Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Examples: a certain PDF file that exists in different and in several hard drives
Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
imported from: Gene Ontology, Version 1.931
alternative term: ribonucleic acid transcriptase activity ribonucleic polymerase activity ribonucleic transcriptase activity RNA nucleotidyltransferase activity RNA transcriptase activity transcriptase C ribonucleic acid formation factors C RNA formation factors ribonucleate nucleotidyltransferase activity ribonucleate polymerase activity ribonucleic acid nucleotidyltransferase ribonucleic acid polymerase activity
editor preferred term: RNA polymerase activity
Definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template.
imported from: Chemical entities of biological interest, Version 1.69
Definition: RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis.
Definition: An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation.
editor preferred term: polyacrylamide gel
term imported from: Ontology for Biomedical Investigations, Version 2009-11-06 Philly (aka version 1.0) Release Candidate
Example Of Usage: Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
definition: A Polyacrylamide Gel is a separation matrix used in electrophoresis of biomolecules, such as proteins or DNA fragments. Traditional DNA sequencing techniques such as Maxam-Gilbert or Sanger methods used polyacrylamide gels to separate DNA fragments differing by a single base-pair in length so the sequence could be read.
definition source: http://en.wikipedia.org/wiki/Polyacrylamide_gel
Example Of Usage: Amplied DNA created by PCR
Definition Editor: PERSON: Alan Ruttenberg
Definition: DNA that has been produced in an enzymatic amplification process
definition: Proofreading DNA polymerases are accurate due to the 3′→5′ exonuclease activity, which can remove a misincorporated nucleotide from a growing DNA chain.
editor preferred term: 3′→5′_exonuclease (proofreading) activity
example of usage: enzyme Pfu DNA polymerase. When the amplified product is to be cloned, expressed or used in mutation analysis, Pfu DNA polymerase is a better choice due to its high fidelity.
definition source: Promega, Protocols & Applications Guide. http://www.promega.com/paguide/chap1.htm#title4
alternative term: Proofreading DNA polymerase
definition: An organic compound having at least one hydroxy group attached to a carbon atom.
definition source: Emerald, Professional Protection Products. http://www.emeraldlatexgloves.com/gloves-101.htm
definition: Vinyl is the first synthetic material available to consumer, is a material composed of polyvinyl chloride and plasticizers that softens the material. These type of gloves are an economical alternative to latex gloves. These gloves offer great for basic hand protection in a low infection environment, good multi-purpose glove for general use and activities that do not require highest degree of tactile precision, but does not fit as well as latex.
definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-N/nucleic_acid_ampl_assay.html
editor preferred term: in vitro nucleic acid amplification
definition: An assay that uses purified enzymes to isolate and then replicate specific nucleic acids to levels where they can be detected. Examples are PCR, TAS, NASBA, etc.
editor preferred term: transferase activity
Definition: Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor).
definition source: Peterson, C., M. Maraia, and C. Deschamp, Scissors. 2007, Fiskars Brands, Inc. (Madison, WI, US) United States. p. 7.
definition: scissors, are a tool used for cutting.
Editor Preferred Term: quality of a single physical entity
Definition: A physical object quality which inheres in a single-bearer.
editor preferred term: taq DNA polymerase
definition: Taq DNA Polymerase is a thermostable DNA Polymerase isolated from an E. coli strain that carries the Taq DNA polymerase gene. Taq DNA Polymerase is the most common polymerase used for PCR* reactions.
alternative term: taq polymerase DNA Polymerase, Taq polymerase, taq polymerase, taq DNA polymerase, taq1 polymerase, thermus aquaticus taq1 Polymerase thermus aquaticus Polymerase aquaticus polymerase, thermus
definition source: GenScript. http://taqpolymerase.net/
Definition: Compounds having the structure R2S=O (R =/= H).
definition: P-20 model, refer to the maximum volume in microliters. P20 is a micropipette designed for dispensing volumes between 2µl and 20µl.
editor preferred term: P-20_micropipette
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123600
definition: TE buffer is a commonly used buffer solution in molecular biology, especially in procedures involving DNA or RNA. "TE" is derived from its components: Tris, a common pH buffer, and EDTA, a molecule chelating cations like Mg2+. The purpose of TE buffer is to protect DNA or RNA from degradation.
