Consensus Sequence
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Base Sequence
Consensus
Amino Acid Sequence
Promoter Regions, Genetic
Binding Sites
Cloning, Molecular
Transcription, Genetic
Sequence Homology, Nucleic Acid
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Sequence Homology, Amino Acid
DNA-Binding Proteins
Transcription Factors
Consensus Development Conferences as Topic
Presentations of summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus--often with findings and recommendations--on a subject of interest. The Conference, consisting of participants representing the scientific and lay viewpoints, is a significant means of evaluating current medical thought and reflects the latest advances in research for the respective field being addressed.
Sequence Analysis, DNA
Plasmids
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Protein Binding
Restriction Mapping
Regulatory Sequences, Nucleic Acid
Mutagenesis, Site-Directed
Mutation
Introns
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Interferon Regulatory Factors
A family of transcription factors that share an N-terminal HELIX-TURN-HELIX MOTIF and bind INTERFERON-inducible promoters to control GENE expression. IRF proteins bind specific DNA sequences such as interferon-stimulated response elements, interferon regulatory elements, and the interferon consensus sequence.
DNA Primers
Genes
Gene Expression Regulation
DNA, Complementary
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Recombinant Fusion Proteins
Repressor Proteins
Conserved Sequence
Transfection
Exons
Oligodeoxyribonucleotides
RNA Splicing
Nucleic Acid Conformation
Gene Expression Regulation, Bacterial
Operon
Amino Acid Motifs
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Enhancer Elements, Genetic
Substrate Specificity
Saccharomyces cerevisiae
Gene Library
Nuclear Proteins
Genes, Regulator
Chloramphenicol O-Acetyltransferase
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.
Delphi Technique
Sequence Analysis
Chromosome Mapping
HeLa Cells
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Models, Molecular
Response Elements
DNA Footprinting
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Oligonucleotide Probes
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Deoxyribonuclease I
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Phosphorylation
Open Reading Frames
Trans-Activators
Zinc Fingers
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Carrier Proteins
Glycosylation
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Transcriptional Activation
Genes, Reporter
Structure-Activity Relationship
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Sp1 Transcription Factor
Point Mutation
Blotting, Northern
Blotting, Southern
Furin
Peptide Fragments
Mutagenesis
Genomic Library
Oligonucleotides
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
RNA Precursors
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Cell Nucleus
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Gene Expression
Evolution, Molecular
Peptide Library
RNA Splice Sites
Cells, Cultured
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Interferon Regulatory Factor-2
TATA Box
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Protein Biosynthesis
Gene Expression Regulation, Enzymologic
Binding, Competitive
Software
Tumor Cells, Cultured
Alternative Splicing
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Membrane Proteins
Electrophoresis, Polyacrylamide Gel
Algorithms
Cricetinae
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
RNA-Binding Proteins
Consensus Development Conferences, NIH as Topic
Articles on conferences sponsored by NIH presenting summary statements representing the majority agreement of physicians, scientists, and other professionals convening for the purpose of reaching a consensus on a subject of interest. This heading is used for NIH consensus conferences as a means of scientific communication. In indexing it is viewed as a type of review article and as a tag for any article appearing in any publication of the NIH Office of Medical Applications of Research (OMAR).
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Protein Structure, Secondary
Sigma Factor
DNA Probes
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Expressed Sequence Tags
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
beta-Galactosidase
5' Untranslated Regions
Chickens
Saccharomyces cerevisiae Proteins
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Serine
Models, Genetic
Cattle
Regulon
Transcription Initiation Site
Interferon Regulatory Factor-1
Lorisidae
A family of Primates of the suborder Strepsirhini containing six genera. The family is distributed in parts of Africa, India, Asia, and the Philippines. The six genera are: Arctocebus (golden potto), GALAGO (bush babies), Loris (slender loris), Nycticebus (slow loris), and Perodicticus (potto). Lorises and pottos are relatively common except for Arctocebus, the golden potto. All are arboreal and nocturnal.
Organ Specificity
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
DNA, Recombinant
RNA, Small Nuclear
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
Luciferases
Reverse Transcriptase Polymerase Chain Reaction
Blotting, Western
Sequence Analysis, Protein
5' Flanking Region
Peptide Mapping
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Mutagenesis, Insertional
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
DNA, Satellite
Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.
Heat-Shock Proteins
Contig Mapping
Replication Origin
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Genetic Complementation Test
3T3 Cells
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
Integration Host Factors
Genetic Vectors
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Proto-Oncogene Proteins
Sequence Homology
Signal Transduction
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Short Interspersed Nucleotide Elements
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
CHO Cells
Macromolecular Substances
Protein Kinases
Operator Regions, Genetic
RNA, Bacterial
Poly A
Gene Deletion
Precipitin Tests
Chromatin Immunoprecipitation
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
Drosophila melanogaster
Protein Sorting Signals
Transcription Factor AP-1
Lac Operon
Proline
Phenotype
COS Cells
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Concomitant activation of pathways downstream of Grb2 and PI 3-kinase is required for MET-mediated metastasis. (1/4818)
The Met tyrosine kinase - the HGF receptor - induces cell transformation and metastasis when constitutively activated. Met signaling is mediated by phosphorylation of two carboxy-terminal tyrosines which act as docking sites for a number of SH2-containing molecules. These include Grb2 and p85 which couple the receptor, respectively, with Ras and PI 3-kinase. We previously showed that a Met mutant designed to obtain preferential coupling with Grb2 (Met2xGrb2) is permissive for motility, increases transformation, but - surprisingly - is impaired in causing invasion and metastasis. In this work we used Met mutants optimized for binding either p85 alone (Met2xPI3K) or p85 and Grb2 (MetPI3K/Grb2) to evaluate the relative importance of Ras and PI 3-kinase as downstream effectors of Met. Met2xPI3K was competent in eliciting motility, but not transformation, invasion, or metastasis. Conversely, MetP13K/Grb2 induced motility, transformation, invasion and metastasis as efficiently as wild type Met. Furthermore, the expression of constitutively active PI 3-kinase in cells transformed by the Met2xGrb2 mutant, fully rescued their ability to invade and metastasize. These data point to a central role for PI 3-kinase in Met-mediated invasiveness, and indicate that simultaneous activation of Ras and PI 3-kinase is required to unleash the Met metastatic potential. (+info)ATF-2-binding regulatory element is responsible for the Ly49A expression in murine T lymphoid line, EL-4. (2/4818)
