• detect
  • The results of the parallel analyses are then used to detect common molecular characteristics of the genetic disorder type, which can subsequently be used in the diagnosis or treatment of the disease. (google.com)
  • This method may also be adapted to detect DNA methylation differences, as seen in Methylation-Sensitive Representational Difference Analysis (MS-RDA). (wikipedia.org)
  • To address these challenges, we have previously developed and validated a pan-viral microarray platform called the Virochip with the capacity to detect all known viruses as well as novel variants on the basis of conserved sequence homology 1 . (jove.com)
  • For known exRNA nucleotide sequences, RT-PCR can be applied to detect their presence within a sample as well as quantify their abundance. (wikipedia.org)
  • Here, we use our study to illustrate the use of Exon Arrays to detect alternative isoforms, to outline the analysis involved, and to point out potential problems that may be encountered by researchers using this technology. (igi-global.com)
  • The method of sequencing cDNA to find transcribed genes also runs into problems, such as failing to detect rare or very short RNA molecules, and so do not detect genes that are active only in response to signals or specific to a time frame. (wikipedia.org)
  • molecular
  • A method is disclosed for rapid molecular profiling of tissue or other cellular specimens by placing a donor specimen in an assigned location in a recipient array, providing copies of the array, and performing a different biological analysis of each copy. (google.com)
  • These integrated genomic and molecular studies provide evidence that the IGF1R pathway is a potential therapeutic target for patients with MPNST. (aacrjournals.org)
  • This information deficit is caused by several constraining factors such as the lack of the complete genomic information or the unavailability of molecular tools, for instance, species-specific antibodies. (hindawi.com)
  • Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (wikipedia.org)
  • Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (wikipedia.org)
  • Polymerase chain reaction (PCR) is a technique used in molecular biology to amplify a single copy or a few copies of a segment of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. (wikipedia.org)
  • Recombinant DNA techniques create molecular clones by conferring on a specific sequence the ability to replicate by inserting it into a vector and introducing the vector into a host cell. (wikipedia.org)
  • In addition to its many applications in basic molecular biological research, PCR promises to play a critical role in the identification of medically important sequences as well as an important diagnostic one in their detection. (wikipedia.org)
  • Some of its major applications include genomics, proteomics, molecular diagnostics, point-of-care diagnostics, tissue engineering, single cell analysis and implantable microdevices. (wikipedia.org)
  • Hybridization
  • Cyanine dyes are commonly used for fluorescent labeling of DNA and RNA oligonucleotides in applications including qPCR, sequencing, fluorescence in situ hybridization, Förster resonance energy transfer, and labeling for microarray hybridization. (jove.com)
  • Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. (wikipedia.org)
  • They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. (wikipedia.org)
  • This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. (wikipedia.org)
  • The sequence signatures are deciphered by the parallel identification of four bases by hybridization to fluorescently labeled encoders (Figure 5). (wikipedia.org)
  • Each of the encoders has a unique label which is detected after hybridization by taking an image of the microbead array. (wikipedia.org)
  • The most important elements are, among others, hybridization ovens, chip scanners, and software packages for subsequent numerical analysis of the raw data. (wikipedia.org)
  • The hybridization signal intensities for each probe are used by specialized software to generate a log2ratio of test/normal for each probe on the array. (wikipedia.org)
  • quantification
  • The principle of these methods is the identification and quantification of up to ten thousands of RNA and proteins species in a tissue, in contrast to the sequential analysis of conventional methods such as PCR and Western blotting. (hindawi.com)
  • Traditional analytical tools for quantification of DNA, RNA, or proteins are restricted to the sequential analysis of one biomolecule specimen at a time. (hindawi.com)
  • The microbeads are then arrayed in a flow cell for sequencing and quantification. (wikipedia.org)
  • In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. (wikipedia.org)
  • transcriptomes
  • However, because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial transcriptomes has been impossible. (bio-medicine.org)
  • In 2008, two human transcriptomes, composed of millions of transcript-derived sequences covering 16,000 genes, were published and, by 2015, transcriptomes had been published for hundreds of individuals. (wikipedia.org)
  • loci
  • Such processes have been suggested to be at least partly responsible for mammalian complexity, which is otherwise difficult to explain in view of our relatively low number of genomic loci - less than 25,000 genes in humans, versus approximately 20,000 in the nematode worm C. elegans (Claverie, 2001). (igi-global.com)
  • Virtual karyotype is the digital information reflecting a karyotype, resulting from the analysis of short sequences of DNA from specific loci all over the genome, which are isolated and enumerated. (wikipedia.org)
  • variants
  • Variants were further analyzed using clinical criteria and segregation analysis, where available. (ahajournals.org)
  • As only a relatively small proportion of the CNV regions overlap with regions found in other studies, the current total of more than 6,000 CNVs detailed in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ) is most likely an underestimate. (pubmedcentralcanada.ca)
  • However, these methods were largely overtaken by high throughput sequencing of entire transcripts, which provided additional information on transcript structure e.g. splice variants. (wikipedia.org)
  • organism's
