			Home About us Contact

Low Copy Numbers (low + copy_number)

Distribution by Scientific Domains

Life Sciences	100%

Selected Abstracts

Development of a strategy for transgenic studies and monitoring of transgene expression in two closely related Moricandia species possessing a C3 or C3,C4 intermediate photosynthetic phenotype

PHYSIOLOGIA PLANTARUM, Issue 1 2003
Vera Thole
In order to establish a model system for comparative studies of C3 and C3,C4 intermediate photosynthesis, the development of efficient transformation systems and the monitoring of transgene behaviour and stability were carried out in two closely related Moricandia species (Brassicaceae): the C3,C4 photosynthetic intermediate species M. arvensis and the C3 species M. moricandioides. In this study the green fluorescent protein (gfp) reporter gene was used as a vital marker gene while the use of the , -glucuronidase (gusA) gene was based on the highly sensitive detection of its activity. For Agrobacterium -mediated transformation of leaf explants, a cauliflower mosaic virus 35S promoter-driven, modified version of gfp, the mgfp5-ER gene and the gusA gene, respectively, were introduced into the new dual binary transformation vector system pGreen/pSoup (Hellens et al. 2000, Plant Mol Bio 42: 819,832). GFP5 produced bright-green fluorescence in transformed tissues that was distinctly detected 5,12 days following transformation in developing calli of the two species. Visual screening, combined with antibiotic selection, enabled early and easy identification of transformation events and contributed to improvements in the transformation strategies. Transgene integration studies demonstrated that mgfp5-ER was inserted with low copy number in the M. arvensis plant lines and the transgene was transmitted in a Mendelian fashion to T1 and T2 progenies. GFP5 expression levels in a population of 100 independent primary transformed M. arvensis plant lines (T0) showed great variation between transformation events (coefficient of variation of 108%). The mgfp5-ER or gusA reporter genes were expressed in 90,95% of the kanamycin-resistant M. arvensis plant lines and in up to 98% of the independent M. moricandioides plant lines. [source]

Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments

ENVIRONMENTAL MICROBIOLOGY, Issue 7 2005
Juan M. Gonzalez
Summary Microbial assessment of natural biodiversity is usually achieved through polymerase chain reaction (PCR) amplification. Deoxyribonucleic acid (DNA) sequences from natural samples are often difficult to amplify because of the presence of PCR inhibitors or to the low number of copies of specific sequences. In this study, we propose a non-specific preamplification procedure to overcome the presence of inhibitors and to increase the number of copies prior to carrying out standard amplification by PCR. The pre-PCR step is carried out through a multiple displacement amplification (MDA) technique using random hexamers as priming oligonucleotides and ,29 DNA polymerase in an isothermal, whole-genome amplification reaction. Polymerase chain reaction amplification using specific priming oligonucleotides allows the selection of the sequences of interest after a preamplification reaction from complex environmental samples. The procedure (MDA-PCR) has been tested on a natural microbial community from a hypogean environment and laboratory assemblages of known bacterial species, in both cases targeting the small subunit ribosomal RNA gene sequences. Results from the natural community showed successful amplifications using the two steps protocol proposed in this study while standard, direct PCR amplification resulted in no amplification product. Amplifications from a laboratory assemblage by the two-step proposed protocol were successful at bacterial concentrations ,,10-fold lower than standard PCR. Amplifications carried out in the presence of different concentrations of fulvic acids (a soil humic fraction) by the MDA-PCR protocol generated PCR products at concentrations of fulvic acids over 10-fold higher than standard PCR amplifications. The proposed procedure (MDA-PCR) opens the possibility of detecting sequences represented at very low copy numbers, to work with minute samples, as well as to reduce the negative effects on PCR amplifications of some inhibitory substances commonly found in environmental samples. [source]

Ticks have R2 retrotransposons but not the consensus transposon target site of other arthropods

INSECT MOLECULAR BIOLOGY, Issue 5 2005
J. Bunikis
Abstract Some copies of the large subunit rRNA genes (LSU rDNA) of most arthropods studied to date are inactivated by R-element retrotransposons at a specific target region that is highly conserved in sequence across all kingdoms of organisms. Here we report finding R2 elements in low copy numbers in the LSU rDNA of hard and soft ticks. Although the elements were inserted at the same LSU rDNA location as in insects, there were substitutions in the consensus R2 endonuclease cleavage site in the ticks and some other parasitiform mites. The substituted region comprises a critical contact point with small subunit rRNA, but in vitro structure probing analysis revealed novel, presumably stabilizing base-pairing. [source]

Construction of a ,unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes

THE PLANT JOURNAL, Issue 5 2002
Ralf Herwig
Summary Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods have to produce massively redundant data to get access to low-abundance genes. Here, we present an improved oligonucleotide fingerprinting (ofp) approach to the genome of sugar beet (Beta vulgaris), a plant for which practically no molecular information has been available. To identify distinct genes and to provide a representative ,unigene' cDNA set for sugar beet, 159 936 cDNA clones were processed utilizing large-scale, high-throughput data generation and analysis methods. Data analysis yielded 30 444 ofp clusters reflecting the number of different genes in the original cDNA sample. A sample of 10 961 cDNA clones, each representing a different cluster, were selected for sequencing. Standard sequence analysis confirmed that 89% of these EST sequences did represent different genes. These results indicate that the full set of 30 444 ofp clusters represent up to 25 000 genes. We conclude that the ofp analysis pipeline is an accurate and effective way to construct large representative ,unigene' sets for any plant of interest with no requirement for prior molecular sequence data. [source]