WorldWideScience

Sample records for ancestry-sensitive dna markers

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. A novel cell permeable DNA replication and repair marker

    OpenAIRE

    Herce, Henry D.; Rajan, Malini; Lättig-Tünnemann, Gisela; Fillies, Marion; Cardoso, M. Cristina

    2014-01-01

    Proliferating Cell Nuclear Antigen (PCNA) is a key protein in DNA replication and repair. The dynamics of replication and repair in live cells is usually studied introducing translational fusions of PCNA. To obviate the need for transfection and bypass the problem of difficult to transfect and/or short lived cells, we have now developed a cell permeable replication and/or repair marker. The design of this marker has three essential molecular components: (1) an optimized artificial PCNA bindin...

  9. 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

  10. 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

  11. 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)

  12. Diagnostic markers of urothelial cancer based on DNA methylation analysis

    International Nuclear Information System (INIS)

    Early detection and risk assessment are crucial for treating urothelial cancer (UC), which is characterized by a high recurrence rate, and necessitates frequent and invasive monitoring. We aimed to establish diagnostic markers for UC based on DNA methylation. In this multi-center study, three independent sample sets were prepared. First, DNA methylation levels at CpG loci were measured in the training sets (tumor samples from 91 UC patients, corresponding normal-appearing tissue from these patients, and 12 normal tissues from age-matched bladder cancer-free patients) using the Illumina Golden Gate methylation assay to identify differentially methylated loci. Next, these methylated loci were validated by quantitative DNA methylation by pyrosequencing, using another cohort of tissue samples (Tissue validation set). Lastly, methylation of these markers was analyzed in the independent urine samples (Urine validation set). ROC analysis was performed to evaluate the diagnostic accuracy of these 12 selected markers. Of the 1303 CpG sites, 158 were hyper ethylated and 356 were hypo ethylated in tumor tissues compared to normal tissues. In the panel analysis, 12 loci showed remarkable alterations between tumor and normal samples, with 94.3% sensitivity and 97.8% specificity. Similarly, corresponding normal tissue could be distinguished from normal tissues with 76.0% sensitivity and 100% specificity. Furthermore, the diagnostic accuracy for UC of these markers determined in urine samples was high, with 100% sensitivity and 100% specificity. Based on these preliminary findings, diagnostic markers based on differential DNA methylation at specific loci can be useful for non-invasive and reliable detection of UC and epigenetic field defect

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

  14. 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

  15. 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)

  16. 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.

  17. Microsatellite markers- A new practice of DNA based markers in molecular genetics

    Directory of Open Access Journals (Sweden)

    Neha Mittal

    2009-01-01

    Full Text Available Microsatellites are randomly interspersed within eukaryotic genomes. These are also known as SSRs (Simple sequence repeats, STRs (Short tandem repeats, STMs (Sequence tagged microsatellites, and VNTRs (Variable number of tandem repeats, are short 1-8 bp long monomer sequences, which randomly repeated in the DNA sequences. Conservation of the flanking sequence of each microsatellite locus allows the design of primers for PCR amplification. Then amplified products are separated by electrophoresis (either on high resolution agarose or acrylamide gels to detect the polymorphism in repeat length. These markers don′t require the radioactivity for detection and these are extremely robust as well as easily exchanged between the laboratories. Multiplex reactions of SSRs can easily be run to speed up the assay, when the products have non-overlapping size ranges. Microsatellites have emerged as the marker of choice for plant genetic resources and molecular genetic applications due to their abundant and uniform distribution throughout the genome, highly variable nature with regard to repeat number, show co-dominant inheritance, ease of transferability and reproducibility, and found highly efficient in the DNA fingerprinting analysis, as well as can also be utilized in the pedigree analysis of different plant species. This marker system has been proven beneficial for crop improvement and for breeding applications in many species. These are also found the useful tools to detect the polymorphisms in low level of intraspecific diversity. Consequently, in the present review we have described the various characteristic features and properties of these highly polymorphic microsatellite markers, which found beneficial in several molecular genetic and breeding applications.

  18. A novel cell permeable DNA replication and repair marker.

    Science.gov (United States)

    Herce, Henry D; Rajan, Malini; Lättig-Tünnemann, Gisela; Fillies, Marion; Cardoso, M Cristina

    2014-01-01

    Proliferating Cell Nuclear Antigen (PCNA) is a key protein in DNA replication and repair. The dynamics of replication and repair in live cells is usually studied introducing translational fusions of PCNA. To obviate the need for transfection and bypass the problem of difficult to transfect and/or short lived cells, we have now developed a cell permeable replication and/or repair marker. The design of this marker has three essential molecular components: (1) an optimized artificial PCNA binding peptide; (2) a cell-penetrating peptide, derived from the HIV-1 Trans Activator of Transcription (TAT); (3) an in vivo cleavable linker, linking the two peptides. The resulting construct was taken up by human, hamster and mouse cells within minutes of addition to the media. Inside the cells, the cargo separated from the vector peptide and bound PCNA effectively. Both replication and repair sites could be directly labeled in live cells making it the first in vivo cell permeable peptide marker for these two fundamental cellular processes. Concurrently, we also introduced a quick peptide based PCNA staining method as an alternative to PCNA antibodies for immunofluorescence applications. In summary, we present here a versatile tool to instantaneously label repair and replication processes in fixed and live cells. PMID:25484186

  19. 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 of......, only two trees did not belong to either of the two clones. Genotyping of commercial common lime trees that would be planted in place of the felled trees during the restoration project was also performed. Samples of 20 newly planted trees all possessed the same genotype as the majority of the old felled...... subsample of the trees had the same genotype. Trees from four other locations with historical avenues/plantings from the 17th century were also genotyped. The two clones registered in the first location were also found at the other four locations. Of 76 trees from the other historical avenues/plantings...

  20. Persistence of mitochondrial DNA markers as fecal indicators in water environments.

    Science.gov (United States)

    He, Xiwei; Chen, Huimei; Shi, Wei; Cui, Yibin; Zhang, Xu-Xiang

    2015-11-15

    Mitochondrial DNA (mtDNA) polymerase chain reaction (PCR) technology has recently been developed to identify sources of fecal contamination, but information regarding environmental fate of mtDNA is limited. In this study, quantitative real-time PCR was used to determine the persistence of three species-specific mtDNA markers (human, pig and chicken) in river microcosms under different laboratory conditions and in dialysis tubes incubated in river environments during different seasons. Human feces had a higher abundance of mtDNA marker than pig and chicken feces. A biphasic decay pattern was observed for the mtDNA markers in microcosms incubated in darkness, and T90 (time needed for 90% reduction) ranged from 2.03 to 13.83 d. Each species-specific mtDNA marker persisted for relatively longer time at lower temperatures, and light exposure and predation increased the decay rates. Field experiments showed that the mtDNA markers could survive for longer time in winter (T90: 1.79-4.37 d) than in summer (T90: 0.60-0.75 d). Field application of mtDNA technology indicated that the markers were mainly distributed on the sites near animal breeding plants and had lower abundance in downstream water of the receiving river. This study expands our knowledge of the environmental fate of mtDNA markers and the results may be useful for practical application of the technology in fecal source tracking. PMID:26172605

  1. 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)

  2. 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.

  3. Tagging of blast resistance gene(s) to DNA markers and marker-assisted selection (MAS) in rice improvement

    International Nuclear Information System (INIS)

    This paper reports progress made on the tagging of blast resistance gene(s) to DNA markers and on the initiation of marker-assisted selection (MAS) for blast resistance in rice improvement. A pair of near isogenic lines, K8OR and K79S, were developed using a Chinese landrace Hong-jiao-zhan as the resistance donor. Ten putatively positive markers were identified by screening 177 mapped DNA markers. Using the F2 population of 143 plants and the derived F3 lines, three Restriction Fragment Length Polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were identified to be closely linked to the blast resistance gene Pi-12(t). The genetic distance between Pi-12(t) and the closest marker RG869 was 5.1 cM. By employing the bulk segregant analysis (BSA) procedure, six of 199 arbitrary primers were found to produce positive Randomly Amplified Polymorphic DNA (RAPD) bands. Tight linkage between Pi-12(t) and three RAPD bands, each from a different primer, was confirmed after amplification of DNA of all F2 individuals. Two fragments were cloned and sequenced, and two sequence characterised amplified re-ion (SCAR) markers were established. In two other F3 populations, Xian-feng I/Tetep and Xian-feng, 1/Hong-jiao-zhan, the blast resistance was found to be controlled by interactions of two or more genes. One resistance gene was located in the vicinity of RG81 in both populations. Work to identify other gene(s) is currently under way. Marker assisted selection for blast resistance was initiated. Crosses were made between elite varieties and blast resistance donors to develop populations for DNA marker-assisted selection of blast resistance. In addition, 48 varieties widely used in current rice breeding programs were provided by rice breeders. DNA marker-based polymorphism among, these varieties and resistance donors were analysed to produce a database for future MAS program. (author)

  4. 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...

  5. Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification

    OpenAIRE

    Waldron Julie; Peace Cameron P.; Searle Iain R.; Furtado Agnelo; Wade Nick; Findlay Ian; Graham Michael W.; Carroll Bernard J.

    2002-01-01

    Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA ma...

  6. 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.

  7. 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.

  8. 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

  9. 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)

  10. Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

    OpenAIRE

    Schneider, Kevin L.; Marrero, Glorimar; Alvarez, Anne M.; Presting, Gernot G.

    2011-01-01

    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...

  11. DNA Fingerprinting Eastern Redbud Cultivars (Cercis canadensis) Using SSR Markers

    Science.gov (United States)

    In this study we present data for a subset of SSR loci, 76 out of the 130 high-quality loci, which were selected out of hundreds of SSR loci identified from a SSR-enriched library. SSR markers are abundant in eukaryotic genomes and are highly reproducible. Previously, we have used SSR markers to e...

  12. 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

  13. 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...

  14. 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

  15. 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

  16. 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.

  17. 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

  18. Development of identification process for insect group using radiation marker DNA

    International Nuclear Information System (INIS)

    Detection of a band pattern for insect groups was tried by using radiation marked DNA clone. A rapid segregation process for poly-type DNA segment was investigated. A band pattern of silkworm was detected by analysis using DNA type transposon, K1.4. The exon regions on genes of hemiptera insect were segregated by in vitro cloning. Band patterns of the silkworm and the other insects were detected by identification process of DNA clone and radiation marker. Family singularity mutation existed in the inserted position of transposon. The family of insect was identified easily by the difference of the detection band patterns. Effective band pattern for family discrimination were obtained by analysis for a part of mitochondria DNA and ribosomal DNA. DNA segregation process was investigated by using the enriched library, also. (M. Suetake)

  19. Z-DNA, a new in situ marker for transcription

    Czech Academy of Sciences Publication Activity Database

    Černá, Adriana; Cuadrado, A.; Jouve, N.; de la Espina, S. M. D.; De la Torre, C.

    2004-01-01

    Roč. 48, č. 1 (2004), s. 49-55. ISSN 1121-760X R&D Projects: GA AV ČR IBS5038351 Institutional research plan: CEZ:AV0Z5038910 Keywords : Allium cepa * Z-DNA immunodetection * in situ run-on transcription Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.845, year: 2004

  20. DNA fingerprinting of groundnut (Arachis hypogaea L.) varieties of Tirupati using SSR markers

    OpenAIRE

    Y. Amaravathi, R.P. Vasanthi, E. Siva Kumar, M. Purushotham and T. Giridhara Krishna

    2014-01-01

    Unambiguous identification of varieties is important for registration and certification of newly released varieties. Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widely used for fingerprinting in a number of crop varieties. In the present study, a set of 12 groundnut varieties released from Regional Agricultural Research Station, Tirupati were fingerprinted employing SSR markers. A total of 300 SSR were screened and fifteen...

  1. DNA damage markers in dermal fibroblasts in vitro reflect chronological donor age

    DEFF Research Database (Denmark)

    Waaijer, Mariëtte E C; Croco, Eleonora; Westendorp, Rudi G J; Slagboom, P Eline; Sedivy, John M; Lorenzini, Antonello; Maier, Andrea B

    2016-01-01

    The aging process is accompanied by an accumulation of cellular damage, which compromises the viability and function of cells and tissues. We aim to further explore the association between in vitro DNA damage markers and the chronological age of the donor, as well as long-lived family membership...... damage markers and long-lived family membership or cardiovascular disease. Results were comparable when fibroblasts were stressed in vitro with rotenone. In conclusion, we found that DNA damage foci of cultured fibroblasts are significantly associated with the chronological age, but not biological age...

  2. 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.

  3. 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.

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

    OpenAIRE

    Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J L; Levesque, C.A.; W. Chen; Crous, P.W.; Boekhout, T.; Damm, U.; Hoog, de, R.; Eberhardt, U.; Groenewald, J.Z.; Groenewald, M.; Hagen, F.

    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 thre...

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

    OpenAIRE

    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 wer...

  6. 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 ...

  7. 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

  8. 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

  9. 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)

  10. 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

  11. 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.

  12. 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

    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

  13. 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

  14. 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.

  15. 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...

  16. 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...

  17. Natural hybridization in tropical spikerushes of Eleocharis subgenus Limnochloa (Cyperaceae): Evidence from morphology and DNA markers

    Czech Academy of Sciences Publication Activity Database

    Košnar, J.; Košnar, Ji.; Macek, Petr; Herbstová, Miroslava; Rejmánková, E.; Stech, M.

    2010-01-01

    Roč. 97, č. 7 (2010), s. 1229-1240. ISSN 0002-9122 Institutional research plan: CEZ:AV0Z60050516; CEZ:AV0Z50510513 Keywords : Belize * Cyperaceae * DNA markers * hybridization Subject RIV: EB - Genetics ; Molecular Biology; EB - Genetics ; Molecular Biology (BU-J) Impact factor: 3.052, year: 2010

  18. 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.

  19. Molecular Characterization of Some Turkish Olive Cultivars Using Random Amplified Polymorphic DNA (RAPD Markers

    Directory of Open Access Journals (Sweden)

    Ergün KAYA

    2015-03-01

    Full Text Available Olive (Olea europea L. is one of the oldest cultivated plants characteristic in the Mediterranean area, where it is the most important oilproducing crop. The cultivated olive (O. europaea L. var. europaea is propagated by cutting or grafting, whereas wild olive (O. europaea L. var. sylvestris is reproduced from seeds. These two olive types are interfertile and have led to a large number of varieties. Morphological descriptions are not entirely reliable, due to numerous synonyms and homonyms in designations, labelling mistakes, the presence of varietal clones, and the uncertain identification methods thus far applied. Molecular markers, as random amplified polymorphic DNA (RAPD markers, are environment-independent and efficient to identify olive varieties and to detect synonymous and homonymous. In this study, fifteen selected RAPD markers are used for determination of relationships among twenty individuals belonging to four important Turkish olive cultivars. Our results showed that RAPD markers can be used to differentiate olive cultivars

  20. 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.

  1. Markers

    Science.gov (United States)

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  2. 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...

  3. 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

  4. 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)

  5. 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...

  6. Oligo(dT) is not a correct native PAGE marker for single-stranded DNA

    Czech Academy of Sciences Publication Activity Database

    Kejnovská, Iva; Kypr, Jaroslav; Vorlíčková, Michaela

    2007-01-01

    Roč. 353, č. 3 (2007), s. 776-779. ISSN 0006-291X R&D Projects: GA AV ČR(CZ) IAA4004201; GA AV ČR(CZ) IAA1004201 Institutional research plan: CEZ:AV0Z50040702 Keywords : polyacrylamide gel electrophoresis * DNA length markers * oligo(dT) Subject RIV: BO - Biophysics Impact factor: 2.749, year: 2007

  7. 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

  8. 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...

  9. 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)

  10. 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.

  11. 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.

  12. Investigation of the Reliability of the Blood Markers in Human Identity Recognition by DNA Finger Printing

    Directory of Open Access Journals (Sweden)

    Morteza Sadeghi

    2014-04-01

    Full Text Available Introduction: Determination of blood groups is the first step in the approval or rejection of blood relation between the two individuals for identity recognition. The aim of this study is to investigate the reliability of common blood grouping systems in DNA finger printing recognition. Methods: In this study, blood samples were obtained from 300 individuals belonging to 150 families. Then, DNA of each individual was purified and DNA finger printing was performed for 10 STR regions using ABI set. Seven human blood group systems including ABH, RH, Kidd, Kell, Mns, Lutheran and p1 were determined with agglutination methods, and the results were compared with DNA sequencing results of the ABI sequencing machine. Results: 300 randomly selected individuals were studied, in 256 cases. There was no difference between the blood grouping and DNA typing results; in 44 cases, the blood relation was approved by DNA typing but antigenic discord was observed in RH, MNS and ABH antigens. Among the blood grouping systems, RH, MNS and ABH,with the error scale of 30.7% (P=0.001, 20.54% (0.04 and 17.6% (P=0.005 respectively, were found to be the weakest systems for human identity recognition. Conclusion: Among the blood grouping systems, RH, MNS and ABH are the weakest markers for blood relation identification, and DNA finger printing must be used as a supplementary test to confirm their results.

  13. Rust resistance evaluation of advanced wheat (triticum aestivum l.) genotypes using pcr-based dna markers

    International Nuclear Information System (INIS)

    The most effective and environmental friendly approach for the control of wheat rust disease is the use of resistant genotypes. The present study was conducted to explore rust resistance potential of 85 elite wheat genotypes (36 varieties and 49 advanced lines) using various types of DNA markers like STS, SCAR and SSR. DNA markers linked with different genes conferring resistance to rusts (Leaf rust=Lr, Yellow rust=Yr and Stem rust=Sr) were employed in this study. A total of 18 genes, consisting of eleven Lr (lr1, lr10, lr19, lr21, lr28, lr34, lr39, lr46, lr47, lr51 and lr52), four Yr (yr5, yr18, yr26 and yr29) and three Sr genes (sr2, sr29, and sr36) were studied through linked DNA markers. Maximum number of Lr genes was found in 17 advanced lines and 9 varieties, Yr genes in 26 advanced lines and 20 wheat varieties, and Sr genes in 43 advanced lines and 27 varieties. Minimum number of Lr genes was found in advanced line D-97 and variety Kohinoor-83, Yr genes in wheat variety Bwp-97 and Sr genes in 6 advanced lines and 8 varieties. Molecular data revealed that genotypes having same origin, from a specified area showed resistance for similar type of genes. In this study, an average similarity of 84% was recorded among wheat genotypes. Out of 18 loci, 15 were found to be polymorphic. (author)

  14. 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.

