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  • genomic
  • Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. (springer.com)
  • TaqMan® Assays are considered the gold standard technology for quantitative gene expression analysis, and are also widely used for analysis of genomic DNA. (thermofisher.com)
  • 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)
  • Paired-end tags (PET) exist in PET libraries with the intervening DNA absent, that is, a PET "represents" a larger fragment of genomic or cDNA by consisting of a short 5' linker sequence, a short 5' sequence tag, a short 3' sequence tag, and a short 3' linker sequence. (wikipedia.org)
  • Fragmented genomic DNA or complementary DNA (cDNA) of interest is cloned into plasmid vectors. (wikipedia.org)
  • Instead of cloning, adaptors containing the endonuclease sequence are ligated to the ends of fragmented genomic DNA or cDNA. (wikipedia.org)
  • modulate
  • Our present study aimed to investigate the effects of recombinant TRAIL on the expression of SOCS1 , a gene known to modulate the sensitivity of both immune cells and pancreatic β-cells to key inflammatory cytokines elevated in diabetes ( 7 - 10 ), in peripheral blood mononuclear cells (PBMCs), and purified human pancreatic islets. (diabetesjournals.org)
  • The core auxin transcriptional response machinery drives the synthesis of proteins that modulate auxin dependent growth processes. (plantcell.org)
  • Through this process one can rapidly identify active compounds, antibodies, or genes that modulate a particular biomolecular pathway. (wikipedia.org)
  • binds
  • Auxin binds to the TRANSPORT INHIBITOR RESPONSE1 (TIR1) receptor or another auxin F-box (AFB) protein, which are E3-ubiquitin ligases that add ubiquitin tags to AUX/IAA transcriptional repressor proteins ( Chapman and Estelle, 2009 ). (plantcell.org)
  • It is a conserved nuclear protein that binds rapidly and directly to both single-strand and double-strand breaks. (aacrjournals.org)
  • mRNA
  • For proteases, specific probes for protease genes and their inhibitors have been developed to view expression patterns on the mRNA transcript level. (wikipedia.org)
  • A more sensitive approach to transcript analysis of a gene is quantitative real-time polymerase chain reaction (qRT-PCR), which has also seen action in quantifying protease mRNA levels. (wikipedia.org)
  • In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. (wikipedia.org)
  • The microRNAs thus generated are short RNA molecules that regulate a wide variety of other genes by interacting with the RNA-induced silencing complex (RISC) to induce cleavage of complementary messenger RNA (mRNA) as part of the RNA interference pathway. (wikipedia.org)
  • transcripts
  • 210,000 assays for human gene transcripts)-all designed using our validated bioinformatics pipeline. (thermofisher.com)
  • A pathway/functional analysis of celecoxib-affected transcripts, using Gene Ontology and Biocarta Pathways and exploring biological association networks, revealed that celecoxib modulates expression of numerous genes involved in a variety of cellular processes, including metabolism, cell proliferation, apoptotic signaling, cell cycle check points, lymphocyte activation, and signaling pathways. (aacrjournals.org)
  • Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid ( IAA ), partitioning into 60 clusters with distinct response kinetics. (plantcell.org)
  • Examples of alternative splicing in immunoglobin gene transcripts in mammals were also observed in the early 1980s. (wikipedia.org)
  • Peptide
  • It encodes a protein known as CGRP (calcitonin gene related peptide). (wikipedia.org)
  • Studies in rodents suggest that the full-length protein, secretogranin II, is involved in the packaging or sorting of peptide hormones and neuropeptides into secretory vesicles. (wikipedia.org)
  • The full-length protein is cleaved to produce the active peptide secretoneurin, which exerts chemotaxic effects on specific cell types, and EM66, whose function is unknown. (wikipedia.org)
  • molecules
  • 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)
  • The regulator of G protein signaling (RGS) proteins are signal transduction molecules that have structural homology to SST2 of Saccharomyces cerevisiae and EGL-10 of Caenorhabditis elegans. (wikipedia.org)
  • quantitative
  • the user specifies eigengene (principal component) of the expression data and treats it as a quantitative response SAM calculates a test statistic for relative difference in gene expression based on permutation analysis of expression data and calculates a false discovery rate. (wikipedia.org)