To understand the mechanism of Ly49A-expression and its significance in T-cell differentiation, we analyzed the 5'-flanking region of the Ly49A gene in a search for the Ly49A-regulatory element. Since very few known regulatory elements have been found in this region, presumably a novel regulatory sequence(s) could exist. Accordingly, we defined the 13-bp regulatory element, 5'-ATGACGAGGAGGA-3', restricted to Ly49A-expression in EL-4 cells in comparison with two other representative cell lines tested. This element, designated as EL13, proved to be previously undiscovered by homology search and is highly homologous with several virus DNAs. Using EL13 as a probe we have cloned a cDNA encoding a binding protein to EL13. Its deduced nucleotide sequence revealed that EL13-binding protein is almost identical with rat ATF-2. Although ATF-2 is known to bind to cyclic AMP responsive element (CRE), EL13 shares five out of eight nucleotides with this consensus sequence. Our results suggested that ATF-2 may play an important role via binding to EL13 for the expression of Ly49A. These data will provide useful information for understanding T-cell and NK-cell differentiation in murine immune system. (+info)Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. (3/4818)
The expression of a luciferase reporter gene under the control of the human glucose 6-phosphatase gene promoter was stimulated by both dexamethasone and dibutyryl cAMP in H4IIE hepatoma cells. A cis-active element located between nucleotides -161 and -152 in the glucose 6-phosphatase gene promoter was identified and found to be necessary for both basal reporter-gene expression and induction of expression by both dibutyryl cAMP and dexamethasone. Nucleotides -161 to -152 were functionally replaced by the consensus sequence for a cAMP response element. An antibody against the cAMP response element-binding protein caused a supershift in gel-electrophoretic-mobility-shift assays using an oligonucleotide probe representing the glucose 6-phosphatase gene promoter from nucleotides -161 to -152. These results strongly indicate that in H4IIE cells the glucose 6-phosphatase gene-promoter sequence from -161 to -152 is a cAMP response element which is important for the regulation of transcription of the glucose 6-phosphatase gene by both cAMP and glucocorticoids. (+info)Analysis of 4-phosphopantetheinylation of polyhydroxybutyrate synthase from Ralstonia eutropha: generation of beta-alanine auxotrophic Tn5 mutants and cloning of the panD gene region. (4/4818)
The postulated posttranslational modification of the polyhydroxybutyrate (PHA) synthase from Ralstonia eutropha by 4-phosphopantetheine was investigated. Four beta-alanine auxotrophic Tn5-induced mutants of R. eutropha HF39 were isolated, and two insertions were mapped in an open reading frame with strong similarity to the panD gene from Escherichia coli, encoding L-aspartate-1-decarboxylase (EC 4.1.1.15), whereas two other insertions were mapped in an open reading frame (ORF) with strong similarity to the NAD(P)+ transhydrogenase (EC 1.6.1.1) alpha 1 subunit, encoded by the pntAA gene from Escherichia coli. The panD gene was cloned by complementation of the panD mutant of R. eutropha Q20. DNA sequencing of the panD gene region (3,312 bp) revealed an ORF of 365 bp, encoding a protein with 63 and 67% amino acid sequence similarity to PanD from E. coli and Bacillus subtilis, respectively. Subcloning of only this ORF into vectors pBBR1MCS-3 and pBluescript KS- led to complementation of the panD mutants of R. eutropha and E. coli SJ16, respectively. panD-encoded L-aspartate-1-decarboxylase was further confirmed by an enzymatic assay. Upstream of panD, an ORF with strong similarity to pntAA from E. coli, encoding NAD(P)+ transhydrogenase subunit alpha 1 was found; downstream of panD, two ORFs with strong similarity to pntAB and pntB, encoding subunits alpha 2 and beta of the NAD(P)+ transhydrogenase, respectively, were identified. Thus, a hitherto undetermined organization of pan and pnt genes was found in R. eutropha. Labeling experiments using one of the R. eutropha panD mutants and [2-14C]beta-alanine provided no evidence that R. eutropha PHA synthase is covalently modified by posttranslational attachment of 4-phosphopantetheine, nor did the E. coli panD mutant exhibit detectable labeling of functional PHA synthase from R. eutropha. (+info)An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (5/4818)
Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus. (+info)Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. (6/4818)
The complete 184,457-bp sequence of the aromatic catabolic plasmid, pNL1, from Sphingomonas aromaticivorans F199 has been determined. A total of 186 open reading frames (ORFs) are predicted to encode proteins, of which 79 are likely directly associated with catabolism or transport of aromatic compounds. Genes that encode enzymes associated with the degradation of biphenyl, naphthalene, m-xylene, and p-cresol are predicted to be distributed among 15 gene clusters. The unusual coclustering of genes associated with different pathways appears to have evolved in response to similarities in biochemical mechanisms required for the degradation of intermediates in different pathways. A putative efflux pump and several hypothetical membrane-associated proteins were identified and predicted to be involved in the transport of aromatic compounds and/or intermediates in catabolism across the cell wall. Several genes associated with integration and recombination, including two group II intron-associated maturases, were identified in the replication region, suggesting that pNL1 is able to undergo integration and excision events with the chromosome and/or other portions of the plasmid. Conjugative transfer of pNL1 to another Sphingomonas sp. was demonstrated, and genes associated with this function were found in two large clusters. Approximately one-third of the ORFs (59 of them) have no obvious homology to known genes. (+info)A binding site for homeodomain and Pax proteins is necessary for L1 cell adhesion molecule gene expression by Pax-6 and bone morphogenetic proteins. (7/4818)
The cell adhesion molecule L1 regulates axonal guidance and fasciculation during development. We previously identified the regulatory region of the L1 gene and showed that it was sufficient for establishing the neural pattern of L1 expression in transgenic mice. In the present study, we characterize a DNA element within this region called the HPD that contains binding motifs for both homeodomain and Pax proteins and responds to signals from bone morphogenetic proteins (BMPs). An ATTA sequence within the core of the HPD was required for binding to the homeodomain protein Barx2 while a separate paired domain recognition motif was necessary for binding to Pax-6. In cellular transfection experiments, L1-luciferase reporter constructs containing the HPD were activated an average of 4-fold by Pax-6 in N2A cells and 5-fold by BMP-2 and BMP-4 in Ng108 cells. Both of these responses were eliminated on deletion of the HPD from L1 constructs. In transgenic mice, deletion of the HPD from an L1-lacZ reporter resulted in a loss of beta-galactosidase expression in the telencephalon and mesencephalon. Collectively, our experiments indicate that the HPD regulates L1 expression in neural tissues via homeodomain and Pax proteins and is likely to be a target of BMP signaling during development. (+info)Functional analysis of the promoter of the yeast SNQ2 gene encoding a multidrug resistance transporter that confers the resistance to 4-nitroquinoline N-oxide. (8/4818)
The yeast gene SNQ2, which encodes a multidrug resistance ABC superfamily protein, is required for resistance to the mutagen 4-nitroquinoline N-oxide (4-NQO). The expression of the SNQ2 gene is under the control of a regulatory network that involves the transcription factor Yrr1p, as well as Pdr1p/Pdr3p (Cui et al., Mol. Microbiol., 29, 1307-1315 (1998)). By 5'-deletion analysis of the promoter by using SNQ2-lacZ fusion constructs, four regions: -745 to -639 (region I), -639 to -578 (region II), -548 to -533 (region III) and -533 to -485 (region IV) were found to be important for SNQ2 expression. Genetic analysis suggested that the site in region IV was responsible for the Yrr1p-mediated SNQ2 expression. A consensus motif known for the binding of Pdr1p/Pdr3p (PDRE) was not found in region IV. (+info)
NIOSHTIC-2 Publications Search - 20038418 - A novel mechanism for p53 to regulate its target gene ECK in signaling apoptosis.
