THE STUDY OF GENETIC DIVERSITY IN VITRO SOMATIC TEA CLONES (CAMELLIA SINENSIS (L.) O. KUNTZE) BY SSR AND ISSR METHODS OF FULL GENOMIC DNA ANALYSIS

ABSTRACT The randomly amplified polymorphic DNA (RAPD) method was used to investigate the genetic diversity in Xanthomonas cynarae, which causes bacterial bract spot disease of artichoke. This RAPD analysis was also intended to identify molecular markers characteristic of this species, in order to develop PCR-based markers which can be used to detect this pathogenic bacterium in artichoke fields. Among the 340 RAPD primers tested, 40 were selected on their ability to produce reproducible and reliable fingerprints in our genetic background. These 40 primers produced almost similar patterns for the 37 X. cynarae strains studied, different from the fingerprints obtained for other Xanthomonas species and other xanthomonad-like bacteria isolated from artichoke leaves. Therefore, X. cynarae strains form a homogeneous genetic group. However, a little DNA polymorphism within this species was observed and the collection of X. cynarae isolates was divided into two groups (one containing three strains, the second one including all other strains). Out of seven RAPD markers characteristic of X. cynarae that were cloned, four did not hybridize to the genomic DNA of strains belonging to other Xanthomonas species. These four RAPD markers were converted into PCR markers (specific characterized amplified regions [SCARs]); they were sequenced, and a PCR primer pair was designed for each of them. Three derived SCARs are good candidates to develop PCR-based tests to detectX. cynarae in artichoke fields.

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Differentiation of Cryptosporidium parvum Isolates by a Simplified Randomly Amplified Polymorphic DNA Technique

Applied and Environmental Microbiology ◽

10.1128/aem.64.5.1954-1957.1998 ◽

1998 ◽

Vol 64 (5) ◽

pp. 1954-1957 ◽

Cited By ~ 8

Author(s):

Ming Qi Deng ◽

Dean O. Cliver

Keyword(s):

Cryptosporidium Parvum ◽

Genomic Dna ◽

Dna Analysis ◽

Immunomagnetic Separation ◽

Randomly Amplified Polymorphic Dna

ABSTRACT Genomic DNA was isolated from Cryptosporidium parvumoocysts by a specific immunomagnetic separation-in vitro excystation procedure and subjected to randomly amplified polymorphic DNA analysis using sequence-independent primers. An estuary C. parvumisolate was easily differentiated from several bovine isolates, while five bovine isolates of the same origin were indistinguishable from each other.

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Genetic Diversity of Gulin-niupicha [Camellia sinensis(L.)O. Kuntze] Germplasm Resources

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2014.02118 ◽

2014 ◽

Vol 40 (12) ◽

pp. 2118

Author(s):

Shao-Jie LIU ◽

Lin CHI ◽

Wen-Gang XIE ◽

Nan HAN ◽

Ying-Hui CHEN ◽

...

Keyword(s):

Genetic Diversity ◽

Camellia Sinensis ◽

Germplasm Resources

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Thinning in mature eastern white pine: 43-year case study

The Forestry Chronicle ◽

10.5558/tfc78539-4 ◽

2002 ◽

Vol 78 (4) ◽

pp. 539-549 ◽

Cited By ~ 3

Author(s):

Paul D Anderson ◽

John C Zasada ◽

Glen W Erickson ◽

Zigmond A Zasada

Keyword(s):

Genetic Diversity ◽

Dna Analysis ◽

Large Diameter ◽

White Pine ◽

Thinning Intensity ◽

Pine Regeneration ◽

Volume Production ◽

Pine Stands ◽

Over Time

A white pine (Pinus strobus L.) stand at the western margin of the species range, approximately 125 years of age at present, was thinned in 1953 from 33.5 m2 ha-1 to target residual basal areas of 18.4, 23.0, 27.5, and 32.1 m2 ha-1 . Repeated measurement over the following 43-years indicated that the greatest total volume production and the greatest number of large diameter trees occurred in the unit of highest residual density. Over time, the distribution of stems was predominantly random although mortality between 1979 and 1996 resulted in a tendency for clumping in the 23.0 and 27.5 m2 ha-1 treatments. DNA analysis indicated that thinning intensity had little effect on the genetic diversity of residual white pine. This study suggests that mature white pine stands in northern Minnesota may be managed at relatively high densities without loss of productivity. However, regardless of overstory density, there was little or no white pine regeneration occurring in this stand. Key words: thinning, growth, genetic diversity, molecular markers, spatial pattern, regeneration

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APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A

Nucleic Acids Research ◽

10.1093/nar/gkaa1201 ◽

2020 ◽

Author(s):

Lai Wong ◽

Frederick S Vizeacoumar ◽

Franco J Vizeacoumar ◽

Linda Chelico

Keyword(s):

Genomic Dna ◽

Cytidine Deaminase ◽

Protein A ◽

Cytosine Deaminase ◽

Cancer Cell Line ◽

Replication Protein A ◽

Lung Cancer Cell Line ◽

Replication Protein ◽

Cancer Evolution

Abstract Many APOBEC cytidine deaminase members are known to induce ‘off-target’ cytidine deaminations in 5′TC motifs in genomic DNA that contribute to cancer evolution. In this report, we characterized APOBEC1, which is a possible cancer related APOBEC since APOBEC1 mRNA is highly expressed in certain types of tumors, such as lung adenocarcinoma. We found a low level of APOBEC1-induced DNA damage, as measured by γH2AX foci, in genomic DNA of a lung cancer cell line that correlated to its inability to compete in vitro with replication protein A (RPA) for ssDNA. This suggests that RPA can act as a defense against off-target deamination for some APOBEC enzymes. Overall, the data support the model that the ability of an APOBEC to compete with RPA can better predict genomic damage than combined analysis of mRNA expression levels in tumors and analysis of mutation signatures.

