BackgroundDNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number.ResultsWe developed a sequencing-based assay of nuclear, mitochondrial, and telomeric ...

DNA Structure and Analysis Molecules Used as Must have 4 Properties: They Must... 1) Be Accurately Evolutionary Change to Occur DNA is Replicated (or Meiosis) Making Completely Copied Set of Chromosomes The 2 Daughter Cells then Receive of DNA Containing Chromosomes Information Stored in the ...

Abstract. Accurate estimation of relative mutation rates of mitochondrial DNA (mtDNA) and single- copy in mitochondrial vs. nuclear genes was unexpected in light of previous reports of a slow rate of mtDNA evolution on mutation rates. Key words: Substitution rate -- Synonymous sites -- ...

Genome-wide RNA expression profiling has yielded tumor subtypes with strong predictive or prognostic value for a wide variety of cancers. Recently, for breast cancer two RNA expression classifiers have been adopted by the World Health Organization (WHO) and approved by the Food and Drug Administration (FDA). Also on the basis of DNA copy number profiles, ...

We have developed a new protocol for using MolecularInversion Probes (MIP) to accurately and specifically measure allele copynumber (ACN). The new protocol provides for significant improvementsincluding the reduction of input DNA (from 2?g) by more than 25 fold (to75ng total genomic DNA), higher overall precision resulting in one ...

Banana is one of the most important subtropical fruit crops. Genetic improvement by traditional breeding strategies is difficult and better knowledge of genomic structure is needed. Repeated sequences are powerful markers for genetic fingerprinting. The method proposed here to determine the copy number of nuclear repetitive elements is based on competitive reverse ...

"An embryonic cell divides again and again. Where there was one cell there are two, then four, then eight,... Each holds all the genetic information needed to create a human being. How, exactly, do these cells make copies of themselves? Hair grows from your head, nonstop, day in and day out. The cells of your hair follicles somehow generate all of the protein that make up this ...

BackgroundThere have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and ?-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, ...

Cancer results from progressive irreversible changes in our genetic material (DNA) that ultimately leads the uncontrolled growth of tumor cells, increased invasiveness to surrounding tissue, and the ability to spread to other organs. A major cause of genetic mutations is chemical damage to DNA. Damaged DNA is not ...

Quantitation of hepatitis B virus (HBV) DNA in serum is a useful method for the monitoring of HBV replication. We attempted to develop a quantitative assay system for HBV DNA that is more sensitive, accurate, and reproducible than existing systems. We detected HBV DNA by real-time detection PCR (RTD-PCR) based on ...

We frequently use competitive PCR in the plateau phase in quantifying DNA species with a small number of cells. However, the basic issues of this method are poorly understood. Here, first we analyze this method theoretically under a generalized condition that competitor and target DNA products accumulate with different amplification efficiencies. We show a ...

Three possible ways in which DNA can replicate are illustrated. The two original strands of DNA are shown in yellow (light); newly synthesized DNA is blue (dark). To explain the phenomenon of heredity, biological information must be accurately copied and transmitted from each cell to all of its ...

Retroviruses encode an enzyme, RNA-independent DNA polymerase (reverse transcriptase), responsible for copying the RNA genome found in the virion into DNA. This copying of viral RNA into DNA is an obligate step in the viral life cycle and the DNA copy ...

Accurate estimation of total DNA concentration (mass concentration, e.g., ng/muL) that is traceable to the International System of Units (SI) is a crucial starting point for improving reproducible measurements in many applications involving nucleic acid testing and requires a DNA reference material which has been certified for its ...

The development of high-throughput screening methods such as array-based comparative genome hybridization (array CGH) allows screening of the human genome for copy-number changes. Current array CGH strategies have limits of resolution that make detection of small (less than a few tens of kilobases) gains or losses of genomic DNA difficult to identify. We ...

Accurate and timely detection of transgene copy number in sugarcane is currently hampered by the requirement to use Southern blotting, needing relatively large amounts of genomic DNA and, therefore, the continued growth and maintenance of bulky plants in containment glasshouses. In addition, the sugarcane genome is both polyploid and ...

DNA is a chemically reactive molecule that is subject to many different covalent modifications from sources that are both endogenous and exogenous in origin. The inherent instability of DNA is a major obstacle to genomic maintenance and contributes in varying degrees to cellular dysfunction and disease in multi-cellular organisms. Investigations into the ...