Radiolabeling of Subtracted cDNA Probes by Random Oligonucleotide Extension
The Natural Complexity of Patent Eligibility - Iowa Law Review - The University of Iowa College of Law
release history
release history
Synthesis of cDNA Probes from mRNA Using Random Oligonucleotide Primers
blockchain - New params of chainparams.cpp. What put on them and how generate? - Bitcoin Stack Exchange
cluster # 2681
20284 (consensus weight case 2b3 does not follow dir-spec)
- Tor Bug Tracker & Wiki
How to Build Consensus in a Collaboration Team | UniversalClass
Bio-software] Software for aligning abi trace files
On the Misgivings of Anthropomorphic Consensus Polling in Defining the Complexity of Life
Wider-than-Expected Q3 Loss at Alnylam
PEDIATRIC ANIMAL MODEL OF GROWTH RETARDATION IN AIDS - UC Davis
Kozak consensus sequence - Wikipedia
Author Search Results
Virus mystery homepage
Virus mystery homepage
OPENSEQ.org - FTSW RODA SPOVE - Pfam Coevolution Predictions
BIP 0123 - Bitcoin Wiki
CCDS Report for Consensus CDS
CCDS Report for Consensus CDS
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination - Page 2
Bitcoin Blasts Through $15,000 - Its A Consensus Hallucination - Page 3
What the critics wrote about the Beatles in 1964 - Daily Press
Secondary structure prediction and consensus sequence o | Open-i
Protein consensus sequence motifs | SpringerLink
Whole-genome consensus sequence analysis of a South African rotavirus SA11 sample reveals a mixed infection with two close...
Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus...
Zinc finger and BTB domain-containing protein 4
P16-13. A greater breadth of HIV-1-specific T cell responses detected using mosaic peptides compare to consensus peptides -...
Hella Heaven: There is no such thing as consensus science Michael Crichton
in-vitro systems
ArchDB - Biological DataBase of Protein Loops
The Markets Assessment of the Probability of Meeting or Beating the Consensus by Guang Ma, Stanimir Markov :: SSRN
Cel-Sci Corporation - Consensus Indicates Potential 62.4% Upside
Copenhagen Consensus: Whats more important, growing more food or controlling the world population?
HP Q1 adj. EPS 92 cents vs. 65 cents a year ago; FactSet consensus 66 cents - The 2020 Bubble - The Year The World Popped
Italys Two Options: Hardball or Consensus
False consensus effect 彙整 - 體驗冒險的職涯實驗室 - Experiencing Experimental Career Lab.
Smo9 project
Interferon regulatory factor 8/interferon consensus sequence binding protein is a critical transcription factor for the...
Rabbit anti IRF8 Antibody (Cross) | Bio-Rad
Characterization of a functionally important and evolutionarily well-conserved epitope mapped to the short consensus repeats of...
Leader-Following Consensus of Linear Multiagent Systems with State Observer under Switching Topologies
BSORF Gene Entry : BG10678
254780372
Consensus Decision Making - ReadWriteThink
No Frakking Consensus: Pachauris Latest Award: Can You Say Conflict-of-Interest?
About myself - Uffe Ravnskov
Narrower-than-Expected Loss at Curis
Consensus sequence
... can also be considered as consensus sequences. Thus a consensus sequence is a model for a putative DNA binding site: it is ... The conserved sequence motifs are called consensus sequences and they show which residues are conserved and which residues are ... Any mutation allowing a mutated nucleotide in the core promoter sequence to look more like the consensus sequence is known as ... A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several ...
Kozak consensus sequence
The Kozak consensus sequence is so common that the similarity of the sequence around the AUG codon to the Kozak Sequence is ... The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein ... Kozak discovered the sequence through a detailed analysis of DNA genomic sequences. The Kozak sequence is not to be confused ... Kozak sequence, and leaderless initiation. Haloarchaea are known to have a variant of the Kozak consensus sequence in their ...
DNA binding site
... restriction sites can be generally represented by consensus sequences. This is because they target mostly identical sequences ... This makes it difficult to accurately represent transcription factor binding sites using consensus sequences, and they are ... Schneider T.D. (2002). "Consensus sequence Zen". Applied Bioinformatics. 1 (3): 111-119. PMC 1852464. PMID 15130839. Bulyk M.L ... can be represented by a consensus sequence. This representation has the advantage of being compact, but at the expense of ...
Sequence motif
... and T for each row should be equal because the PFM is derived from aggregating several consensus sequences. The sequence motif ... Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence ... a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be ... See also consensus sequence. Consider the N-glycosylation site motif mentioned above: Asn, followed by anything but Pro, ...
Consensus CDS Project
A common start site is defined within Kozak consensus sequence: (GCC) GCCACCAUGG in vertebrates. The sequence in brackets (GCC ... Exact nucleotide sequence and protein sequence of the specific coding sequence are also displayed in the section of CCDS ... The Consensus Coding Sequence (CCDS) Project is a collaborative effort to maintain a dataset of protein-coding regions that are ... There are variations within Kozak consensus sequence, such as G or A is observed three nucleotides upstream (at position -3) of ...
Glossary of genetics (0-L)
canonical sequence See consensus sequence. carboxyl terminus See C-terminus. carrier An individual who has inherited a ... insertion sequence (IS) Any nucleotide sequence that is inserted naturally or artificially into another sequence. The term is ... consensus sequence A calculated order of the most frequent residues (of either nucleotides or amino acids) found at each ... in-frame 1. (of a gene or sequence) Read or transcribed in the same reading frame as another gene or sequence; not requiring a ...
