measurement of mitochondrial dna copy number

... of the data Page of 12 We have developed a software tool called FISH Oracle combining the most important features of the above mentioned software tools for visualizing array CGH data: First of ... the number of array CGH experiments to be visualized at once This is important since a large number of experiments is often necessary to obtain accurate results, a fact confirmed by the large number ... flexible visualization of DNA copy number data in a genomic context Journal of Clinical Bioinformatics 2011 1:20 Submit your next manuscript to BioMed Central and take full advantage of: • Convenient...

Ngày tải lên: 10/08/2014, 09:22

... major direct role of DNA copy number alteration in the transcriptional program of human breast tumors,” Proceedings of the National Academy of Sciences of the United States of America, vol 99, ... i=1 wi equals the total number of observations on the chromosome (3) For window j, determine the number of subintervals j with lengths t1 , .,t j (4) Count the number of biomarkers, mi , in ... probability function of (20) combined with the sliding window approach signals two or more possible copy number changes on chromosome of GM01524, chromosome of GM03134, chromosomes 10 and 11 of EURASIP...

Ngày tải lên: 21/06/2014, 11:20

... each FlcDNA Out of 3,497 FlcDNAs, 1,073 were covered entirely The length of target sequence (part of the cDNA covered by capture baits) per cDNA was selected based on the previous estimates of genetic ... highlighted in grey (b) An example of CNV due to the deletion of a homoeologous copy of a gene Deletion of a gene in the A genome of Td resulted in the disappearance of three bases, T, A and A, in ... We then mixed 13 μl of hybridization solution, μl of the library, μl of pre-warmed (65°C) mix of SureSelect Oligo Capture Library, μl of water and μl of RNase block A drop of mineral oil (Sigma,...

Ngày tải lên: 09/08/2014, 23:20

... Ontology system (data not shown) The total number of genes in the population of the biological process system was 13,802 Population hits show the number of genes that belong to the respective gene ... the pathways of oxidative phosphorylation (ATP6, COX1, COX3, CYTB, ND1, and ND2), in which three are relevant to mitochondrial dysfunction Because the expressions of DNA repair and mtDNAencoded ... three of them (COX1, COX3, and CYTB) also lead to mitochondrial dysfunction Also worth noting is that repairs of UV-induced DNA damage by ERCC2/XPD and ERCC5/XPG requires ATP The ATP and DNA binding...

Ngày tải lên: 12/08/2014, 15:23

... domesticated in various parts of the world [5,16,20-25] The time of divergence between European and Asian pig mitochondrial DNAs (mtDNAs) was long before the time of possible pig domestication, ... parentheses aNumbers refer to the proportion of individuals that are grouped into this haplogroup in each region bNumber of haplotypes in each region The values in parentheses refer to the number of unique ... median network of domestic pig and wild boar mitochondrial DNAs (mtDNAs) belonging to haplogroup D1 based on the sequence variation of control region and coding region fragments The mtDNA control...

Ngày tải lên: 14/08/2014, 08:20

... before the discovery of the structure of DNA — the duplication of a DNA segment containing the Bar gene in Drosophila melanogaster In 1936, Bridges discovered that the copy number of a chromosomal ... 2009) CNV is a class of variations where the copy number of a DNA segment is varied between different genomes of the same species When genes are located in CNV regions, the dosage of genes are changed, ... underlying copy number ratios 1.3 Development of DNA Sequencing Technologies The rapid development of sequencing technologies is continuously increasing the speed and decreasing the cost of DNA sequencing...

Ngày tải lên: 11/09/2015, 10:01

... to the monomer size of linear Fig The state of mtDNA in Sc pombe is affected by the loss of Ydc2 Agarose gel electrophoresis of undigested or XhoI-digested total cellular DNA from strain FO101 ... dominant-negative effects of truncated and point mutants The results of this experiment are shown in Fig 7B Expression of wild-type Ydc2–GFP resulted in a clear reduction of the mtDNA content of the cells ... complement the mtDNA deficiency of ydc2D cells These results show clearly that maintaining a normal content of mtDNA in fission yeast depended on the catalytic activity of Ydc2 The effect of expressing...