  • In a particular type of cell or tissue, only a small subset of an organism's genomic DNA will be expressed as mRNAs at any given time. (wikipedia.org)
  • Illumina
  • The Sanger method of sequencing was predominant until the advent of high-throughput methods such as sequencing by synthesis (Solexa/Illumina). (wikipedia.org)
  • The toolkit comprises user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. (wikipedia.org)
  • organisms
  • Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved. (wikipedia.org)
  • differences
  • Representational difference analysis (RDA) is a technique used in biological research to find sequence differences in two genomic or cDNA samples. (wikipedia.org)
  • We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. (biomedcentral.com)
  • The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). (wikipedia.org)
  • It was concluded that the fluorescence ratios obtained were accurate and that differences between genomic DNA from different cell types were detectable, and therefore that CGH was a highly useful cytogenetic analysis tool. (wikipedia.org)
  • species
  • However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. (pubmedcentralcanada.ca)
  • When the two species are mixed, the driver sequence is added in excess to tester. (wikipedia.org)
  • Although many mammalian host species may be compatible with MICROB Enrich , only human, mouse and rat rRNA sequences were used for the design and optimization of the capture oligonucleotides. (bio-medicine.org)
  • transcripts
  • Gene set enrichment analysis (GSEA) revealed that several of the transcripts encoded transporters associated with the endomembrane system, especially zinc transport. (biomedcentral.com)
  • In the 1980s, low-throughput sequencing using the Sanger method was used to sequence random transcripts, producing Expressed Sequence Tags (ESTs). (wikipedia.org)
  • So if there are 50 copies of a specific transcript in the biological sample, these transcripts will be captured onto 50 different microbeads, each bead holding roughly 100,000 amplified copies of the specific signature sequence. (wikipedia.org)
  • Traditional methods of gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. (wikipedia.org)
  • tumors
  • From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. (bcgsc.ca)
  • The first report of CGH analysis was by Kallioniemi and colleagues in 1992 at the University of California, San Francisco, who utilised CGH in the analysis of solid tumors. (wikipedia.org)
  • proteins
  • This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. (biomedcentral.com)
  • We have determined genome sequences of B strains [ 5 , 6 ] - REL606, which has been applied to the study of long-term experimental evolution, and BL21(DE3), which has been used as a cell-factory for overproducing recombinant proteins, biofuels, and a variety of bioproducts on an industrial scale. (biomedcentral.com)
  • Other proteins allow the identification of promoter regions, enhancers, repressors and silencing elements, insulators, boundary elements, and sequences that control DNA replication. (wikipedia.org)
  • DNA sequencing is also the most efficient way to sequence RNA or proteins (via their open reading frames). (wikipedia.org)
  • commercially
  • However, in 1994 a review was published which described an easily understood protocol in detail and the image analysis software was made available commercially, which allowed CGH to be utilised all around the world. (wikipedia.org)
  • strains
  • The cynS gene that encodes cyanase was identified among bacterial, fungal, and plant sequences in public databases, and the gene was particularly prevalent among cyanobacteria, including numerous Prochlorococcus and Synechococcus strains. (embl-heidelberg.de)
  • We demonstrate here that marine cyanobacteria have a functionally active cyanase, the transcriptional regulation of which varies among strains and reflects the genomic context of cynS. (embl-heidelberg.de)
  • protein
  • Structural analysis of the protein suggests that Annexin VII is a membrane binding protein with diverse properties including voltage-sensitive calcium channel activity, ion selectivity and membrane fusion. (wikipedia.org)
  • This includes nucleotide and amino acid sequences, protein domains, and protein structures. (wikipedia.org)
  • For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (wikipedia.org)
  • Tiling arrays aid in transcriptome mapping as well as in discovering sites of DNA/protein interaction (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of sensitivity to DNase (DNase Chip) and array CGH. (wikipedia.org)
  • In addition, proteases recruited from remote sources like nearby tissues are ignored by these DNA based arrays, reiterating the need for protein based methods to confirm the presence and activity of functional enzymes when transcriptome analysis is performed. (wikipedia.org)
  • It also suffers from the same limitation of microarray analysis regarding the lack of correlation between transcript and protein levels. (wikipedia.org)
  • tissue samples
  • Genomic characterization of 51 MPNST tissue samples identified several frequently amplified regions harboring 2,599 genes and regions of deletion including 4,901 genes. (aacrjournals.org)
  • amplification
  • There is some amplification of the starting material so, in the end, approximately 1,000,000 sequence reads are obtained per experiment. (wikipedia.org)
  • Again, total RNA is extracted and used to generate cDNA for PCR amplification. (wikipedia.org)
  • PCR is not generally considered to be a recombinant DNA method, as it does not involve cutting and pasting DNA, only amplification of existing sequences. (wikipedia.org)
  • parallel
  • Fluorescent imaging captures the signal from all of the beads, while affixed to a 2-dimensional surface, so DNA sequences are determined from all the beads in parallel. (wikipedia.org)
  • Firstly, drug discovery in the last decades leading up to the 1990s had been limited due to the time and cost of running many chromatographic analyses in parallel on macroscopic equipment. (wikipedia.org)
  • mammalian
  • In the first step of the MICROB Enrich procedure, host-bacterial total RNA is incubated with an optimized mixture of capture oligonucleotides that bind to the mammalian 18S and 28S rRNAs and polyadenylated RNAs. (bio-medicine.org)