Collagen, type III, alpha 1
"Report for CCDS2297.1". Consensus Coding Sequence (CDS) Database. National Center for Biotechnology Information (NCBI). Byers, ... June 1993). "Sequencing of cDNA from 50 unrelated patients reveals that mutations in the triple-helical domain of type III ... This (Gly-X-Y)n sequence is repeated 343 times in the type III collagen molecule. Proline or hydroxyproline is often found in ... June 2015). "Vascular Ehlers-Danlos Syndrome in siblings with biallelic COL3A1 sequence variants and marked clinical ...
Colin Dingwall
Nuclear targeting sequences-a consensus?. Trends in biochemical sciences. 1991 Jan 1;16:478-81. According to Google Scholar, ... Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences--a consensus?". Trends in Biochemical Sciences. 16 (12): ... Detailed mapping of the sequence in nucleoplasmin revealed a longer sequence motif within which two domains of basic amino ... nuclear localization sequence has emerged as the major nuclear localization sequence in cellular proteins and the sequence ...
SV40 large T antigen
Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences - a consensus?". Trends Biochem. Sci. 16 (12): 478-81. doi: ... Glu sequence, nor in the positions immediately flanking this sequence. The pRb-binding motif and negatively charged region ... The NLS sequence is PKKKRKV. SV40 large TAg, other polyomavirus large T antigens, adenovirus E1a proteins, and oncogenic human ... Figge J, Smith TF (14 July 1988). "Cell division sequence motif". Nature. 334 (6178): 109. doi:10.1038/334109a0. PMID 3290690. ...
Nuclear localization sequence
proposed the consensus sequence K-K/R-X-K/R for monopartite NLSs. A Chelsky sequence may, therefore, be part of the downstream ... Dingwall C, Laskey RA (December 1991). "Nuclear targeting sequences--a consensus?". Trends in Biochemical Sciences. 16 (12): ... A nuclear localization signal or sequence (NLS) is an amino acid sequence that 'tags' a protein for import into the cell ... The first NLS to be discovered was the sequence PKKKRKV in the SV40 Large T-antigen (a monopartite NLS). The NLS of ...
Glossary of genetics
canonical sequence See consensus sequence. carboxyl terminus See C-terminus. carrier An individual who has inherited a ... sequence See nucleic acid sequence. sequence-tagged site (STS) Any DNA sequence that occurs exactly once within a particular ... palindromic sequence A nucleic acid sequence of a double-stranded DNA or RNA molecule in which the unidirectional sequence (e.g ... Sanger sequencing A method of DNA sequencing based on the in vitro replication of a DNA template sequence, during which ...
GLIS1
It has the consensus sequence GACCACCCAC. The individual zinc finger motifs are separated from one another by the amino acid ... to interact with target DNA sequences to regulate gene transcription. The domain interacts sequence specifically with the DNA, ... The protein's termini are fairly unusual, and have no strong sequence similarity other proteins. Glis1 can be used as one of ... a change in a single nucleotide of the DNA sequence of the gene, has been implicated as a risk factor in the neurodegenerative ...
Circular chromosome
B) The consensus sequence of Ter. [3] The Ter sites specifically interact with the replication terminator protein called Tus in ... a 9-mer repeat with a highly conserved consensus sequence 5' - TTATCCACA - 3', that are recognized by the DnaA protein. DnaA ... Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52 ... The E. coli bacterial replication origin, called oriC consists of DNA sequences that are recognised by the DnaA protein, which ...
Short Oligonucleotide Analysis Package
SOAPsnp is a consensus sequence builder. This tool uses the output from SOAPaligner to generate a consensus sequence which ... and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data. All programs in ... 2009). "The sequence and de novo assembly of the giant panda genome". Nature. 463 (7279): 311-317. doi:10.1038/nature08696. ... The first release of SOAP consisted only of the sequence alignment tool SOAPaligner. SOAP v2 extended and improved on SOAP v1 ...
Nucleic acid structure prediction
The quality of the alignment determines the accuracy of the consensus structure model. Consensus sequences are folded using ... Chiu D.K.; Kolodziejczak T. (1991). "Inferring consensus structure from nucleic acid sequences". Comput. Appl. Biosci. 7 (3): ... Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but ... A less widely used approach is to fold the sequences using single sequence structure prediction methods and align the resulting ...
Duplex sequencing
... single-strand consensus sequences (SSCS) and duplex consensus sequences (DCS) assembly. Duplex sequencing theoretically can ... A consensus sequence is then generated for each family using the identical sequences in each position of the remaining reads. ... The remaining reads are assembled to consensus sequences using SSCS and DCS assemblies. Trimmed sequences from the previous ... The consensus sequence is called the SSCS. It increases the NGS accuracy to about 20 fold higher; however, this method relies ...
Shine-Dalgarno sequence
... terminal 16S rRNA sequence can restore translation. Kozak consensus sequence, the sequence that targets the ribosome to the ... The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while the shorter GAGG ... Given the complementary relationship between rRNA and the Shine-Dalgarno sequence in mRNA, it was proposed that the sequence at ... The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome ...
Expressed sequence tag
Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W (Jan 2001). "STACK: Sequence Tag Alignment and Consensus ... In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene ... Because of the way ESTs are sequenced, many distinct expressed sequence tags are often partial sequences that correspond to the ... Alternatively, if the genome of the organism that originated the EST has been sequenced, one can align the EST sequence to that ...
ChIL-sequencing
SELEX: Employed to determine consensus binding sequences. Competition-ChIP: Measures relative replacement dynamics on DNA. ... ChIL sequencing (ChIL-seq), also known as Chromatin Integration Labeling sequencing, is a method used to analyze protein ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ... ChIL-sequencing combines antibody-targeted controlled cleavage by Tn5 transposase with massively parallel DNA sequencing to ...
CUT&Tag sequencing
SELEX: Employed to determine consensus binding sequences. Competition-ChIP: Measures relative replacement dynamics on DNA. ... Sensitivity of sequencing depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ... The data is then collected and analyzed using software that aligns sample sequences to a known genomic sequence to identify the ...
Alternative splicing
... the consensus around this sequence varies somewhat. In humans the branch site consensus sequence is yUnAy. The branch site is ... The typical eukaryotic nuclear intron has consensus sequences defining important regions. Each intron has the sequence GU at ... The intron upstream from exon 4 has a polypyrimidine tract that doesn't match the consensus sequence well, so that U2AF ... Gao K, Masuda A, Matsuura T, Ohno K (April 2008). "Human branch point consensus sequence is yUnAy". Nucleic Acids Research. 36 ...
