Diagnosis

    OpenAIRE

    Hatt, Lotte; Aagaard, Mads M.; Graakjaer, Jesper; Bach, Cathrine; Sommer, Steffen; Inge E Agerholm; Kølvraa, Steen; Bojesen, Anders

    2015-01-01

    Epigenetic markers for cell free fetal DNA in the maternal blood circulation are highly interesting in the field of non-invasive prenatal testing since such markers will offer a possibility to quantify the amount of fetal DNA derived from different chromosomes in a maternal blood sample. The aim of the present study was to define new fetal specific epigenetic markers present in placental DNA that can be utilized in non-invasive prenatal diagnosis. We have conducted a high-resolution methylati...

  5. DNA amplification polymorphisms of the cultivated mushroom Agaricus bisporus.

    OpenAIRE

    Khush, R S; Becker, E; Wach, M.

    1992-01-01

    Single 10-bp primers were used to generate random amplified polymorphic DNA (RAPD) markers from commercial and wild strains of the cultivated mushroom Agaricus bisporus via the polymerase chain reaction. Of 20 primers tested, 19 amplified A. bisporus DNA, each producing 5 to 15 scorable markers ranging from 0.5 to 3.0 kbp. RAPD markers identified seven distinct genotypes among eight heterokaryotic strains; two of the commercial strains were shown to be related to each other through single-spo...

  6. A four-gene methylation marker panel as triage test in high-risk human papillomavirus positive patients

    NARCIS (Netherlands)

    Eijsink, J. J. H.; Lendvai, A.; Deregowski, V.; Klip, H. G.; Verpooten, G.; Dehaspe, L.; de Bock, G. H.; Hollema, H.; van Criekinge, W.; Schuuring, E.; van der Zee, A. G. J.; Wisman, G. B. A.

    2012-01-01

    Cervical neoplasia-specific biomarkers, e.g. DNA methylation markers, with high sensitivity and specificity are urgently needed to improve current population-based screening on (pre)malignant cervical neoplasia. We aimed to identify new cervical neoplasia-specific DNA methylation markers and to desi

  7. The Swift Turbidity Marker

    Science.gov (United States)

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  8. Magik Markers Trehvis

    Index Scriptorium Estoniae

    2008-01-01

    Müra-rock'i viljelevast USA duost Magik Markers (ansambel osaleb režissöör Veiko Õunapuu uue mängufilmi "Püha Tõnu kiusamine" võtetel, kontsert 15. nov. Tartus klubis Trehv, vt. www.magikmarkers.audiosport.org.)

  9. Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests

    NARCIS (Netherlands)

    Addisalem, A.B.; Esselink, G.; Bongers, F.; Smulders, M.J.M.

    2015-01-01

    Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree spec

  10. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

    Directory of Open Access Journals (Sweden)

    Angela A G van Tilborg

    Full Text Available Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance.

  11. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids.

    Science.gov (United States)

    Lu, X; Zhou, H; Pan, Y-B; Chen, C Y; Zhu, J R; Chen, P H; Li, Y-R; Cai, Q; Chen, R K

    2015-01-01

    No information is available on segregation analysis of DNA markers involving both pollen and self-progeny. Therefore, we used capillary electrophoresis- and fluorescence-based DNA fingerprinting together with single pollen collection and polymerase chain reaction (PCR) to investigate simple sequence repeat (SSR) marker segregation among 964 single pollens and 288 self-progenies (S1) of sugarcane cultivar LCP 85-384. Twenty SSR DNA fragments (alleles) were amplified by five polymorphic SSR markers. Only one non-parental SSR allele was observed in 2392 PCRs. SSR allele inheritance was in accordance with Mendelian laws of segregation and independent assortment. Highly significant correlation coefficients were found between frequencies of observed and expected genotypes in pollen and S1 populations. Within the S1 population, the most frequent genotype of each SSR marker was the parental genotype of the same marker. The number of genotypes was higher in pollen than S1 population. PIC values of the five SSR markers were greater in pollen than S1 populations. Eleven of 20 SSR alleles (55%) were segregated in accordance with Mendelian segregation ratios expected from pollen and S1 populations of a 2n = 10x polyploid. Six of 20 SSR alleles were segregated in a 3:1 (presence:absence) ratio and were simplex markers. Four and one alleles were segregated in 77:4 and 143:1 ratios and considered duplex and triplex markers, respectively. Segregation ratios of remaining alleles were unexplainable. The results provide information about selection of crossing parents, estimation of seedling population optimal size, and promotion of efficient selection, which may be valuable for sugarcane breeders. PMID:26782486

  12. 利用微卫星DNA标记分析贵州3个地方猪种的遗传多样性%Genetic Diversity Analysis of Three Guizhou Local Pig Breeds Using Microsatellite DNA Markers

    Institute of Scientific and Technical Information of China (English)

    郭宏宇; 林家栋

    2009-01-01

    [Objective] The research aimed to provide the genetic basis for the protection, development and utilization of Guizhou local pig breeds. [Method] From 27 pairs of porcine microsatellite primers recommended by Food and Agriculture Organization of the United Nations (FAO) and International Society for Animal Genetics (ISAG), six pairs (S0155, SW240, IGF1, SW951, SW857, SW24) were selected for microsatellite DNA detection of three Guizhou local pig breeds, including Nuogu Pig, Kele Pig and Guanling Pig. Subsequently, their genetic diversities were analyzed. [Result] The three pig breeds were high polymorphic at the six microsatellite loci (PIC>0.5). The Neis standard genetic distance of them was 0.206 3-0.481 5. The genetic distance between Nuogu Pig and Kele Pig was the closest, and that between Nuogu Pig and Guanling Pig was the furthest. [Conclusion] The three Guizhou local pig breeds are in high genetic diversities. Nuogu Pig is a special type of Kele Pig, an excellent Chinese local pig breed.

  13. Bovine and equine forensic DNA analysis

    NARCIS (Netherlands)

    van de Goor, L.H.P.

    2011-01-01

    Animal forensic DNA analysis is being used for human criminal investigations (e.g traces from cats and dogs), wildlife management, breeding and food safety. The most common DNA markers used for such forensic casework are short tandem repeats (STR). Rules and guidelines concerning quality assurance (

  14. 油莎豆SRAP指纹图谱构建及遗传多样性分析%Construction of DNA Fingerprinting and Analysis of Genetic Diversity with SRAP Markers for Tigernut(Cyperus esculentus L.)

    Institute of Scientific and Technical Information of China (English)

    赵永国; 郭瑞星; 罗丽霞

    2013-01-01

    利用SRAP分子标记构建了14份不同地理来源、表型具有差异的油莎豆品系的分子指纹图谱并进行遗传多样性分析.结果表明100对引物中共有多态性引物42对,扩增出多态性带328条,平均每对引物7.8条.28对引物在12个品系上具有特征谱带,除品系4和14外,均可用1对引物进行鉴定;采用引物组合法仅用Me2/Em6和Me8/Em11这2对引物就可将14份材料区分开,并利用这2对引物构建了上述品系的数字指纹图谱.UPGMA聚类分析表明,所有参试材料间的遗传距离在0.12~0.75之间,平均为0.42,表明我国不同地理来源的油莎豆品系遗传差异较大,具有较为丰富的遗传多样性.%The fingerprinting and genetic diversity of 14 tigernut accessions collected from different geographical regions were investigated with SRAP molecular markers. The results showed there were 42 polymorphic primers among 100 primers,and 328 polymorphic bands were detected among the tested accessions,with an average of 7. 8 bands per primer. Twelve accessions had unique bands by 28 primer pairs, which could be identified with one pair of specific primer expect No. 4 and No. 14. All 14 accessions could be distinguished by two primer combinations (Me2/Em6 and Me8/Emll) at least,and digital fingerprinting code was also established. Clustering with UPGMA method revealed that the genetic distance ranged from 0. 12 to 0. 75 with an average of 0.42,which indicated that there was abundant genetic diversity among all 14 accessions.