  15. 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.

  16. Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity.

    Science.gov (United States)

    Carranza, Juan; Salinas, María; de Andrés, Damián; Pérez-González, Javier

    2016-02-01

    Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages. PMID:26843924

  17. DNA fingerprinting of groundnut (Arachis hypogaea L. varieties of Tirupati using SSR markers

    Directory of Open Access Journals (Sweden)

    Y. Amaravathi, R.P. Vasanthi, E. Siva Kumar, M. Purushotham and T. Giridhara Krishna

    2014-12-01

    Full Text Available Unambiguous identification of varieties is important for registration and certification of newly released varieties. Molecular markers are powerful tools, which help in differentiating plant varieties at the DNA level and have been widely used for fingerprinting in a number of crop varieties. In the present study, a set of 12 groundnut varieties released from Regional Agricultural Research Station, Tirupati were fingerprinted employing SSR markers. A total of 300 SSR were screened and fifteen potential markers were employed for fingerprinting of groundnut varieties. The SSR markers generated alleles ranging from 2 to 7 with an average of four per locus. The polymorphism information content (PIC values ranged from 0 to 0.85. The genotypic data from all the loci provided unique SSR allelic fingerprints which helped in varietal identification of groundnut. Core set of highly informative primers viz., PM 377, TC1A02, TC5A06 and GM1489 identified in this study has the potential to identify most of the groundnut varieties. Cluster analysis using SSR marker grouped 12 groundnut varieties into two major clusters. Finger printing of the groundnut genotypes provide information about phylogenetic relationships and assists groundnut breeders in varietal registration and protection of intellectual property rights.

  18. Sensitive voltammetric detection of DNA damage at carbon electrodes using DNA repair enzymes and an electroactive osmium marker

    Czech Academy of Sciences Publication Activity Database

    Havran, Luděk; Vacek, Jan; Cahová, Kateřina; Fojta, Miroslav

    2008-01-01

    Roč. 391, č. 5 (2008), s. 1751-1758. ISSN 1618-2642 R&D Projects: GA AV ČR(CZ) IAA4004402; GA AV ČR(CZ) IAA400040611; GA ČR(CZ) GA203/07/1195; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA damage * electroactive marker * carbon electrodes Subject RIV: BO - Biophysics Impact factor: 3.328, year: 2008

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

    OpenAIRE

    Suprun I. I.; Kovalev V. S.; Shilovskiy V. N.

    2013-01-01

    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

  20. The Use of Random Amplified Polymorphic DNA (RAPD) Markers in Sex Discrimination in Nile Tilapia, Oreochromis niloticus (Pisces: Cichlidae)

    OpenAIRE

    Bardakci, Fevzi

    2000-01-01

    Random amplified polymorphic DNA (RAPD) markers were successfully used in discrimination of sexes in Nile tilapia fish ( Oreochromis niloticus) using linear discriminant function analysis. The results provide support for the view that major genetical sex determining factors exist in tilapia.

  1. 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

  2. A Randomly Amplified Polymorphic DNA Marker Specific for the Bacillus cereus Group Is Diagnostic for Bacillus anthracis

    OpenAIRE

    Daffonchio, Daniele; Borin, Sara; Frova, Giuseppe; Gallo, Romina; Mori, Elena; Fani, Renato; Sorlini, Claudia

    1999-01-01

    Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B. cereus, B. thuringiensis, B. anthracis, and B. mycoides was identified. This fragment included a pu...

  3. 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...

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. [Sex determination in ten crane species by DNA marker EE0.6].

    Science.gov (United States)

    2013-12-01

    Using a unique DNA sequence of W-chromosome EE0.6, we carried out molecular sex determination in 383 individuals often species of cranes (Grusgrus L., G. leucogeranus Pallas, G. japonensis Muller, G. vipio Pallas, G. Canadensis L., G. antigone L., G. monacha Temminck, Anthropoides virgo L., Balearica regulorum Bennett, and B. pavonia L.) kept in zoos and other centers of captive propagation. In 211 birds, sex was determined or verified for the first time. The efficiency of using the sex marker EE0.6 for chicks and immature and adult cranes of different species, as well as for interspecific hybrids was shown. PMID:25508137

  15. 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.

  16. 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

  17. 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)

  18. Species markers for equine strongyles detected in intergenic rDNA by PCR-RFLP.

    Science.gov (United States)

    Gasser, R B; Stevenson, L A; Chilton, N B; Nansen, P; Bucknell, D G; Beveridge, I

    1996-10-01

    Five species of equine strongyle belonging to the subfamily Strongylinae (Strongylus edentatus, S. equinus, S. vulgaris, Oesophagodontus robustus and Triodontophorus serratus) and 11 species belonging to the subfamily Cyathostominae (Poteriostomum imparidentatum, P. ratzii, Cylicocyclus insignis, Cc. leptostomus, Cc. nassatus, Cylicostephanus calicatus, Cs. longibursatus, Cs. goldi, Cyathostomum catinatum, Cy. labiatum and Cy. pateratum) were characterized using a polymerase chain reaction-linked restriction fragment length polymorphism technique (PCR-RFLP). Internal transcribed spacer ribosomal DNA was amplified from genomic DNA by polymerase chain reaction (PCR) using conserved primers, digested separately with six restriction endonucleases (AluI, BfaI, CfoI, Hae III, VSpI and XbaI) and the fragments separated by agarose gel electrophoresis. The PCR products of the three Strongylus species were approx. 90-100 bp smaller in size compared with those of the other 13 species. The PCR-RFLP analysis of the rDNA region spanning the first and second internal transcribed spacers plus the 5.85 rDNA gene (ITS+) produced characteristic patterns for each of the 16 species examined, and no variation in RFLP patterns was detected within the species Cy. catinatum, where multiple isolates were analysed. The study demonstrates that the internal transcribed spacer sequences provide genetic markers for the species identification of a range of equine strongyles. These markers will be of use for the identification of egg and larval stages, where morphological characters alone are unreliable. The results also indicate that the spacer sequences will be of use to study the systematics of equine strongyles. PMID:8910892

  19. Identification and evaluation of age-correlated DNA methylation markers for forensic use.

    Science.gov (United States)

    Park, Jong-Lyul; Kim, Jong Hwan; Seo, Eunhye; Bae, Dong Hyuck; Kim, Seon-Young; Lee, Han-Chul; Woo, Kwang-Man; Kim, Yong Sung

    2016-07-01

    In forensics, age prediction is useful to narrow down the number of potential suspects because it can provide some general characteristics for predicting appearance. Previous genome-wide studies based on DNA methylation have reported age prediction algorithms using a penalized multivariate regression method known as elastic net and a few dozen to hundreds of CpG sites. Although more CpG sites may provide better accuracy than fewer CpG sites, this approach is not applicable to forensics because the amounts of crime-scene DNA are usually limited. In this study, we selected three age-correlated CpG sites, namely cg16867657 (ELOVL2), which is known to be an excellent age predictor, cg04208403 (ZNF423), and cg19283806 (CCDC102B), from HumanMethylation450 BeadChip datasets of 1415 individuals. Furthermore, we evaluated these markers in a 535-sample training set and a 230-sample validation set from Korean individuals using a pyrosequencing platform. From the training set, an age prediction model using the multiple linear regression method explained 91.44% of age-correlated variation in DNA methylation patterns. The standard error of estimate and mean absolute deviation were 6.320 and 3.156 years, respectively. In the validation set, the standard error of estimate and mean absolute deviation were estimated as 6.853 and 3.346 years, respectively. For the validation set, the model explained 91.08% of the variation in methylation and predicted age (±6years) with accuracy of 77.30% in the <60years age group and 57.30% in the older group (≥60 years). These results suggest that our three DNA methylation markers may be useful for age prediction in samples from Asian populations. PMID:27017110

  20. 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

  1. 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。

  2. 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

  3. Cross-species amplification of microsatellite markers in Mycteria leucocephala Pennant 1769: molted feathers as successful DNA source.

    Science.gov (United States)

    Sharma, Bharat Bhushan; Mustafa, Mohd; Sharma, Tusha; Banerjee, Basu Dev; Urfi, Abdul Jamil

    2014-10-01

    DNA from molted feathers is being increasingly used for genetic studies on birds. However, the DNA obtained from such non-invasive sources is often not of enough quantity and quality for isolation of new microsatellite markers. The present study examined the potential of shed feathers of near threatened Painted Stork as a source of its DNA for cross-species amplification of microsatellites. Thirty-one shed feathers of varying conditions ('good' and 'deteriorated') and sizes ('large', 'intermediate' and 'small') collected in a north Indian population were used to isolate DNA by a standard isopropanol method and 11 microsatellite markers already developed in the Wood Stork were screened for amplification. Nine plucked feathers from two dead Painted Storks were also used to compare the DNA yield and amplification success. The DNA yield of feathers varied significantly in relation to the calamus size and condition. Among molted feathers, 'good' and 'large' samples provided more DNA than 'deteriorated' and 'small' ones, respectively. 'Large' plucked feathers yielded more DNA than 'large' molted feathers. DNA was almost degraded in all the samples and ratio of absorbance at 260/280 nm varied from 1.0 to 1.8, indicating impurity in many samples. Independent of DNA yields, all microsatellites were cross-amplified in all kinds of feathers, with > 80% success in different feather categories. It is concluded that the shed feathers can be successfully used to isolate DNA in the Painted Stork and for cross-species amplification of microsatellites. PMID:25345251

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. [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

  13. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas

    Science.gov (United States)

    Porter, Teresita M.; Shokralla, Shadi; Baird, Donald; Golding, G. Brian; Hajibabaei, Mehrdad

    2016-01-01

    Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence. PMID:26731732

  14. 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

    OBJECTIVES: The pathophysiological mechanisms underlying bipolar disorder and its multi-system nature are unclear. Oxidatively generated damage to nucleosides has been demonstrated in metabolic disorders; however, the extent to which this occurs in bipolar disorder in vivo is unknown. We...... 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...... 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...

  15. Brown trout ( Salmo trutta ) stocking impact assessment using microsatellite DNA markers

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Ruzzante, D.E.; Eg Nielsen, Einar; Mensberg, Karen-Lise Dons

    2001-01-01

    The genetic integrity of many salmonid fish populations is threatened by stocking of domesticated conspecifics. The purpose of this study was to assess the utility of microsatellite DNA markers for detecting loss of genetic diversity in hatchery strains, for estimating their genetic relationships...... diversity was distributed between the wild and hatchery populations. We assessed whether wild populations were introgressed by stocked hatchery trout by performing assignment tests to determine population of origin and estimating maximum potential introgression rates. The results suggested that genetic...... introgression by hatchery trout had occurred for only two of the five populations potentially influenced by stocking. In one of these two rivers, microsatellite data obtained from a limited number of old scale samples indicated that individuals from the original population were genetically divergent from these...

  16. 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.

  17. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.;

    2016-01-01

    Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type....... kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence of...... hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region...

  18. Establishment of dna fingerprinting in clonal tea improved cultivars from yunnan of china using issr markers

    International Nuclear Information System (INIS)

    In this study, DNA fingerprints were constructed by using ISSR markers for 20 clonal improved varieties developed by two breeding institutes in Yunnan province. Seven core ISSR primers were selected from 15 primers. A total of 110 bands were generated by PAGE with seven core primers, 93 of which were polymorphic bands, the percentage of polymorphic band (PPB) was 84.54%, and the mean value of polymorphism information content (PIC) reached 0.417; the genetic similarity coefficient of the cultivars was 0.574-0.854. The two primers, UBC835 and ISSR2, had high PIC values, and could be used to distinguish all cultivars, presenting the most efficient single primers. Among the all of primer combinations from the seven core primers, the three combinations, UBC835/UBC811, UBC835/ISSR2, and UBC835/ISSR3 showed lower similar coefficients, and more efficient in identifying the 20 improved varieties than the other primer combinations. Then these three primer combinations were further scored in 15 traditional cultivars. The results showed that UBC835/ISSR2 was the optimal primer combination, which could be used to distinguish each material among the 20 clonal improved varieties and 15 traditional cultivals. Finally, the DNA fingerprints of the 20 clonal improved varieties were constructed based on country and region code, breeding institute, core primer name and ISSR marker data. The established fingerprints could provide reliable scientific base for the protection of intellectual property right for these clonal improved varieties, and the important molecular information contained in these fingerprints would be useful for the authenticity identification and genetic relationship analysis of tea varieties. (author)

  19. Genetic Diversity of Eurycoma longifolia Jack Based on Random Amplified Polymorphic DNA Marker

    Directory of Open Access Journals (Sweden)

    Rosmaina Rosmaina

    2013-08-01

    Full Text Available Eurycoma longifolia Jack is one of the extensively exploited medicinal plants in Indonesia. The objectives of this study were to obtain information on genetic diversity and population genetic structure of E. longifolia to formulate effective conservation plan. RAPD marker was used to assess the genetic diversity of E. longifolia collected from 5 natural populations in Riau Province. A total of 25 plants were analyzed using 5 RAPD primers, which amplified produced 44 scored DNA bands. The mean observed number of alleles per locus (No, number of effective alleles (Ne, and percentage of polymorphic loci (PPL of E. longifolia were 1.57, 1.34, and 56.80%, respectively. The degree of differentiation among populations of E. longifolia was 0.31 (Ht = 0.29; Hs = 0.20.  The mean value of estimated gene flow among populations of E. longifolia was 1.11 individual per generation. The UPGMA dendogram formed 2 significant clusters. The first cluster consisted of Pelalawan and Kampar populations, while the second cluster was formed from Kuansing, Rohul, and Rohil population. The genetic diversity information in this study is very important to perform efficient conservation and effective future management of its genetic resources.Keywords: Eurycoma longifolia, RAPD marker, genetic variation, conservation DOI: 10.7226/jtfm.19.2.138

  20. DNA fingerprinting and diversity analysis in Aus genotypes using microsatellite markers

    Directory of Open Access Journals (Sweden)

    MD. MONIRUL ISLAM

    2015-08-01

    Full Text Available DNA fingerprinting and genetic diversity of 94 Aus (6 BRRI released Aus variety and 88 local Aus landraces genotypes were carried out to protect the Aus landraces from biopiracy. A total of 91 microsatellite markers were tested for screening the genotypes. Among 91 amplified products, 56% have polymorphic bands giving 195 alleles. The number of alleles per locus ranged from four (RM25 and RM147 to twenty seven (RM519, where average allele number was 9.76. The Polymorphism Information Contents (PIC lied between 0.455 (RM5 to 0.934 (RM519. Most robust marker was found RM519 since it provided the highest PIC value (0.934. Pair-wise genetic dissimilarity co-efficient showed the lowest genetic dissimilarity was found BRRI dhan42 and BRRI dhan43 and the highest genetic dissimilarity was found local landraces each other. Here it is shown that most Aus landraces is recognized to have broad genetic base. Thus it is recommended to use these landraces for future breeding program or include new and untouched local landraces to incorporate new genes and broaden genetic base.

  1. 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.

  2. 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.

  3. 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

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

    OpenAIRE

    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 n...

  5. 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

  6. Investigation of the somaclonal and mutagen induced variability in barley by the application of protein and DNA markers

    International Nuclear Information System (INIS)

    Barley, Hordeum vulgare L., is one of the most important crop species for Bulgaria. The characterisation of the genetic pool is of great necessity for the Bulgarian barley breeding programme which is directed toward improving quantitative and qualitative traits. Molecular markers [protein, restriction fragment length polymorphisms (RFLP) and randomly amplified polymorphic DNA (RAPD)] have been applied to characterise the Bulgarian barley cultivars and their regenerants. The changes in DNA loci coding for 26S, 5.8S and 18S rRNA repeats, C hordein locus and mitochondrial DNA organisation have been investigated. The potential for ribosomal DNA length polymorphism in Bulgarian barley cultivars appear to be limited to three different repeat lengths (10.2, 9.5 and 9.0kb) and three plant rDNA phenotypes. Polymorphism was not observed in ribosomal DNA repeat units in somaclonal variants. Variation concerning C hordein electrophoretic pattern was observed in one line from cultivar Jubiley. Analysis of the HorI locus reveals RFLPs in sequences coding for C hordeins in this line. Mitochondrial molecular markers are convenient for detection of DNA polymorphisms in the variant germplasm as well as for the somaclonal variants derived from it. Two lines from Ruen revealed polymorphic bands after hybridisation with mitochondrial DNA probe. RAPD assays have been carried out by using 20 different 10-mer primers. Heritable polymorphism in several tissue culture derived (TCD) lines was observed. RAPD assay is a sensitive and representative approach to distinguish the variability created by tissue culture and mutagenesis

  7. 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.

  8. 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

  9. 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.

  10. Species specific cpDNA markers useful for studies on the hybridisation between Pinus mugo and P. sylvestris

    Directory of Open Access Journals (Sweden)

    Witold Wachowiak

    2014-02-01

    Full Text Available PCR-RFLP technique has been used to detect species-specific mutations of organelles DNA for closely related dwarf mountain pine (Pinus mugo and Scots pine (P. sylvestris. Restriction fragment patterns have been compared of amplification products for trnL-trnF cpDNA and for coxI and orf25 genes of mtDNA. The difference has been found in the Dral and Hinfl restriction patterns of the amplification products for trnL-trnF region of cpDNA with two haplotypes detected. The haplotype M is characteristic for P. mugo and the haplotype S for P. sylvestris. These markers may be useful for the analysis of the natural hybridisation and introgression between these species postulated for some sympatric populations on the basis of morphological analysis. No differences have been disclosed in the studied mtDNA regions.

  11. 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)

  12. Genetic characterization of Moroccan and the exotic bread wheat cultivars using functional and random DNA markers linked to the agronomic traits for genomics-assisted improvement

    OpenAIRE

    Henkrar, Fatima; El-Haddoury, Jamal; Ouabbou, Hassan; Bendaou, Najib; Udupa, Sripada M.

    2016-01-01

    Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most importan...

  13. 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...

  14. 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. PMID:24345408

  15. GeneMarker® Genotyping Software: Tools to Increase the Statistical Power of DNA Fragment Analysis

    Science.gov (United States)

    Hulce, D.; Li, X.; Snyder-Leiby, T.; Johathan Liu, C.S.