DNAi Location: Genome>The Project>Putting it together>Animations>Sanger sequencing The DNA sequencing method developed by Fred Sanger forms the basis of automated "cycle" sequencing reactions today. Scaling up to sequence In the 1980s, two key developments allowed researchers to believe that sequencing the entire genome could be possible. The first was a technique ...

Humans differ not only at the level of DNA sequence. It has been recently discovered that humans can also differ in the number of copies of each gene. These are called copy number variants.

DNA is used as a template for copying information. Knowing the structure of DNA, scientists speculated and then proved that DNA is the template for copying the genetic code.

Every time a cell divides, billions of base pairs of information must be accurately copied in the face of an onslaught of DNA damage. Homologous recombination (HR) provides a critical mechanism for tolerating and repairing damaged DNA. Although HR is generally beneficial, misalignments during HR can lead to ...

BackgroundThe transposon-based gene delivery technique is emerging as a method of choice for gene therapy. The Sleeping Beauty (SB) system has become one of the most favored methods, because of its efficiency and its random integration profile. Copy-number determination of the delivered transgene is a crucial task, but a universal method for measuring this is lacking. In this ...

For bacterial genes to be inherited to the next bacterial generation, the gene containing DNA sequences must be duplicated before cell division so that each daughter cell contains a complete set of genes. The duplication process is called DNA replication and it starts at one defined site on the DNA molecule called the origin of ...

We have constructed a hybrid plasmid by insertion of the thymidine kinase (TK) gene of Herpes simplex virus (HSV) type I at the BamHI site on Escherichia coli plasmid pBR322. The restriction endonuclease cleavage site map for the viral DNA fragment was determined for ten nucleases, and the insert in the recombinant plasmid has the same restriction nuclease digestion pattern as ...

The copy number variation in beta-defensin genes on human chromosome 8 has been proposed to underlie susceptibility to inflammatory disorders, but presents considerable challenges for accurate typing on the scale required for adequately powered case-control studies. In this work, we have used accurate methods of ...

Polymerase chain reaction (PCR) enables researchers to produce millions of copies of a specific DNA sequence in approximately two hours. This automated process bypasses the need to use bacteria for amplifying DNA.

Interviewee: Kary Mullis DNAi Location:Manipulation>Techniques>amplifying Finding the DNA to copy Kary Mullis speaks about the process of find a specific fragment of DNA amongst many pieces in a complex mixture.

High-fidelity DNA polymerases copy DNA rapidly and accurately by adding correct deoxynucleotide triphosphates to a growing primer strand of DNA. Following nucleotide incorporation, a series of conformational changes translocate the DNA substrate by one base pair step, ...

Transpositions of mtDNA sequences to the nuclear genome have been documented in a wide variety of individual taxa, but little is known about their taxonomic frequency or patterns of variation. We provide evidence of nuclear sequences homologous to the mtDNA control region in seven species of diving ducks (tribe Aythyini). Phylogenetic analysis places ...

DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis-syn thymine dimers. We present structural and ...

Motivation: The complexity of a large number of recently discovered copy number polymorphisms is much higher than initially thought, thus making it more difficult to detect them in the presence of significant measurement noise. In this scenario, separate normalization and segmentation is prone to lead to many false detections of changes in copy number. New ...

BackgroundCopy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) ...

Rice (Oryza sativa) is a main staple food in the world, and several genetically modified (GM) rice events have been approved for commercialization. To accurately quantify GM contents in rice derived products, we have evaluated the variation of seed DNA density and nuclear DNA content in the hull, endosperm, and embryo of rice seeds ...

Mitochondria have their own DNA (mitochondrial DNA [mtDNA]). Although mtDNA copy number is dependent on tissues and its decrease is associated with various neuromuscular diseases, detailed distribution of mtDNA copies in the brain remains uncertain. ...

Visceral Leishmaniasis is an endemic disease in Brazil caused by Leishmania infantum chagasi and its main vector species is the sand fly Lutzomyia longipalpis. Epidemiological studies have used conventional PCR techniques to measure the rate of infection of sand flies collected in the field. However, real-time PCR can detect lower parasite burdens, reducing the number of false negatives and ...