  • Either way, these assays use 10-500 times less sample input than traditional protein analysis methods (5-500 cells, or tissue lysate containing 1-100 ng total protein) and provide sensitive quantitative data in less than 4 hours. (thermofisher.com)
  • Quantitative microRNA analysis with state-of-the-art TaqMan® Assay performance, these assays are also available on 384-well TaqMan® Array Cards for profiling all microRNAs in the miRBase database. (thermofisher.com)
  • Altered expression of many of the genes by celecoxib was confirmed by quantitative PCR and at the protein level by Western blotting. (aacrjournals.org)
  • To determine the metabolism location of the extra-cellular matrix proteins in fugu (Takifugu rubripes), we cloned the cDNAs of the fugu gelatinases, matrix metalloproteinase-2 (MMP-2) and MMP-9, and examined their expressions in various adult tissues using a quantitative real-time PCR. (biomedsearch.com)
  • bioinformatics
  • Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. (booktopia.com.au)
  • Focusing on design, statistical inference, and data analysis from a Bayesian perspective, this volume explores statistical challenges in bioinformatics data analysis and modeling and offers solutions to these problems. (booktopia.com.au)
  • interactions
  • Molecular biology /məˈlɛkjʊlər/ concerns the molecular basis of biological activity between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, and proteins and their biosynthesis, as well as the regulation of these interactions. (wikipedia.org)
  • nuclear
  • BET proteins feature characteristic tandem N-terminal bromodomains that function to interact with N-acetyl lysine residues on histones and nuclear proteins ( 1-4 ). (aacrjournals.org)
  • Inhibition of PARP also affected activator protein-1 (AP-1) activation but not nuclear factor-κB (NF-κB). (aacrjournals.org)
  • Numerous intracellular signaling, including cytokines, mitogens, phorbol esters, growth factors, environmental, and ionizing radiation, converge with the activation of nuclear factor-κB (NF-κB) and activator protein-1 (AP-1), which act independently or coordinately to regulate expression of target genes. (aacrjournals.org)
  • Both processes activate the catalytic capacity of the enzyme, which in turn modulates the activity of a wide range of nuclear proteins by covalent attachment of branching chains of ADP-ribose moieties. (aacrjournals.org)
  • inhibits
  • The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. (wikipedia.org)
  • activators
  • Such proteins include splicing activators that promote the usage of a particular splice site, and splicing repressors that reduce the usage of a particular site. (wikipedia.org)
  • RGS proteins are involved in the regulation of heterotrimeric G proteins by acting as GTPase activators. (wikipedia.org)
  • transcriptome
  • 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)
  • patterns
  • Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. (springer.com)
  • A cDNA array representing 2927 unique genes based on a large EST (expressed sequence tag) database of M. grisea strain Y34 was constructed and used to profile the gene expression patterns at mycelium and appressorium maturation stages. (springer.com)
  • Gene Expression Patterns. (wikipedia.org)
  • Assays
  • We offer a wide array of simple and easy to use genetic analysis assays to meet the unique demands of translational and clinical research. (thermofisher.com)
  • More than 2,700 unique assays to detect polymorphisms in 221 genes that code for drug metabolism enzymes (DMEs) and drug transporters shown to significantly impact drug efficacy and toxicity. (thermofisher.com)
  • Detect and quantitate key mutations in targets including KRAS, BRAF, and EGFR genes, using assays from our expanding portfolio. (thermofisher.com)
  • TaqMan® PreAmp Pools can be constructed from individual TaqMan® Assays or purchased as a preconfigured pool in conjunction with a TaqMan® Array Card. (thermofisher.com)
  • Moreover, the transcriptional activity of hypoxia-inducible factor-1α (HIF-1α) was compromised by PARP inhibition or in PARP-1-deficient cells, as measured by gene reporter assays and the expression of key target genes for HIF-1α. (aacrjournals.org)
  • It is a 2D array on a solid substrate (usually a glass slide or silicon thin-film cell) that assays large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods. (wikipedia.org)
  • pathways
  • This study reveals that DENSPM potently activates the mitogen-activated protein kinase (MAPK) pathways in melanoma cells and investigates the role of this response in determining cellular outcomes. (aacrjournals.org)
  • Results from gene profiling studies (reported here) with SK-MEL-28 and MALME-3M cells have focused our attention on EGR-1 signaling and the upstream MAPK pathways. (aacrjournals.org)