    2011-01-01

    The discriminatory power of post-genotyping analyses, such as kinship or clustering analysis, is dependent on the amount of genetic information obtained from the DNA fragment/genotyping analysis. The number of microsatellite loci amplified in one multiplex is limited by the number of dyes and overlapping loci boundaries; requiring researchers to amplify replicate samples with 2 or more multiplexes in order to obtain a genotype for 12–15 loci. AFLP is another method that is limited by the number of dyes, often requiring multiple amplifications of replicate samples to obtain more complete results. Traditionally, researchers export the genotyping results into a spread sheet, manually combine the results for each individual and then import into a third software package for post-genotyping analysis. GeneMarker is highly accurate, user-friendly genotyping software that allows all of these steps to be done in one software package, avoiding potential errors from data transfer to different programs and decreasing the amount of time needed to process the results. The Merge Project tool automatically combines the results from replicate samples processed with different primer sets. Replicate animal (diploid) DNA samples were amplified with three different multiplexes, each multiplex provided information on 4–6 loci. The kinship analysis using the merged results provided a 1017 increase in statistical power with a range of 108 when 5 loci were used versus 1025 when 15 loci were used to determine potential relationship levels with identity by descent calculations. These same sample sets were used in clustering analysis to diagram dendrograms. The dendrogram based on a single multiplex resulted in three branches at a given Euclidian distance. In comparison, the dendrogram that was constructed using the merged results had eight branches at the same Euclidian distance.

  16. 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)

  17. 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.

  18. 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

  19. 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...

  20. 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 ...

  1. 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...

  2. Analysis of Microsatellite DNA Markers Reveals no Genetic Differentiation between Wild and Hatchery Populations of Pacific Threadfin in Hawaii

    Directory of Open Access Journals (Sweden)

    Gang Pan, Jinzeng Yang

    2010-01-01

    Full Text Available Pacific threadfin, Polydactylus sexfilis, is popular fish in recreational fishing, as well as aquaculture in Hawaii. Its natural population has been continuously declining in the past several decades. Microsatellite DNA markers are useful DNA-based tool for monitoring Pacific threadfin populations. In this study, fifteen Microsatellite (MS DNA markers were identified from a partial genomic Pacific threadfin DNA library enriched in CA repeats, and six highly-polymorphic microsatellite loci were employed to analyze genetic similarity and differences between the wild population and hatchery population in Oahu Island. A total of 37 alleles were detected at the six MS loci in the two populations. Statistical analysis of fixation index (FST and analysis of molecular variance (AMOVA showed no genetic differentiation between the wild and hatchery populations (FST=0.001, CI95%= -0.01-0.021. Both high genetic diversity (Ho=0.664-0.674 and He=0.710-0.715 and Hardy-Weinberg equilibrium were observed in the wild and hatchery populations. Results of genetic bottleneck analysis indicated that the hatchery was founded with sufficient numbers of brooders as inbreeding coefficient is very low (FIS=0.052-0.072 in both wild and hatchery populations. Further studies are needed for comprehensive determinations of genetic varieties of primary founder broodstocks and successive offspring of the hatchery and wild populations with increased number of Pacific threadfin sample collections.

  3. 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.

  4. Epigenome-wide methylation in DNA from peripheral blood as a marker of risk for breast cancer.

    Science.gov (United States)

    Severi, Gianluca; Southey, Melissa C; English, Dallas R; Jung, Chol-hee; Lonie, Andrew; McLean, Catriona; Tsimiklis, Helen; Hopper, John L; Giles, Graham G; Baglietto, Laura

    2014-12-01

    Aberrant DNA methylation is a key feature of breast carcinoma. We aimed to test the association between breast cancer risk and epigenome-wide methylation in DNA from peripheral blood. Nested case-control study within the prospective Melbourne Collaborative Cohort Study. DNA was extracted from before-diagnosis blood samples (420 incident cases and matched controls). Methylation was measured with the Illumina Infinium Human Methylation 450 BeadChip array. Odds ratio (OR) for epigenome-wide methylation, quantified as the mean beta values across the CpGs, in relation to breast cancer risk were estimated using conditional logistic regression. Overall, the OR for breast cancer was 0.42 (95% CI 0.20-0.90) for the top versus bottom quartile of epigenome-wide DNA methylation and the OR for a one standard deviation increment was 0.69 (95% CI 0.50-0.95; test for linear trend, p = 0.02). Epigenome-wide DNA methylation of CpGs within functional promoters was associated with an increased risk, whereas epigenome-wide DNA methylation of genomic regions outside promoters was associated with decreased risk (test for heterogeneity, p = 0.0002). The increased risk associated with epigenome-wide DNA methylation in functional promoters did not vary by time between blood collection and diagnosis, whereas the inverse association with epigenome-wide DNA methylation outside functional promoters was strongest when the interval from blood collection to diagnosis was less than 5 years and weakest for the longest interval. Epigenome-wide methylation in DNA extracted from peripheral blood collected before diagnosis may have potential utility as markers of breast cancer risk and for early detection. PMID:25407397

  5. 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.

  6. 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)...

  7. Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

    Science.gov (United States)

    In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

  8. 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

  9. 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

  10. 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.

  11. 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...

  12. 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...

  13. 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...

  14. Isolation and characterization of 10 microsatellite DNA markers in the oriental honey buzzard (Pernis ptilorhyncus).

    Science.gov (United States)

    Weng, Guo-Jing; Li, Shou-Hsien; Severinghaus, Lucia Liu

    2009-05-01

    We designed 10 new microsatellite markers for the oriental honey buzzard (Pernis ptilorhyncus) and tested them on 44 individuals. The number of alleles ranged from two to 12 with an average of five, while the observed heterozygosity ranged from 0.273 to 1.0. Linkage disequilibrium was not found. These markers are being used in a study of the ecology of this species in Taiwan. We also tested their utility on eight other raptor species. PMID:21564794

  15. A 6. 5-Mb yeast artificial chromosome contig incorporating 33 DNA markers on the human X chromosome at Xq22

    Energy Technology Data Exchange (ETDEWEB)

    Vetrie, D.; Kendall, E.; Coffey, A.; Hassock, S.; Collins, J.; Todd, C.; Bobrow, M.; Bentley, D.R. (Paediatric Research Unit, London (United Kingdom)); Lehrach, H. (Imperial Cancer Research Fund, London (United Kingdom)); Harris, A. (John Radcliffe Hospital, Oxford (United Kingdom))

    1994-01-01

    The Xq22 region of the human X chromosome contains genes for a number of inherited disorders. Sixty-nine yeast artificial chromosome clones have been isolated and assembled into a 6.5-Mb contig that contains 33 DNA markers localized to this region. This contig extends distally from DXS366 to beyond DXS87 and includes the genes involved in X-linked agammaglobulinemia (btk), Fabry disease (GLA), and Pelizaeus-Merzbacher disease (PLP). The order of markers in this contig is consistent with the known genetic and physical mapping information of Xq22. This cloned material provides a source from which to isolate other genes located in this part of the X chromosome. 45 refs., 2 figs., 2 tabs.

  16. Investigation of the Reliability of the Blood Markers in Human Identity Recognition by DNA Finger Printing

    OpenAIRE

    Morteza Sadeghi; Alireza Sabouri

    2014-01-01

    Introduction: Determination of blood groups is the first step in the approval or rejection of blood relation between the two individuals for identity recognition. The aim of this study is to investigate the reliability of common blood grouping systems in DNA finger printing recognition. Methods: In this study, blood samples were obtained from 300 individuals belonging to 150 families. Then, DNA of each individual was purified and DNA finger printing was performed for 10 STR regions using A...

  17. Developmental validation studies of epigenetic DNA methylation markers for the detection of blood, semen and saliva samples.

    Science.gov (United States)

    Silva, Deborah S B S; Antunes, Joana; Balamurugan, Kuppareddi; Duncan, George; Alho, Clarice S; McCord, Bruce

    2016-07-01

    Determining the type and origin of body fluids in a forensic investigation can provide important assistance in reconstructing crime scenes. A set of epigenetic markers, ZC3H12D, BCAS4 and cg06379435, have been developed to produce unique and specific patterns of DNA methylation that can be used to identify semen, saliva, and blood, respectively. To ensure the efficacy of these markers, developmental validation studies were performed to determine the conditions and limitations of this new tool for forensic analysis. DNA was extracted from human samples and bisulfite modified using commercial bisulfite modification kits. Specific primers were used to amplify the region of interest and the methylation profile of the CpG sites were determined by pyrosequencing. The percent methylation values at each CpG site were determined in multiple samples and averaged for each tissue type. The versatility of these new markers is presented by showing the results of validation studies on sensitivity, human specificity, stability and mixture resolution. When testing the markers using different organisms, we did obtain positive results for certain non-human primate samples, however, all other tested species were negative. The lowest concentration consistently detected varied from 0.1 to 10ng, depending on the locus, indicating the importance of primer design and sequence in the assay. The method also proved to be effective when inhibitors were present in the samples or when samples were degraded by heat. Simulated case- samples were also tested. In the case of mixtures of different cell types, the overall methylation values varied in a consistent and predictable manner when multiple cell types were present in the same sample. Overall, the validation studies demonstrate the robustness and effectiveness of this new tool for body fluid identification. PMID:27010659

  18. 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.

  19. DNA Markers and FCSS Analyses Shed Light on the Genetic Diversity and Reproductive Strategy of Jatropha curcas L.

    Directory of Open Access Journals (Sweden)

    Daria Gigliola Ambrosi

    2010-05-01

    Full Text Available Jatropha curcas L. (2n = 2x = 22 is becoming a popular non-food oleaginous crop in several developed countries due to its proposed value in the biopharmaceutical industry. Despite the potentials of its oil-rich seeds as a renewable source of biodiesel and an interest in large-scale cultivation, relatively little is known with respect to plant reproduction strategies and population dynamics. Here, genomic DNA markers and FCSS analyses were performed to gain insights into ploidy variation and heterozygosity levels of multiple accessions, and genomic relationships among commercial varieties of Jatropha grown in different geographical areas. The determination of ploidy and the differentiation of either pseudogamous or autonomous apomixis from sexuality were based on the seed DNA contents of embryo and endosperm. The presence of only a high 2C embryo peak and a smaller 3C endosperm peak (ratio 2:3 is consistent with an obligate sexual reproductive system. Because of the lack of either 4C or 5C endosperm DNA estimates, the occurrence of gametophytic apomixis seems unlikely in this species but adventitious embryony cannot be ruled out. The investigation of genetic variation within and between cultivated populations was carried out using dominant RAPD and Inter-SSR markers, and codominant SSR markers. Nei’s genetic diversity, corresponding to the expected heterozygosity, was equal to He = 0.3491 and the fixation index as low as Fst = 0.2042. The main finding is that seeds commercialized worldwide include a few closely related genotypes, which are not representative of the original Mexican gene pool, revealing high degrees of homozygosity for single varieties and very low genetic diversity between varieties.

  20. 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...

  1. 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

  2. Development of specific ITS markers for plant DNA identification within herbivorous insects.

    Science.gov (United States)

    Pumariño, L; Alomar, O; Agustí, N

    2011-06-01

    DNA-based techniques have proved to be very useful methods to study trophic relationships between pests and their natural enemies. However, most predators are best defined as omnivores, and the identification of plant-specific DNA should also allow the identification of the plant species the predators have been feeding on. In this study, a PCR approach based on the development of specific primers was developed as a self-marking technique to detect plant DNA within the gut of one heteropteran omnivorous predator (Macrolophus pygmaeus) and two lepidopteran pest species (Helicoverpa armigera and Tuta absoluta). Specific tomato primers were designed from the ITS 1-2 region, which allowed the amplification of a tomato DNA fragment of 332 bp within the three insect species tested in all cases (100% of detection at t=0) and did not detect DNA of other plants nor of the starved insects. Plant DNA half-lives at 25°C ranged from 5.8 h, to 27.7 h and 28.7 h within M. pygmaeus, H. armigera and T. absoluta, respectively. Tomato DNA detection within field-collected M. pygmaeus suggests dietary mixing in this omnivorous predator and showed a higher detection of tomato DNA in females and nymphs than males. This study provides a useful tool to detect and to identify plant food sources of arthropods and to evaluate crop colonization from surrounding vegetation in conservation biological control programs. PMID:21092379

  3. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.

    Science.gov (United States)

    Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

    2011-05-01

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne. PMID:21344184

  4. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers.

    Science.gov (United States)

    Takahashi, Hiroshi; Møller, Peter R; Shedko, Sergei V; Ramatulla, Temirbekov; Joen, Sang-Rin; Zhang, Chun-Guang; Sideleva, Valentina G; Takata, Keisuke; Sakai, Harumi; Goto, Akira; Nishida, Mutsumi

    2016-06-01

    Pungitius is a highly diversified genus of sticklebacks (Gasterosteidae) occurring widely in northern parts of the Northern Hemisphere. Several ecologically and genetically divergent types that are largely isolated reproductively but occasionally hybridize in sympatry have been discovered in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type localities of the described species. Phylogenetic analyses based on 2683 polymorphic AFLP loci confirmed seven species, each of which (except for one entirely allopatric species P. platygaster) was clearly differentiated from one or two other sympatric species and constituted a highly supported monophyletic clade with conspecific allopatric populations. The phylogeny showed that two lineages arose early; one gave rise to two species (circumpolar species P. pungitius and Paratethys species P. platygaster) and the other to five species endemic to Northeast Asia (P. sinensis, P. tymensis, P. polyakovi, P. kaibarae, and P. bussei). The brackish-water, freshwater, and Omono types previously discovered in Japan were reidentified as P. pungitius, P. sinensis, and P. kaibarae, respectively. A marked incongruence was noted between the phylogenies of AFLP and mtDNA markers, suggesting the occasional occurrence of hybridization and mtDNA introgression among distinct species. Our results highlight that the marginal seas of Northeast Asia played a key role as barriers to or facilitators of gene flow in the evolution of species diversity of Pungitius concentrated in this region. PMID:26997522

  5. 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.

  6. 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.

  7. 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.

  8. 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

  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. 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...

  11. 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...

  12. 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...

  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. 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

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

    Lifescience Database Archive (English)

    Full Text Available Kasalath Nipponbare band size (kb) Southern band size of Nipponbare (kb) Kasalath band size (kb) Southern ba...l of RAPD and STS markers Image file name Southern image file name Joomla SEF URLs by Artio About This Datab

  17. 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. PMID:26966393

  18. A novel microsatellite DNA marker at locus D7S1870 detects hemizygosity in 75% of patients with Williams syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert-Dussardier, B. [Hopital des Enfants-Malades, Paris (France)]|[Hopital Dupuytren, Limoges (France); Bonneau, D. [Hopital des Enfants-Malades, Paris (France)]|[Hopital Jean Bernard, Poitiers (France); Gigarel, N.; Le Merrer, M.; Bonnet, D.; Lyonnet, S.; Munnich, A. [Hopital des Enfants-Malades, Paris (France); Philip, N.; Mattei, M.G. [Hopital de La Timone, Marseille (France)] [and others

    1995-02-01

    Williams syndrome (WS) is a predominantly sporadic developmental disorder characterized by dysmorphic facial features, infantile hypercalcemia, premature aging of skin, mental retardation and gregarious personality. Supravalvular aortic stenosis (SVAS) and other vascular diseases caused by the narrowing of large elastic arteries are present in almost 80% of cases. Recently, hemizygosity at the elastin locus has been shown in sporadic WS, suggesting that this disease is caused by deletions encompassing the elastin gene on chromosome 7q11.23. Taking advantage of a large series of sporadic WS (27 cases), we have explored the potential application of novel microsatellite DNA markers in the rapid detection of hemizygosity in WS. We report here a highly informative marker at locus D7S1870, which detected failure of parental inheritance in almost 75% of cases of WS in our series. This marker can be regarded therefore as a reliable and useful diagnostic tool in suspected cases of WS as well as in complicated forms of supravalvular aortic stenosis. 10 refs., 2 figs.

  19. Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction

    OpenAIRE

    Behzadi, Payam; Najafi, Ali; BEHZADI, Elham; Ranjbar, Reza

    2016-01-01

    Introduction Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of ...

  20. 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...

  1. The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers

    OpenAIRE

    Jin, Han-Jun; Tyler-Smith, Chris; Kim, Wook

    2009-01-01

    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 ...

  2. 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...

  3. 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. 

  4. 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.

  5. Cloned fragment of human alphoid DNA: molecular marker of pericentromeric region of 18th chromosome

    International Nuclear Information System (INIS)

    Two recombinant plasmids were isolated from the collection of cloned human DNA fragments which contain sequences of alphoid DNA. It was shown using in situ hybridization on metaphase chromosomes that both cloned sequences hybridize preferentially with the region of pericentromeric heterochromatin of chromosome 18, less intensively with pericentric regions of chromosomes 2, 9, and 20, and are characterized by polymorphism according to number of copies in homologous chromosomes. These sequences may prove useful for cytogenetic analysis of chromosome reorganizations and study of polymorphism of regions of pericentromeric heterochromatin in human chromosomes

  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. 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

  8. 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.

  9. 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). PMID:22136768

  10. 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...... interrelationship between protein tumor markers, the global DNA hypomethylation, and hypermethylated genes in serum from patients with advanced disease. Twenty-nine patients with histologically proven advanced breast cancer received first-line chemotherapy with epirubicin. Samples were collected prior to each...... treatment and prospectively analyzed for CA 15-3, CEA, and TPA. The same samples were retrospectively analyzed for the concentration of hypermethylated RASSF1A and for global DNA hypomethylation using LINE-1. Among patients with elevated concentrations of the protein markers, concordance could be observed...