  15. NMR structural studies of intramolecular (Y+)n·(R+)n(Y-)n DNA triplexes in solution: Imino and amino proton and nitrogen markers of G·TA base triple formation

    International Nuclear Information System (INIS)

    The authors reported previously on NMR studies of (Y+)n·(R+)n(Y-)nDNA triple helices containing one oligopurine strand (R)n and two oligopyrimidine strands (Y)n stabilized by T·AT and C+·GC base triples. Recently, it has been established that guanosine can recognize a thymidine·adenosine base pair to form a G·TA triple in an otherwise (Y+)n·(R+)n(Y-)n triple-helix motif. The present study extends the NMR research to the characterization of structural features of a 31-mer deoxyoligonucleotide that folds intramolecularly into a 7-mer (Y+)n·(R+)n(Y-)n triplex with the strands linked through two T5 loops and that contains a central G·TA triple flanked by T·AT triples. The NMR data are consistent with the proposed pairing alignment for the G·TA triple where the guanosine in an anti orientation pairs through a single hydrogen bond from one of its 2-amino protons to the 4-carbonyl group of thymidine in the Watson-Crick TA pair. They detect a set of NOEs between adjacent triples that establishes that the G·TA triple stacks between flanking T·AT triples in the G·TA triplex. These results demonstrate the capabilities of the NMR approach in monitoring individual base triples and their pairing alignments, as well as establishing that the G·TA triple can be readily accommodated in an otherwise intramolecular (Y+)n (R+)n(Y-)n triple helix in solution

  16. Human identification & forensic analyses of degraded or low level DNA

    OpenAIRE

    Westen, Antoinette-Andrea

    2013-01-01

    DNA-based human identification is employed in varying situations, such as disaster victim identification, relationship testing and forensic analyses. When DNA is of low quality and/or quantity, standard methods for DNA profiling may not suffice. The research described in this thesis is aimed at the development of additional or alternative methods to extract information from a person’s DNA. The explored methods include: optimised sampling, the use of smaller and/or other types of DNA markers, ...

  17. DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

    OpenAIRE

    Chang Liu; Linchun Shi; Xiaolan Xu; Huan Li; Hang Xing; Dong Liang; Kun Jiang; Xiaohui Pang; Jingyuan Song; Shilin Chen

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three diff...

  18. DNA damage in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Coppedè, Fabio, E-mail: fabio.coppede@med.unipi.it; Migliore, Lucia, E-mail: lucia.migliore@med.unipi.it

    2015-06-15

    Highlights: • Oxidative DNA damage is one of the earliest detectable events in the neurodegenerative process. • The mitochondrial DNA is more vulnerable to oxidative attack than the nuclear DNA. • Cytogenetic damage has been largely documented in Alzheimer's disease patients. • The question of whether DNA damage is cause or consequence of neurodegeneration is still open. • Increasing evidence links DNA damage and repair with epigenetic phenomena. - Abstract: Following the observation of increased oxidative DNA damage in nuclear and mitochondrial DNA extracted from post-mortem brain regions of patients affected by neurodegenerative diseases, the last years of the previous century and the first decade of the present one have been largely dedicated to the search of markers of DNA damage in neuronal samples and peripheral tissues of patients in early, intermediate or late stages of neurodegeneration. Those studies allowed to demonstrate that oxidative DNA damage is one of the earliest detectable events in neurodegeneration, but also revealed cytogenetic damage in neurodegenerative conditions, such as for example a tendency towards chromosome 21 malsegregation in Alzheimer's disease. As it happens for many neurodegenerative risk factors the question of whether DNA damage is cause or consequence of the neurodegenerative process is still open, and probably both is true. The research interest in markers of oxidative stress was shifted, in recent years, towards the search of epigenetic biomarkers of neurodegenerative disorders, following the accumulating evidence of a substantial contribution of epigenetic mechanisms to learning, memory processes, behavioural disorders and neurodegeneration. Increasing evidence is however linking DNA damage and repair with epigenetic phenomena, thereby opening the way to a very attractive and timely research topic in neurodegenerative diseases. We will address those issues in the context of Alzheimer's disease

  19. DNA damage in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Highlights: • Oxidative DNA damage is one of the earliest detectable events in the neurodegenerative process. • The mitochondrial DNA is more vulnerable to oxidative attack than the nuclear DNA. • Cytogenetic damage has been largely documented in Alzheimer's disease patients. • The question of whether DNA damage is cause or consequence of neurodegeneration is still open. • Increasing evidence links DNA damage and repair with epigenetic phenomena. - Abstract: Following the observation of increased oxidative DNA damage in nuclear and mitochondrial DNA extracted from post-mortem brain regions of patients affected by neurodegenerative diseases, the last years of the previous century and the first decade of the present one have been largely dedicated to the search of markers of DNA damage in neuronal samples and peripheral tissues of patients in early, intermediate or late stages of neurodegeneration. Those studies allowed to demonstrate that oxidative DNA damage is one of the earliest detectable events in neurodegeneration, but also revealed cytogenetic damage in neurodegenerative conditions, such as for example a tendency towards chromosome 21 malsegregation in Alzheimer's disease. As it happens for many neurodegenerative risk factors the question of whether DNA damage is cause or consequence of the neurodegenerative process is still open, and probably both is true. The research interest in markers of oxidative stress was shifted, in recent years, towards the search of epigenetic biomarkers of neurodegenerative disorders, following the accumulating evidence of a substantial contribution of epigenetic mechanisms to learning, memory processes, behavioural disorders and neurodegeneration. Increasing evidence is however linking DNA damage and repair with epigenetic phenomena, thereby opening the way to a very attractive and timely research topic in neurodegenerative diseases. We will address those issues in the context of Alzheimer's disease

  20. The urine marker test

    DEFF Research Database (Denmark)

    Elbe, Anne-Marie; Jensen, Stine Nylandsted; Elsborg, Peter;

    2016-01-01

    BACKGROUND: Urine sample collection for doping control tests is a key component of the World Anti-Doping Agency's fight against doping in sport. However, a substantial number of athletes experience difficulty when having to urinate under supervision. Furthermore, it cannot always be ensured...... that athletes are actually delivering their own urine. A method that can be used to alleviate the negative impact of a supervised urination procedure and which can also identify urine as coming from a specific athlete is the urine marker test. Monodisperse low molecular weight polyethylene glycols (PEGs......) are given orally prior to urination. Urine samples can be traced to the donor by analysis of the PEGs previously given. OBJECTIVE: The objective of this study was to investigate the use of the urine marker during urine doping control testing. METHODS: Two studies investigated athletes' acceptance...

  1. A genetic marker test for brachyspina and fertility in cattle

    DEFF Research Database (Denmark)

    2010-01-01

    This invention relates to methods for the detection of bovine that are affected by or carriers of Brachyspina (BS). The present invention provides a method for determining whether a bovine is affected by or earner of BS by analyzing its genomic DNA or its RNA. The method can be used to perform...... marker assisted selection or genomic selection for increased fertility in said bovine....

  2. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids

    Science.gov (United States)

    Although the microsatellite (SSR) DNA markers have been extensively used in sugarcane breeding research, little is known about its inheritance mechanism. To address this problem, a high throughput molecular genotyping experiment was conducted on 964 single pollen grains and a 288-self progeny S1 map...

  3. Lipoprotein marker for hypertriglyceridemia

    Science.gov (United States)

    Cubicciotti, Roger S.; Karu, Alexander E.; Krauss, Ronald M.

    1986-01-01

    Methods and compositions are provided for the detection of a particular low density lipoprotein which has been found to be a marker for patients suffering from type IV hypertriglyceridemia. A monoclonal antibody capable of specifically binding to a characteristic epitopic site on this LDL subspecies can be utilized in a wide variety of immunoassays. Hybridoma cell line SPL.IVA5A1 was deposited at the American Type Culture Collection on Mar. 29, 1984, and granted accession no. HB 8535.

  4. The prognostic molecular markers in hepatocellular carcinoma

    Institute of Scientific and Technical Information of China (English)

    Lun-Xiu Qin; Zhao-You Tang

    2002-01-01

    The prognosis of hepatocellular carcinoma (HCC) stillremains dismal, although many advances in its clinicalstudy have been made. It is important for tumor control toidentity the factors that predispose patients to death. Withnew discoveries in cancer biology, the pathological andbiological prognostic factors of HCC have been studied quiteextensively. Analyzing molecular markers (biomarkers) withprognostic significance is a complementary method. A largenumber of molecular factors have been shown to associatewith the invasiveness of HCC, and have potential prognosticsignificance. One important aspect is the analysis ofmolecular markers for the cellular malignancy phenotypeThese include alterations in DNA ploidy, cellularproliferation markers (PCNA, Ki-67, Mcm2, MIB1, MIA, andCSE1L/CAS protein), nuclear morphology, the p53 geneand its related molecule MDM2, other cell cycle regulators(cyclin A, cyclin D, cyclin E, cdc2, p27, p73), oncogenesand their receptors (such as ras, c-myc, c-fms, HGF, c-met, and erb-B receptor family members ), apoptosisrelated factors (Fas and FasL), as well as telomeraseactivity. Another important aspect is the analysis ofmolecular markers involved in the process of cancerinvasion and metastasis. Adhesion molecules (E-cadherin,catenins, serum intercellular adhesion molecule-1, CD44variants), proteinases involved in the clegradation ofextracellular matrix (MMP-2, MMP-9, uPA, uPAR, PAl), aswell as other molecules have been regarded as biomarkersfor the malignant phenotype of HCC, and are related toprognosis and therapeutic outcomes. Tumor angiogenesisis critical to both the growth and metastasis of cancersincluding HCC, and has drawn much attention in recentyears. Many angiogenesis-related markers, such as vascularendothelial growth factor (VEGF), basic fibroblast growthfactor (bFGF), platelet-derived endothelial cell growth factor( PD-ECGF ), thrombospondin ( TSP ), angiogenin,pleiotrophin, and endostatin (ES) levels, as well asinratumor

  5. Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...he DNA marker list, the QTL list, the list of related databases and/or the genomic analysis information. Data file File name: pgd...bj_dna_marker_linkage_map_plant_species_list_en.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgd...bj-dna-marker-linkage-map/LATEST/pgdbj_dna_marker_linkage_map_plant_...species_list_en.zip File size: 20.0 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_dn

  6. [Microsatellite markers and applications in the barley genome].