definition source: http://en.wikipedia.org/wiki/TE_buffer
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F144801
definition: P-2 model, refer to the maximum volume in microliters. P2 is a micropipette designed for dispensing volumes between 0.2µl and 2µl.
editor preferred term: nucleotidyltransferase activity
Definition: Catalysis of the transfer of a nucleotidyl group to a reactant.
alternative term: Ameisensaeureamid Formamid formimidic acid carbamaldehyde Methanamid Methanamide CH3NO
Definition: A member of the formamides that has formula CH3NO.
definition: The AMV reverse transcriptase (AMV RT), is isolated from Avian Myeloblastosis Virus as the beta holoenzyme of molecular weight 157,000 daltons, using a modification of the method described by Houts et al. (1979). AMV RT is qualified for cDNA synthesis and also for dideoxy sequencing of DNA and RNA. Using AMV Reverse Transcriptase, the reverse transcription step can be carried out at elevated temperatures up to 70 °C. High temperature increases the specificity of priming and helps to increase the efficiency by reducing RNA secondary structures.
editor preferred term: AMV reverse transcriptase
definition source: Finnzymes, Tools for Molecular Biology. http://www.finnzymes.fi/rt-pcr/amv_reverse_transcriptase.html
Definition: A family of enzymes that catalyze the endonucleolytic cleavage of RNA.
imported from: Medical Subject Headings, Version 2010_2009_08_17
Definitions: A secondary alcohol that has formula C3H8O.
alternative term: 2-hydroxypropane Isopropylalkohol sec-propanol IPA 1-methylethanol i-Propylalkohol 1-methylethyl alcohol i-propanol isopropyl alcohol 2-Propanol Isopropanol C3H8O CC(C)O
definition source: Chemical entities of biological interest, Version 1.68
Definitions: A chemical compound containing three hydroxyl groups.
editor preferred term: polyacrylamide gel electrophoresis instrument
definition source: http://www.tesa.co.uk/AdhesiveTapeRange/MaskingTape/general_purpose
definition: General purpose masking tapes comprise of a paper backing or carrier and a natural rubber adhesive. The adhesive have a limited temperature resistance and should not be left longer than 24 hours or 3 days before removal otherwise they may leave adhesive residues.
definition: TBE buffer is commonly used in all DNA electrophoresis applications (both for acrylamide and for agarose gels), including sequencing. In general, TBE buffer offers better resolution of 0.1 to 3 kb fragments; TBE is better suited for high-voltage (>150V) electrophoresis because of its higher buffering capacity and lower conductivity than TAE.
definition source: http://www.interchim.com/interchim/bio/produits_uptima/product_line/electrobuffer_tae_tbe.htm#tbe_buffer
alternative term: Tris-Borate-EDTA buffer
Example Of Usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
Definition: a material processing in which components of an input material become segregated in space
Editor Preferred Term: material component separation
definition: The recommended primer concentration for PCR is between 0.1μM and 1μM of each primer. The use of higher concentrations of primers can have the following effects: 1. If the primers are capable of forming dimers, raising their concentration only results in the creation of primer-dimers and does not improve the amplification of the desired PCR product. Primer-derived oligomers will possibly contaminate the reaction. 2. If the primers do not form primer-dimers, it is likely that raising the primer concentration will lead to non-specific primer binding and the creation of spurious, undesirable PCR products. Raising the primer concentration does not therefore cause an increase in the effective concentration of the primers. Low primer concentration generally ensures cleaner product and lower background.
editor preferred term: 0.1uM reverse primer
alternative term: 0.1uM_downstream_primer 0.1uM_antisense_primer
definition source: PCR Troubleshooting: Primer Concentration. http://www.caister.com/molecular-biology-blog/2008/10/pcr-troubleshooting-primer.html
definition source: http://en.wikipedia.org/wiki/Distilled_water
definition: Distilled water is water that has many of its impurities removed through distillation. Distillation involves boiling the water and then condensing the steam into a clean container.