  11. Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD markers in farmed Atlantic salmon

    Directory of Open Access Journals (Sweden)

    Houston Ross D

    2012-06-01

    Full Text Available Abstract Background Restriction site-associated DNA sequencing (RAD-Seq is a genome complexity reduction technique that facilitates large-scale marker discovery and genotyping by sequencing. Recent applications of RAD-Seq have included linkage and QTL mapping with a particular focus on non-model species. In the current study, we have applied RAD-Seq to two Atlantic salmon families from a commercial breeding program. The offspring from these families were classified into resistant or susceptible based on survival/mortality in an Infectious Pancreatic Necrosis (IPN challenge experiment, and putative homozygous resistant or susceptible genotype at a major IPN-resistance QTL. From each family, the genomic DNA of the two heterozygous parents and seven offspring of each IPN phenotype and genotype was digested with the SbfI enzyme and sequenced in multiplexed pools. Results Sequence was obtained from approximately 70,000 RAD loci in both families and a filtered set of 6,712 segregating SNPs were identified. Analyses of genome-wide RAD marker segregation patterns in the two families suggested SNP discovery on all 29 Atlantic salmon chromosome pairs, and highlighted the dearth of male recombination. The use of pedigreed samples allowed us to distinguish segregating SNPs from putative paralogous sequence variants resulting from the relatively recent genome duplication of salmonid species. Of the segregating SNPs, 50 were linked to the QTL. A subset of these QTL-linked SNPs were converted to a high-throughput assay and genotyped across large commercial populations of IPNV-challenged salmon fry. Several SNPs showed highly significant linkage and association with resistance to IPN, and population linkage-disequilibrium-based SNP tests for resistance were identified. Conclusions We used RAD-Seq to successfully identify and characterise high-density genetic markers in pedigreed aquaculture Atlantic salmon. These results underline the effectiveness of RAD

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

    Science.gov (United States)

    Leng, Bingjie; Zheng, Wenfei; He, Ze; Zuo, Manzhen; Chen, Aihua

    2016-01-01

    Background 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. Methods 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. Results 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. Conclusions 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. PMID:27253331

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

    Czech Academy of Sciences Publication Activity Database

    Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J.L.; Levesque, C.A.; Chen, W.; Bolchacova, E.; Voigt, K.; Crous, P.W.; Miller, A.N.; Wingfield, M.J.; Aime, M.C.; An, K.D.; Bai, F.Y.; Barreto, R.W.; Bergeron, M.J.; Blackwell, M.; Boekhout, T.; Bogale, M.; Boonyuen, N.; Burgaz, A.R.; Buyck, B.; Cai, L.; Cai, Q.; Cardinali, G.; Chaverri, P.; Coppins, B.J.; Crespo, A.; Cubas, P.; Cummings, C.; Damm, U.; de Beer, Z.W.; de Hoog, G.S.; Del-Prado, R.; Dentinger, B.; Dieguez-Uribeondo, J.; Divakar, P.K.; Douglas, B.; Duenas, M.; Duong, T.A.; Eberhardt, U.; Edwards, J.E.; Elshahed, M.S.; Fliegerová, Kateřina; Furtado, M.; Garcia, M.A.; Ge, Z.W.; Griffith, G.W.; Griffiths, K.; Groenewald, J.Z.; Groenewald, M.; Grube, M.; Gryzenhout, M.; Guo, L.D.; Hagen, F.; Hambleton, S.; Hamelin, R.C.; Hansen, K.; Harrold, P.; Heller, G.; Herrera, C.; Hirayama, K.; Hirooka, Y.; Ho, H.M.; Hoffmann, K.; Hofstetter, V.; Hognabba, F.; Hollingsworth, P.M.; Hong, S.B.; Hosaka, K.; Houbraken, J.; Hughes, K.; Huhtinen, S.; Hyde, K.D.; James, T.; Johnson, E.M.; Johnson, J.E.; Johnston, P.R.; Jones, E.B.; Kelly, L.J.; Kirk, P.M.; Knapp, D.G.; Koljalg, U.; Kovacs, G.M.; Kurtzman, C.P.; Landvik, S.; Leavitt, S.D.; Liggenstoffer, A.S.; Liimatainen, K.; Lombard, L.; Luangsa-Ard, J.J.; Lumbsch, H.T.; Maganti, H.; Maharachchikumbura, S.S.; Martin, M.P.; May, T.W.; McTaggart, A.R.; Methven, A.S.; Meyer, W.; Moncalvo, J.M.; Mongkolsamrit, S.; Nagy, L.G.; Nilsson, R.H.; Niskanen, T.; Nyilasi, I.; Okada, G.; Okane, I.; Olariaga, I.; Otte, J.; Papp, T.; Park, D.; Petkovits, T.; Pino-Bodas, R.; Quaedvlieg, W.; Raja, H.A.; Redecker, D.; Rintoul, T.; Ruibal, C.; Sarmiento-Ramirez, J.M.; Schmitt, I.; Schussler, A.; Shearer, C.; Sotome, K.; Stefani, F.O.; Stenroos, S.; Stielow, B.; Stockinger, H.; Suetrong, S.; Suh, S.O.; Sung, G.H.; Suzuki, M.; Tanaka, K.; Tedersoo, L.; Telleria, M.T.; Tretter, E.; Untereiner, W.A.; Urbina, H.; Vagvolgyi, C.; Vialle, A.; Vu, T.D.; Walther, G.; Wang, Q.M.; Wang, Y.; Weir, B.S.; Weiss, M.; White, M.M.; Xu, J.; Yahr, R.; Yang, Z.L.; Yurkov, A.; Zamora, J.C.; Zhang, N.; Zhuang, W.Y.; Schindel, D.

    2012-01-01

    Roč. 109, č. 16 (2012), s. 6241-6246. ISSN 0027-8424 Institutional research plan: CEZ:AV0Z50450515 Keywords : DNA barcoding * fungal biodiversity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.737, year: 2012

  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. Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers

    OpenAIRE

    Antolin, M F; Bosio, C. F.; COTTON, J; W. Sweeney; Strand, M.R.; Black-IV, W. C.

    1996-01-01

    The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a d...

  16. Development, applications and distribution of DNA markers for genetic information for sorghum and maize improvement

    International Nuclear Information System (INIS)

    This final report summarizes the progress made towards the enhancement and distribution of genetic resources (e.g. genetic stocks, seed and DNA clones) used for basic and applied aspects of the genetic improvement of maize and sorghum. The genetic maps of maize and sorghum were improved through comparative mapping of RFLP loci detected by 124 maize cDNA clones and through the development of a new mapping population of maize. Comparative mapping between maize and sorghum and maize and rice, using the set of 124 maize cDNA clones (and other clones) in each study, substantiated previous observations of extensive conservation of locus order but it also provided strong evidence of numerous large-scale chromosomal rearrangements. The new mapping population for maize (intermated B73xMo17, 'IBM') was created by random intermating during the first segregating generation. Intermating for four generations prior to the derivation of recombinant inbred lines (RILs) increased the frequency of recombinants at many regions of the maize genome and provided better genetic resolution of locus order. Expansion of the maize genetic map was not uniform along the length of a linkage group and was less than the theoretical expectation. The 350 IBM RILs were genotyped at 512 loci detected by DNA clones, including 76 of the 124 supported by this contract. The production of the sorghum mapping population of RILs from the cross CK60xPI229828 has been delayed by weather conditions that were not conducive to plant growth and seed development. Seed of the IBM RILs have been distributed (approximately 5000 RILs in total) to 16 research organizations in the public and private sector. The DNA clones have been distributed (1,206 in total) to nine research labs. Further distribution of the seed and clones will be managed by curators at stock centers in the public domain. (author)

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. High-resolution fluorescence mapping of 46 DNA markers to the short arm of human chromosome 1

    Energy Technology Data Exchange (ETDEWEB)

    Van Roy, N.; Speleman, F.; Laureys, G. (University Hospital, Gent (Belgium)); Versteeg, R. (Academic Medical Center, Amsterdam (Netherlands)); Opdenakker, G. (Univ. of Leuven (Belgium))

    1993-10-01

    The authors describe a high-resolution cytogenetic map for 46 DNA markers previously assigned to the short arm of human chromosome 1. Using fluorescence in situ hybridization on simultaneously R-banded prometaphase chromosomes, a refined map position was found for 45 probes. For 6 of these probes, additional hybridization sites were observed and for another 7 probes, conflicting results were found with regard to previous localizations. For some probes with overlapping map positions, probe order could be determined by dual-color hybridization on elongated chromosomes. The present high-resolution map can be used to refine the previously published composite map and also provides additional landmarks for the construction of a contig map of the short arm of chromosome 1. 56 refs., 2 figs., 2 tabs.

  4. Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces.

    Science.gov (United States)

    Sun, Da; Duan, Chuanren; Shang, Yaning; Ma, Yunxia; Tan, Lili; Zhai, Jun; Gao, Xu; Guo, Jingsong; Wang, Guixue

    2016-04-01

    The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST). PMID:26743644

  5. 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.

  6. 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...

  7. Evaluation of blood, buccal swabs, and hair follicles for DNA profiling technique using STR markers

    OpenAIRE

    Chaudhary, Garima; Dogra, T. D.; Raina, Anupuma

    2015-01-01

    Aim To study the short tandem repeat (STR) pattern of DNA from the blood, buccal swabs, and hair follicles of the recipients of allogenic hematopoietic stem cell transplantation to examine whether these tissues contain donor derived cells. Methods The study enrolled 25 patients who sustained engraftment. Peripheral blood, buccal swabs, and hair follicles were collected on days 21-30, 90, and 180 after transplantation and the chimeric status of the recipients was evaluated. Results Donor deriv...

  8. 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

  9. A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers.

    Science.gov (United States)

    Misof, B; Anderson, C L; Hadrys, H

    2000-04-01

    We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups. PMID:10764530

  10. Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

    Science.gov (United States)

    Quinn, J S; Guglich, E; Seutin, G; Lau, R; Marsolais, J; Parna, L; Boag, P T; White, B N

    1992-02-01

    The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa. PMID:1572527

  11. 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.

  12. 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

  13. 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.

  14. Microarray long oligo probe designing for Escherichia coli: an in-silico DNA marker extraction

    Science.gov (United States)

    Behzadi, Payam; Najafi, Ali; Behzadi, Elham

    2016-01-01

    Introduction Urinary tract infections are predominant diseases which may be caused by different pathogenic microorganisms, particularly Escherichia coli (E.coli). DNA microarray technology is an accurate, rapid, sensitive, and specific diagnostic tool which may lead to definite diagnosis and treatment of several infectious diseases. DNA microarray is a multi-process method in which probe designing plays an important. Therefore, the authors of the present study have tried to design a range of effective and proper long oligo microarray probes for detection and identification of different strains of pathogenic E.coli and in particular, uropathogenic E.coli (UPEC). Material and methods E.coli O26 H11 11368 uid41021 was selected as the standard strain for probe designing. This strain encompasses the largest nucleotide sequence and the most number of genes among other pathogenic strains of E.coli. For performing this in silico survey, NCBI database, GReview Server, PanSeq Server, Oligoanalyzer tool, and AlleleID 7.7 were used to design accurate, appropriate, effective, and flexible long oligo microarray probes. Moreover, the genome of E.coli and its closely related microorganisms were compared. Results In this study, 15 long oligo microarray probes were designed for detecting and identifying different strains of E.coli such as UPEC. These probes possessed the best physico-chemical characteristics. The functional and structural properties of the designed probes were recognized by practical tools and softwares. Conclusions The use of reliable advanced technologies and methodologies for probe designing guarentees the high quality of microarray probes and makes DNA microarray technology more flexible and an effective diagnostic technique.

  15. 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

  16. 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

  17. 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

  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. 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.

  20. Variabilidade genética de etnovariedades de mandioca, avaliada por marcadores de DNA Genetic diversity of cassava folk varieties assessed by DNA markers

    Directory of Open Access Journals (Sweden)

    Gilda Santos Mühlen

    2000-06-01

    reference. Among these, 38 were bitter varieties and 17 sweet. Three different types of DNA markers were used: RAPD (randomly amplified polymorphic DNA, AFLP (amplified fragment length polymorphism and microsatellites. Analysis of the results consisted of a description of band patterns, a calculation of similarity indexes (Nei & Li and a principal coordinate analysis (PCoA for each marker type. Heterozygosity, diversity indexes (DI, Weir and genetic differentiation coefficients (G ST were calculated for the microsatellite loci.Genetic variability was more concentrated within regions, then among regions (G ST = 0.07. Mean heterozygosity was 56%. Mean similarity indexes were dependent on the marker used: S = 0.89 for RAPD, S = 0.85 for AFLP and S = 0.59 for microsatellites. PCoA analysis revealed groups, distinguishing bitter from sweet varieties.

  1. 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.

  2. 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.

  3. 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

  4. [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

  5. 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

  6. Admixture analysis of stocked brown trout populations using mapped microsatellite DNA markers: indigenous trout persist in introgressed populations.

    Science.gov (United States)

    Hansen, Michael M; Mensberg, Karen-Lise D

    2009-10-23

    Admixture between wild and captive populations is an increasing concern in conservation biology. Understanding the extent of admixture and the processes involved requires identification of admixed and non-admixed individuals. This can be achieved by statistical methods employing Bayesian clustering, but resolution is low if genetic differentiation is weak. Here, we analyse stocked brown trout populations represented by historical (1943-1956) and contemporary (2000s) samples, where genetic differentiation between wild populations and stocked trout is weak (pairwise F(ST) of 0.047 and 0.053). By analysing a high number of microsatellite DNA markers (50) and making use of linkage map information, we achieve clear identification of admixed and non-admixed trout. Moreover, despite strong population-level admixture by hatchery strain trout in one of the populations (70.8%), non-admixed individuals nevertheless persist (7 out of 53 individuals). These remnants of the indigenous population are characterized by later spawning time than the majority of the admixed individuals. We hypothesize that isolation by time mediated by spawning time differences between wild and hatchery strain trout is a major factor rescuing a part of the indigenous population from introgression. PMID:19515653

  7. Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae).

    Science.gov (United States)

    Buerki, Sven; Forest, Félix; Acevedo-Rodríguez, Pedro; Callmander, Martin W; Nylander, Johan A A; Harrington, Mark; Sanmartín, Isabel; Küpfer, Philippe; Alvarez, Nadir

    2009-05-01

    The economically important soapberry family (Sapindaceae) comprises about 1900 species mainly found in the tropical regions of the world, with only a few genera being restricted to temperate areas. The infrafamilial classification of the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae - which have now been included in an expanded definition of Sapindaceae (i.e., subfamily Hippocastanoideae) - have been debated for decades. Here we present a phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family. Our study comprises 997 new sequences of Sapindaceae from 152 specimens. Despite presenting 18.6% of missing data our complete data set produced a topology fully congruent with the one obtained from a subset without missing data, but including fewer markers. The use of additional information therefore led to a consistent result in the relative position of clades and allowed the definition of a new phylogenetic hypothesis. Our results confirm a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Our study confirms that the Chinese monotypic genus Xanthoceras is sister to the rest of the family, in which subfamily Hippocastanoideae is sister to a clade comprising subfamilies Dodonaeoideae and Sapindoideae. On the basis of the strong support demonstrated in Sapindoideae, Dodonaeoideae and Hippocastanoideae as well as in 14 subclades, we propose and discuss informal groupings as basis for a new classification of Sapindaceae. PMID:19405193

  8. 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

  9. 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

  10. 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...

  11. Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

    Science.gov (United States)

    In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers wer...

  12. D-loop somatic mutations and ∼5 kb "common" deletion in mitochondrial DNA: important molecular markers to distinguish oral precancer and cancer.

    Science.gov (United States)

    Datta, Sayantan; Chattopadhyay, Esita; Ray, Jay Gopal; Majumder, Mousumi; Roy, Puspita Das; Roy, Bidyut

    2015-04-01

    Apart from genomic DNA, mutations at mitochondrial DNA (mtDNA) have been hypothesized to play vital roles in cancer development. In this study, ∼5 kb deletion and D-loop mutations in mtDNA and alteration in mtDNA content were investigated in buccal smears from 104 healthy controls and 74 leukoplakia and 117 cancer tissue samples using Taqman-based quantitative assay and re-sequencing. The ∼5 kb deletion in mtDNA was significantly less (9.8 and 10.5 folds, P mutations in D-loop, investigated in 54 controls, 50 leukoplakias and 56 cancer patients, were found to be significantly more in cancer tissues, but not in leukoplakia tissues, compared to control (Z-score = 5.4). MtDNA contents were observed to be significantly more in leukoplakia (2.1 folds, P = 0.004) and cancer (1.6 folds, P = 0.03) tissues compared to control tissues. So, D-loop somatic mutations and ∼5 kb deletion patterns could be used as distinguishing markers between precancer and cancer tissues. This observation further suggests that somatic mutations in D-loop may facilitate carcinogenesis and cancer cells with less ∼5 kb deletion, i.e., intact mtDNA, may become resistant to apoptosis. PMID:25527154

  13. 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

  14. Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker.

    Science.gov (United States)

    Baurens, Franc-Christophe; Nicolleau, Joris; Legavre, Thierry; Verdeil, Jean-Luc; Monteuuis, Olivier

    2004-04-01

    Genomic DNA methylation was analyzed in Acacia mangium Willd. microshoots micropropagated in vitro from juvenile and mature explants, and in relation to leaf morphology of the microshoots, which is considered a phase change indicator. Based on high performance liquid chromatography (HPLC) analyses, we found more DNA methylation in microshoots exhibiting juvenile leaf morphology (22.4%) than in microshoots of the mature phyllode morphological type (20.7%), irrespective of the age of the source material. Overall, the degree of DNA methylation in A. mangium microshoots was consistent with values reported for other angiosperms. Complementary investigations based on methylation sensitive amplification polymorphism (MSAP) techniques established that, of 1204 fragments revealed by the different primer pairs used, 49 (i.e., 4.08%) were derived from C(5m)CGG methylated sites. Three of these C(5m)CGG sites were exclusive to the juvenile plant material, and three sites were exclusive to the mature source. No fragments were associated specifically with leaf morphology, rather than with plant age. Thus, although the two age classes could not be distinguished based on a quantitative HPLC measure of DNA methylation, qualitative differences existed, as demonstrated by the six age-specific markers identified by MSAP. The reliability of the MSAP data was confirmed on a larger sample of juvenile plant material, which suggested that the total of six methylation markers detected is probably an underestimation of the age-related differences in DNA methylation that may exist between juvenile and mature plant materials. PMID:14757579

  15. 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...

  16. 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.