    Science.gov (United States)

    Feng, Zong-yun; Zhang, Yi-zheng; Ling, Hong-qing

    2002-11-01

    Microsatellites, also called simple sequence repeats (SSR), are simple, tandemly repeated DNA sequences with a repeat length of a few base pairs,and are very ideally used as molecular markers because of their abundance, high level of polymorphism, co-dominance and ease of assay with the polymerase chain reaction (PCR) by selecting primers as the conserved DNA sequences flanking the SSRs,as well as better stability. The experiments showed that SSRs are randomly distributed throughout the barley genome,and there are 3-18 alleles at a single SSR locus,up to 37 alleles/locus. SSR markers have being widely applied in the construction of molecular genetic map, the study of genetic diversity,the identification of germplasm, gene mapping for important traits and molecular marker-assisted selection. Meanwhile,most of markers are strongly clustered around the centromeric regions of all seven linkage groups. As a result of the clustering,genome coverage with SSRs remains incomplete with an obvious lack of markers on the long arms of chromosomes 1H and 5H and short arm of chromosome 6H. Therefore,it is very potential and necessary to further develop SSR markers in barley. PMID:15979979

  7. DNA fingerprinting of water yam (Dioscorea alata cultivars in Brazil based on microsatellite markers Diversidade genética de cultivares de inhame (Dioscorea alata no Brasil utilizando microssatélites

    Directory of Open Access Journals (Sweden)

    Marcos VBM Siqueira

    2012-12-01

    Full Text Available This study aimed to fingerprint 36 water yam (Dioscorea alata accessions using microsatellite markers. Ten accessions were collected in local markets from several municipalities in Brazil, eight were obtained from the 'Instituto Agronômico de Campinas' (IAC germplasm collection and eighteen were collected directly from growers from São Paulo state. A total of nine microsatellite loci were used in the analysis. Loci revealed high polymorphism verified by elevated PIC values (0.57-0.77, and by high gene diversity and Shannon-Wiener indices (0.69 and 1.29 on average, respectively. The accessions were classified into two groups based on clustering analysis. One group contained mostly accessions from the IAC collection, including a commercial cultivar acquired in a market in the city of Cuiabá, Mato Grosso state. The second group was composed of most accessions, including those collected directly from growers and markets in São Paulo, a few accessions from the IAC collection, and an accession from Puerto Rico, named 'Florida', which is the most cultivated in Brazil. Several duplicates were identified in this study, including accessions obtained from two farmers in Mogi Guaçu and Mogi Mirim, São Paulo state. However, some of these accessions were allocated in different sub-groups, within this second group. Results suggested the hypothesis of different origins for accessions currently cultivated in Brazil. Similar accessions obtained from different municipalities revealed the commercialization of the same accessions at different locations.Este estudo teve como objetivo a análise genética de 36 acessos de inhame (Dioscorea alata utilizando marcadores microssatélites. Dez acessos foram coletados em mercados locais de vários municípios no Brasil, oito foram obtidos no banco de germoplasma do Instituto Agronômico de Campinas (IAC, e dezoito foram coletados diretamente com os agricultores no estado de São Paulo. Um total de nove locos de

  8. DNA fingerprinting in forensics: past, present, future

    Science.gov (United States)

    2013-01-01

    DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework examples. Benefits and risks of expanding forensic DNA databases are discussed and we ask what the future holds for forensic DNA fingerprinting. PMID:24245688

  9. NMR structural studies of intramolecular (Y+) sub n ter dot (R+) sub n (Y minus ) sub n DNA triplexes in solution: Imino and amino proton and nitrogen markers of Gter dot TA base triple formation

    Energy Technology Data Exchange (ETDEWEB)

    Radhakrishnan, I.; de los Santos, C.; Patel, D.J. (Columbia Univ., New York, NY (United States)); Gao, Xiaolian (Glaxo Research Inst., Research Triangle Park, NC (United States)); Live, D. (California Inst. of Tech., Pasadena (United States))

    1991-09-17

    The authors reported previously on NMR studies of (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n}DNA triple helices containing one oligopurine strand (R){sub n} and two oligopyrimidine strands (Y){sub n} stabilized by T{center dot}AT and C{sup +}{center dot}GC base triples. Recently, it has been established that guanosine can recognize a thymidine{center dot}adenosine base pair to form a G{center dot}TA triple in an otherwise (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triple-helix motif. The present study extends the NMR research to the characterization of structural features of a 31-mer deoxyoligonucleotide that folds intramolecularly into a 7-mer (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triplex with the strands linked through two T{sub 5} loops and that contains a central G{center dot}TA triple flanked by T{center dot}AT triples. The NMR data are consistent with the proposed pairing alignment for the G{center dot}TA triple where the guanosine in an anti orientation pairs through a single hydrogen bond from one of its 2-amino protons to the 4-carbonyl group of thymidine in the Watson-Crick TA pair. They detect a set of NOEs between adjacent triples that establishes that the G{center dot}TA triple stacks between flanking T{center dot}AT triples in the G{center dot}TA triplex. These results demonstrate the capabilities of the NMR approach in monitoring individual base triples and their pairing alignments, as well as establishing that the G{center dot}TA triple can be readily accommodated in an otherwise intramolecular (Y+){sub n}{center dot}(R+){sub n}(Y{minus}){sub n} triple helix in solution.

  10. DNA fingerprinting in forensics: past, present, future

    OpenAIRE

    Roewer, Lutz

    2013-01-01

    DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework ex...

  11. Short Tandem Repeat DNA Internet Database

    Science.gov (United States)

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  12. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  13. Testing a Short Nuclear Marker for Inferring Staphylinid Beetle Diversity in an African Tropical Rain Forest

    OpenAIRE

    Birthe Thormann; Raupach, Michael J.; Thomas Wagner; Johann W Wägele; Marcell K Peters

    2011-01-01

    BACKGROUND: The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, the...

  14. Forensic DNA methylation profiling from evidence material for investigative leads.

    Science.gov (United States)

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-07-01

    DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369]. PMID:27099236

  15. Forensic DNA methylation profiling from evidence material for investigative leads.

    Science.gov (United States)

    Lee, Hwan Young; Lee, Soong Deok; Shin, Kyoung-Jin

    2016-07-01

    DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369].

  16. Forensic DNA typing in China.

    Science.gov (United States)

    Hou, Y P

    2009-04-01

    In the field of forensic genetics, essential developmental impulses come from the advances of the molecular biology and human genome projects. This paper overviews existing technologies for forensic genetics in China and gives a perspective of forensic DNA analysis. In China, work has been done in the development of blood group serology of the conventional markers. Forensic scientists in China also contributed to the progress of DNA analysis by the validation of numerous test methods and by optimization of these methods. During these years, forensic DNA analysis in China has experienced tremendous progress towards development of robust, efficient and precise protocols, including the development of short tandem repeat analysis, mitochondrial DNA and Y-chromosome analysis. Forensic scientists are constantly looking for new methods to further improve DNA typing. Therefore, this paper also focuses on emerging new technologies in China, which represent an interest for forensic genetics.

  17. A redesigned CRISPR/Cas9 system for marker-free genome editing in Plasmodium falciparum

    OpenAIRE

    Lu, Junnan; TONG, Ying; Pan, Jiaqiang; Yang, Yijun; Liu, Quan; Tan, Xuefang; Zhao, Siting; Qin, Li; Chen, Xiaoping

    2016-01-01

    Background A highly efficient CRISPR/Cas9-based marker-free genome editing system has been established in Plasmodium falciparum (Pf). However, with the current methods, two drug-selectable markers are needed for episome retention, which may present hurdles for consecutive genome manipulations due to the limited number of available selectable markers. The loading capacity of donor DNA is also unsatisfactory due to the large size of the Cas9 nuclease and sgRNA co-expression system, which limits...

  18. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution▿ †

    OpenAIRE

    Shanks, Orin C.; Atikovic, Emina; Blackwood, A. Denene; Lu, Jingrang; Noble, Rachel T.; Domingo, Jorge Santo; Seifring, Shawn; Sivaganesan, Mano; Haugland, Richard A.

    2007-01-01

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described bovine feces-specific genetic markers and a method for the enumeration of these markers using a Markov chain Monte Carlo approach. Both assays exhibited a range of quantification from 25 to 2 × 106 copies of target DNA, with a coeff...