The replisome is a multi-component molecular machine responsible for rapidly and accurately copying the genome of an organism. A central member of the bacterial replisome is DnaB, the replicative helicase, which separates the parental duplex to provide templates for newly synthesized daughter strands. A unique RNA polymerase, the ...

Genome replication is the most fundamental element of the continuity of life. In eukaryotes, DNA replication is regulated by an elegant network of many different protein factors to ensure the timely and accurate copying of their entire genome once per cell cycle. The replication factors include the maintenance (MCM) proteins, Cdt1, ...

To develop a method to modify genomic sequences in Ascobolus immersus by precisely reintroducing defined DNA segments previously manipulated in vitro, we investigated the effect of transforming DNA conformation on recombination with chromosomal sequences. Circular single-stranded DNA carrying the met2 gene and double-stranded ...

Along the transformation process, cells accumulate DNA aberrations, including mutations, translocations, amplifications, and deletions. Despite numerous studies, the overall effects of amplifications and deletions on the end point of gene expression�the level of proteins�is generally unknown. Here we use large-scale and high-resolution proteomics combined with gene ...

Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray ...

The P1 plasmid partition site acts like a centromere, promoting accurate segregation of copies to daughter cells. A 34 bp segment is essential for partition and binds the plasmid ParB protein. Additional sequences act as specificity elements that direct the choice of copies for partition. They include a second ParB binding site and a ...

BackgroundCurrent methods for measurement of copy number do not combine all the desirable qualities of convenience, throughput, economy, accuracy and resolution. In this study, to improve the throughput associated with Multiplex Amplifiable Probe Hybridisation (MAPH) we aimed to develop a modification based on the 3-Dimensional, Flow-Through Microarray Platform from PamGene ...

Occurrence of retinoblastoma is associated with inactivation of Rb1 gene which is located in 13q14. According to published data the inactivation of Rb1 gene occurred in 90% retinoblastoma was resulted from either deletion or point mutation or methylation of Rb1 gene. Denaturing high performance liquid chromatography (DHPLC) is capable to detect point mutation simply, rapidly and ...

DNA polymerase (blue) makes many copies of DNA (red) in a cycle of the polymerase chain reaction (PCR).

... an internal control for the efficiency of PCR utilizing globin DNA or heparin cofactor II DNA, present at the level of one copy per haploid genome. 13 ...

BACKGROUND & AIMS: It is not clear whether risk for hepatocellular carcinoma can be accurately determined from long-term changes in serum levels of hepatitis B virus (HBV) DNA or alanine aminotransferase (ALT). METHODS: We measured serum levels of HBV DNA and ALT at enrollment and during follow-up analysis of 3160 participants in ...

BackgroundGenotyping platforms such as single nucleotide polymorphism (SNP) arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV) and allelic imbalance including loss-of-heterozygosity (LOH) beyond that obtained from the total ...

Interviewee: Kary Mullis DNAi Location:Manipulation>Techniques>amplifying Making many DNA copies Kary Mullis talks about his discovery of the polymerase chain reaction (PCR), a process that allows chemists to produce many copies of a specific fragment of DNA.

... of DNA or RNA and therefore does not require the use of PCR. ... Rapid, accurate and sensitive detection and identification of biological agents is ...

Microarray-based Comparative Genomic Hybridization (array-CGH) has been applied for a decade to screen for submicroscopic DNA gains and losses in tumor and constitutional DNA samples. This method has become increasingly flexible with the integration of new biological resources generated by genome sequencing projects. In this chapter, we describe ...

Maintenance of genome integrity requires that chromosomes be accurately and faithfully replicated. We are using Tetrahymena thermophila as a model system for studying the initiation and regulation of eukaryotic DNA replication. This organism contains a diploid micronucleus and polyploid macronucleus. During macronuclear development, the five diploid ...

Affymetrix SNP arrays have been widely used for single-nucleotide polymorphism (SNP) genotype calling and DNA copy number variation inference. Although numerous methods have achieved high accuracy in these fields, most studies have paid little attention to the modeling of hybridization of probes to off-target allele sequences, which can affect the accuracy ...