CUT&RUN sequencing
SELEX: Employed to determine consensus binding sequences. Competition-ChIP: Measures relative replacement dynamics on DNA. ... Sensitivity of sequencing depends on the depth of the sequencing run (i.e. the number of mapped sequence tags), the size of the ... Sequencing of prepared DNA libraries and comparison to whole-genome sequence databases allows researchers to analyze the ... The data is then collected and analyzed using software that aligns sample sequences to a known genomic sequence to identify the ...
Richard M. Durbin
Eddy, S. R.; Mitchison, G; Durbin, R (1995). "Maximum discrimination hidden Markov models of sequence consensus". Journal of ... c. Elegans Sequencing, C. (1998). "Genome sequence of the nematode C. Elegans: A platform for investigating biology". Science. ... More recently Durbin has returned to sequencing and has developed low coverage approaches to population genome sequencing, ... Birney, Ewan (2000). Sequence alignment in bioinformatics. cam.ac.uk (PhD thesis). University of Cambridge. OCLC 894597337. ...
Protein methylation
Nevertheless, PRMTs with non-GAR consensus sequences exist. PRMTs are present in the nucleus as well as in the cytoplasm. In ... Proteins containing the consensus motif H2N-X-Pro-Lys- (where X can be Ala, Pro or Ser) after removal of the initiator ...
Ras GTPase
The G5 motif contains a SAK consensus sequence. The A is alanine146, which provides specificity for guanine rather than adenine ... Dynamic electrostatic interactions between its positively charged basic sequence with negative charges at the inner leaflet of ... or the combination of prenylation and a polybasic sequence adjacent to the prenylation site (KRAS). The C-terminal CaaX box of ...
Initiator element
The consensus sequence of Inr in humans was inferred to be YYANWYY. The consensus sequence in Drosophila is TCAKTY. Studies ... It has the consensus sequence YYANWYY in humans. Similarly to the TATA box, the Inr element facilitates the binding of ... Out of those sequences with the TATA box, 62% contained the Inr element as well. Though the Inr element is not fully understood ... This sequence encompasses where the RNA polymerase will begin transcribing. The Inr element is located about ~20 bp downstream ...
BRCA1
"Novel consensus DNA-binding sequence for BRCA1 protein complexes". Mol. Carcinog. 38 (2): 85-96. doi:10.1002/mc.10148. PMID ... When this happens, it is difficult for the repair mechanism to "know" how to replace the correct DNA sequence, and there are ... Zheng L, Pan H, Li S, Flesken-Nikitin A, Chen PL, Boyer TG, Lee WH (October 2000). "Sequence-specific transcriptional ... Classical methods for mutation detection (sequencing) are unable to reveal these types of mutation. Other methods have been ...
Tektin
They have the consensus amino acid sequence of RPNVELCRD. Different types of tektins, designated as A (53 kDa), B (51 kDa), C ( ... Amino acid sequences of tektins are well conserved, with significant similarity between mouse and human homologs. Tubulin ... The 2 segments are similar in sequence, indicating a gene duplication event. Along each tektin rod, cysteine residues occur ...
Lipid-anchored protein
No consensus sequence for protein palmitoylation has been identified. Palmitoylated proteins are mainly found on the ... In the CaaX box sequence, the C represents the cysteine that is prenylated, the A represents any aliphatic amino acid and the X ... This reaction is facilitated by N-myristoyltransferase . These proteins usually begin with a Met-Gly sequence and with either a ...
Sequence alignment
For multiple sequences the last row in each column is often the consensus sequence determined by the alignment; the consensus ... Sequenced RNA, such as expressed sequence tags and full-length mRNAs, can be aligned to a sequenced genome to find where there ... Schneider TD; Stephens RM (1990). "Sequence logos: a new way to display consensus sequences". Nucleic Acids Res. 18 (20): 6097- ... Sequence homology Sequence mining BLAST String searching algorithm Alignment-free sequence analysis UGENE Needleman-Wunsch ...
American Horror Story: Hotel
The site's consensus reads, "Favoring garish style over effective storytelling, the fifth American Horror Story strands a ... Same day the title sequence of the season was released by Murphy, consisting of the same soundtrack like previous seasons, ... Woerner, Meredith (October 1, 2015). "'American Horror Story: Hotel' title sequence is a germaphobe's nightmare". Los Angeles ... Bryant, Jacob (October 1, 2015). "Watch: 'American Horror Story: Hotel' Opening Sequence Gets Biblical". Variety. Archived from ...
Protocol Wars
ISBN 978-1-4669-3935-6. Russell, Andrew L. (July-September 2006). "'Rough Consensus and Running Code' and the Internet-OSI ... independently of other packets whereas a connection-oriented virtual circuit transports packets between terminals in sequence. ...
Antonius Suwanto
Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR)". HAYATI ... DNA sequence and mechanism of transfer". Journal of Bacteriology. 182 (1): 81-90. doi:10.1128/jb.182.1.81-90.2000. PMC 94243. ...
Pirates of the Caribbean: Dead Men Tell No Tales
The website's consensus reads, "Pirates of the Caribbean: Dead Men Tell No Tales proves that neither a change in directors nor ... and Bruckheimer had previously mentioned that there might be a sequence in Louisiana. However, a spokesman for Australian Arts ...
Game of Thrones (season 7)
Hooton, Christopher (January 23, 2017). "Game of Thrones season 7: Bastille 'film cameo in battle sequence'". The Independent. ... with the site's consensus reading, "After a year-long wait, Game of Thrones roars back with powerful storytelling and a focused ...
Prokaryotic DNA replication
... which have a highly conserved 9 bp consensus sequence 5' - TTATC/ACACA ) are high affinity DnaA boxes. They bind to DnaA-ADP ... These sequences allow the two replication forks to pass through in only one direction, but not the other. DNA replication ... In E. coli, the direction for orisome assembly are built into a short stretch of nucleotide sequence called as origin of ... Termination of DNA replication in E. coli is completed through the use of termination sequences and the Tus protein. ...
Slobbovia
In the end, the determining factor was just plain strakhfulness and consensus.) The head of a Great Family was considered a ... The Slobbovians justified their conquest by reversing the sequence.] The latter, ruled by the Rabinsky family, were held to be ...
A Mighty Heart (film)
The site's consensus states: "Angelina Jolie conveys the full emotional range of a woman in a desperate situation in A Mighty ... The production also shot multiple scenes in Austin, Texas in early 2007, including a key sequence with Marianne Pearl giving an ...
Childeric I
99-100), following his teacher Eugen Ewig, believes that the exile story reflects a real sequence of events whereby Childeric ... there is no consensus on this, because the reference in this case is not apparently to events near the Loire.[citation needed] ... gives a sequence of events which are very difficult to interpret. In 463 Childeric and Aegidius successfully repelled the ...