  19. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Science.gov (United States)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  20. Application of resistance gene analog markers to analyses of genetic structure and diversity in rice.

    Science.gov (United States)

    Ren, Juansheng; Yu, Yuchao; Gao, Fangyuan; Zeng, Lihua; Lu, Xianjun; Wu, Xianting; Yan, Wengui; Ren, Guangjun

    2013-07-01

    Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known RGAs and used to map resistance genes. We used genome-wide RGA markers for genetic analyses of structure and diversity in a global rice germplasm collection. Of the 472 RGA markers, 138 were polymorphic and these were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported from SSR markers, including cluster of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster of geographic origins. These results suggest that RGA markers are applicable for analyses of genetic structure and diversity in rice. However, unlike SSR markers, the RGA markers failed to differentiate temperate japonica, tropical japonica, and aromatic subgroups. The restricted way for developing RGA markers from the cDNA sequence might limit the polymorphism of RGA markers in the genome, thus limiting the discriminatory power in comparison with SSR markers. Genetic differentiation obtained using RGA markers may be useful for defining genetic diversity of a suite of random R genes in plants, as many studies show a differentiation of resistance to a wide array of pathogens. They could also help to characterize the genetic structure and geographic distribution in crops, including rice, wheat, barley, and banana. PMID:24099390

  1. Human age estimation from blood using mRNA, DNA methylation, DNA rearrangement, and telomere length.

    Science.gov (United States)

    Zubakov, Dmitry; Liu, Fan; Kokmeijer, Iris; Choi, Ying; van Meurs, Joyce B J; van IJcken, Wilfred F J; Uitterlinden, André G; Hofman, Albert; Broer, Linda; van Duijn, Cornelia M; Lewin, Jörn; Kayser, Manfred

    2016-09-01

    Establishing the age of unknown persons, or persons with unknown age, can provide important leads in police investigations, disaster victim identification, fraud cases, and in other legal affairs. Previous methods mostly relied on morphological features available from teeth or skeletal parts. The development of molecular methods for age estimation allowing to use human specimens that possess no morphological age information, such as bloodstains, is extremely valuable as this type of samples is commonly found at crime scenes. Recently, we introduced a DNA-based approach for human age estimation from blood based on the quantification of T-cell specific DNA rearrangements (sjTRECs), which achieves accurate assignment of blood DNA samples to one of four 20-year-interval age categories. Aiming at improving the accuracy of molecular age estimation from blood, we investigated different types of biomarkers. We started out by systematic genome-wide surveys for new age-informative mRNA and DNA methylation markers in blood from the same young and old individuals using microarray technologies. The obtained candidate markers were validated in independent samples covering a wide age range using alternative technologies together with previously proposed DNA methylation, sjTREC, and telomere length markers. Cross-validated multiple regression analysis was applied for estimating and validating the age predictive power of various sets of biomarkers within and across different marker types. We found that DNA methylation markers outperformed mRNA, sjTREC, and telomere length in age predictive power. The best performing model included 8 DNA methylation markers derived from 3 CpG islands reaching a high level of accuracy (cross-validated R(2)=0.88, SE±6.97 years, mean absolute deviation 5.07 years). However, our data also suggest that mRNA markers can provide independent age information: a model using a combined set of 5 DNA methylation markers and one mRNA marker could provide

  2. Functional molecular markers for crop improvement.

    Science.gov (United States)

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered. PMID:26171816

  3. Exon-primed intron-crossing (EPIC markers as a tool for ant phylogeography

    Directory of Open Access Journals (Sweden)

    Patrícia R. Ströher

    2013-12-01

    Full Text Available Exon-primed intron-crossing (EPIC markers as a tool for ant phylogeography. Due to their local abundance, diversity of adaptations and worldwide distribution, ants are a classic example of adaptive radiation. Despite this evolutionary and ecological importance, phylogeographical studies on ants have relied largely on mitochondrial markers. In this study we design and test exon-primed intron-crossing (EPIC markers, which can be widely used to uncover ant intraspecific variation. Candidate markers were obtained through screening the available ant genomes for unlinked conserved exonic regions interspersed with introns. A subset of 15 markers was tested in vitro and showed successful amplification in several phylogenetically distant ant species. These markers represent an important step forward in ant phylogeography and population genetics, allowing for more extensive characterization of variation in ant nuclear DNA without the need to develop species-specific markers.

  4. Impact of the DNA extraction method on 2-LTR DNA circle recovery from HIV-1 infected cells

    OpenAIRE

    Badralmaa, Yunden; Natarajan, Ven

    2013-01-01

    Detection of episomal 2-LTR DNA circles is used as a marker for the ongoing virus replication in patients infected with HIV-1, and efficient extraction of episomal DNA is critical for accurate estimation of the 2-LTR circles. The impact of different methods of DNA extraction on the recovery of 2-LTR circles was compared using mitochondrial DNA extracted as an internal control. The bacterial plasmid DNA isolation method extracted less than 10% of cellular DNA, 40% of mitochondrial DNA and 12-2...

  5. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

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

  6. Cancer and tumour markers

    International Nuclear Information System (INIS)

    Cancer has been a major cause of death world wide and in Nigeria there are six commonest forms of manifestation of cancer known. Of these prostrate cancer is the highest with 16% occurrence of all known cancers according to a study by the Histopathology Department of the UCH. Many factors, amongst them dietary, environmental, lifestyle, age and sedentary work are possible causes. With the global rise in incidents, the IAEA initiated the Tumour Marker Project as a means of screening cancers in 15 African countries including Nigeria. In Nigeria, 4 groups of the commonest cancers have been chosen for screening. These are prostrate cancer, primary liver cancer, cancer of the GI tract and trophoblastic cancer

  7. Development of a SCAR (sequence-characterised amplified region) marker for acid resistance-related gene in Lactobacillus plantarum.

    Science.gov (United States)

    Liu, Shu-Wen; Li, Kai; Yang, Shi-Ling; Tian, Shu-Fen; He, Ling

    2015-03-01

    A sequence characterised amplified region marker was developed to determine an acid resistance-related gene in Lactobacillus plantarum. A random amplified polymorphic DNA marker named S116-680 was reported to be closely related to the acid resistance of the strains. The DNA band corresponding to this marker was cloned and sequenced with the induction of specific designed PCR primers. The results of PCR test helped to amplify a clear specific band of 680 bp in the tested acid-resistant strains. S116-680 marker would be useful to explore the acid-resistant mechanism of L. plantarum and to screen desirable malolactic fermentation strains.

  8. Analysis of Genetic Diversity and Development of SCAR Markers in a Mycogone perniciosa Population.

    Science.gov (United States)

    Wang, Wei; Li, Xiao; Chen, Bingzhi; Wang, Shuang; Li, Chenghuan; Wen, Zhiqiang

    2016-07-01

    The fungus Mycogone perniciosa is a major pathogen of the common button mushroom Agaricus bisporus. Analysis of genetic diversity in M. Perniciosa may assist in developing methods for prophylaxis and treatment of M. Perniciosa infections. For this, it is necessary to classify M. Perniciosa into relevant class groups quickly and efficiently. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and sequence-related amplified polymorphism (SRAP) markers were used to obtain genetic fingerprints and assess the genetic variation among 49 strains of M. perniciosa collected from different areas of Fujian Province in China. Analysis of DNA sequence polymorphism revealed two major distinct groups (Group I and Group II). Specific DNA fragments that were identified through RAPD, ISSR, and SRAP markers were sequenced and used for the designing of stable sequence-characterized amplified region (SCAR) markers. The resulting SCAR markers were then validated against the classified groups of M. perniciosa. PMID:26960290

  9. Molecular taxonomy of Plagioscion Heckel (Perciformes, Sciaenidae and evidence from mtDNA RFLP markers for an invasive species in the Paraná river, Southern Brazil Taxonomia molecular de Plagioscion Heckel (Perciformes, Sciaenidae e evidências de marcadores moleculares RFLPs de mtDNA para uma espécie invasora no rio Paraná, Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Rodrigo A. Torres