  • Among these processes, cell proliferation and apoptotic signaling consistently ranked as the highest-scoring Gene Ontology terms and Biocarta Pathways in both COX-2 expresser and nonexpresser cell lines. (aacrjournals.org)
  • In particular, specific proteins and molecular pathways, affecting cell cycle progression and apoptosis, have been extensively studied and shown to be targeted by celecoxib ( 12 - 17 ). (aacrjournals.org)
  • Fusarium oxysporum G-protein beta subunit Fgbl regulates hyphal growth, development, and virulence through multiple signalling pathways. (springer.com)
  • Activation of the signaling pathways that mediate these responses causes profound and rapid increases in gene expression in well characterized gene families, including AUXIN/INDOLE-3-ACETIC ACID ( AUX/IAA ), GRETCHEN HAGEN3 ( GH3 ), and SMALL AUXIN UP-REGULATED ( SAUR ) families ( Chapman and Estelle, 2009 ). (plantcell.org)
  • chromosomal
  • It is a single copy gene that maps to 6q27, a region associated with human malignancies and chromosomal rearrangement. (wikipedia.org)
  • Transcript
  • The production of alternatively spliced mRNAs is regulated by a system of trans-acting proteins that bind to cis-acting sites on the primary transcript itself. (wikipedia.org)
  • Researchers found that the primary RNA transcript produced by adenovirus type 2 in the late phase was spliced in many different ways, resulting in mRNAs encoding different viral proteins. (wikipedia.org)
  • In 1981, the first example of alternative splicing in a transcript from a normal, endogenous gene was characterized. (wikipedia.org)
  • This gene consists of at least 13 exons and its alternative splicing generates at least 2 transcript variants. (wikipedia.org)
  • genetic
  • In some embodiments, the specimens may be tissue specimens from different tumors, which are subjected to multiple parallel molecular (including genetic and immunological) analyses. (google.com)
  • 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)
  • Other data suggested that sporadic or inherited genetic mutations in some critical genes regulating cell cycle, programmed cell death or differentiation and adhesion might be the actual cause of tumorigenesis. (pubmedcentralcanada.ca)
  • Genetic approaches have provided insight into the function of proteins that mediate auxin signaling and transcriptional responses. (plantcell.org)
  • The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being oversimplified, still provides a good starting point for understanding the field. (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)
  • In the future, in-depth work on selected genes will determine if these genes may serve as potential molecular targets for more effective chemopreventive strategies. (aacrjournals.org)
  • Analysis of gene expression profiles of appressorium development provides insight into the molecular basis of pathogenicity and control of this fungal plant disease. (springer.com)
  • In the early 2000s, the study of gene structure and function, molecular genetics, has been among the most prominent sub-fields of molecular biology. (wikipedia.org)
  • citation needed] One of the most basic techniques of molecular biology to study protein function is molecular cloning. (wikipedia.org)
  • regulatory
  • Poly(ADP-ribose) polymerase (PARP)-1, an enzyme that catalyzes the attachment of ADP ribose to target proteins, acts as a component of enhancer/promoter regulatory complexes. (aacrjournals.org)
  • This protein, together with X11L, may play an important role in the regulatory system of amyloid precursor protein metabolism and beta-amyloid generation. (wikipedia.org)
  • HUMAN
  • The protein encoded by this gene is a member of a family of human VCX/Y genes. (genecards.org)
  • RESEARCH DESIGN AND METHODS Recombinant TRAIL was added in vitro to primary human and mouse peripheral blood mononuclear cells (PBMCs) and isolated human islets to evaluate the expression of the immunoregulatory gene SOCS1 . (diabetesjournals.org)
  • Rapid, simple analysis of copy number variations (CNVs) in human genomes. (thermofisher.com)
  • FZD10 protein, human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from the United States National Library of Medicine, which is in the public domain. (wikipedia.org)
  • RRP1B (ribosomal RNA processing 1 homolog B), also known as KIAA0179, is a human gene which is located on Chromosome 21. (wikipedia.org)
  • The other two human enzymes that participate in the processing and activity of miRNA are the Dicer and Argonaute proteins. (wikipedia.org)
  • Human NECAB3 genome location and NECAB3 gene details page in the UCSC Genome Browser. (wikipedia.org)