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IN VITRO INHIBITION OF HELICOBACTER PYLORI UREASE WITH NON AND SEMI FERMENTED CAMELLIA SINENSIS

Indian Journal of Medical Microbiology ◽

10.1016/s0255-0857(21)01749-7 ◽

2009 ◽

Vol 27 (1) ◽

pp. 30-34

Author(s):

AR Shoae Hassani ◽

N Ordouzadeh ◽

A Ghaemi ◽

N Amirmozafari ◽

K Hamdi ◽

...

Keyword(s):

Helicobacter Pylori ◽

Camellia Sinensis ◽

In Vitro Inhibition

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Nuclear-encoded tobacco chloroplast ribosomal protein L24. Protein identification, sequence analysis of cDNAs encoding its cytoplasmic precursor, and mRNA and genomic DNA analysis.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)36669-4 ◽

1992 ◽

Vol 267 (30) ◽

pp. 21705-21711

Author(s):

G.A. Elhag ◽

D.P. Bourque

Keyword(s):

Sequence Analysis ◽

Ribosomal Protein ◽

Genomic Dna ◽

Protein Identification ◽

Dna Analysis ◽

Tobacco Chloroplast

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Influence of Cytokinins in Combination with GA3on Shoot Multiplication and Elongation of Tea Clone Iran 100 (Camellia sinensis(L.) O. Kuntze)

The Scientific World JOURNAL ◽

10.1155/2014/943054 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Reza Azadi Gonbad ◽

Uma Rani Sinniah ◽

Maheran Abdul Aziz ◽

Rosfarizan Mohamad

Keyword(s):

Camellia Sinensis ◽

Woody Plants ◽

Clonal Propagation ◽

Shoot Multiplication ◽

Shoot Elongation ◽

Nodal Segments ◽

Nodal Segment ◽

Liquid Form ◽

Solid Media

The use ofin vitroculture has been accepted as an efficient technique for clonal propagation of many woody plants. In the present research, we report the results of a number of experiments aimed at optimizing micropropagation protocol for tea (Camellia sinensis(L.) O. Kuntze) (clone Iran 100) using nodal segments as the explant. The effect of different combinations and concentrations of plant growth regulators (PGR) (BAP, TDZ, GA3) on shoot multiplication and elongation was assessed. The influence of exposure to IBA in liquid form prior to transfer to solid media on rooting of tea microshoots was investigated. The results of this study showed that the best treatment for nodal segment multiplication in terms of the number of shoot per explant and shoot elongation was obtained using 3 mg/L BAP in combination with 0.5 mg/L GA3. TDZ was found to be inappropriate for multiplication of tea clone Iran 100 as it resulted in hyperhydricity especially at concentrations higher than 0.05 mg/L. Healthy shoots treated with 300 mg/L IBA for 30 min followed by transfer to 1/2 strength MS medium devoid of PGR resulted in 72.3% of shoots producing roots and upon transferring them to acclimatization chamber 65% survival was obtained prior to field transfer.

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Absence of Replication-Competent Human-Tropic Porcine Endogenous Retroviruses in the Germ Line DNA of Inbred Miniature Swine

Journal of Virology ◽

10.1128/jvi.78.5.2502-2509.2004 ◽

2004 ◽

Vol 78 (5) ◽

pp. 2502-2509 ◽

Cited By ~ 46

Author(s):

Linda Scobie ◽

Samantha Taylor ◽

James C. Wood ◽

Kristen M. Suling ◽

Gary Quinn ◽

...

Keyword(s):

Genomic Dna ◽

Germ Line ◽

Human Cells ◽

Endogenous Retroviruses ◽

Open Reading Frames ◽

Miniature Swine ◽

Dna Libraries ◽

Porcine Endogenous Retroviruses ◽

Perv Transmission

ABSTRACT The potential transmission of porcine endogenous retroviruses (PERVs) has raised concern in the development of porcine xenotransplantation products. Our previous studies have resulted in the identification of animals within a research herd of inbred miniature swine that lack the capacity to transmit PERV to human cells in vitro. In contrast, other animals were capable of PERV transmission. The PERVs that were transmitted to human cells are recombinants between PERV-A and PERV-C in the post-VRA region of the envelope (B. A. Oldmixon, J. C. Wood, T. A. Ericsson, C. A. Wilson, M. E. White-Scharf, G. Andersson, J. L. Greenstein, H. J. Schuurman, and C. Patience, J. Virol. 76:3045-3048, 2002); these viruses we term PERV-A/C. This observation prompted us to determine whether these human-tropic replication-competent (HTRC) PERV-A/C recombinants were present in the genomic DNA of these miniature swine. Genomic DNA libraries were generated from one miniature swine that transmitted HTRC PERV as well as from one miniature swine that did not transmit HTRC PERV. HTRC PERV-A/C proviruses were not identified in the germ line DNAs of these pigs by using genomic mapping. Similarly, although PERV-A loci were identified in both libraries that possessed long env open reading frames, the Env proteins encoded by these loci were nonfunctional according to pseudotype assays. In the absence of a germ line source for HTRC PERV, further studies are warranted to assess the mechanisms by which HTRC PERV can be generated. Once identified, it may prove possible to generate animals with further reduced potential to produce HTRC PERV.

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