    2006-12-01

    Full Text Available Mitochondrial RFLP markers were developed to examine whether Plagioscion squamosissimus (Heckel, 1840 is invasive in natural environments of the congener P. ternetzi in the Paraná river, in southern Brazil. Specimens of P. squamosissimus and of the putative P. ternetzi (Boulenger, 1895 were obtained from the Negro river (Manaus, Amazonas, Brazil and from Paraná river, respectively. Fragments of the cytochrome b gene (900bp were amplified by PCR and four restriction enzymes (Eco RI, Mbo I, Bam HI and Alu I yielded the mitochondrial markers. An additional RFLP analysis with a cytochrome b gene sequence of Plagioncion sp. from GeneBank was carried out to validate the prior analysis. No genetic differentiation was found among either sample. While molecular variation in the cytochrome b analysis was no substantial among individuals, the combined analysis was important for demonstrating that there is no evidence for differentiation of the putative sample P. ternetzi from that of P. squamosissimus. The ecological implications of the introduced occurrence of P. squamosissimus, as well as the role of molecular taxonomic approaches for biodiversity studies are discussed.Marcadores RFLPs mitocondriais foram desenvolvidos para verificar se Plagioscion squamosissimus (Heckel, 1840 é invasora nos ambientes naturais da espécie congênere P. ternetzi no rio Paraná, no sul do Brasil. Exemplares de Plagioscion squamosissimus e supostamente de P. ternetzi (Boulenger, 1895 foram obtidos, respectivamente, do rio Negro (Manaus, AM, Brasil e rio Paraná (Foz do Iguaçu, PR, Brasil. Foram amplificados, via PCR, fragmentos de cerca de 900pb do Citocromo b e foram utilizadas quatro enzimas de restrição (Eco RI, Mbo I, Bam HI e Alu I para os fins de geração dos marcadores moleculares. Foi desenvolvida, a partir de uma seqüência de Citocromo b de Plagioscion sp. (genebank, uma análise de RFLP adicional, objetivando validar a primeira análise acima mencionada

  10. Biochemical markers of bone turnover

    International Nuclear Information System (INIS)

    Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

  11. Discrimination of Wild Tea Germplasm Resources (Camellia sp.) Using RAPD Markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Liang; WANG Ping-sheng; Yamaguchi Satoshi

    2002-01-01

    Discrimination of 24 wild tea germplasm resources ( Camellia sp. ) using RAPD markers was conducted. The result showed that RAPD markers were very effective tool and method in wild tea germplasm discrimination. There were 3 independent ways to discriminate tea germplasms, a) unique RAPD markers, b)specific band patterns and c) a combination of the band patterns or DNA fingerprinting provided by different primers. The presence of 16 unique RAPD markers and the absence of 3 unique markers obtained from 12 primers made it possible to discriminate 14 germplasms. Using the unique band patterns of primer OPO-13 could discriminate 10 tea germplasms. It was of much importance using minimum primers to obtain maximum discrimination capacity. All the 24 wild tea germplasms could be discriminated easily and entirely by the band patterns combination or DNA fingerprinting obtained from OPO-13, OPO-18, OPG-12 and OPA-13, including two wild tea trees of very similar morphological characteristics and chemical components.

  12. Development and validation of new SSR markers from expressed regions in the garlic genome

    OpenAIRE

    Meryem Ipek; Nihan Sahin; Ahmet Ipek; Asuman Cansev; Simon, Philipp W

    2015-01-01

    Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs we...

  13. New sequence-tagged site molecular markers for identification of sex in Distichlis spicata.

    Science.gov (United States)

    Eppley, Sarah M; O'Quinn, Robin; Brown, Anna L

    2009-09-01

    Sex-linked molecular markers have become valuable tools for understanding sex ratio evolution and sex-specific physiology in pre-reproductive plants. To develop new accurate methods for sexing Distichlis spicata juveniles and nonflowering individuals, we converted a random amplified polymorphic DNA-polymerase chain reaction marker that co-segregated with the female phenotype into a set of sequence-tagged site markers. We tested the marker pair on known males and females from populations in Oregon and California. A single band was obtained for all female samples but never for males.

  14. [DNA adducts in human female genital organs].

    Science.gov (United States)

    Postawski, Krzysztof; Przadka-Rabaniuk, Dorota; Monist, Marta; Baranowski, Włodzimierz

    2007-12-01

    DNA adducts, one of genetic damages markers, precede and finally can lead to oncogenic mutations. They appear in genome as a result of DNA bases damages caused by various and numerous environmental factors eg. ultraviolet light, ionic radiation, toxins and also endogenic substances, for example estrogens. It is believed that the creation of DNA adducts is a necessary but insufficient process for the neoplastic transformation of the cell. The following review presents concise knowledge about the DNA adducts creation and their sequels served in healthy and cancerous tissues of the female genital organs, on the base of the available data. PMID:18411923

  15. EXTRACELLULAR DNA AND THE LEVEL OF ITS METHYLATION IN DIFFERENT RHEUMATIC DISEASES

    Directory of Open Access Journals (Sweden)

    N O Shubayeva

    2012-01-01

    Conclusion. RDs are characterized by the higher concentration of apoptotic and necrotic DNA, impaired exDNA methylation, varying complexification of exDNA with monometinic proteins, which is associated with the hyperproduction of autoantibodies (including anti-exDNA antibodies and inflammatory markers.

  16. QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD...nism name, papers and trait. Data file File name: pgdbj_dna_marker_linkage_map_pl...ant_qtl_list.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-dna-marker-linkage-map/LATEST/pgdbj_dna_...marker_linkage_map_plant_qtl_list.zip File size: 22.6 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/pgd...Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

  17. A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles

    Directory of Open Access Journals (Sweden)

    Ansell Ricky

    2010-11-01

    Full Text Available Abstract Background Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights of the capillary electrophoresis electropherograms. Results We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009 951-958. FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. Conclusions The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification.

  18. Inheritance of chloroplast DNA in Chlamydomonas reinhardtii

    OpenAIRE

    Grant, David M; Nicholas W. Gillham; Boynton, John E.

    1980-01-01

    Two symmetrically located deletions of approximately 100 base pairs each have been identified in chloroplast DNA of Chlamydomonas reinhardtii. Although present in a mutant strain that requires acetate for growth, both deletions have been shown to be distinct from the nonphotosynthetic phenotype of this strain. These physical markers in the chloroplast genome and maternally inherited genetic markers showed strict cotransmission in reciprocal crosses. Thus, our results are consistent with the l...

  19. Developing SCAR markers to study predation on Trialeurodes vaporariorum.

    Science.gov (United States)

    Agustí, N; de Vicente, M C; Gabarra, R

    2000-06-01

    DNA markers of Trialeurodes vaporariorum were developed to detect remains of these whitefly in the gut of the predator Dicyphus tamaninii. A 2400-bp DNA fragment of T. vaporariorum, absent in other closely related prey species and in the predator banding pattern, was identified by random amplified polymorphic DNA (RAPD) analysis. After cloning and sequencing this fragment, two pairs of sequence-characterized amplified region (SCAR) primers were developed, amplifying single bands of 2100 bp and 310 bp, respectively. Detection of T. vaporariorum DNA in the predator gut was only possible using the primers that amplified the shortest fragment. Specificity tests performed with this pair of primers showed the presence of the 310-bp band for T. vaporariorum in all stages.

  20. Salivary markers of oxidative stress in oral diseases

    Directory of Open Access Journals (Sweden)

    Ľubomíra eTóthová

    2015-10-01

    Full Text Available Saliva is an interesting alternative diagnostic body fluid with several specific advantages over blood. These include non-invasive and easy collection and related possibility to do repeated sampling. One of the obstacles that hinders the wider use of saliva for diagnosis and monitoring of systemic diseases is its composition, which is affected by local oral status. However, this issue makes saliva very interesting for clinical biochemistry of oral diseases. Periodontitis, caries, oral precancerosis and other local oral pathologies are associated with oxidative stress. Several markers of lipid peroxidation, protein oxidation and DNA damage induced by reactive oxygen species can be measured in saliva. Clinical studies have shown an association with oral pathologies at least for some of the established salivary markers of oxidative stress. This association is currently limited to the population level and none of the widely used markers can be applied for individual diagnostics. Oxidative stress seems to be of local oral origin, but it is currently unclear whether it is caused by an overproduction of reactive oxygen species due to inflammation or by the lack of antioxidants. Interventional studies, both, in experimental animals as well as humans indicate that antioxidant treatment could prevent or slow-down the progress of periodontitis. This makes the potential clinical use of salivary markers of oxidative stress even more attractive. This review summarizes basic information on the most commonly used salivary markers of oxidative damage, antioxidant status and carbonyl stress and the studies analyzing these markers in patients with caries or periodontitis.

  1. Aspergillus and Penicillium identification using DNA sequences: Barcode or MLST?

    Science.gov (United States)

    Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through...

  2. Markers of renal function tests

    Directory of Open Access Journals (Sweden)

    Shivaraj Gowda

    2010-04-01

    Full Text Available Background: The markers of renal function test assess the normal functioning of kidneys. These markers may be radioactive and non radioactive. They indicate the glomerular filtration rate, concentrating and diluting capacity of kidneys (tubular function. If there is an increase or decrease in the valves of these markers it indicates dysfunction of kidney. Aim: The aim of this review is to compare and analyze the present and newer markers of renal function tests which help in diagnosis of clinical disorders. Material & Methods: An extensive literature survey was done aiming to compare and compile renal function tests makers required in diagnosis of diseases. Results: Creatinine, urea, uric acid and electrolytes are makers for routine analysis whereas several studies have confirmed and consolidated the usefulness of markers such as cystatin C and β-Trace Protein. Conclusion: We conclude that further investigation is necessary to define these biomarkers in terms of usefulness in assessing renal function.