  • transcriptional
  • First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. (springer.com)
  • cell
  • The sources of exposure include cell phones and their base stations (towers, masts and simply antennas), bluetooth, blackberry, wireless computer networks at work, schools and homes, cordless phones in most homes, even wireless baby monitors and a whole array of new products coming into the market everyday that may or may not be apparent in their wirelessness. (freewebs.com)
  • Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. (plantcell.org)
  • Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA -regulated root growth and development. (plantcell.org)
  • The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development. (plantcell.org)
  • The protein encoded by this gene is only expressed in the S and G2 phases of the cell cycle, where it colocalizes with cytoplasmic tubulin and microtubules. (wikipedia.org)
  • DNA coding for a protein of interest is now inside a cell, and the protein can now be expressed. (wikipedia.org)
  • A variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. (wikipedia.org)
  • Genomics
  • He is known for his research in the area of plant genomics and biotechnology, particularly for his contribution in the decoding of rice, tomato and pigeonpea genomes and understanding of wheat seed storage proteins and their effect on wheat quality. (wikipedia.org)
  • Sequences
  • These displaying phages can then be screened against other proteins, peptides or DNA sequences, in order to detect interaction between the displayed protein and those other molecules. (wikipedia.org)
  • Applications of phage display technology include determination of interaction partners of a protein (which would be used as the immobilised phage "bait" with a DNA library consisting of all coding sequences of a cell, tissue or organism) so that the function or the mechanism of the function of that protein may be determined. (wikipedia.org)
  • Instead of probing for sequences of known or predicted genes that may be dispersed throughout the genome, tiling arrays probe intensively for sequences which are known to exist in a contiguous region. (wikipedia.org)
  • In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible. (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)
  • isolated the lin-4 gene, they found that instead of producing an mRNA encoding a protein, it produced short non-coding RNAs, one of which was a ~22-nucleotide RNA that contained sequences partially complementary to multiple sequences in the 3' UTR of the lin-14 mRNA. (wikipedia.org)
  • In rat hepatic cells, LIMP-2 exhibited a half-life for internalization and lysosomal transport of 32 min and 2.0 h, respectively, which resembled that of well-known lysosomal proteins, lamp-1 and lamp-2, albeit different amino acid sequences in their cytoplasmic tails. (wikipedia.org)
  • Cloning
  • Multiple cloning sites are sometimes used to ensure that the fragments are inserted in all three possible reading frames so that the cDNA fragment is translated in the proper frame. (wikipedia.org)
  • Peptides
  • Phage display was first described by George P. Smith in 1985, when he demonstrated the display of peptides on filamentous phage by fusing the peptide of interest onto gene III of filamentous phage. (wikipedia.org)
  • biochemical
  • Biochemical and immunohistochemical analyses discovered that LIMP-2 interacts with N-cadherin at intercalated discs, a function outside of lysosomal membranes. (wikipedia.org)
  • sequence
  • GO annotations related to this gene include sequence-specific DNA binding and RNA polymerase II repressing transcription factor binding . (genecards.org)
  • Phage eluted in the final step can be used to infect a suitable bacterial host, from which the phagemids can be collected and the relevant DNA sequence excised and sequenced to identify the relevant, interacting proteins or protein fragments. (wikipedia.org)
  • Further analysis narrowed the site to syndecan-1's N-terminal 51 amino acids, and subsequently to the N-terminal sequence GAGAL that is conserved in syndecan-1's from different species. (wikipedia.org)
  • GC-rich sequence DNA-binding factor homolog is a protein that in humans is encoded by the PAXBP1 gene. (wikipedia.org)
  • These genes have an intron immediately upstream of the initiator Met codon, which separates the site of transcription initiation from protein coding sequence. (wikipedia.org)
  • The alleles of this gene exhibit an unusual amount of sequence variation, such that the alleles were once thought to represent two separate genes, beta II and beta III. (wikipedia.org)
  • vectors