Gliese 581
There is no current consensus and 3-planet, 4-planet, 5-planet and 6-planet models have been proposed to address the available ... M-type main-sequence stars, BY Draconis variables, Objects with variable star designations, Durchmusterung objects, Libra ( ... The planet remained unconfirmed as consensus for its existence could not be reached. Additional reanalysis only found evidence ... was at the time the least massive confirmed exoplanet identified around a main-sequence star. On 29 September 2010, astronomers ...
Marsupial mole
Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Molecular Phylogenetics and Evolution ... reflecting the consensus of older studies, Archer et al. (2011) report the presence of four molars (typical for marsupials) in ... An analysis of marsupial interordinal relationships based on 12S rRNA, tRNA valine, 16S rRNA, and cytochrome b sequences. ... Phillips MJ, McLenachan PA, Down C, Gibb GC, Penny D. Combined mitochondrial and nuclear DNA sequences resolve the ...
Interferon
"NIH Consensus Statement on Management of Hepatitis C: 2002". NIH Consensus and State-Of-The-Science Statements. 19 (3): 1-46. ... Zoon KC, Smith ME, Bridgen PJ, Anfinsen CB, Hunkapiller MW, Hood LE (February 1980). "Amino terminal sequence of the major ... Inside the nucleus, the ISGF3 complex binds to specific nucleotide sequences called IFN-stimulated response elements (ISREs) in ... amino acid analysis and amino terminal amino acid sequence". Science. 207 (4430): 525-6. Bibcode:1980Sci...207..525K. doi: ...
Issue tracking system
... order sequence, etc.[citation needed] Finished tasks can also be foreseen with the report, showing what exactly has been done ... ", "fixed", or a group consensus that the issue is not worth solving, such as "not a problem" or "won't fix"); that each issue ...
Esthesioneuroblastoma
There is no consensus on an appropriate treatment approach of esthesioneuroblastoma because of the rarity of the disease. Most ... 2012). "Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma". PLOS ONE. 7 (5): e37029. ...
Insular India
... though the general consensus appears to be that they are non-placental eutherians and that there are non known Cretaceous ... inferred from mitochondrial rRNA gene sequences, Department of Zoology, The Natural History Museum, London SW7 5BD, UK b ...
CADASIL
Depending on the nature and position of each mutation, a consensus significant loss of betasheet structure of the Notch3 ... The definitive test is sequencing the whole Notch 3 gene, which can be done from a sample of blood. However, as this is quite ...
Promoter (genetics)
... has the consensus sequence TATAAT. The sequence at -35 (the -35 element) has the consensus sequence TTGACA. The above consensus ... consensus sequence 5'-AAAAAARNR-3' when centered in the -42 region; consensus sequence 5'-AWWWWWTTTTT-3' when centered in the - ... Promoter DNA sequences provide an enzyme binding site. The -10 sequence is TATAAT. -35 sequences are conserved on average, but ... we may call the most common sequence in a population the wild-type sequence. It may not even be the most advantageous sequence ...
Trials HD
Tournament mode sees the player attempt to complete a number of courses in sequence, trying to achieve a fast overall time with ... Gallegos, Anthony (2009-08-12). "The Consensus: Trials HD Review". GameSpy. IGN Entertainment. Retrieved 2010-10-13. "Trials HD ...
Children of Men
The site's critical consensus states: "Children of Men works on every level: as a violent chase thriller, a fantastical ... Children of Men used several lengthy single-shot sequences in which extremely complex actions take place. The longest of these ... In an interview with Variety, Cuarón acknowledged this nature of the "single-shot" action sequences: "Maybe I'm spilling a big ... Debruge, Peter (19 February 2007). "Editors cut us in on tricky sequences". Variety. Wagner, Annie (28 December 2006). " ...
Hairspray (2007 film)
The site's consensus states: "Hairspray is an energetic, wholly entertaining musical romp; a fun Summer movie with plenty of ... A PCC streetcar with Toronto Transit Commission livery is seen in the opening sequence. Some of the signs for the 1960s-era ... in that great sequence in Funny Girl. Shankman, Adam (July 25, 2007). "The Director's Chair: Adam Shankman's Hairspray Diary # ... Shankman based Edna's dancing style on the hippo ballerinas in the Dance of the Hours sequence in Walt Disney's 1940 animated ...
Serenity (2005 film)
The sequence where the crew is pursued by Reavers after a bank robbery was filmed along the Templin Highway north of Santa ... The site's critical consensus states: "Snappy dialogue and goofy characters make this Wild Wild West soap opera in space fun ... The videos, sequenced out of chronological order, depict excerpts of counseling sessions between River Tam, played by Summer ... The shoot typically would have lasted 30 days, but the production completed filming the sequence in five days. Pyrotechnics ...
Zinc deficiency
"Copenhagen Consensus Center". Retrieved 30 August 2014. Raulin J (1869). "Chemical studies on vegetation". Annales des Sciences ... Animal studies indicate that maternal zinc deficiency can upset both the sequencing and efficiency of the birth process. An ... to humans is one of the four solutions to major global problems identified in the Copenhagen Consensus from an international ...
Droseraceae
Molecular studies over the past 30 years have led to a wide consensus that Darwin was correct, with studies showing that ... and matK DNA sequences", American Journal of Botany, 89 (1): 132-144, doi:10.3732/ajb.89.1.132, PMID 21669721 Albert, V. A.; ... based on chloroplast rbcL and nuclear 18S ribosomal DNA Sequences". American Journal of Botany. 90 (1): 123-130. doi:10.3732/ ... a cladistic analysis of rbcL sequence and morphological data", American Journal of Botany, 81 (8): 1027-1037, doi:10.2307/ ...
Ant-Man and the Wasp
The flashback sequences featuring a younger Hank Pym were set around the same time as the flashback sequences of Ant-Man, so ... The website's critical consensus reads, "A lighter, brighter superhero movie powered by the effortless charisma of Paul Rudd ... The film's main credits sequence is a "table-top" version of its action sequences, and was created by Elastic. An alternative ... Eric Eisenberg of Cinema Blend opined that a standalone adventure with Pym and the cut sequence would be a good candidate to ...
Stanislaw Ulam
Ulam's work on non-Euclidean distance metrics in the context of molecular biology made a significant contribution to sequence ... After extensive discussion, the participants reached a consensus that his ideas were worthy of further exploration. A few weeks ... Goad, Walter B (1987). "Sequence Analysis: Contributions of Ulam to Molecular Genetics" (PDF). Los Alamos Science. Los Alamos ... challenged conclusions of Walter by writing that Ulam had only modest influence on early development of sequence alignment ...