Definition: A scanner is an image acquistion device that generates a digital representation of an image for data input to a computer.
imported from: Sample processing and separation techniques, Version 1.070708
definition: nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere.
alternative term: N - Nitrogen N2 - Nitrogen Nitrogen (substance) Nitrogen, NOS
definition source: http://en.wikipedia.org/wiki/Nitrogen
editor preferred term: 0.1uM forward primer
alternative term: 0.1uM upstream primer 0.1uM sense primer
Definition Source: PERSON: Daniel Schober
Definition: A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
Example Of Usage: A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
alternative term: deoxynucleate polymerase activity deoxyribonucleate nucleotidyltransferase activity deoxyribonucleic acid polymerase activity deoxyribonucleic polymerase activity DNA nucleotidyltransferase activity
Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
editor preferred term: DNA polymerase activity
definition: betaine is an agent that has been used successfully for increasing yield and specificity of PCR products. Betaine, an isostabilizing agent, equalizes the contribution of GC- and AT- base pairing to the stability of the DNA duplex.
definition source: Frackman, S., et al., Betaine and DMSO: Enhancing Agents for PCR. 1998, Promega Corporation. p. 4.
Definition: Compounds (NH4(+))Y(-) and derivatives, in which one or more of the hydrogens bonded to nitrogen have been replaced with univalent groups.
editor preferred term: ammonium compound
Example Of Usage: Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells.
Definition Source: http://www.medterms.com/script/main/art.asp?articlekey=18426
Definition: An incubator is an instrument in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
alternative term: Tris-Acetate-EDTA buffer
definition source: http://www.interchim.com/interchim/bio/produits_uptima/product_line/electrobuffer_tae_tbe.htm#tae_buffer
definition: TAE buffer is commonly used in DNA electrophoresis on agarose gel.
example of usage: Better resolution of fragments greater than 4 kb.
Definition Editor: Melanie Courtot Trish Whetzel
alternative term: ~#en DNA_amplifier ~#en PCR_machine ~#en thermocycler ~#en Polymerase_Chain_Reaction_ machine
Example Of Usage: Piko(tm) 96-well Thermal Cycler
Definition: An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
definition: In a transcription-based amplification system (TAS) each cycle of the TAS is composed of two steps. The first is a cDNA synthesis step that produces one copy of a double-stranded DNA template for each copy of RNA or DNA target nucleic acid. During the course of this cDNA synthesis step, a sequence recognized by a DNA-dependent RNA polymerase is inserted into the cDNA copy of the target sequence to be amplified. The second step is the amplification of the target sequence by the transcription of the cDNA template into multiple copies of RNA.
editor preferred term: transcription-based amplification system
definition source: Kwoh, D.Y., et al., Transcription-Based Amplification System and Detection of Amplified Human Immunodeficiency Virus Type-1 with a Bead-Based Sandwich Hybridization Format. Proceedings of the National Academy of Sciences of the United States of America, 1989. 86(4): p. 1173-1177.
definition: ribonuclease (RNase), is an enzyme which degrades RNA by cleaving the phosphodiester bond. It is ubiquitous in living organisms and is exceptionally stable. The prevention of RNase activity is the primary problem in handling RNA.
definition source: Eurofins MWG Operon's Glossary of Biotechnical Terms. http://www.operon.com/products/custom_oligos/glossary.aspx
editor preferred term: DNA extraction buffer
definition: an extraction buffer with correct pH, gets rid of the cell components, but retains the organelles.
definition source: http://wiki.answers.com/Q/What_is_an_extraction_buffer
Definition: A nucleotide is a nucleoside phosphate. It is composed of a nucleobase, a sugar moiety and one to three phosphate groups.
editor preferred term: boron molecular entity
The role a peptide plays in accelerating a biochemical reaction
editor preferred term: degenerate primer role
definition: Degenerate primers are useful for pulling out one part of a gene sequence when you only know the gene sequence in related organisms. The more distant those related organsims, the more difficult it can be to design primers.
definition source: *http://hcgs.unh.edu/protocol/basic/pcrdegenpri.html *http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29#PCR_primer_design
Definition: A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
alternative term: Endoribonuclease H RNAase H RNase H Ribonuclease H, Calf Thymus
Definition Editor: person:Allyson Lister person:Alan Ruttenberg PERSON: Lawrence Hunter
Definition Source: group:OBI OBI_0000240
Definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
alternative term: (C12H18O9)n (1->4)-3,6-anhydro-alpha-L-galactopyranosyl-(1->3)-beta-D-galactopyranan
definition: A polysaccharide that has formula (C12H18O9)n.