Ngày tải lên: 20/02/2014, 11:20

... represents an important step in assembly of the holoenzyme Results In vitro import and assembly of nDNA-encoded complex IV subunits The assembly of a number of nDNA-encoded complex IV subunits was ... assembly that involve formation of the catalytic core consisting of the mtDNA-encoded subunits CO1, CO2 and CO3 Thus details of the latter stages in which the majority of nDNA-encoded subunits that ... these differences is that further analysis of the biogenesis of the mammalian enzyme is required Assembly of nDNA-encoded complex IV subunits Of the five nDNA-encoded subunits investigated in this...

Ngày tải lên: 07/03/2014, 00:20

... were an artefact of the genotyping assay or a result of unequal allele distribution CYP17 copy number determination Relative copy number determinations were performed for each of the three putative ... the distribution of the two CYP17 isoforms in the South African Angora population, goats were genotyped on the basis of a restriction digest assay It was determined that 29% of the goats genotyped ... difference observed in their CYP17 composition and copy number The physiological effect of this novel finding was investigated by testing goats of each genotype for their ability to produce cortisol...

Ngày tải lên: 07/03/2014, 06:20

... Resistance of mitochondrial DNA- depleted cells against cell death: role of mitochondrialsuperoxide dismutase J Biol Chem 279, 7512–7520 17 Chandel, N.S & Schumacker, P.T (1999) Cells depleted of mitochondrial ... protein)1, with unit of SOD activity being defined as the amount of proteins causing half-maximal inhibition of the rate of NBT reduction GST activity was assayed in the supernatant of cell lysates, ... used for measurements of intracellular fluorescence Dead cells were excluded by electronically gating data on the basis of forward- vs side-scatter profiles; a minimum of · 104 cells of interest...

Ngày tải lên: 16/03/2014, 18:20

... homogeneity of isochore can be defined by an index h [17,20], which is defined as the variance of GC content of the region divided by that of the whole genome If h ( 1, the variance of GC content of the ... a series of nodes P0, P1, P2, …, PN, whose coordinates xn, yn and zn (n ¼ 0, 1, 2, …, N, where N is the length of the DNA sequence being studied) are calculated by the Z-transform of DNA sequence ... genomic distribution of the major family of interspersed repeats of mouse DNA Proc Natl Acad Sci USA 79, 355– 359 12 Soriano P, Meunier-Rotival M & Bernardi G (1983) The distribution of interspersed...

Ngày tải lên: 30/03/2014, 20:20

... intensity of the PCR product when about 14 ng of PCR-purified mtDNA was amplified by PCR from control SF The PCR analysis revealed the presence of extracellular mtDNA in the SF of 38 of 54 (70%) of ... amplification of mtDNA from plasma and synovial fluid (SF) samples of patients with rheumatoid arthritis (RA) SDS–polyacrylamide-gel electrophoresis of PCR-amplified mitochondrial DNA (mtDNA) fragments ... spiked with 10 ng of purified mtDNA Statistical analyses Figure Differences between the groups in the levels of PCRamplified mitochondrial DNA in plasma and SF, and in the levels of 8-oxodG in SF,...

Ngày tải lên: 09/08/2014, 01:23

... World Journal of Surgical Oncology 2010, 8:92 http://www.wjso.com/content/8/1/92 Page of Figure A Histologic appearance of combinations of small, ductal and squamous cellular components of the tumor ... for publication of this case report and accompanying images A copy of the written consent is available for review by the Editor-in-Chief of this journal Acknowledgements We thank Professor Ling-Ling ... from EGFR copy number analysis in each component of the tumor, no EGFR amplification was found EGFR targeting agents might have limited roles in this rare tumor Huang et al World Journal of Surgical...