Paleolithic
Ewen, Callaway (22 September 2011). "First Aboriginal genome sequenced". Nature News. doi:10.1038/news.2011.551. Bocquet-Appel ... societies may have made decisions by communal consensus decision making rather than by appointing permanent rulers such as ...
Pinales
conifers) (1) Gymnosperm (Acrogymnospermae) taxonomy has been considered controversial, and lacks consensus. As taxonomic ... Evidence from rbcL Sequences". Systematic Botany. 19 (2): 253. doi:10.2307/2419600. JSTOR 2419600. Chamberlain, Charles Joseph ... with the intention of reaching a consensus. Gymnosperms form a group of four subclasses among the spermatophytes (seed bearing ... "A new classification and linear sequence of extant gymnosperms" (PDF). Phytotaxa. 19 (1): 55-70. doi:10.11646/phytotaxa.19.1.3 ...
Chinese alligator
There is still not a consensus among biologists that the American and Chinese alligators belong to the same genus, despite ... Wu, Ziaobang; Zhou, Kaiya; Wang, Yiquan; Zhu, Weiquan (October 2003). "Complete mitochondrial DNA sequence of Chinese alligator ... "Complete mitochondrial DNA sequence of Chinese alligator, Alligator sinensis, and phylogeny of crocodiles". Chinese Science ...
Jackass Forever
The website's consensus reads, "A gleefully gonzo franchise revival, Jackass Forever will make you worry more than ever for the ... Dave England also burnt his right hand during the opening sequence. Zach Holmes got an infection after he glided into the ... producer Spike Jonze's father Lionel Boyce Cameos in the intro sequence include Arthur H. Spiegel III, Errol Chatham, Alia ...
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College...
... sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and ... previously developed guidance for the interpretation of sequence variants.(1) In the past decade, ... Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College ... sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and ...
Calculate consensus sequence - MATLAB seqconsensus
- MathWorks España
... for a multiply aligned set of sequences (Seqs), returns a character vector with the consensus sequence (CSeq). ... for a multiply aligned set of sequences (. Seqs. ), returns a character vector with the consensus sequence (. CSeq. ). The ... returns a character vector with the consensus sequence (. CSeq. ) from a sequence profile (. Profile. ). ... Sequence. .. Profile. Sequence profile. Enter a profile from the function seqprofile. . Profile. is a matrix of size [20 (or 4 ...
Puma concolor Mitochondrial DNA Consensus Sequence Files
... Files from the Illumina MiSeq and HiSeq 2500 sequencing runs were ... Consensus mtDNA genome sequences for each sample were constructed using the Samtools mpileup command with the -C50 parameter to ... We required minimums of 2X non-redundant sequence coverage and 80% site identity per site for consensus base calling ... processed as described (see description for Puma concolor Mitochondrial DNA Sequence Files from Illumina HiSeq 2500/MiSeq ...
sam consensus v3: 4f3585e2f14b env/lib/python3.9/site-packages/boto/sdb/db/sequence.py
... return self.sequence_string[(self.sequence_string.index(val) + 1) % len(self.sequence_string)] # # Simple Sequence Functions # ... sequence_string self.sequence_length = len(sequence_string[0]) self.rollover = rollover self.last_item = sequence_string[-1] ... self.sequence_length: return self.sequence_string[0] last_value = val[-self.sequence_length:] if (not self.rollover) and (last_ ... param sequence_string: The string or list that explains how to generate the next item in the sequence :type sequence_string: ...
Convergent Solid-Phase Synthesis of N-Glycopeptides Facilitated by Pseudoprolines at Consensus-Sequence Ser/Thr Residues -...
A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest | SpringerLink
Macro-haplogroup consensus sequences reliability. Based on the hypothesis that the mtDNA variants spread and fixed in one or ... Macro-haplogroup consensus sequences (MHCS) phylogeny. The robustness of 32 MHCSs was tested by generating a phylogenetic tree ... The consistency of MHCSs as consensus is supported by the clustering of such sequences with real genomes belonging to the same ... 2013). In this context, we used the Macro Haplogroup Consensus Sequences to move the fixed evolutionary variants to the ...
Generating consensus sequences from unaligned reads -
SEQanswers
I would like to determine consensus sequences in unaligned reads. I know that the usual way is to first align them to a ... I would like to determine consensus sequences in unaligned reads. I know that the usual way is to first align them to a ... Generating consensus sequences from unaligned reads 09-06-2022, 06:08 AM. ...
Perform consensus or template alignments on protein sequences - Benchling
Perform protein alignments from Template You can use our protein alignment tool to perform consensus alignments for proteins or ... Name your Consensus AA Sequencing, save it in a folder and click on "Create Alignment." ... How can I see all alignments Ive performed with a protein sequence?. Open your DNA or amino acid sequence. Click on the ... button to designate the AA sequence as your template. To change the template AA sequence, simply click on "Unset Template." ...
Rapid sequence induction: where did the consensus go? | Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine |...
Rapid Sequence Induction (RSI) was introduced to minimise the risk of aspiration of gastric contents during emergency tracheal ... Avery, P., Morton, S., Raitt, J. et al. Rapid sequence induction: where did the consensus go?. Scand J Trauma Resusc Emerg Med ... Rapid sequence induction: where did the consensus go?. *Pascale Avery. ORCID: orcid.org/0000-0002-0110-04121, ... Rapid Sequence Induction (RSI) was introduced to minimise the risk of aspiration of gastric contents during emergency tracheal ...
Consensus based recommendations for diagnosis and medical management of Poland syndrome (sequence) | Orphanet Journal of Rare...
Being Poland syndrome a rare syndrome most recommendations here presented are good clinical practice based on the consensus of ... books and guidelines were reviewed and final recommendations were reached by consensus. ... Consensus based recommendations for diagnosis and medical management of Poland syndrome (sequence). Access & Citations. * 8735 ...
Biblio | Page 30 | Linus Pauling Institute | Oregon State University
CDD Conserved Protein Domain Family: FCP1 euk
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes | BMC Bioinformatics | Full Text
... but also provides basic statistics of the CRISPR sequences, and the consensus sequences of DRs/spacers across the input strains ... CrisprVi is a convenient tool for visualizing and analyzing the CRISPR sequences and it would be helpful for users to inspect ... orders and components of the CRISPR sequences in a global view. In comparison to other CRISPR visualization tools such as ... label and align the CRISPR sequences, which help researchers investigate the locations, ...