  17. DNA marker-assisted evaluation of potato genotypes for potential resistance to potato cyst nematode pathotypes not yet invading into Japan

    OpenAIRE

    Asano, Kenji; Kobayashi, Akira; Tsuda, Shogo; Nishinaka, Mio; Tamiya, Seiji

    2012-01-01

    One of major objectives of crop breeding is conferring resistance to diseases and pests. However, large-scale phenotypic evaluation for many diseases and pests is difficult because strict controls are required to prevent their spread. Detection of disease resistance genes by using DNA markers may be an alternative approach to select potentially resistant accessions. Potato (Solanum tuberosum L.) breeders in Japan extensively use resistance gene H1, which confers nearly absolute resistance to ...

  18. 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...

  19. 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. ...

  20. 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

  1. 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.

  2. 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

  3. 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.)

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Random amplified polymorphic DNA markers for DNA fingerprinting and genetic variability assessment of minute parasitic wasp species (Hymenoptera: Mymaridae and Trichogrammatidae) used in biological control programs of phytophagous insects.

    Science.gov (United States)

    Landry, B S; Dextraze, L; Boivin, G

    1993-06-01

    Biological control of insects that feed on our crops has become more practical in recent years by mass release of egg parasitoid microhymenoptera. Trichogramma species are now commercially reared and spread in commercial fields to control specific insect pests. Microhymenoptera species are, however, very small and morphologically indistinguishable within species, although strains of a given species differ in their efficiency to control specific insect pests. Traditional taxonomy is unable to differentiate microhymenoptera species at the strain level. It is becoming increasingly important to develop a reliable system to monitor genetic variations both within and between strains of commercially important microhymenoptera, to detect genetic drift occurring during several generations of multiplication, to protect patents, and to certify the lots of commercially released microhymenoptera. We have developed a system based on DNA markers to rapidly characterize individuals of five species of microhymenoptera from the genus Anaphes and Trichogramma including a new species of Anaphes not previously described. The main components of our system are a rapid and simple DNA micro-extraction method and fast DNA polymorphism analyses based on random amplified polymorphic DNA markers. PMID:8349128

  12. Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species.

    Science.gov (United States)

    Baharum, Syarul Nataqain; Nurdalila, A'wani Aziz

    2012-05-01

    The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics. PMID:22167328

  13. 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...

  14. 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...

  15. 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...

  16. 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.

  17. 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

    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. The...... implications of these results for the conservation status of North Sea houting are discussed in the light of current definitions of evolutionary significant units. Both mtDNA and microsatellite data indicated that postglacial recolonization by C. lavaretus in Denmark was less likely to have taken place from...... the Baltic Sea. Instead, the data suggested a recent common origin of all Danish whitefish populations, including North Sea houting, probably by recolonization via the postglacial Elbe River system. Estimates of genetic differentiation among populations based on mtDNA and microsatellites were...

  18. 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.

  19. Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.).

    Science.gov (United States)

    Cuveliers, E L; Bolle, L J; Volckaert, F A M; Maes, G E

    2009-05-01

    Historical otolith collections are crucial in assessing the evolutionary consequences of natural and anthropogenic changes on the demography and connectivity of commercially important fish species. Hence, it is important to define optimal protocols for purifying DNA from such valuable information sources while avoiding any damage to the physical structure of the otolith. Before being able to conclude on the harmlessness of a method, it is important to validate protocols on different kinds of otoliths by testing purification methodologies under standardized conditions. Here we compare the effect of two DNA extraction methods on the success in identifying the age in an overexploited marine fish, the common sole (Solea solea L.). To ensure optimal future population genetic and demographic analyses, we assessed DNA quantity and tested the DNA quality by investigating the amplification success of a mitochondrial and nuclear marker. Our results show that the choice of the DNA extraction method had a significant effect on the success of using these otoliths in age and growth analyses. Standard commercial and published protocols resulted in a severe damaging of the otolith structure, hampering accurate preparation and analyses of the morphological structures of the otoliths. Shortening the lysis time and lowering the EDTA (ethylene diamine tetraacetic acid) and SDS (sodium dodecylsulphate) concentration turned out to be beneficial for the stability of otolith structure, while maintaining an overall high DNA quality measured through polymerase chain reaction amplification success. We therefore recommend that care should be taken when choosing the extraction method for a molecular study on archived samples, in order to enable the maximal use of information embedded in historical material. PMID:21564731

  20. DNA marker-assisted evaluation of potato genotypes for potential resistance to potato cyst nematode pathotypes not yet invading into Japan.

    Science.gov (United States)

    Asano, Kenji; Kobayashi, Akira; Tsuda, Shogo; Nishinaka, Mio; Tamiya, Seiji

    2012-06-01

    One of major objectives of crop breeding is conferring resistance to diseases and pests. However, large-scale phenotypic evaluation for many diseases and pests is difficult because strict controls are required to prevent their spread. Detection of disease resistance genes by using DNA markers may be an alternative approach to select potentially resistant accessions. Potato (Solanum tuberosum L.) breeders in Japan extensively use resistance gene H1, which confers nearly absolute resistance to potato cyst nematode (Globodera rostochiensis) pathotype Ro1, the only pathotype found in Japan. However, considering the possibility of accidental introduction of the other pathotypes, breeding of resistant varieties is an important strategy to prevent infestation by non-invading pathotypes in Japan. In this study, to evaluate the prevalence of resistance genes in Japanese genetic resources, we developed a multiplex PCR method that simultaneously detects 3 resistance genes, H1, Gpa2 and Gro1-4. We revealed that many Japanese varieties possess not only H1 but Gpa2, which are potentially resistant to other pathotypes of potato cyst nematode. On the other hand, no genotype was found to have the Gro1-4, indicating importance of introduction of varieties having Gro1-4. Our results demonstrate the applicability of DNA-marker assisted evaluation of resistant potato genotypes without phenotypic evaluation. PMID:23136525

  1. 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

  2. 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

  3. 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...

  4. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, S.V.; Nadeau, J.H.; Tanzi, R.E.; Watkins, P.C.; Jagadesh, J.; Taylor, B.A.; Haines, J.L.; Sacchi, N.; Gusella, J.F. (Harvard Medical School, Boston, MA (USA))

    1988-08-01

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid {beta} precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS.

  5. Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17

    International Nuclear Information System (INIS)

    Mouse trisomy 16 has been proposed as an animal model of Down syndrome (DS), since this chromosome contains homologues of several loci from the q22 band of human chromosome 21. The recent mapping of the defect causing familial Alzheimer disease (FAD) and the locus encoding the Alzheimer amyloid β precursor protein (APP) to human chromosome 21 has prompted a more detailed examination of the extent of conservation of this linkage group between the two species. Using anonymous DNA probes and cloned genes from human chromosome 21 in a combination of recombinant inbred and interspecific mouse backcross analyses, the authors have established that the linkage group shared by mouse chromosome 16 includes not only the critical DS region of human chromosome 21 but also the APP gene and FAD-linked markers. Extending from the anonymous DNA locus D21S52 to ETS2, the linkage map of six loci spans 39% recombination in man but only 6.4% recombination in the mouse. A break in synteny occurs distal to ETS2, with the homologue of the human marker D21S56 mapping to mouse chromosome 17. Conservation of the linkage relationships of markers in the FAD region suggests that the murine homologue of the FAD locus probably maps to chromosome 16 and that detailed comparison of the corresponding region in both species could facilitate identification of the primary defect in this disorder. The break in synteny between the terminal portion of human chromosome 21 and mouse chromosome 16 indicates, however, that mouse trisomy 16 may not represent a complete model of DS

  6. 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...

  7. 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.

  8. 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.

  9. 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

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

    OpenAIRE

    Correa, M. C. G.; Zaviezo, T.; Le Maguet, Jean; HERRBACH, Etienne; Malausa, Thibaut

    2014-01-01

    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 in...

  11. Diversity and genetic structure of teak (Tectona grandis L.f) in its natural range using DNA microsatellite markers

    OpenAIRE

    Fofana, Inza Jesus; Ofori, Daniel; Poitel, Mireille; Verhaegen, Daniel

    2009-01-01

    Teak (Tectona grandis L.f.) is considered to be an extraordinarily durable building timber with a worldwide reputation. Its widespread use has entailed the over- exploitation of natural forests and a large reduction in natural diversity. Fifteen micro- satellite markers were used to study the genetic variability and structure of 166 teak trees distributed over the whole natural area of teak. Analysis showed that in the teak natural area there were four main centers of genetic variability. Two...

  12. 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...

  13. 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.

  14. 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...

  15. 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

  16. Phylogenetic Study of Mangifera laurina and its Related Species Using cpDNA trnL-F Spacer Markers

    Directory of Open Access Journals (Sweden)

    FITMAWATI

    2010-03-01

    Full Text Available Phylogenetic study of cpDNA intergenic spacer trnL-F of Mangifera laurina and their related species within the genus Mangifera in Indonesia was conducted using Rutaceae as the outgroup. This study was to reconstruct phylogenetic relationships and to understand infraspecific relationships within Mangifera based on cpDNA trnL-F intergenic spacer sequences. The results showed that Mangifera sp. Hiku (mangga hiku as the basic cultivar in the clade, and it supported the monophyletic group in Mangifera. And phylogenetic construction indicated that Mangifera sp. Hiku was the progenitor of M. laurina and their related species.

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

    International Nuclear Information System (INIS)

    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

  18. 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 to d...

  19. 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

  20. Detection of monoclonal integration of bovine leukemia virus proviral DNA as a malignant marker in two enzootic bovine leukosis cases with difficult clinical diagnosis.

    Science.gov (United States)

    Miura, Saori; Horiuchi, Noriyuki; Matsumoto, Kotaro; Kobayashi, Yoshiyasu; Kawazu, Shin-Ichiro; Inokuma, Hisashi

    2015-07-01

    Monoclonal integration of bovine leukemia virus (BLV) proviral DNA into bovine genomes was detected in peripheral blood from two clinical cases of enzootic bovine leukosis (EBL) without enlargement of superficial lymph nodes. A BLV-specific probe hybridized with 1 to 3 EcoRI and HindIII fragments in these 2 atypical EBL cattle by Southern blotting and hybridization, as well as in 3 typical EBL cattle. The probe also hybridized to a large number of EcoRI and HindIII fragments in 5 cattle with persistent leukosis. These results suggest that the detection of monoclonal integration of BLV provirus into the host genome may serve as a marker of monoclonal proliferation and malignancy in difficult to diagnose EBL cattle. PMID:25766769

  1. Biomonitoring of diesel exhaust-exposed workers. DNA and hemoglobin adducts and urinary 1-hydroxypyrene as markers of exposure

    DEFF Research Database (Denmark)

    Nielsen, Per Sabro; Andreassen, Åshild; Farmer, Peter B.;

    1996-01-01

    Diesel exhaust-exposed workers have been shown to have an increased risk of lung cancer. A battery of biomarkers were evaluated for their ability to assess differences in exposure to genotoxic compounds in bus garage workers and mechanics and controls. Lymphocyte DNA adducts were analyzed using t....... The study indicated that skin absorption of polycyclic aromatic hydrocarbons (PAH) might be an important factor to consider when studying PAH exposure from air pollution sources....... correlated with HPU but not with DNA adducts. The levels of HPU in urine were 0.11 micromol/mol creatinine compared to 0.05 in controls. All three assays applied were sensitive enough to evaluate a low level of exposure to environmental pollutants, with postlabelling and GC-MS as the most sensitive assays...

  2. UTILIZATION OF DNA MARKERS BASED ON MICROSATELLITE POLYMORPHISM FOR IDENTIFICATION OF POTATO VARIETIES CULTIVATED IN THE CZECH REPUBLIC

    Directory of Open Access Journals (Sweden)

    Alena Nováková

    2011-01-01

    Full Text Available In the year 2007, there were one hundred and seventy-eight potato varieties enlisted in the Czech list of registered potato varieties. The classical morphometric approach to characterization is not effective for such a number of varieties especially for identification at the level of tubers. The needfulness of variety identification at the level of tubers is important mainly for trade aspect. The Czech law no.110/1997 Sb. about the food-stuff and tobacco products and the consequential ordinance (MZe č. 332 / 1997 Sb. require guarantee of variety declaration in commercial relation for table potato. In this study we analyzed twenty potato varieties (Solanum tuberosum L. cultivated in the Czech Republic. Every variety was represented by four independent replicates. This set of samples was analyzed by methods of PCR-SSR (Simple Sequence Repeats and PCR-ISSR (Inter Simple Sequence Repeats. We discovered that both of tested methods afford sufficient polymorphism for variety identification, but the method of PCR-ISSR is not utilizable, because we observed the variability within variety. For outright identification of the whole set of potato varieties cultivated in the Czech Republic we recommend to use SSR, AFLP and retrotransposene-based markers as well as morphological markers.

  3. PCR amplification of species-specific repeat for meat DNA identification via genetic markers in cattle and sheep

    OpenAIRE

    Ahmed M.M.

    2005-01-01

    The designed and evaluated four assays based upon PCR amplification of species-specific repeat (SSR) for detection, identification and authentication of cattle and sheep on the DNA level. SSR primers were applied in the polymerase chain reaction (PCR), the products has been used for the specific identification of cattle and sheep meat. PCR amplification size of the gene encoding SSR region in cattle and sheep meat was 603 bp and 374 bp respectively. The results showed that SSR analysis produc...

  4. 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

  5. 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

  6. 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.

  7. Identifikasi Trenggiling (Manis javanica Menggunakan Penanda Cytochrome B Mitokondria DNA (IDENTIFICATION OF PANGOLIN (MANIS JAVANICA DESMAREST, 1822 USING CYTOCHROME B mtDNA MARKER

    Directory of Open Access Journals (Sweden)

    Wirdateti .

    2013-12-01

    Full Text Available The aim of this study was to identify the gentic profile of Malay pangolin (Manis javanica and originpatterns of confiscated specimens.  Tissue samples of Malay pangolin were collected from several confiscatedmaterials in Tangerang, Medan, and Lampung. Wild collections tissue were also conducted in Lampungand Sukabumi. The study was conducted using  conserved Cytochrome b (Cyt. B DNA mitochondria(mtDNA. The results showed that based on nucleotide base lentgh of 420 nt, confiscated pangolin wasdistributed in three clades and two groups. Haplotype variations was high, consisted of 19 haplotypes in19 individuals (TR1-TR19. On fisrt clade (TR4,7,16,9,19 high substitution occured in adenin base, cladetwo (TR14,17,1,2,15,3,8,13 high substitution occured in guanin base and clade three  (TR5,6,10,11,12 incytosin. It was concluded that haplotipe variation of each populations  was high and for genetic distancebetween individuals was low. Mutation rates was dominated by transition  from guanine to adenine

  8. 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

  9. 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

  10. 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.

  11. 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

  12. Preliminary study of the genetic diversity of eastern Assamese macaques (Macaca assamensis assamensis) in Thailand based on mitochondrial DNA and microsatellite markers.

    Science.gov (United States)

    Sukmak, Manakorn; Malaivijitnond, Suchinda; Schülke, Oliver; Ostner, Julia; Hamada, Yuzuru; Wajjwalku, Worawidh

    2014-04-01

    Human overpopulation, deforestation, invasion of agricultural areas, and livestock are the primary causes for population fragmentation of wildlife. The distribution range of species of the genus Macaca is constantly decreasing and becoming increasingly fragmented due to forest deterioration. Assamese macaques (M. assamensis) are classified as near threatened in the International Union for Conservation of Nature (IUCN) Red List of Threatened Animals (2008) and have been declared a protected wildlife animal according to Wildlife Preservation and Protection Act, B.E.2535 (1992) of Thailand. As studies of the population history and genetic diversity of Assamese macaques in Thailand are currently lacking, we aimed at a first investigation of their genetic diversity based on mitochondrial DNA [hypervariable regions 1 and 2 (HV1, HV2) and cytochrome B (CYTB) regions], as well as 15 microsatellite markers of five sampling sites distributed across Thailand. Our results indicate that Assamese macaques in Thailand are diverse, with eight maternal haplotypes and a low inbreeding coefficient in the Phu Khieo Wildlife Sanctuary (PKWS) population. Moreover, our phylogenetic and median-joining network analysis based on mitochondrial (mt)DNA suggests a population distribution in accordance with the evolutionary scenario proposed for M. sinica. Today, the population of Assamese macaques is fragmented, and conservation strategies are needed to ensure the maintenance of genetic diversity of this primate species. PMID:24142419

  13. 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

  14. Relationship between changes of blood HBV-DNA viral load and serum liver fibrosis markers (HA, LN, IV-C, PCIII) levels in patients with chronic hepatitis B

    International Nuclear Information System (INIS)

    Objective: To investigate the relationship between changes of blood HBV DNA viral load and serum liver fibrosis markers levels in patients with chronic hepatitis B. Methods: In 2002, 20 patients with hepatitis B were divided into two groups: Group A treated with antiviral ageat (n=10), Group B not treated.Five years later (2007) the blood viral load (with FQ-PCR) and serum levels of hepatic fibrosis markers (with RIA) were determined in these patients. Results: The average log viral load in serum in the tow groups were 3.56 ± 1.12 (treated group) and 7.76 ± 1.23 respectively with significant difference (P<0.05). In 2002, serum liver fibrosis markers (HA, LN, IV-C, PCIII) levels were about the same in the two groups were (82.72 ± 30.62μg/ml, 71.18 ± 26.71μg/ml, 93.77 ± 69.87μg/ml, 91.4 ± 18.64μg/ml and 79.32 ± 31.34μg/ml, 70.25 ± 28.23)μg/ml, 90.35 ± 67.81μg/ml, 85.77 ± 20.56μg/ml respectively). In 2007, in the treated patients, serum liver fibrosis markers HA, LN, IV-C, PCIII levels were 85.72 ± 29.52μg/ml, 70.18 ± 25.4μg/ml, 94.2 ± 70.92μg/ml, 93.4 ± 19.32μg/ml respectively However, in the non-treated groups, the serum HA, LN, IV-C, PCIII levels were105.67 ± 28.54μg/ml, 97.75 ± 26.25μg/ml, 132 ± 72.13μg/ml, 120.72 ± 19.87μg/ml, being significantly higher than those in the treated group (P<0.05). Conclusion: Effective decrease of the viral load might control the progress of hepatic fibrosis in patients with chronic hepatitis B. (authors)

  15. 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...