  3. MarkerSet: a marker selection tool based on markers location and informativity in experimental designs

    Directory of Open Access Journals (Sweden)

    Demeure Olivier

    2008-03-01

    Full Text Available Abstract Background The recent sequencing of full genomes has led to the availability of many SNP markers which are very useful for the mapping of complex traits. In livestock production, there are still no commercial arrays and many studies use home-made sets of SNPs. Thus, the current methodologies for SNP genotyping are still expensive and it is a crucial step to select the SNPs to use. Indeed, the main factors affecting the power of the linkage analyses are the density of the genetic map and the heterozygosity of markers in tested animal parents. Findings This is why we have developed a PERL program selecting a defined number of markers based on their locations on the genome and their informativity in specific experimental designs. As an option, different experimental designs can be combined in order to select the best possible common marker set. The program has been tested using different conditions of marker informativity and density with both real and simulated datasets. The results show the efficiency of our program to select the most informative markers even if there is a wide range of informativity for whole genome scan mapping analyses. In case of combination of different experimental crosses, the multidesign mode can optimize the SNP markers selection. Conclusion Written in PERL, it assures a maximum portability to other operating systems (OS and the source code availability for user modifications. Except for the simulation mode which could be time consuming, MarkerSet can compute results in a very short time.

  4. APPLICATION OF MOLECULAR MARKERS IN FARM ANIMAL IMPROVEMENT: PROSPECTS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    V.N. EBEGBULEM

    2013-05-01

    Full Text Available The discovery of genetic polymorphism at the DNA sequence level has been exploited as markers to explain the observed phenotypic variability in animals. Molecular markers have proven to be more reliable than other forms of genetic markers. The overview of the applications of molecular markers in the areas of genetic diversity conservation, identification of disease carriers, parentage determination, marker-assisted selection, transgenesis, sex-determination; and the enumeration of some challenges to the application of these markers in the developing countries, especially Nigeria, form the crux of this paper. Some of the challenges include economic factors, mechanical and logistics factors, lack of funding/grants for research, IPR issues and lack of adequately trained personnel in areas of molecular genetics.

  5. Marker-Assisted Selection Backgrounder

    OpenAIRE

    Van Eenennaam, Alison

    2004-01-01

    DNA (deoxyribonucleic acid) is a molecule that is shaped like a double helix and made up of pairs of nucleotides. DNA transmits genetic information. DNA is packaged into chromosomes which are located within the nucleus of all cells. Every cell in the body contains all of the chromosomes that collectively make up the genome of that organism. DNA codes for amino acids which are linked together to make proteins. A gene is a stretch of DNA that specifies all of the amino acids that make up a sing...

  6. Genetic characterization of Barbari goats using microsatellite markers

    OpenAIRE

    Ramamoorthi, J.; K.Thilagam; Sivaselvam, S. N.; Karthickeyan, S. M. K.

    2009-01-01

    Genetic variation in Barbari goats, a highly prolific breed distributed widely in the northern part of India, known for better milk and meat quality, was studied as a part of genetic characterization and conservation. The genomic DNA from 50 unrelated Barbari goats were amplified via PCR with a panel of 21 microsatellite markers, and resolved through 6 per cent denaturing polyacrylamide gel electrophoresis followed by silver staining. The number of alleles ranged from 4 to 11, with allele siz...

  7. Circulating cell free DNA as a predictor of systemic lupus erythematosus severity and monitoring of therapy

    Directory of Open Access Journals (Sweden)

    Olfat M. Hendy

    2016-01-01

    Conclusion: Our findings support that the measurement of cf-DNA appears to be a useful marker in addition to laboratory tests used in SLE diagnosis. High correlation with markers of disease severity suggesting its role in disease pathogenesis and decreasing its level after therapy makes it to be a marker of treatment follow-up.

  8. Cell-Free Fetal DNA and Cell-Free Total DNA Levels in Spontaneous Abortion with Fetal Chromosomal Aneuploidy

    OpenAIRE

    Ji Hyae Lim; Min Hyoung Kim; You Jung Han; Da Eun Lee; So Yeon Park; Jung Yeol Han; Moon Young Kim; Hyun Mee Ryu

    2013-01-01

    BACKGROUND: Cell-free fetal DNA and cell-free total DNA in maternal circulation have been proposed as potential markers for noninvasive monitoring of the placental condition during the pregnancy. However, the correlation of and change in cell-free fetal DNA and cell-free total DNA in spontaneous abortion (SA) with fetal chromosomal aneuploidy have not yet been reported. Therefore, we investigated cell-free fetal DNA and cell-free total DNA levels in SA women with fetal chromosomal aneuploidy....

  9. Recent innovation in microbial source tracking using bacterial real-time PCR markers in shellfish

    International Nuclear Information System (INIS)

    Highlights: ► DNA extraction from intravalvular liquid is promising for microbial source tracking in oysters. ► Host-associated bacterial markers in shellfish digestive tissues were difficult to assess with real-time PCR. ► DNA extracts from shellfish flesh appeared to have low inhibitor levels but low marker levels. ► Protocol transfer from one shellfish species to another does not appear possible. -- Abstract: We assessed the capacity of real-time PCR markers to identify the origin of contamination in shellfish. Oyster, cockles or clams were either contaminated with fecal materials and host-associated markers designed from Bacteroidales or Catellicoccus marimammalium 16S RNA genes were extracted from their intravalvular liquid, digestive tissues or shellfish flesh. Extraction of bacterial DNA from the oyster intravalvular liquid with FastDNA spin kit for soil enabled the selected markers to be quantified in 100% of artificially contaminated samples, and the source of contamination to be identified in 13 out of 38 naturally contaminated batches from European Class B and Class C areas. However, this protocol did not enable the origin of the contamination to be identified in cockle or clam samples. Although results are promising for extracts from intravalvular liquid in oyster, it is unlikely that a single protocol could be the best across all bacterial markers and types of shellfish

  10. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

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

  11. DNA glue

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  12. Authentication of shankhpushpi by RAPD markers

    Directory of Open Access Journals (Sweden)

    Showkat Hussain Ganie

    2012-05-01

    Full Text Available Background: “Shankhpushpi”, an important indigenous drug of Ayurveda, an ancient system of Indian medicine, improves memory power and intellect. It is used in many Ayurvedic formulations, either singly or in combination with other herbs, meant for sleeplessness, epilepsy, hallucinations and anxiety. At least three different plant species viz., Clitoria ternatea, Convolvulus pluricaulis and Evolvulus alsinoides are as the source of this drug in the different parts of the country. Because of increased demand and high price, shankhpushpi is often adulterated in the trade by other related species. Therefore, a reliable authentication method is needed to facilitate differentiation/identification of the genuine material from its adulterants. The present study was aimed at developing RAPD-based markers for identification of C. pluricaulis, E. alsinoides and C. ternatea, and analyzing the market samples of the drug to ascertain their authenticity. Material and Methods: Fresh samples of source plants of shankhpushpi were collected from Ghaziabad and Delhi. The market samples were procured from the crude-drug markets of different geographical regions of India. The amplified polymorphic DNA (RAPD technique was employed for characterization of genuine and market samples. Twenty-five 11-mer oligonucleotide primers were used to amplify the DNA isolated. Results: Out of 25 primers, only four (OPN-03, OPN-04, OPN-05 and OPN-06 yielded amplification products that produced clear and reproducible bands, which were used to characterize the market samples. RAPD profile of some market samples did not match with the authentic samples, indicating that these samples were either adulterated or spurious. Conclusion: The RAPD markers developed in this study may provide guidance for the authentication of plant materials traded as shankhpushpi.

  13. DNA microsatellite analysis for tomato genetic differentiation

    OpenAIRE

    Miskoska-Milevska Elizabeta; Popovski Zoran T.; Dimitrievska Blagica; Bandzo Katerina

    2015-01-01

    Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11) in genetic differentiation of six morphologically different tomato v...

  14. Inferring ethnicity from mitochondrial DNA sequence

    OpenAIRE

    Lee, Chih; Măndoiu, Ion I; Nelson, Craig E.

    2011-01-01

    Background The assignment of DNA samples to coarse population groups can be a useful but difficult task. One such example is the inference of coarse ethnic groupings for forensic applications. Ethnicity plays an important role in forensic investigation and can be inferred with the help of genetic markers. Being maternally inherited, of high copy number, and robust persistence in degraded samples, mitochondrial DNA may be useful for inferring coarse ethnicity. In this study, we compare the per...