  • Genetic combinatorial marking using lentiviral vectors encoding fluorescent proteins (FPs) enabled cell fate mapping through advanced microscopy imaging. (jove.com)
  • amino
  • In HIV, a synthetic peptide corresponding to the immunosuppressive domain (amino acids 574-592) of HIV-1 gp41 downregulates the expression of fatty acid binding protein 3 (FABP3) in peptide-treated PBMCs. (wikipedia.org)
  • The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. (wikipedia.org)
  • putative
  • There are both heterochromatin and euchromatin structures within D4Z4 and one putative gene called DUX4. (wikipedia.org)
  • human
  • This gene is also a candidate tumor suppressor gene for human breast cancer. (wikipedia.org)
  • Human NECAB3 genome location and NECAB3 gene details page in the UCSC Genome Browser. (wikipedia.org)
  • WAP four-disulfide core domain protein 2 - also known as Human Epididymis Protein 4 (HE4) - is a protein that in humans is encoded by the WFDC2 gene. (wikipedia.org)
  • FZD10 protein, human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from the United States National Library of Medicine, which is in the public domain. (wikipedia.org)
  • The human genome may encode over 1000 miRNAs, which are abundant in many mammalian cell types and appear to target about 60% of the genes of humans and other mammals. (wikipedia.org)
  • The weight discrepancy between its theoretical (54.3 kDa) and observed (85 kDa) is due to the presence of 10 high mannose-type N-linked oligosaccharide chains in the human form of this protein, compared to 11 in mouse and rat. (wikipedia.org)
  • Out of 143 differentially-regulated genes, LIMP-2 was identified to be significantly upregulated in heart failure-prone rat cardiac muscle biopsies, which also proved true in human heart failure. (wikipedia.org)
  • Targets
  • By immobilizing a relevant DNA or protein target(s) to the surface of a microtiter plate well, a phage that displays a protein that binds to one of those targets on its surface will remain while others are removed by washing. (wikipedia.org)
  • For example, an analysis of the miRNAs highly conserved in vertebrates shows that each has, on average, roughly 400 conserved targets. (wikipedia.org)
  • Genetic
  • The second mechanism is a "toxic gain of function" of the DUX4 gene, which is the first time in genetic research that a "dead gene" has been found to "wake up" and cause disease. (wikipedia.org)
  • On 19 August 2010, a paper entitled A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy was published in Science showing that the candidate gene DUX4 undergoes a "toxic gain of function" as a result of single nucleotide polymorphisms in the region distal to the last D4Z4 repeat. (wikipedia.org)
  • qPCR
  • While RT-PCR is used to qualitatively detect gene expression through creation of complementary DNA (cDNA) transcripts from RNA, qPCR is used to quantitatively measure the amplification of DNA using fluorescent dyes. (wikipedia.org)
  • In addition to the qualitative study of gene expression, quantitative PCR can be utilized for quantification of RNA, in both relative and absolute terms, by incorporating qPCR into the technique. (wikipedia.org)
  • genomes
  • He has also made significant advances in comparative analysis of rice and wheat genomes and mapping of genes for salt tolerance and basmati quality traits in rice. (wikipedia.org)
  • transcript variants
  • These DNA primer pairs were designed by prioritizing the gene regions most commonly found in transcript variants. (bio-rad.com)
  • Multiple transcript variants encoding several different isoforms have been found for this gene. (wikipedia.org)
  • At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues. (wikipedia.org)
  • Alternative splicing of this gene results in three transcript variants encoding different isoforms. (wikipedia.org)
  • primers
  • The selected pathways were used to design panels of real-time PCR primers tailored for the top-ranked genes for differential gene expression analysis. (bio-rad.com)
  • To streamline reference gene selection, we offer PCR primers for a set of commonly used reference genes that can be used individually, easily screened using our preplated 96-well and 384-well reference panels or added to custom-designed plates. (bio-rad.com)
  • Gene-specific PCR primers for the unbiased preamplification of small quantities of cDNA for subsequent use in downstream gene expression analysis. (bio-rad.com)
  • reveal
  • Volumetric analyses over large areas reveal that spectrally coded HSPC-derived cells can be detected non-invasively in various intact tissues, including the bone marrow (BM), for extensive periods of time following transplantation. (jove.com)