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

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

    Science.gov (United States)

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

    2016-01-15

    Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world. PMID:26481237

  2. 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

  3. Linkage analysis of bipolar illness with X-chromosome DNA markers: A susceptibility gene in Xq27-q28 cannot be excluded

    Energy Technology Data Exchange (ETDEWEB)

    De bruyn, A.; Raeymaekers, P.; Raes, G. [Univ. of Antwerp (Belgium)] [and others

    1994-12-15

    Transmission studies have supported the presence of a susceptibility gene for bipolar (BP) illness on the X-chromosome. Initial linkage studies with color blindness (CB), glucose-6-phosphate dehydrogenase (G6PD) deficiency, and the blood coagulation factor IX (F9) have suggested that a gene for BP illness is located in the Xq27-q28 region. We tested linkage with several DNA markers located in Xq27-q28 in 2 families, MAD3 and MAD4, that previously were linked to F9, and 7 newly ascertained families of BP probands. Linkage was also examined with the gene encoding the {alpha}3 subunit of the gamma-amino butyric acid receptor (GABRA3), a candidate gene for BP illness located in this region. The genetic data were analyzed with the LOD score method using age-dependent penetrance of an autosomal dominant disease gene and narrow and broad clinical models. In MAD3 and MAD4 the multipoint LOD score data suggested a localization of a BPI gene again near F9. In the 7 new families the overall linkage data excluded the Xq27-q28 region. However, if the families were grouped according to their proband`s phenotype BPI or BPII, a susceptibility gene for BPI disorder at the DXS52-F8 cluster could not be excluded. 48 refs., 2 figs., 3 tabs.

  4. 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.

  5. Evaluation of genetic fidelity among micropropagated plants of Gloriosa superba L. using DNA-based markers--a potential medicinal plant.

    Science.gov (United States)

    Yadav, Kuldeep; Aggarwal, Ashok; Singh, Narender

    2013-09-01

    Malabar glory lily (Gloriosa superba L.) is a medicinally potent plant species used for the production of alkaloid colchicine. With ever increasing demand, there is a pressing need to conserve it through biotechnological approaches. A large number of complete plantlets were obtained by direct regeneration from the non-dormant tuber explants on Murashige and Skoog (MS) medium supplemented with 2.0 mg/l 6-benzylaminopurine (BAP)+0.5 mg/l α-naphthalene acetic acid (NAA). Large number of plants can be produced in vitro under aseptic conditions, but there is always a danger of producing somaclonal variants by tissue culture technology. Thus, the genetic stability of micropropagated clones was evaluated using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analysis. During the study a total of 80 (50 RAPD and 30 ISSR) primers were screened, out of which 10 RAPD and 7 ISSR primers produced a total of 98 (49 RAPD and 49 ISSR) clear, distinct and reproducible amplicons. The amplification products of the regenerated plants showed similar banding patterns to that of the mother plant thus demonstrating the homogeneity of the micropropagated plants. This is the first report that evaluates the use of genetic markers to establish genetic fidelity of micropropagated G. superba using RAPD and ISSR, which can be successfully applied for the mass multiplication, germplasm conservation and further genetic transformation assays for colchicine production to meet the ever increasing demand of this medicinally potent plant for industrial and pharmaceutical uses. PMID:23811099

  6. 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.

  7. A Comparative Analysis of Bio marker Expression and Molecular Subtypes of Pure Ductal Carcinoma In Situ and Invasive Breast Carcinoma by Image Analysis: Relationship of the Subtypes with Histologic Grade, Ki67, p53 Overexpression, and DNA Ploidy

    International Nuclear Information System (INIS)

    There is a paucity of data regarding molecular subtypes of pure ductal carcinoma in situ (pDCIS). We evaluated the expression of ER, PR, HER2, Ki67, and p53 and DNA ploidy in 118 pDCIS and 100 invasive breast carcinomas (IBCAs) by routine IHC and classified them according to molecular subtypes. Quantification of bio markers and DNA ploidy was performed by image analysis. Expression of ER, PR, and high ki67 was more frequent in pDCIS compared to IBCA. High-grade tumors had lower ER and PR expression, high Ki67, overexpression of HER2 and p53, and DNA aneuploidy. Luminal A and HER2 subtypes were more common in pDCIS, and triple negative was more prevalent in IBCA. In both groups, HER2 and triple negative subtypes were characterized by high ki67, overexpression of p53, and DNA aneuploidy compared to luminal subtypes. Molecular subtypes of IBCA are distinct from those of pDCIS. Invasion is characterized by change in phenotype in some tumors.Pathology.Pathology.Bio marker staining nuclei, and staining intensity expression

  8. 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 ...

  9. 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

  10. 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

  11. Histone H2AX phosphorylation as a measure of DNA double-strand breaks and a marker of environmental stress and disease activity in lupus

    Science.gov (United States)

    Namas, Rajaie; Renauer, Paul; Ognenovski, Mikhail; Tsou, Pei-Suen; Sawalha, Amr H

    2016-01-01

    Objective Defective or inefficient DNA double-strand break (DSB) repair results in failure to preserve genomic integrity leading to apoptotic cell death, a hallmark of systemic lupus erythematosus (SLE). Compelling evidence linked environmental factors that increase oxidative stress with SLE risk and the formation of DSBs. In this study, we sought to further explore genotoxic stress sensitivity in SLE by investigating DSB accumulation as a marker linking the effect of environmental stressors and the chromatin microenvironment. Methods DSBs were quantified in peripheral blood mononuclear cell subsets from patients with SLE, healthy controls, and patients with rheumatoid arthritis (RA) by measuring phosphorylated H2AX (phospho-H2AX) levels with flow cytometry. Phospho-H2AX levels were assessed in G0/G1, S and G2 cell-cycle phases using propidium iodide staining, and after oxidative stress using 0.5 µM hydrogen peroxide exposure for 0, 2, 5, 10, 30 and 60 min. Results DSB levels were significantly increased in CD4+ T cells, CD8+ T cells and monocytes in SLE compared with healthy controls (p=2.16×10−4, 1.68×10−3 and 4.74×10−3, respectively) and RA (p=1.05×10−3, 1.78×10−3 and 2.43×10−2, respectively). This increase in DSBs in SLE was independent of the cell-cycle phase, and correlated with disease activity. In CD4+ T cells, CD8+ T cells and monocytes, oxidative stress exposure induced significantly higher DSB accumulation in SLE compared with healthy controls (60 min; p=1.64×10−6, 8.11×10−7 and 2.04×10−3, respectively). Conclusions Our data indicate that SLE T cells and monocytes have increased baseline DSB levels and an increased sensitivity to acquiring DSBs in response to oxidative stress. Although the mechanism underlying DSB sensitivity in SLE requires further investigation, accumulation of DSB may serve a biomarker for disease activity in SLE and help explain increased apoptotic cell accumulation in this disease. PMID:27158526

  12. 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.

  13. DNA isolation from teeth by organic extraction and identification of sex of the individual by analyzing the AMEL gene marker using PCR

    OpenAIRE

    Subramanian Thangaraj Praveen Kumar; Nalini Aswath

    2016-01-01

    Background: To identify the sex of the deceased individual from dental hard tissue such as enamel and dentine. Objective: To isolate the DNA from dental hard tissue (enamel and dentin) from teeth extracted for prophylactic purpose, to assess the quality and purity of DNA and to identify the sex using polymerized chain reactor (PCR). Materials and Methods: DNA was extracted following phenol/chloroform (organic) extraction from 20 male and 20 female teeth. The samples that contain the amelogeni...

  14. 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,

  15. 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℃.

  16. 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; Sørensen, Kirsten Kørup; Nielsen, Kåre Lehmann

    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 is dis...

  17. Transformation of tobacco cpDNA with fusion E7GGG/GUS gene and homologous recombination mediated elimination of the marker gene

    Czech Academy of Sciences Publication Activity Database

    Bříza, Jindřich; Vlasák, Josef; Ryba, Š.; Ludvíková, V.; Niedermeierová, Hana

    2013-01-01

    Roč. 27, č. 2 (2013), s. 3644-3648. ISSN 1310-2818 R&D Projects: GA AV ČR IAA500960903 Institutional support: RVO:60077344 Keywords : E7GGG oncogene * chloroplast transformation * marker-free plant * homologous recombination Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.379, year: 2013

  18. 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...

  19. 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.

    OpenAIRE

    Mariën J; Roelofs D; Timmermans MJTN; Straalen NM van

    2008-01-01

    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. Resu...

  20. Nuclear and mitochondrial DNA markers indicate unidirectional gene flow of Indo-Pacific to Atlantic bigeye tuna (Thunnus obesus) populations, and their admixture off southern Africa

    OpenAIRE

    Durand, Jean-Dominique; Collet, Adeline; Chow, S; Guinand, B.; Borsa, Philippe

    2005-01-01

    A sharp genetic break separates Atlantic from Indo-Pacific bigeye tuna (Thunnus obesus) populations, as the frequencies of two major mitochondrial (mt) DNA types (alpha and beta) found in this species are different across the tip of southern Africa. The level of nucleotide divergence between mtDNA types alpha and beta is of the same order as that between reproductively isolated taxa. To further investigate the genetic structure of bigeye tuna over its distribution range and in the contact zon...

  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. Close linkage of the locus for X chromosome-linked severe combined immunodeficiency to polymorphic DNA markers in Xq11-q13

    Energy Technology Data Exchange (ETDEWEB)

    de Saint Basile, G.; Arveiler, B.; Oberle, I.; Malcolm, S.; Levinsky, R.J.; Lau, Y.L.; Hofker, M.; Debre, M.; Fischer, A.; Griscelli, C.; Mandel, J.L.

    1987-11-01

    The gene for X chromosome-linked severe combined immunodeficiency (SCID), a disease characterized by a block in early T-cell differentiation, has been mapped to the region Xq11-q13 by linkage analysis with restriction fragment length polymorphisms. High logarithm of odds (lod) scores were obtained with the marker 19.2 (DXS3) and with the marker cpX73 (DXS159) that showed complete cosegregation with the disease locus in the informative families analyzed. Other significant linkages were obtained with several markers from Xq11 to q22. With the help of a recently developed genetic map of the region, it was possible to perform multipoint linkage analysis, and the most likely genetic order is DXS1-(SCID, DXS159)-DXYS1-DXYS12-DXS3, with a maximum multipoint logarithm of odds score of 11.0. The results demonstrate that the SCID locus (gene symbol IMD4) is not closely linked to the locus of Bruton's agammaglobulinemia (a defect in B-cell maturation). They also provide a way for a better estimation of risk for carrier and antenatal diagnosis.

  5. Clonal evolution and progression of 20-methylcholanthrene-induced squamous cell carcinoma of mouse epidermis as revealed by DNA instability and other malignancy markers

    Directory of Open Access Journals (Sweden)

    K Hirai

    2009-12-01

    Full Text Available We examined the clonal evolution of skin malignant lesions by repeated topical applications of 20- methylcholanthrene (20-MC to the skin, which induces hyperplastic epidermis, papillomatous lesion and invasive carcinoma in mice. The lesions were examined histologically and immunohistochemically with anti-single-stranded DNA after acid hydrolysis (DNA-instability test, p53, VEGF, DFF45, PCNA and AgNORs parameters analyses. Multiple clones with increased DNA instability comparable to that of invasive carcinoma were noted in early-stage (2-6 weeks hyperplastic epidermis, and their number increased in middle (7-11 weeks, and late-stages (12-25 weeks of hyperplastic epidermis, indicating that they belong to the malignancy category. All papillomatous lesions and invasive carcinomas showed a positive DNA-instability test. Positive immunostaining for various biomarkers and AgNORs parameters appeared in clones with a positive DNA-instability test in earlyor middle-stage hyperplastic epidermis, and markedly increased in late-stage hyperplastic epidermis, papillomatous lesions and invasive carcinomas. The percentage of PCNA-positive vascular endothelial cells was significantly higher in VEGFpositive lesions with a positive DNA-instability test and became higher toward the late-stage of progression. Cut-woundings were made to papillomatous and invasive carcinoma lesions, and the regeneration activity of vascular endothelial cells was determined by using flash labeling with tritiated thymidine (3H-TdR. In small papillomatous lesions, vascular endothelial cells showed regenerative response, but the response was weak in large lesions. No such response was noted in invasive carcinomas; rather, cut-wounding induced collapse of blood vessels, which in turn induced massive coagulative necrosis of cancer cells. These responses can be interpreted to reflect exhausted vascular growth activity due to excessive stimulation by VEGF-overexpression, which was persistently

  6. Hybridization between three crested newt species (Triturus cristatus superspecies) in the Czech Republic and Slovakia: comparison of nuclear markers and mitochondrial DNA

    Czech Academy of Sciences Publication Activity Database

    Mikulíček, Peter; Horák, Aleš; Zavadil, V.; Kautman, J.; Piálek, Jaroslav

    2012-01-01

    Roč. 61, 3-4 (2012), s. 202-218. ISSN 0139-7893 R&D Projects: GA ČR GA206/01/0695 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : hybrid zone * introgression * mtDNA * microsatellites * RAPD * Salamandridae Subject RIV: EG - Zoology Impact factor: 0.494, year: 2012

  7. 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.

  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. DNA isolation from teeth by organic extraction and identification of sex of the individual by analyzing the AMEL gene marker using PCR

    Directory of Open Access Journals (Sweden)

    Subramanian Thangaraj Praveen Kumar

    2016-01-01

    Full Text Available Background: To identify the sex of the deceased individual from dental hard tissue such as enamel and dentine. Objective: To isolate the DNA from dental hard tissue (enamel and dentin from teeth extracted for prophylactic purpose, to assess the quality and purity of DNA and to identify the sex using polymerized chain reactor (PCR. Materials and Methods: DNA was extracted following phenol/chloroform (organic extraction from 20 male and 20 female teeth. The samples that contain the amelogenin gene (amel were amplified by PCR. The products of the PCR were run on agarose gel with ethidium bromide staining on gel documentation system. Results: The results on the gel showed the presence of X-specific bands at 212 bp and Y-specific bands at 218 bp. Males were distinguished from females by the presence of two bands whereas female samples showed only one, that is, X-specific band on the gel. The gender from the known samples was determined with complete accuracy, and the results were analyzed statistically by the Chi-square test. Conclusion: In our study, the PCR-based method showed 100% specificity and sensitivity.

  12. 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

  13. Comparative cytogenetic study on two species of the genus Entedon Dalman, 1820 (Hymenoptera, Eulophidae using DNA-binding fluorochromes and molecular and immunofluorescent markers

    Directory of Open Access Journals (Sweden)

    Nadezhda Bolsheva

    2012-02-01

    Full Text Available Karyotypes of Entedon cionobius Thomson, 1878 and E. cioni Thomson, 1878 (Hymenoptera: Eulophidae were studied using DNA-binding ligands with different base specificity (propidium iodide, chromomycin A3, methyl green and DAPI; all these ligands, except for the last one, were used for the first time in parasitic wasps, C-banding, fluorescence in situ hybridization (FISH with a 45S rDNA probe and 5-methylcytosine immunodetection. Female karyotypes of both species contain five pairs of relatively large metacentric chromosomes and a pair of smaller acrocentric chromosomes (2n = 12. As in many other Hymenoptera, males of both Entedon Dalman, 1820 species have haploid chromosome sets (n = 6. Fluorochrome staining revealed chromosome-specific banding patterns that were similar between the different fluorochromes, except for the CMA3- and PI-positive and DAPI-negative band in the pericentromeric regions of the long arms of both acrocentric chromosomes. The obtained banding patterns were virtually identical in both species and allowed for the identification of each individual chromosome. C-banding revealed a pattern similar to DAPI staining, although centromeric and telomeric regions were stained more intensively using the former technique. FISH detected a single rDNA site in the same position on the acrocentric chromosomes as the bright CMA3-positive band. Immunodetection of 5-methylcytosine that was performed for the first time in the order Hymenoptera revealed 5-methylcytosine-rich sites in the telomeric, centromeric and certain interstitial regions of most of the chromosomes.

  14. 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...

  15. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    OpenAIRE

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10...

  16. 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.

  17. A maternally inherited DNA marker, descended from Solanum demissum (2n = 6x = 72) to S. tuberosum (2n = 4x = 48)

    OpenAIRE

    Sanetomo, Rena; Hosaka, Kazuyoshi

    2011-01-01

    A Mexican hexaploid wild potato species, Solanum demissum (dms), was only used as a female in previous breeding programs. The resulting clones with dms cytoplasm produced abundant, but non-functional pollen. A 170 bp DNA fragment, named Band 1, was originally detected in the F1 hybrid between dms and S. tuberosum. In this study, the sequenced region was extended to 1,032 bp; nevertheless, it did not show any homology to known sequences. This extended region harboring Band 1 was, without intro...

  18. Detection of monoclonal integration of bovine leukemia virus proviral DNA as a malignant marker in two enzootic bovine leukosis cases with difficult clinical diagnosis

    OpenAIRE

    MIURA, Saori; HORIUCHI, Noriyuki; MATSUMOTO, Kotaro; Kobayashi, Yoshiyasu; Kawazu, Shin-ichiro; INOKUMA, Hisashi

    2015-01-01

    Monoclonal integration of bovine leukemia virus (BLV) proviral DNA into bovine genomes was detected in peripheral blood from two clinical cases of enzootic bovine leukosis (EBL) without enlargement of superficial lymph nodes. A BLV-specific probe hybridized with 1 to 3 EcoRI and HindIII fragments in these 2 atypical EBL cattle by Southern blotting and hybridization, as well as in 3 typical EBL cattle. The probe also hybridized to a large number of EcoRI and HindIII fragments in 5 cattle with ...

  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. 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.

  1. 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.

  2. 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

  3. 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

    Science.gov (United States)

    Anderson, D.; Andrais, B.; Mirzayans, R.; Siegbahn, E. A.; Fallone, B. G.; Warkentin, B.

    2013-06-01

    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.

  4. 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.

  5. 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

  6. 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.

  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. 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.

  9. 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...

  10. 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.