  15. Identification of RAPD markers and their use for molecular mapping in pea (Pisum sativum L.).

    Science.gov (United States)

    Cheghamirza, Kianoosh; Koveza, Oksana; Konovalov, Fedor; Gostimsky, Sergei

    2002-01-01

    The RAPD method (Random Amplified Polymorphic DNA) was used for identifying and mapping new molecular markers in pea. RAPD analysis of various cultivars and lines of pea was carried out using 10-mer random primers. The presence of multiple polymorphism between cultivars and lines was revealed; at least one fragment for any given primer was present in the DNA of one form of pea and absent in the DNA of another line or cultivar. To detect molecular markers linked to the genes of chi-15, xa-18 and also to the 12 morphological markers of the L-1238 line, the F2 populations (Chi-15 ? L-1238), (Vio ? L-1238), (Xa-18 ? L-1238), (L-111 ? Chi-15) and (L-84 ? Xa-18) were studied via bulked segregant analysis. DNA molecular analysis of F1 hybrids revealed the presence of parental polymorphic fragments in all of the populations. The study of the F2 plants showed that the obtained fragments are inherited as Mendelian factors. 13 RAPD-markers linked to genes of A/a (flower color), I/i (seed color), Gp/gp (pod color), R/r (seed form), S/s (seeds linkage), and also to genes of Chi-15/chi-15 (leaf color) and Xa-18/xa-18 (leaf color) were discovered. The study of individual plant DNA from the F2 populations allowed us to determine the genetic distances between genes and the RAPD markers linked to them.

  16. A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers

    OpenAIRE

    ASHWANI KUMAR; NEELAM VERMA

    2012-01-01

    Kumar A, Verma N. 2012. A comparative phylogenetic analysis of medicinal plant Tribulus terrestris in Northwest India revealed by RAPD and ISSR markers. Biodiversitas 13: 107-113. Several DNA marker systems and associated techniques are available today for fingerprinting of plant varieties. A total of 5 RAPD and 8 ISSR primers were used. Amplification of genomic DNA of the 6 genotypes, using RAPD analysis, yielded 164 fragments that could be scored, of which 47 were polymorphic, with an avera...

  17. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    OpenAIRE

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open readin...

  18. [DNA computing].

    Science.gov (United States)

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

    2011-01-01

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

  19. DNA probes

    International Nuclear Information System (INIS)

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

  20. Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents

    DEFF Research Database (Denmark)

    Birkbak, Nicolai J.; Wang, Zhigang C.; Kim, Ji-Young;

    2012-01-01

    DNA repair competency is one determinant of sensitivity to certain chemotherapy drugs, such as cisplatin. Cancer cells with intact DNA repair can avoid the accumulation of genome damage during growth and also can repair platinum-induced DNA damage. We sought genomic signatures indicative...... of defective DNA repair in cell lines and tumors and correlated these signatures to platinum sensitivity. The number of subchromosomal regions with allelic imbalance extending to the telomere (NtAI) predicted cisplatin sensitivity in vitro and pathologic response to preoperative cisplatin treatment in patients....... Thus, accumulation of telomeric allelic imbalance is a marker of platinum sensitivity and suggests impaired DNA repair. SIGNIFICANCE: Mutations in BRCA genes cause defects in DNA repair that predict sensitivity to DNA damaging agents, including platinum; however, some patients without BRCA mutations...

  1. [Tumor markers for hepatocellular carcinoma].

    Science.gov (United States)

    Tateishi, Ryosuke; Enooku, Kenichiro; Shiina, Shuichiro; Koike, Kazuhiko

    2012-05-01

    Three tumor markers for hepatocellular carcinoma (HCC) are available in Japan: alpha-fetoprotein (AFP), protein induced by vitamin K absence or antagonists-II (PIVKA-II), and Lens culinaris agglutinin-reactive fraction of alpha-fetoprotein (AFP-L3). Although AFP has drawbacks in its specificity, it is widely utilized in treatment evaluation and prognosis prediction. PIVKA-II is a unique marker that does not correlate with AFP value and can predict microvascular invasion. AFP-L3 is a highly specific marker and strong predictor of poor prognosis. These three markers are indispensable in every aspect of clinical practice of hepatocellular carcinoma including surveillance, diagnosis, treatment evaluation, and prognosis prediction.

  2. Serum Markers of Intrahepatic Cholangiocarcinoma

    Directory of Open Access Journals (Sweden)

    Giulia Malaguarnera

    2013-01-01

    Full Text Available Cholangiocarcinoma (CCA is a relatively rare type of primary liver cancer that originates in the bile duct epithelium. It is an aggressive malignancy typified by unresponsiveness to chemotherapy and radiotherapy. Despite advances in radiologic techniques and laboratory diagnostic test, the diagnosis of CCA remains highly challenging. Development in molecular techniques has led to go into the possible use of serum markers in diagnosing of cholangiocarcinoma. This review summarizes the principal characteristics of serum markers of cholangiocarcinoma. The tumour markers used frequently such as Carbohydrate antigen 19-9 (CA 19-9, Carcinogenic Embryonic antigen (CEA, and Cancer Antigen 125 have shown sufficient sensitivity and specificity to detect and monitor CCA. In particular, the combination of these tumour markers seems to increase their efficiency in diagnosing of cholangiocarcinoma. New markers such as Soluble fragment of cytokeratin 19 (CYFRA 21-1 Mucins, Tumour Markers2- pyruvate-Kinase (TuM2- PK and metalloproteinase-7 (MMP-7 have been recently shown to help in the diagnosis of CCA, with in some cases a prognostic value.

  3. One hundred fifty-four genetic markers for the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Knutson, Todd P; Chaves, Lee D; Hall, Majken K; Reed, Kent M

    2004-12-01

    Identifying and selectively breeding for improved traits is one of the ultimate goals of genetic research in agriculturally important species. Genome characterization and analysis are important first steps in this process. Genetic linkage maps based on the linear order of polymorphic DNA markers are typically developed through statistical analysis of inheritance patterns in pedigreed families. To develop microsatellite markers for further improvement of the turkey genetic linkage map, small-insert genomic libraries were screened for tandem repeats. Oligonuclotide primers were designed to amplify 164 microsatellite-containing fragments from genomic DNA. Genetic polymorphisms at 154 markers were determined by genotyping the F(1) individuals of two resource populations. Markers determined as segregating in the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) reference population were used to genotype F(2) individuals and a two-point linkage analysis was performed.

  4. DNA data

    Data.gov (United States)

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

  5. Molecular markers of nuclear restoration gene Rf1 in sunflower using bulked segregant analysis-RAPD

    Institute of Scientific and Technical Information of China (English)

    季静; 王罡; E.Belhassen; H.Serieys; A.Berville

    1996-01-01

    Restoration of cytoplasmic male sterility (CMS) in sunflower was demonstrated to be controlled by polygenes by analysing 982 effective crosses among 109 self-crossed lines and 16 CMS lines. Two self-crossed lines and one CMS line with distinct genotypes were applied to creation of segregating populations for DNA bulks of the target gene Rfl. Bulked DNA was prepared in order to investigate single gene Rfl and its gene marker among polygenic characters at the same genetic background. Using 80 10-mer operon primers, 620 RAPD reactions were carried out between fertile and sterile DNA bulks. In about 800 loci, primary results showed that 8 were related to the restoration genes. Furthermore. 2 were confirmed as RAPD markers for gene Rfl by examining 9 maintenance and 7 restoration lines. This method is the improvement for bulked segregant analysis[1] with which markers of single gene of target can be identified rapidly among polygenic characters.

  6. New environmental metabarcodes for analysing soil DNA

    DEFF Research Database (Denmark)

    Epp, Laura S.; Boessenkool, Sanne; Bellemain, Eva P.;

    2012-01-01

    Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for ta....... The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool....

  7. Exposures that may affect sperm DNA integrity

    DEFF Research Database (Denmark)

    Håkonsen, L B; Spano, M; Bonde, J P;

    2012-01-01

    Prenatal lifestyle exposures are linked to alterations in conventional semen characteristics. Sperm DNA integrity is another marker of semen quality shown to be altered in mice prenatally exposed to chemicals. From a Danish pregnancy cohort established in 1984-1987, sons were selected for a follo...