Ngày tải lên: 09/08/2014, 03:22

... qiangs@mail.tmmu.com.cn -1- Abstract Background: Mitochondrial DNA (mtDNA) alterations, including mtDNA copy number and mtDNA 4977bp common deletion (CD), are key indicators of irradiation-induced damage The ... due to its high copy number One of possible radio-protective mechanism is that enhanced replication of mtDNA reduces the mutation frequency of total mtDNA and delays the onset of lethal radiation ... alteration of the copy number of mitochondrial DNA in human leukocytes Free Radic Res 2003, 37:1307-1317 Figure Legends Figure TaqMan PCR assay for measuring the common mitochondrial deletion in DNA...

Ngày tải lên: 09/08/2014, 09:21

... copy number is locally constant Consequently, the final CNV calling step takes advantage of this fact, smoothing or segmenting the raw copy numbers into discrete segments of consistent copy number ... objective function is defined by the observed data (raw copy number) and is a function of inferred state (copy number call) The sequence of copy number calls (states) that optimizes the objective ... versions of the Affymetrix platform, Illumina arrays, or array comparative genomic (a) 2.5 Raw copy number Raw copy number 3.0 hybridization Any platform that produces a measure of raw copy number...

Ngày tải lên: 09/08/2014, 20:20

... BeadChips, which generate allele-specific signals (with the exception of subsets of non-genotyping copy number probes) To observe copy number events on our arrays, we processed our probe signals with ... AAGACTCAAG Matsuzaki et al R125.5 Number of probes Number of unique probes Figure Examples of loss events detected by segmentation analysis [22] in two Yoruba DNAs, NA19132 and NA19101, at putative ... be harboring a fair proportion of common and more older CNVs, similar to the occurrence of common SNPs [1] A number of previous CNV studies also used some or all of the Yoruba individuals, making...

Ngày tải lên: 09/08/2014, 20:20

... distance is chosen Generation of the copy number profile of the common precursor of two samples At each step of the algorithm, the profile of the common precursor of the two nodes joined, CP(a ... Segmentation of the profiles and generation of the amplitude vectors Generation of the amplitude matrix (a) Discretized copy number profiles of three tumors for a given chromosome (yellow, ‘normal copy number ; ... considering each segment in the copy number profile as a character, with a discrete number of values (-2 to 2) As the number of tumors increases, so does the number of successive steps in the simulated...

Ngày tải lên: 09/08/2014, 20:22

... on other chromosomes of the same sample are plotted in grey The number of possible variants of allele-specific copy number increases with the total copy number Lower copy numbers are more affected ... and single -copy gains and losses is the best indicator of copy number two Find the Allelic Imbalance Ratio of cn1, cn2m1 (2 with minor copy number 1) and cn2m0 (2 with minor copy number 0, i.e ... lower copy number variants (such as cn1, cn2m1 and cn2m0 for copy number 3) to predict the Allelic Imbalance Ratio of copy number variants (such as cn3m1 and cn3m0) Set them to the median* of any...

Ngày tải lên: 09/08/2014, 23:20

... been fully characterized The copy number variations (CNVs) can contribute to variable levels of gene expressions [11], and thus fine-scale copy number (CN) profiling of cancer can enhance our knowledge ... frequencies of CN gains, and bottom dots represent the frequencies of CN losses Figure Comparisons of copy number variation patterns between colorectal cancer subtypes (a) the average number of CN-changed ... also known as copy number alterations/aberrations (CNAs), are frequently observed, e.g., gains of oncogenes and losses of tumor suppresser genes [12] Furthermore, the DNA CN states of CRC cases...

Ngày tải lên: 10/08/2014, 05:21

... vitiligo, the distribution of copy number for total C4, C4 isotypes as well as C4 polymorphisms did not associate with the occurrence of myxedema (Table 3) The distribution of copy number for total C4, ... CY: Gene copy- number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is ... SD, standard deviation; N, number Page of Liu et al Journal of Biomedical Science 2011, 18:71 http://www.jbiomedsci.com/content/18/1/71 Page of Table Distribution of C4 polymorphisms in individuals...

Ngày tải lên: 10/08/2014, 10:20