  11. On identification problems requiring linked autosomal markers.

    Science.gov (United States)

    Egeland, Thore; Sheehan, Nuala

    2008-06-01

    This paper considers identification problems based on DNA marker data. The topics we discuss are general, but we will exemplify them in a simple context. There is DNA available from two persons. There is uncertainty about the relationship between the two individuals and a number of hypotheses describing the possible relationship is available. The task is to determine the most likely pedigree. This problem is fairly standard. However, there are some problems that cannot be solved using DNA from independently segregating loci. For example, the likelihoods for (i) grandparent-grandchild, (ii) uncle-niece and (iii) half-sibs coincide for such DNA data and so these relations cannot be distinguished on the basis of markers normally used for forensic identification problems: the likelihood ratio comparing any pair of hypotheses will be unity. Sometimes, but not in the examples we consider, other sources of DNA like mtDNA or sex chromosomes can help to distinguish between such equally likely possibilities. Prior information can likewise be of use. For instance, age information can exclude alternative (i) above and also indicate that alternative (iii) is apriori more likely than alternative (ii). More generally, the above problems can be solved using linked autosomal markers. To study the problem in detail and understand how linkage works in this regard, we derive an explicit formula for a pair of linked markers. The formula extends to independent pairs of linked markers. While this approach adds to the understanding of the problem, more markers are required to obtain satisfactory results and then the Lander-Green algorithm is needed. Simulation experiments are presented based on a range of scenarios and we conclude that useful results can be obtained using available freeware (MERLIN and R). The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed

  12. 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.)

  13. 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...

  14. CREATION OF RICE BREEDING LINES, CARRYING BROAD SPECTRUM BLAST RESISTANCE GENE Pi-40 USING DNA-MARKERS METHODS Создание селекционных форм риса, несущих ген широкого спектра устойчивости к пирикуляриозу Pi-40, с использованием методов ДНК-маркирования

    Directory of Open Access Journals (Sweden)

    Suprun I. I.

    2013-02-01

    Full Text Available The results of development of rice breeding lines, carrying the wide range resistance gene to rice blast disease - Pi-40. For identification of the dominant allele of the gene the DNA - marker analysis was used. With co-dominant DNA markers plants from inbred populations that carry a dominant allele of this gene in the homozygous state were selected

  15. Characterization of Fluorescent Eye Markers for Mammalian Transgenic Studies

    OpenAIRE

    Cornett, Jonathan C.; Landrette, Sean F.; Xu, Tian

    2011-01-01

    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 tran...

  16. 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...

  17. 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...

  18. 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)

  19. 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...

  20. Methodology: simplified preparation of a DNA ladder using PCR.

    Science.gov (United States)

    Wang, T-Y; Wang, L; Wang, F

    2011-01-01

    Serving as a DNA molecular weight standard, the DNA ladder has been widely used in molecular biology applications. We developed a simple method for the preparation of a DNA marker, which involves designing primers to amplify 100- to 1000-bp DNA fragments using lambda DNA as a template for polymerase chain reaction, followed by extraction with phenol/chloroform, precipitation with ethanol and mixing. Fragments of 100- to 1000-bp DNA were successfully amplified; the sequences showed 100% identity with lambda DNA. This prepared DNA marker displayed clear bands, indicating that it can be used for molecular studies. PMID:21863555

  1. 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.

  2. 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.

  3. 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...

  4. 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.

  5. 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

  6. 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...

  7. 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.

  8. Radiopaque anastomosis marker

    International Nuclear Information System (INIS)

    This invention relates to split ring markers fabricated in whole or in part from a radiopaque material, usually metal, having the terminal ends thereof and a medial portion formed to define eyelets by means of which said marker can be sutured to the tissue at the site of an anastomosis to provide a visual indication of its location when examined fluoroscopically

  9. Localization of ribosomal genes in three Pimelodus species (Siluriformes, Pimelodidae of the São Francisco River: 5S genes as species markers and conservation of the 18S rDNA sites

    Directory of Open Access Journals (Sweden)

    Caroline Garcia

    2008-01-01

    Full Text Available Pimelodidae is one of the most representative of Neotropical catfish families. However, these fish are still poorly studied in terms of cytogenetics, especially regarding the application of more accurate techniques such as the chromosomal localization of ribosomal genes. In the present work, fluorescent in situ hybridization with 5S and 18S rDNA probes was employed for rDNA site mapping in Pimelodus sp., P. fur and P. maculatus from the São Francisco River in the Três Marias municipality - MG. The results from the application of the 18S probe confirmed the previous data obtained by silver nitrate staining, identifying a simple nucleolar organizing region system for these species. However, the labeling results from the 5S rDNA probe demonstrated a difference in the number and localization of these sites between the analyzed species. The obtained data allowed inferences on the possible processes involved in the karyotypic evolution of this genus.

  10. Localization of ribosomal genes in three Pimelodus species (Siluriformes, Pimelodidae) of the São Francisco River: 5S genes as species markers and conservation of the 18S rDNA sites

    OpenAIRE

    Caroline Garcia; Orlando Moreira Filho

    2008-01-01

    Pimelodidae is one of the most representative of Neotropical catfish families. However, these fish are still poorly studied in terms of cytogenetics, especially regarding the application of more accurate techniques such as the chromosomal localization of ribosomal genes. In the present work, fluorescent in situ hybridization with 5S and 18S rDNA probes was employed for rDNA site mapping in Pimelodus sp., P. fur and P. maculatus from the São Francisco River in the Três Marias municipality - MG...

  11. New molecular marker technologies for pearl millet improvement

    Directory of Open Access Journals (Sweden)

    MD Gale

    2005-12-01

    Full Text Available The first molecular marker-based genetic linkage map of pearl millet (Pennisetum glaucum was built with restriction fragment length polymorphisms (RFLP, the marker system of choice in the early 1990s. This map has served as the basis for subsequent pearl millet marker-based studies at the John Innes Centre. The RFLP framework in the consensus map is presented and is based on 173 (out of 500 available mapped PstI genomic clones from inbred line Tift 23DB, which has now become the base genotype for pearl millet molecular genetics. Molecular marker techniques have now moved on particularly with the development of polymerase chain reaction (PCR and a programme at ICRISAT has developed the first microsatellite markers (simple sequence repeats; SSR. Some 100 markers, of which 60 are mapped, are available either as DNA primers or as DNA sequences of the flanking regions of the SSR. The integration of the pearl millet map in the grass consensus map is briefly described along with the establishment of the plant genome database MilletGenes. MilletGenes collates as genome related data (maps, markers, DNA sequences and images on pearl millet, finger millet (Eleusine coracana, foxtail millet (Setaria italica and tef (Eragrostis tef.

  12. Screening and characterization of RAPD markers in viscerotropic Leishmania parasites.

    Directory of Open Access Journals (Sweden)

    Imen Mkada-Driss

    Full Text Available Visceral leishmaniasis (VL is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5' end transversions, and presence of inter- and intra- taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers

  13. Screening and characterization of RAPD markers in viscerotropic Leishmania parasites.

    Science.gov (United States)

    Mkada-Driss, Imen; Lahmadi, Ramzi; Chakroun, Ahmed S; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M; Cupolillo, Elisa; Mukhtar, Moawia M; Guizani, Ikram

    2014-01-01

    Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5' end transversions, and presence of inter- and intra- taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop

  14. 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...

  15. 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.

  16. 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.

  17. 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

  18. 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...

  19. 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)

  20. 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.

  1. DNA Book

    OpenAIRE

    Kawai, Jun; Hayashizaki, Yoshihide

    2003-01-01

    We propose herein a new method of DNA distribution, whereby DNA clones or PCR products are printed directly onto the pages of books and delivered to users along with relevant scientific information. DNA sheets, comprising water-soluble paper onto which DNA is spotted, can be bound into books. Readers can easily extract the DNA fragments from DNA sheets and amplify them using PCR. We show that DNA sheets can withstand various conditions that may be experienced during bookbinding and deli...

  2. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    Science.gov (United States)

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.)

  10. 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...

  11. 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...

  12. Iododeoxyuridine (IdUrd) incorporation into DNA of human hematopoietic cells, normal liver and hepatic metastases in man: as a radiosensitizer and as a marker for cell kinetic studies

    International Nuclear Information System (INIS)

    Iododeoxyuridine (IdUrd) was administered as a continuous infusion for 14 days to patients with glioblastoma and sarcoma, and for 3 days to patients with metastatic colorectal carcinoma. In the first group, the maximum incorporation of IdUrd into DNA was determined, taking granulocytes as parameter. In the second group, selective incorporation into DNA of normal liver and hepatic metastases of colorectal cancer was investigated. The highest dose of 675 mg/sq.m./day for 14 days produced IdUrd plasma concentrations of 1.8 +/- 0.3 microM, and a substitution of dThd by IdUrd in the range of 7.1-11.7%. Coadministration of fluorodeoxyuridine did not show significant enhancement of IdUrd-incorporation in granulocytes. Three-day intravenous infusions of IdUrd 1000 mg/sq.m./day produced 1.7-4.5% IdUrd-incorporation in hepatic metastases. Three-day intraarterial infusions (hepatic artery) produced 3.8-10.5% dThd-replacement, whereas, in 9/10 patients this was less than 1% in normal liver. In tumor tissue there was a trend towards FdUrd-modulated enhancement of IdUrd-incorporation, although there was considerable scatter. Cell kinetic studies revealed that IdUrd-incorporation in monocytes and granulocytes was very similar. In lymphocytes, a much lower fraction incorporated IdUrd. Liver tumor contained a considerably higher fraction of IdUrd-labeled cells, compared with normal liver. Potential doubling times for the tumors were estimated to be 10 days

  13. 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.

  14. 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.

  15. DNA Polymorphism Among American Watermelon Cultivars Based on DNA Methylation

    Science.gov (United States)

    American watermelon heirlooms are diverse in their growth habits, fruit qualities and responses to biotic and abiotic stress. Wide ranging DNA marker tools resolved a narrow molecular diversity among these collections. The current research explored additional insights such as extent of diversity a...

  16. 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

  17. 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.)

  18. Database Description - 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 published literature. And we provide databases for general plant information and web...about DNA marker, QTL, and website links by keywords such as marker name, agricultural trait, and classification of web...Cell Physiol (2014) 55 (1): e8 Pubmed ID: 24363285 Original website information Database maintenance site Ka...zusa DNA Research Institute URL of the original website http://pgdbj.jp/en/dna-marker-linkage-map.html Opera

  19. 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, ...

  20. DNA supercoiling inhibits DNA knotting.

    OpenAIRE

    Burnier Y.; Dorier J.; Stasiak A.

    2008-01-01

    Despite the fact that in living cells DNA molecules are long and highly crowded, they are rarely knotted. DNA knotting interferes with the normal functioning of the DNA and, therefore, molecular mechanisms evolved that maintain the knotting and catenation level below that which would be achieved if the DNA segments could pass randomly through each other. Biochemical experiments with torsionally relaxed DNA demonstrated earlier that type II DNA topoisomerases that permit inter- and intramolecu...

  1. 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...

  2. 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.

  3. Plasmid marker rescue transformation proceeds by breakage-reunion in Bacillus subtilis

    International Nuclear Information System (INIS)

    Bacillus subtilis carrying a plasmid which replicates with a copy number of about 1 was transformed with linearized homologous plasmid DNA labeled with the heavy isotopes 2H and 15N, in the presence of 32Pi and 6-(p-hydroxyphenylazo)-uracil to inhibit DNA replication. Plasmid DNA was isolated from the transformed culture and fractionated in cesium chloride density gradients. The distribution of total and donor plasmid DNA was examined, using specific hybridization probes. The synthesis of new DNA, associated with the integration of donor moiety, was also monitored. Donor-specific sequences were present at a density intermediate between that of light and hybrid DNA. This recombinant DNA represented 1.4% of total plasmid DNA. The latter value corresponded well with the transforming activity (1.7%) obtained for the donor marker. Newly synthesized material associated with plasmid DNA at the recombinant density amounted to a minor portion of the recombinant plasmid DNA. These data suggest that, like chromosomal transformation, plasmid marker rescue transformation does not require replication for the integration of donor markers and, also like chromosomal transformation, proceeds by a breakage-reunion mechanism. The extent of donor DNA replacement of recipient DNA per plasmid molecule of 54 kilobases (27 kilobase pairs) was estimated as 16 kilobases

  4. 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

  5. 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

  6. 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...

  7. 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

  8. 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...

  9. 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

  10. 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

  11. 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

  12. 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...

  13. 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...

  14. 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.

  15. 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.

  16. DNA vaccines

    OpenAIRE

    Coban, Cevayir; Kobiyama, Kouji; Jounai, Nao; Tozuka, Miyuki; Ishii, Ken J.

    2013-01-01

    Since the introduction of DNA vaccines two decades ago, this attractive strategy has been hampered by its low immunogenicity in humans. Studies conducted to improve the immunogenicity of DNA vaccines have shown that understanding the mechanism of action of DNA vaccines might be the key to successfully improving their immunogenicity. Our current understanding is that DNA vaccines induce innate and adaptive immune responses in two ways: (1) encoded protein (or polypeptide) antigen(s) by the DNA...

  17. Development of genomic and EST-SSR markers in radish (Raphanus sativus L.)

    OpenAIRE

    Nakatsuji, Ryoichi; Hashida, Tomoko; Matsumoto, Naoko; Tsuro, Masato; Kubo, Nakao; Hirai, Masashi

    2011-01-01

    Radish (Raphanus sativus L.) belongs to Brassicaceae family and is a close relative of Brassica. This species shows a wide morphological diversity, and is an important vegetable especially in Asia. However, molecular research of radish is behind compared to that of Brassica. For example, reports on SSR (simple sequence repeat) markers are limited. Here, we designed 417 radish SSR markers from SSR-enriched genomic libraries and the cDNA data. Of the 256 SSR markers succeeded in PCR, 130 showed...

  18. AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.)

    OpenAIRE

    Altinkut A.; Kazan K.; Gozukirmizi N.

    2003-01-01

    The amplified fragment length polymorphism (AFLP) assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA) was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive), which w...

  19. 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...

  20. 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...

  1. 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

  2. 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.

  3. 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

  4. Beyond STRs: The Role of Diallelic Markers in Forensic Genetics.

    Science.gov (United States)

    Schneider, Peter M

    2012-06-01

    Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situations, additional robust markers with negligible mutations rates such as single nucleotide polymorphisms (SNPs) and insertion/deletion markers (indels) can be used as adjuncts to provide decisive genetic information in favor for or against the assumed relationship. Both SNPs and indels can now be typed more easily using multiplexes of up to 50 loci based on fragment length analysis on instruments available in all routine forensic and paternity testing laboratories, thus making it possible to extend the range of markers beyond the currently used STRs. PMID:22851932

  5. 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

  6. Using Monomorphic Microsatellite Markers in Oil Palm (Elaeisguineensis Jacq..

    Directory of Open Access Journals (Sweden)

    Emad Omer Hama-Ali

    2014-12-01

    Full Text Available Molecular markers in oil palm characterization and breeding began two decades ago. Microsatellite markers are a system that is commonly used in oil pal m research since its development. Monomorphic SSR markers have been eliminated from all evolutionary and population genetics studies by researchers because of their lack of genetic variability. The goals of this study were to review polymorphic DNA microsa tellite marker system also known as simple sequence repeats(SSR in oil palm research since its development and to employa monomorphic SSR marker for detection of illegitimacy in oil palm breeding programs. Ten monomorphic SSR markers and two half - sib fami lies were used in this study. Illegitimate offspring IDs 97 and 180 were found by four monomorphic locimEgCIR0425, mEgCIR3477, mEgCIR3769, and mEgCIR3902 in Family - 1and Family - 2. In addition, five loci (mEgCIR3574, mEgCIR3607, mEgCIR3672, mEgCIR3785 and mE gCIR3807 detect one illegitimate offspring ID 180.This study showed that monomorphic SSR markers are suitable for the detection of illegitimate offsprings in oil palm breeding programs

  7. 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

  8. 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.

  9. 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...

  10. Fingerprints for two grain amaranthus varieties KBGA1 and Suvarna using RAPD and legume based SSR markers

    Directory of Open Access Journals (Sweden)

    Meera N., Lohithaswa HC, Niranjana Murthy and Shailaja Hittalmani

    2014-09-01

    Full Text Available 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 genetic variation within and between the species of amaranthus and suggest that cultivated varieties of Amaranthus have significant genetic variation. The differences generated by the markers can be used as fingerprints for detecting the varieties. This is the first report of the utilization of legume microsatellite markers in Amaranthus.

  11. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M

    2015-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  12. DNA looping.

    OpenAIRE

    Matthews, K S

    1992-01-01

    DNA-looping mechanisms are part of networks that regulate all aspects of DNA metabolism, including transcription, replication, and recombination. DNA looping is involved in regulation of transcriptional initiation in prokaryotic operons, including ara, gal, lac, and deo, and in phage systems. Similarly, in eukaryotic organisms, the effects of enhancers appear to be mediated at least in part by loop formation, and examples of DNA looping by hormone receptor proteins and developmental regulator...

  13. DNA structure

    OpenAIRE

    Bowater, R

    2003-01-01

    Deoxyribonucleic acid (DNA) is a polymer of nucleotides. In the cell, DNA usually adopts a double-stranded helical form, with complementary base-pairing holding the two strands together. The most stable conformation is called B-form DNA, although other structures can occur under specific conditions.

  14. 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

  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. 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.

  17. 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...

  18. [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

  19. 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

  20. Genome analysis methods - 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 PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Genome analysis methods... Data detail Data name Genome analysis methods Description of data contents The current status and re...ion of genomic database are shown in this list. Data file File name: pgdbj_dna_marker_linkage_map_genome_analysis_methods...r-linkage-map/LATEST/pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip File size: 5.8 KB Simple se...arch URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_dna_marker_linkage_map_genome_analysis_methods_en

  1. 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

  2. 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.

  3. 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

  4. Changes in allelic frequency over time in European bread wheat (Triticum aestivum L.) varieties revealed using DArT and SSR markers

    DEFF Research Database (Denmark)

    Orabi, Jihad; Jahoor, Ahmed; Backes, Gunter Martin

    2014-01-01

    A collection of 189 bread wheat landraces and cultivars, primarily of European origin, released between 1886 and 2009, was analyzed using two DNA marker systems. A set of 76 SSR markers and ~7,000 DArT markers distributed across the wheat genome were employed in these analyses. All of the SSR mar...

  5. 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...

  6. 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...