Sequence Alignment
- MATLAB & Simulink
... and profile sequence alignments using dynamic programming algorithms; BLAST searches and alignments; standard and custom ... Calculate consensus sequence. seqprofile. Calculate sequence profile from set of multiply aligned sequences. ... Compare Sequences Using Sequence Alignment Algorithms. Determining the similarity between two sequences is a common task in ... Sequence Alignments. You can select from a list of analysis methods to compare nucleotide or amino acid sequences using ...
Parallel G-quadruplexes recruit the HSV-1 transcription factor ICP4 to promote viral transcription in herpes virus-infected...
The reported ICP4 consensus sequence42,60,61 was used as positive control; a G-rich non-folding sequence (scrambled, S) was ... In addition, HIV-1 LTR-III i-motif forming sequence (LTR-IIIc) and the reported ICP4 consensus sequence (IE3) were used as non- ... as well as the reported consensus sequence (Fig. 3a and Supplementary Fig. S10b): the two best bound sequences were ICP4-146532 ... IE-CS is the reported ICP4 consensus sequence42, 60, 61; SCR is a G-rich unfolded oligo; CTR is a control lane loaded with ...
Agronomy | Free Full-Text | In Silico Characterization and Expression Profiles of Heat Shock Transcription Factors (HSFs) in...
Table 4. Conserved motif sequence of Zea mays HSFs.. Motif. Consensus Sequence. ... Sequence Analysis. The coding sequence (CDS) and genomic DNA sequences were obtained from the maize genome database (MaizeGDB ... Sequence Alignment and Phylogenetic Analysis. The protein sequences of Arabidopsis thaliana, Oryza sativa, Brachypodium ... cis-regulatory region sequence-specific DNA binding (GO:0000987), RNA polymerase II transcription regulatory region sequence- ...
Future Applications: Phasing and Sequencing of Viral Mixtures - Speaker Deck
... build a consensus sequence from the reads Align the consensus sequences to a HLA-A sequence database to find the best match ... Single-Molecule Circular Consensus Sequence (CCS) and Multi-Molecule Consensus Single-Molecule CCS: Multi-Molecule Consensus: ... Test the Consensus Algorithm on HIV Data (~9 kb Amplicons) Difference between PacBio® Consensus vs. Sanger Assembly Consensus ... 2nd Generation Sequencing Can Help Resolve Ambiguities 28 If the SNPs that need to be phased are in the sequenced exons and ...
Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from...
... and conquer processing algorithm for SMRT amplicon-sequence data that generates accurate consensus sequences and local sequence ... Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences ... comprised of multiple low quality subreads from which higher quality circular consensus sequences are formed) to cluster raw ... C3S-LAA produced accurate consensus sequences and assemblies of overlapping amplicons from single sample and multiplexed ...
Their LRRs have a specific consensus pattern with characteristic differences from the previously described consensus sequences...
Repbase Reports - 2010, Volume 10, Issue 4 - SINE-1B ACar
Bioconductor - single
SINGLe corrects for systematic errors in nanopore sequencing reads of gene libraries and it retrieves true consensus sequences ... Accurate consensus sequence from nanopore reads of a gene library. Bioconductor version: Release (3.16) ... Accurate consensus sequence from nanopore reads of a DNA gene library. ...
foxa2 antibody
The consensus coding sequences of human breast and colorectal cancers.. October 2, 2021. September 30, 2021. by Jose ... To start out a scientific analysis of such alterations, we determined the sequence of well-annotated human protein-coding genes ... The elucidation of the human genome sequence has made it potential to ascertain genetic alterations in cancers in unprecedented ...
Kenny HELSENS | PhD | Ghent University, Gent | UGhent | VIB Department of Medical Protein Research
Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in...
... to produce finalized consensus sequences.. We aligned our sequences and those available in GenBank (Table S1) using MUSCLE ( ... Finally, two mtDNA sequences from captive-bred P. aurotaenia of unknown origin (sequenced by Grant et al. [2006] and Santos et ... Meyer, M., & Kircher, M. (2010). Illumina sequencing library preparation for highly multiplexed target capture and sequencing. ... Sun, Y.-B., Xiong, Z.-J., Xiang, X.-Y., Liu, S.-P., Zhou, W.-W., Tu, X.-L.,…Zhang, Y.-P. (2015). Whole-genome sequence of the ...
Dirk Aerts
Biblio | Page 5 | Linus Pauling Institute | Oregon State University
Leishmania tropica Infection in Golden Jackals and Red Foxes, Israel - Volume 16, Number 12-December 2010 - Emerging Infectious...
... and consensus sequences representing each animal were created. These consensus sequences were deposited in GenBank under ... Sequences obtained were compared for similarity to sequences in GenBank by using the BLAST program (www.ncbi.nlm.nih.gov/BLAST ... This sequence was closest (99.5% identity over 222 bp) to L. infantum (Table). DNA sequences from all the positive tissues ... Sequences were compared with the following Leishmania sequences deposited in GenBank: L. tropica FJ595949 and FJ595950 from ...
Frontiers | ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in...
DNA encoding consensus TFBS sequences were inserted upstream of PTK. Fluc was then replaced with a unique DNA reporter sequence ... Oka, T., Rairkar, A., and Chen, J. H. (1991). Structural and functional analysis of the regulatory sequences of the ets-1 gene ... Transcription factor binding sites (TFBS) that are found in conserved non-coding sequences (CNS), taking into consideration ... Antibody for E26 transformation-specific sequence-1 (ETS1) detection was purchased from Novus Biologicals (Centennial, CO). ...
Volume 39 Issue 4 | Southwestern Entomologist
Sequences were aligned and a consensus sequence deduced for each species. A pair of oligonucleotides was designed in high ... Sequences of cytochrome oxidase subunit I (COI) gene from nine species of Diptera of forensic importance registered in GenBank ... was identified by sequencing internal transcribed spacer regions of ribosomal DNA (rDNA). Assays against immature sweetpotato ... we found the following sequence: Latin® , Peokubo® , Polar Star® , Leonidas® , Royal Bacara® , Haylander® , Ben Hur®. In ...
GATA1 Promotes Gemcitabine Resistance in Pancreatic Cancer through Antiapoptotic Pathway
GATA1 regulates its target genes through binding to consensus DNA sequence. GATA1 was first found critical for the formation of ... Primer sequences used were listed in Table S4b.. 2.9. Dual-Luciferase Reporter Assay. Cells were seeded into 24-well plates at ... Primer sequences used were listed in Table S4c.. 2.11. Flow Cytometry Assay. Cell apoptosis was analyzed using an Annexin V-APC ... Lentiviral vector of GATA1 was constructed by cloning PCR-amplified full length sequences into pCDH (System Biosciences). The ...