  8. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

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

  9. Biochemical Markers of Myocardial Damage.

    Science.gov (United States)

    Bodor, Geza S

    2016-04-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  10. Imaging markers for Alzheimer disease

    Science.gov (United States)

    Bocchetta, Martina; Chételat, Gael; Rabinovici, Gil D.; de Leon, Mony J.; Kaye, Jeffrey; Reiman, Eric M.; Scheltens, Philip; Barkhof, Frederik; Black, Sandra E.; Brooks, David J.; Carrillo, Maria C.; Fox, Nick C.; Herholz, Karl; Nordberg, Agneta; Jack, Clifford R.; Jagust, William J.; Johnson, Keith A.; Rowe, Christopher C.; Sperling, Reisa A.; Thies, William; Wahlund, Lars-Olof; Weiner, Michael W.; Pasqualetti, Patrizio; DeCarli, Charles

    2013-01-01

    Revised diagnostic criteria for Alzheimer disease (AD) acknowledge a key role of imaging biomarkers for early diagnosis. Diagnostic accuracy depends on which marker (i.e., amyloid imaging, 18F-fluorodeoxyglucose [FDG]-PET, SPECT, MRI) as well as how it is measured (“metric”: visual, manual, semiautomated, or automated segmentation/computation). We evaluated diagnostic accuracy of marker vs metric in separating AD from healthy and prognostic accuracy to predict progression in mild cognitive impairment. The outcome measure was positive (negative) likelihood ratio, LR+ (LR−), defined as the ratio between the probability of positive (negative) test outcome in patients and the probability of positive (negative) test outcome in healthy controls. Diagnostic LR+ of markers was between 4.4 and 9.4 and LR− between 0.25 and 0.08, whereas prognostic LR+ and LR− were between 1.7 and 7.5, and 0.50 and 0.11, respectively. Within metrics, LRs varied up to 100-fold: LR+ from approximately 1 to 100; LR− from approximately 1.00 to 0.01. Markers accounted for 11% and 18% of diagnostic and prognostic variance of LR+ and 16% and 24% of LR−. Across all markers, metrics accounted for an equal or larger amount of variance than markers: 13% and 62% of diagnostic and prognostic variance of LR+, and 29% and 18% of LR−. Within markers, the largest proportion of diagnostic LR+ and LR− variability was within 18F-FDG-PET and MRI metrics, respectively. Diagnostic and prognostic accuracy of imaging AD biomarkers is at least as dependent on how the biomarker is measured as on the biomarker itself. Standard operating procedures are key to biomarker use in the clinical routine and drug trials. PMID:23897875

  11. Development and characterization of microsatellite markers for lippia (Phyla canescens: Verbenaceae).

    Science.gov (United States)

    Fatemi, M; Gross, C L

    2008-11-01

    Lippia (Phyla canescens: Verbenaceae) is a serious weed of wetlands, riparian zones and floodplains, particularly in eastern Australia where many Ramsar wetlands are threatened by hydrological changes precipitated by soil-accreting lippia mats. Enriched genomic DNA libraries were used to develop nine informative microsatellite markers. These markers will be valuable tools to understand the genetic structure of the lippia populations in different regions throughout the world. PMID:21586039

  12. Proliferating cell nuclear antigen: a marker for hepatocellular proliferation in rodents.

    OpenAIRE

    Eldrige, S R; Butterworth, B E; Goldsworthy, T L

    1993-01-01

    Two different markers for quantitating cell proliferation were evaluated in livers of control and chemically treated mice and rats. Proliferating cell nuclear antigen (PCNA), an endogenous cell replication marker, and bromodeoxyuridine (BrdU), an exogenously administered DNA precursor label, were detected in formalin-fixed, paraffin-embedded tissues using immunohistochemical techniques. The percentage of cells in S phase (labeling indexes, LI) evaluated as PCNA- or BrdU-positive hepatocellula...

  13. [DNA-technologies application for early detection of caries predisposition].

    Science.gov (United States)

    Gorbunova, I L

    2006-01-01

    In the paper the possible use of modern DNA-technologies for estimation of gene pool, dental hard tissue resistance to caries prognosis, hereditary predisposition to the main oral diseases diagnosis are presented. Application potentialities of DNA-markers for multiple testing in population are identified. Today very little information is available concerning Russia gene pool characteristics in genome polymorphism, DNA-markers-allelic gene variants, related to the caries predisposition. These characteristics are needed to solve the problems concerning dental diseases prophylaxis and treatment.

  14. What Is Mitochondrial DNA?

    Science.gov (United States)

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

  15. DNA and RNA sensor

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  16. Tumour markers in gastrointestinal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Lamerz, R.

    1988-02-01

    For non-endocrine gastrointestinal tumours the following tumour markers are of clinical interest: For esophageal cancer CEA (sensitivity, s: 40-60%) and SCC (squamous cell carcinoma antigen, x: 20-50%); for gastric cancer CEA (s: 30-40%) as well as CA 19-9 (s: 30-40%) because of complementary results (additive s: 50-60); for hepatocellular cancer AFP (first choice, s: 70-90%; second choice CA 19-9, s: 50-70%); for cholangiocellular cancer CA 19-9 (s: 40-70%); for secondary liver cancer in general CEA; for biliary tract cancer CA 19-9 (s: 40-70%) as well as for excretory pancreatic cancer (s: 70-90%); for colorectal cancer CEA (s: 40-70%) as a first choice marker, and CA 19-9 (s: 20-60%) as a second choice marker, and for anal cancer SCC. The frequency of tumour marker determinations depends on follow-up care recommendations for different tumour diseases (e.g. 1-3 monthly during the 1st and 2nd postoperative year, following chemotherapy courses, on change of therapy, on restaging and at unclear alteration of the clinical state). Tumour markers are only valuable adjuncts to the medical care of tumour patients and therefore useless as solitary findings or on missing therapeutic consequence.

  17. New markers for old stains: Stable mRNA markers for blood and saliva identification from up to 16-year-old stains

    NARCIS (Netherlands)

    D. Zubakov; M. Kokshoorn; A. Kloosterman; M. Kayser

    2009-01-01

    In forensic science, the unequivocal identification of the cellular origin of crime scene samples used for DNA profiling can provide crucial information for crime scene reconstruction. We have previously shown that various mRNA markers from genes with expression patterns specific for blood and saliv

  18. DNA vaccines

    Science.gov (United States)

    Gregersen, Jens-Peter

    2001-12-01

    Immunization by genes encoding immunogens, rather than with the immunogen itself, has opened up new possibilities for vaccine research and development and offers chances for new applications and indications for future vaccines. The underlying mechanisms of antigen processing, immune presentation and regulation of immune responses raise high expectations for new and more effective prophylactic or therapeutic vaccines, particularly for vaccines against chronic or persistent infectious diseases and tumors. Our current knowledge and experience of DNA vaccination is summarized and critically reviewed with particular attention to basic immunological mechanisms, the construction of plasmids, screening for protective immunogens to be encoded by these plasmids, modes of application, pharmacokinetics, safety and immunotoxicological aspects. DNA vaccines have the potential to accelerate the research phase of new vaccines and to improve the chances of success, since finding new immunogens with the desired properties is at least technically less demanding than for conventional vaccines. However, on the way to innovative vaccine products, several hurdles have to be overcome. The efficacy of DNA vaccines in humans appears to be much less than indicated by early studies in mice. Open questions remain concerning the persistence and distribution of inoculated plasmid DNA in vivo, its potential to express antigens inappropriately, or the potentially deleterious ability to insert genes into the host cell's genome. Furthermore, the possibility of inducing immunotolerance or autoimmune diseases also needs to be investigated more thoroughly, in order to arrive at a well-founded consensus, which justifies the widespread application of DNA vaccines in a healthy population.

  19. DNA nanotechnology

    Directory of Open Access Journals (Sweden)

    Nadrian C Seeman

    2003-01-01

    We are all aware that the DNA found in cells is a double helix consisting of two antiparallel strands held together by specific hydrogen-bonded base pairs; adenine (A always pairs with thymine (T, and guanine (G always pairs with cytosine (C. The specificity of this base pairing and the ability to ensure that it occurs in this fashion (and not some other1 is key to the use of DNA in materials applications. The double helical arrangement of the two molecules leads to a linear helix axis, linear not in the geometrical sense of being a straight line, but in the topological sense of being unbranched. Genetic engineers discovered in the 1970s how to splice together pieces of DNA to add new genes to DNA molecules2, and synthetic chemists worked out convenient syntheses for short pieces of DNA (up to ∼100–150 units in the 1980s3. Regardless of the impact of these technologies on biological systems, hooking together linear molecules leads only to longer linear molecules, with circles, knots, and catenanes perhaps resulting from time to time.

  20. Biological Markers and Salivary Cortisol

    DEFF Research Database (Denmark)

    Hansen, Åse Marie; Gunnarsson, Lars-Gunnar; Harris, Anette;

    2011-01-01

    This chapter focuses on salivary cortisol in relation to biological markers. Specifically, associations with conventional cardiovascular risk factors and metabolic abnormalities (body mass index, waist circumference, waist/hip ratio, lipid status, glucose, blood pressure, heart rate and heart rate...... variations and pharmacological interventions were also excluded. After meeting all exclusion criteria, 42 papers remained. In total, 273 associations between salivary cortisol and any of the markers mentioned were studied, comprising 241 associations on metabolic abnormalities, 30 on inflammation, and 2...... on stress hormones. Of the salivary cortisol measures reported for evaluations of all markers tested were 136 (49%) single time points, 100 (37%) deviations, 36 (13%) AUC, and 1 (1%) dexamethasone test. Of these, 72 (26%) were statistically significant, and 201 (74%) indicated non-significant findings...