Buccal smears from 3 women and 1 man were probed with alpha satellite DNA probes for chromosomes 8, 18, X, and Y. Buccal smears were also collected from an adolescent phenotypic female with uterine agenesis, as well as from newborn infants with suspected trisomy 18 and trisomy 21. The clinical cases were confirmed with conventional cytogenetic studies of peripheral ...

Human parvovirus B19 infections are common in the general population, and infection during pregnancy may cause hydrops fetalis and fetal death. To initiate adequate treatment, accurate laboratory diagnosis is essential. The most sensitive tests are nested PCR systems, but these assays provide semiquantitative results at best. A parvovirus B19 DNA assay was ...

Mitochondrial DNA (mtDNA) depletion is characterized by a profound reduction of mtDNA copy number. The maintenance of mtDNA copy number requires several nuclear-encoded factors involved in replication and in dNTP supply. In the past decade mutations in several of these ...

Transposable elements (TEs) are repetitive DNA sequences that are ubiquitous, extremely abundant and dynamic components of practically all genomes. Much effort has gone into annotation of TE copies in reference genomes. The sequencing cost reduction and the newly available next-generation sequencing (NGS) data from multiple strains within a species offer ...

Structural variation of human genome such as duplications and deletions, collectively termed copy number variation (CNV), is one of the major genetic variations. Reliable and efficient measurement of CNV will be essential to develop diagnostic tools for CNV-related diseases. We established a strategy based on multiplex PCR and capillary electrophoresis (CE) for reliable CNV ...

Mammalian mitochondrial DNA (mtDNA) is a small, maternally inherited genome that codes for 13 essential proteins in the respiratory chain. Mature oocytes contain more than 150 000 copies of mtDNA, at least an order of magnitude greater than the number in most somatic cells, but sperm contain only approximately 100 ...

Mammalian mitochondrial DNA (mtDNA) is a small, maternally inherited genome that codes for 13 essential proteins in the respiratory chain. Mature oocytes contain more than 150?000 copies of mtDNA, at least an order of magnitude greater than the number in most somatic cells, but sperm contain only approximately 100 ...

We used real-time PCR to quantify the denitrifying nitrite reductase gene (nirS), a functional gene of biogeochemical significance. The assay was tested in vitro and applied to environmental samples. The primer-probe set selected was specific for nirS sequences that corresponded approximately to the Pseudomonas stutzeri species. The assay was linear from 1 to 10⁶ gene ...

Utilizing the principle of competitive PCR, we developed two assays to enumerate Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus Nitrospira. The specificities of two primer sets, which were designed for two target regions, the amoA gene and Nitrospira 16S ribosomal DNA (rDNA), were verified by ...

BackgroundQuantitative Polymerase Chain Reaction (qPCR) is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise) results. The fundamental problem is that qPCR methods use mathematical models that explicitly or ...

The accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes. Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have ...

BackgroundSingle nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no ...

DNA Replication and RecombinationDNA Replication and Recombination of Eukaryote DNA is a Huge Task in a Million), would Still Mean that Mistakes were Made Every Time the DNA was Copied Consequently an DNA an Idea for (Called the Semi Conservative Model) Based on ...

Motivation: Genomic instability is one of the fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array comparative genomic hybridization (aCGH), developed based on expression microarray technology, can reveal the chromosomal ...

The free, linear macronuclear ribosomal RNA genes (rDNA) of Tetrahymena are derived from a unique copy of micronuclear rDNA during development. We have injected cloned copies of the micronuclear rDNA that have been altered in vitro into developing macronuclei and obtained transformants that ...

An important force in evolutionary selection may be informational efficiency, which results in a balance between the energy expended to maintain a high level of fidelity and the energy lost from errors or mutations in the production of defective offspring. The accuracy of DNA replication may be limited by the average accuracy of protein synthesis if the major source of enzymes ...

Comparative genome hybridization (CGH) to DNA microarrays (array CGH) is a technique capable of detecting deletions and duplications in genomes at high resolution. However, array CGH studies of the human genome noting false negative and false positive results using large insert clones as probes have raised important concerns regarding the suitability of this approach for ...

GSTT1 and GSTM1 genes possess an inherited deletion associated with a lack of enzyme activity. The heterozygous condition of this deletion is difficult to determine in low-quality DNA with existing PCR protocols. We designed and validated a multiplex real-time PCR assay by adapting the DeltaDeltaCt relative quantification method for the analysis of GSTT1 and GSTM1 markers to ...