  7. Identification of ISSR markers associated with productivity traits in silkworm, Bombyx moni L.

    Science.gov (United States)

    Chatterjee, S N; Mohandas, T P

    2003-06-01

    Bombyx mori L., commonly recognised around the world as the mulberry silkworm, is characterized by a wide variability in yield and developmental traits, which have been proven through conventional genetic analysis to be of polygenic nature. A large number of morpho-biochemical traits and RFLP and RAPD markers are mapped on different linkage groups, but to this point very little attention has been given to unravelling the genetics of yield traits. To address this issue, polymorphic profiles of 147 markers generated with 12 ISSR primers on the genomic DNA of 20 silkworm stocks of diverse yield status were subjected to multiple regression and discriminant function analyses (DFA). This led to the identification of eight markers generated by six primers, which demonstrated high beta-coefficient indices of -0.451 to -0.940. Furthermore, a significant difference between the yield traits for stocks with and without the specific marker could also be established. The inheritance pattern of one marker, L13800bp, identified at the first step of selection of markers through stepwise regression analyses for five yield parameters is discussed in the context of applying multiple regression analysis for establishing association, if not linkage, between a group of DNA markers and a particular yield trait of polygenic nature and using such markers in molecular marker-assisted breeding programs. PMID:12834060

  8. Sequence-Related Amplified Polymorphism (SRAP Markers: A Potential Resource for Studies in Plant Molecular Biology

    Directory of Open Access Journals (Sweden)

    Daniel W. H. Robarts

    2014-07-01

    Full Text Available 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 reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use. highly variable marker with inherent biological significance.

  9. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  10. Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus.

    Science.gov (United States)

    Kolomyjec, Stephen H; Grant, Tom R; Blair, David

    2008-09-01

    We identified and optimized 10 microsatellite loci for the platypus, Ornithorhynchus anatinus (Monotremata: Ornithorhynchidae), and screened 21 individuals from the southern tablelands area of New South Wales, Australia. Each polymorphic locus possessed between two and 12 alleles with observed heterozygosities between 0.118 and 0.950. The intent of this effort was to provide informative loci for studies on the population genetics of this species. PMID:21585993

  11. Molecular genetics of vaccinia virus: demonstration of marker rescue.

    OpenAIRE

    Nakano, E.; Panicali, D; E. Paoletti

    1982-01-01

    Two genomic variants of vaccinia virus isolated from serially propagated stocks were used to demonstrate marker rescue. The smaller (S variant) virus contains a 6.3 megadalton (MDal) deletion of unique DNA sequences present in the 123-MDal larger (L variant) virus. The deletion was mapped at 6.85 MDal from the left terminus of the genome, just outside of the inverted terminal repetition. Rescue of the unique deleted DNA sequences by infectious S variant virus was obtained in CV-1 cells by usi...

  12. DNA Immunization

    OpenAIRE

    Wang, Shixia; Lu, Shan

    2013-01-01

    DNA immunization was discovered in early 1990s and its use has been expanded from vaccine studies to a broader range of biomedical research, such as the generation of high quality polyclonal and monoclonal antibodies as research reagents. In this unit, three common DNA immunization methods are described: needle injection, electroporation and gene gun. In addition, several common considerations related to DNA immunization are discussed.

  13. Markers of renal function tests

    Directory of Open Access Journals (Sweden)

    Shivaraj Gowda

    2010-01-01

    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.

  14. DNA deoxyribophosphodiesterase.

    OpenAIRE

    Franklin, W A; Lindahl, T

    1988-01-01

    A previously unrecognized enzyme acting on damaged termini in DNA is present in Escherichia coli. The enzyme catalyses the hydrolytic release of 2-deoxyribose-5-phosphate from single-strand interruptions in DNA with a base-free residue on the 5' side. The partly purified protein appears to be free from endonuclease activity for apurinic/apyrimidinic sites, exonuclease activity and DNA 5'-phosphatase activity. The enzyme has a mol. wt of approximately 50,000-55,000 and has been termed DNA deox...

  15. 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.

  16. 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....

  17. 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

  18. Screening and Characterization of RAPD Markers in Viscerotropic Leishmania Parasites.

    OpenAIRE

    Mkada-Driss, Imen; Lahmadi, Ramzi; Chakroun, Ahmed S; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M; Cupolillo, Elisa; Mukhtar, Moawia M; Guizani, Ikram

    2013-01-01

    Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characte...

  19. Beyond STRs: The Role of Diallelic Markers in Forensic Genetics

    OpenAIRE

    Schneider, Peter M.

    2012-01-01

    Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situation...

  20. 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...

  1. Microbial Risk Markers for Childhood Caries in Pediatricians’ Offices

    OpenAIRE

    Kanasi, E.; Johansson, I; Lu, S.C.; Kressin, N.R.; Nunn, M.E.; Kent, R; Tanner, A.C.R.

    2010-01-01

    Dental caries in pre-school children has significant public health and health disparity implications. To determine microbial risk markers for this infection, this study aimed to compare the microbiota of children with early childhood caries with that of caries-free children. Plaque samples from incisors, molars, and the tongue from 195 children attending pediatricians’ offices were assayed by 74 DNA probes and by PCR to Streptococcus mutans. Caries-associated factors included visible plaque, ...

  2. 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.

  3. 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...

  4. 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...

  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. Cleaving DNA with DNA

    OpenAIRE

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

    1998-01-01

    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 domai...

  7. 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.

  8. 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...

  9. 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...

  10. DNA glue

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  11. Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury

    OpenAIRE

    Dutta, Suhrid R.; Kar, Prasanta K.; Ashok K. Srivastava; Sinha, Manoj K.; Jai Shankar; Ghosh, Ananta K.

    2012-01-01

    The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and l...

  12. 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...... mutation. 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...

  13. 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

  14. [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

  15. Biological Markers and Salivary Cortisol

    DEFF Research Database (Denmark)

    Hansen, Åse Marie; Gunnarsson, Lars-Gunnar; Harris, Anette;

    2011-01-01

    variability), markers related to inflammation (C-reactive protein, cytokines and tumor necrosis factor-alpha) and other stress hormones (adrenaline and noradrenaline) were studied. The focus was on healthy adult populations; studies on patient populations and pregnant women were excluded. Studies on genome....... Several of the markers tested showed low or no association with any of the measurements of salivary cortisol. The number of studies exploring the association between cortisol in saliva and markers for inflammation is low, which limits the possibility of interpretation. The number of studies on adrenaline...... and noradrenaline is also low. To sum up, the proportion of non-significant findings was considerable. This may be due to a large number of studies with relatively small study populations. This is true for metabolic abnormalities, markers related to inflammation as well as other stress hormones...

  16. EST and EST-SSR marker resources for Iris

    Directory of Open Access Journals (Sweden)

    Taylor Christopher A

    2009-06-01

    Full Text Available Abstract Background Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae, a monocot genus of 200–300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars. Results Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72 and I. fulva (IF174, and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons. We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526 amplified alleles from IB72 and IF174 and 84% (335/399 were polymorphic between IB25 and IF174, the parents of I. brevicaulis × I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species – 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona, whereas 42–52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica. Ecotypes and cultivars were genetically diverse – the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76. Conclusion Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within

  17. 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

  18. 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...

  19. 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...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  20. 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.,...

  1. Ancient DNA

    OpenAIRE

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of t...

  2. DNA Photolyasen

    OpenAIRE

    Maul, Melanie

    2009-01-01

    Neben der fehlerfreien Weitergabe der genetischen Information während der Zellteilung durch einen intakten Replikationsapparat, ist auch die Aufrechterhaltung der genetischen Integrität der DNA durch Reparaturenzyme entscheidend für das Überleben der Zellen, sowie für einen gesunden Organismus. Um die genomische Integrität zu wahren, entwickelten sich im Laufe der Evolution verschiedene Mechanismen, u.a. die Exzisionreparatur von geschädigter DNA oder die direkte chemische R...

  3. DNA damage

    OpenAIRE

    Kumari, Sunita; Rastogi, Rajesh P.; Singh, Kanchan L.; Singh, Shailendra P; Sinha, Rajeshwar P.

    2008-01-01

    Even under the best of circumstances, DNA is constantly subjected to chemical modifications. Several types of DNA damage such as SSB (single strand break), DSB (double strand break), CPDs (cyclobutane pyrimidine dimers), 6-4PPs (6-4 photoproducts) and their Dewar valence isomers have been identified that result from alkylating agents, hydrolytic deamination, free radicals and reactive oxygen species formed by various photochemical processes including UV radiation. There are a n...

  4. 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

  5. Human papillomaviruses and DNA ploidy in anal condylomata acuminata

    OpenAIRE

    Rihet, S.; Bellaich, P.; Lorenzato, M; Bouttens, D.; Bernard, P.; Birembaut, P.; Clavel, C.

    2000-01-01

    Previous studies have emphasized the usefulness of DNA ploidy measurement and Human Papillomavirus (HPV) detection as pronostic markers in low grade cervical lesions. We addressed the eventual relationship between HPV type, DNA profile, and p53 tumor suppressor protein expression in anal condylomata acuminata to eventually determine parameters which may be considered as predictive risk factors for the development of cancer. DNA ploidy was assessed by image ...

  6. 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 ...

  7. 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.

  8. 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

  9. Live cell microscopy of DNA damage response in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Pinela da Silva, Sonia Cristina; Gallina, Irene; Eckert-Boulet, Nadine Valerie; Lisby, Michael

    Fluorescence microscopy of the DNA damage response in living cells stands out from many other DNA repair assays by its ability to monitor the response to individual DNA lesions in single cells. This is particularly true in yeast, where the frequency of spontaneous DNA lesions is relatively low...... live cell imaging allows for multiple cellular markers to be monitored over several hours. This chapter reviews useful fluorescent markers and genotoxic agents for studying the DNA damage response in living cells and provides protocols for live cell imaging, time-lapse microscopy, and for induction of...

  10. Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

    Indian Academy of Sciences (India)

    D. E. Jarvis; O. R. Kopp; E. N. Jellen; M. A. Mallory; J. Pattee; A. Bonifacio; C. E. Coleman; M. R. Stevens; D. J. Fairbanks; P. J. Maughan

    2008-04-01

    Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

  11. Study on the sex-related AFLP marker of the Yangtze finless porpoise

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The sex-related molecular marker of the Yangtze finless porpoise was screened using Amplified Fragment Length Polymorphism (AFLP) technique combined with the bulked segregant analysis. Totally 36 AFLP primer combinations were used to detect the genome DNA bulks of the female and male porpoises, and one sex-related AFLP marker was finally obtained. The marker can be applied to sex identification, and provides a base for further cloning of sex-related genes and analyzing of Y chromosome haplotypes of the Yangtze finless porpoise.

  12. Specific gut microbiota features and metabolic markers in postmenopausal women with obesity

    DEFF Research Database (Denmark)

    Brahe, Lena Kirchner; Le Chatelier, E; Prifti, E;

    2015-01-01

    BACKGROUND: Gut microbial gene richness and specific bacterial species are associated with metabolic risk markers in humans, but the impact of host physiology and dietary habits on the link between the gut microbiota and metabolic markers remain unclear. The objective of this study was to identify...... gut metagenomic markers associated with estimates of insulin resistance, lipid metabolism and inflammation in obesity, and to explore whether the associations between metagenomic and metabolic markers persisted after adjustment for body fat, age and habitual dietary intake. METHODS: Faecal DNA from 53......; however, the negative correlation with insulin resistance observed for B. longum and F. prausnitzii appeared to be modified by the intake of dietary fibre and fat, respectively. CONCLUSIONS: This study shows that several gut bacterial species are linked to metabolic risk markers in obesity, also after...

  13. [Cloning and analyzing of the female-specific marker in the dioecious species Asparagus officinalis L].

    Science.gov (United States)

    Lu, Long Dou; Li, Rui Li; Gao, Wu Jun; Deng, Chuan Liang; Wang, Lian Jun

    2006-06-01

    Sex-linked molecular markers are being obtained, which would be essential to be used in the screening of different sex of dioecious plants at the seedling stage. Furthermore, it is important in cloning the gene related to the sex. In this study the random amplified polymorphic DNA (RAPD) technique was employed with the objective to find markers linked to sex determination in Asparagus. A total of 100 primers were tested with the same PCR cycling procedure. A female-associated fragment with a length of about 867bp was generated with S12 primer. The fragment was cloned and sequenced, showing it is abundant in AT and contains 2 shorter open reading frames. In order to convert the RAPD marker into SCAR (sequence characterized amplified regions) marker, 24bp specific primers were constructed and used for PCR amplifying. The female-linked dominant SCAR marker was obtained, which would be efficient to identify the different sex of Asparagus officinalis L. PMID:16944605

  14. Mitochondrial DNA under siege in avian phylogeography.

    Science.gov (United States)

    Zink, Robert M; Barrowclough, George F

    2008-05-01

    Mitochondrial DNA (mtDNA) has been the workhorse of research in phylogeography for almost two decades. However, concerns with basing evolutionary interpretations on mtDNA results alone have been voiced since the inception of such studies. Recently, some authors have suggested that the potential problems with mtDNA are so great that inferences about population structure and species limits are unwarranted unless corroborated by other evidence, usually in the form of nuclear gene data. Here we review the relative merits of mitochondrial and nuclear phylogeographical studies, using birds as an exemplar class of organisms. A review of population demographic and genetic theory indicates that mitochondrial and nuclear phylogeographical results ought to concur for both geographically unstructured populations and for populations that have long histories of isolation. However, a relatively common occurrence will be shallow, but geographically structured mtDNA trees--without nuclear gene corroboration--for populations with relatively shorter periods of isolation. This is expected because of the longer coalescence times of nuclear genes (approximately four times that of mtDNA); such cases do not contradict the mtDNA inference of recent isolation and evolutionary divergence. Rather, the nuclear markers are more lagging indicators of changes in population structure. A review of the recent literature on birds reveals the existence of relatively few cases in which nuclear markers contradict mitochondrial markers in a fashion not consistent with coalescent theory. Preliminary information from nuclear genes suggests that mtDNA patterns will prove to be robust indicators of patterns of population history and species limits. At equilibrium, mitochondrial loci are generally a more sensitive indicator of population structure than are nuclear loci, and mitochondrial estimates of F(ST)-like statistics are generally expected to exceed nuclear ones. Hence, invoking behavioural or ecological

  15. Identification and Validation of a New Male Sex-Specific ISSR Marker in Pointed Gourd (Trichosanthes dioica Roxb.

    Directory of Open Access Journals (Sweden)

    Sinchan Adhikari

    2014-01-01

    Full Text Available The aim of the present study was to develop a genetic sex marker for the pointed gourd (Trichosanthes dioica Roxb. to allow gender determination at any stage in the life cycle. Screening of genomic DNA with intersimple sequence repeat (ISSR primers was used to discover sex-specific touch-down polymerase chain reaction (Td-PCR amplification products. Using pooled DNA from male and female genotypes and 42 ISSR primers, a putative male specific marker (~550 bp was identified. DNA marker specific to male is an indication of existence of nonepigenetic factors involved in gender development in pointed gourd. The ISSR technique has proved to be a reliable technique in gender determination of pointed gourd genotypes at the seedling phenophase. The sex marker developed here could also be used as a starting material towards sequence characterization of sex linked genes for better understanding the developmental as well as evolutionary pathways in sexual dimorphism.

  16. Theory and modeling of particles with DNA-mediated interactions

    Science.gov (United States)

    Licata, Nicholas A.

    2008-05-01

    In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

  17. Prediction of Physicochemical Properties of Indonesian Indica Rice Using Molecular Markers

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    PUJI LESTARI

    2014-06-01

    Full Text Available Physicochemical properties determine the palatability and cooking quality of rice, which must be determined efficiently in order to satisfy consumer demand. To date, little information exists on the use of molecular markers to predict physicochemical properties of the “indica” rice varieties found in Indonesia. The objective of this study was to investigate physicochemical properties and genetic variation of Indonesian rice varieties, and to formulate regression equations to analyze sets of DNA markers which could predict amylose content (AC, protein content (PC and pasting properties of the varieties. A total of 24 Indonesian indica rice varieties were chosen based on their genetic background and agricultural characteristics. We then measured selected physicochemical properties, and genotyped the varieties using 30 DNA markers. The chosen varieties showed favorable values for PC, AC, and six rapid viscosity analyzer (RVA pasting properties, which was supported by molecular data. As demonstrated by principal component analysis (PCA, markers could provide a complementary method for differentiating rice varieties, as an alternative to measuring physicochemical properties. PCA analysis also allowed us to establish marker sets using multiple regression analysis. We formulated eight model regression equations comprising data regarding 15 to 19 markers with high coefficients (R2=0.98-0.99. The formulas provided results that consistently correlated and therefore predicted the physicochemical properties of indica rice. Further validation of these marker sets may provide rapid and efficient means for predicting the physicochemical properties of Indonesian-bred indica rice in the future.

  18. Acute hypoxia and hypoxic exercise induce DNA strand breaks and oxidative DNA damage in humans

    DEFF Research Database (Denmark)

    Møller, P; Loft, S; Lundby, C;

    2001-01-01

    The present study investigated the effect of a single bout of exhaustive exercise on the generation of DNA strand breaks and oxidative DNA damage under normal conditions and at high-altitude hypoxia (4559 meters for 3 days). Twelve healthy subjects performed a maximal bicycle exercise test......; lymphocytes were isolated for analysis of DNA strand breaks and oxidatively altered nucleotides, detected by endonuclease III and formamidipyridine glycosylase (FPG) enzymes. Urine was collected for 24 h periods for analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a marker of oxidative DNA damage....... Urinary excretion of 8-oxodG increased during the first day in altitude hypoxia, and there were more endonuclease III-sensitive sites on day 3 at high altitude. The subjects had more DNA strand breaks in altitude hypoxia than at sea level. The level of DNA strand breaks further increased immediately after...

  19. DNA nanotechnology

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    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. Serum markers of liver fibrosis

    DEFF Research Database (Denmark)

    Veidal, Sanne Skovgård; Bay-Jensen, Anne-Christine; Tougas, Gervais;

    2010-01-01

    BACKGROUND: Fibrosis is a central histological feature of chronic liver diseases and is characterized by the accumulation and reorganization of the extracellular matrix. The gold standard for assessment of fibrosis is histological evaluation of a percutaneous liver biopsy. Albeit a considerable......-epitopes, may be targeted for novel biochemical marker development in fibrosis. We used the recently proposed BIPED system (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) to characterise present serological markers. METHODS: Pubmed was search for keywords; Liver fibrosis, neo...... systematic use of the neo-epitope approach, i.e. the quantification of peptide epitopes generated from enzymatic cleavage of proteins during extracellular remodeling, may prove productive in the quest to find new markers of liver fibrosis....