We have ligated two cosmids through an oligonucleotide linker to produce a single fragment spanning 70 kb of the human alpha-globin cluster, in which the alpha-like globin genes (zeta 2, alpha 2 and alpha 1), their regulatory element (HS-40) and erythroid-specific DNase I hypersensitive sites accurately retain their normal genomic organization. The zeta (embryonic) and alpha ...

We have ligated two cosmids through an oligonucleotide linker to produce a single fragment spanning 70 kb of the human alpha-globin cluster, in which the alpha-like globin genes (zeta 2, alpha 2 and alpha 1), their regulatory element (HS-40) and erythroid-specific DNase I hypersensitive sites accurately retain their normal genomic organization. The zeta (embryonic) and alpha ...

BackgroundThe accurate determination of the number of copies of a gene in the genome (gene dosage) is essential for a number of genetic analyses. Quantitative real time PCR (qPCR) with TaqMan detection has shown advantages over traditional Southern-blot and FISH techniques, however the high costs of the required labeled probes is an important limitation of ...

... obtains PDGF-BB by DNA recombinant technology using a strain of the yeast Succharon ... listing of the fifteen cases is shown below and the relevant hard copy of ...

Duplication is a kind of mutation caused by the production of one or more copies of any piece of DNA, including a gene or even an entire chromosome.

Subtractive hybridization is being used to identify additional families of repetitive human DNA sequences.

Subtractive hybridization is being used to identify additional families of repetitive human DNA sequences.

A mitochondrion has several copies of its own genome, and there are several hundred mitochondria per cell. (image of mitochondrion)

... Page 3. 2895 IYSNRDL-TR-555 Copy 2 April 1962 C= I*ONOVALENT CATION EFFECTS ON C A DNA-SYNTHESIZING SYSTEM U. ...

... to cut DNA at the sites of mismatches, such as ... is paired with a copy of the normal DNA. ... The CEL I mismatch detection (CMD) assay has shown high ...

Subtractive hybridization is being used to identify additional families of repetitive human DNA sequences.

DNA Shearing; Not a pan-generic primer; Assumed #copies/bact; % efficiency in removing DNA from soil; Interference of humic acid in amplification ...

Small parasites and larval stages pose a problem for molecular analyses because limited amounts of DNA template are available. Isothermal methods for faithfully copying DNA have the potential to revolutionize studies of such organisms. We evaluated the fidelity of multiple displacement amplification (MDA) for amplifying ...

The development of DNA cloning techniques for complementary DNA (cDNA) copies of messenger RNA (mRNA) molecules has been of great value in the study of eukaryotic genes. The invention relates to vectors for molecular cloning of DNA segments, particularly ...

... to be made when they are copying their DNA. These DNA changes can eventually lead to cancer (see below). ... great progress in understanding how certain changes in DNA can cause normal cells to become cancerous. DNA ...

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution ...

Detection of human cytomegalovirus (CMV) DNA in clinical specimens is considered a cornerstone in the diagnosis of CMV disease. The aim of this study was to evaluate a newly designed LightCycler-based quantitative CMV PCR. Specimens of human origin (n = 200) were tested using the LightCycler PCR, the quantitative COBAS AMPLICOR CMV MONITOR (CACM) assay, and a qualitative ...

Puccinia horiana Henn. is a quarantine organism and one of the most important fungal pathogens of Chrysanthemum x morifolium cultivars grown for cut flower or potted plant production (florist's chrysanthemum) in several regions of the world. Highly specific primer pairs were identified for conventional, nested, and real-time PCR detection of P. horiana based on the specific and sensitive PCR ...

Integration of human papillomavirus (HPV) DNA into the host cell genome is a frequent event in cervical carcinogenesis, even though this phenomenon does not seem to be mandatory for cervical cancer development. Our objective was to describe the load and physical state of HPV type 16 (HPV16) DNA in a series of cervical samples representative of the natural ...

This thesis is concerned with the development of the polymerase chain reaction (PCR) as an accurate and reliable measure of specific DNA copy number. This development is motivated by the need to quantify the number of copies of HIV in infected cells. In particular the extent of HIV infection, in terms of proviral ...

Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols ? and ?. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, helps to maintain ...