Example Of Usage: PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
Editor Note: We are using PCR and not the written out words, as this is the most common used.
Definition Editor: GROUP: OBI BIomaterial Branch
Definition: is double stranded DNA that is the specified output of a polymerase chain reaction
Definition Source: GROUP: OBI BIomaterial Branch
definition: PCR buffer is necessary to create optimal conditions for activity of Taq DNA polymerase. Buffers often contain Tris-Hcl, KCl, and sometimes MgCl2. PCR buffers are often available in 10X concentration and are sometimes Taq formulation-specific.
definition source: *http://www.eeescience.utoledo.edu/Faculty/Sigler/RESEARCH/Protocols/PCR/PCR.pdf * http://www.pcrlinks.com/glossary/B.htm
Definition: A test substance that is added to a system in order to bring about a reaction or to see whether a reaction occurs.
definition: A refrigerator is a cooling appliance comprising a thermally insulated compartment and a heat pump-chemical or mechanical means-to transfer heat from it to the external enviroment, cooling the contents to a temperature below ambient.
definition source: http://en.wikipedia.org/wiki/Refrigerator
alternative term: Refrigerator, device Refrigerator, device (physical object) Icebox fridge
Definition: An organosulfur compound is a compound containing at least one carbon-sulfur bond.
editor preferred term: organosulfur compound
editor preferred term: image acquisition device
Definition: An image acquisition device is a device which captures a digitiesed image of an object.
Definition Editor: Frank Gibson Bill Bug Daniel Schober Melanie Courtot
Definition: A separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
Editor Preferred Term: separation function
definition: microcentrifuge is a centrifuge used in laboratories to separate materials from small samples (specially of biological material).
definition source: http://en.wiktionary.org/wiki/microcentrifuge
Definition: A primer list is a report of the names or identifiers of primers used in a studio or have been put together for the purpose of an analysis.
Example: primer list may be collected from the literature, data-bases or may be designed to be used in a particular studio (e.g, marker Assisted Selection).
Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
alternative term: revertase activity RNA revertase activity RNA-dependent deoxyribonucleate nucleotidyltransferase activity RNA-dependent DNA polymerase activity RNA-directed DNA polymerase, group II intron encoded RNA-directed DNA polymerase, transposon encoded RNA-instructed DNA polymerase activity RT deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity DNA nucleotidyltransferase (RNA-directed) activity reverse transcriptase activity
editor preferred term: RNA-directed DNA polymerase activity
example of usage: enzyme reverse transcriptase is a RNA-directed DNA_polymerase activity.
Definition: A family of enzymes that catalyze the exonucleolytic cleavage of DNA.
editor preferred term: exodeoxyribonuclease
alternative term: DNA Exonuclease Exonuclease, DNA
Definition: Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
Editor Preferred Term: molecular_function
Definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Editor Preferred Term: catalytic activity
editor preferred term: nucleoside triphosphate
alternative term: Glycane Glycan polisacarido Glykane Glykan
definition: A macromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
Definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
Editor Preferred Term: primary structure of DNA macromolecule
Example Of Usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples.
Editor Preferred Term: processed material
Definition: Is a material entity that is created or changed during material processing.
imported from: Ontology for Biomedical Investigations, Version 2009-11-06 Philly (aka version 1.0) Release Candidate
Definition Source: *(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer *http://es.wikipedia.org/wiki/Cebador
Definition: primer role is inheres to nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
editor preferred term: P-200 micropipette
definition: P-200 model, refer to the maximum volume in microliters. P200 is a micropipette designed for dispensing volumes between 50µl and 200µl.
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123601
Definition: the conformational arrangement (α-helix, β-pleated sheet, etc.) of the backbone segments of a macromolecule such as nucleic acids, a polypeptide chain of a protein without regard to the conformation of the side chains or the relationship to other segments.
definition source: PAC, 1996, 68, 2193 (Basic terminology of stereochemistry (IUPAC Recomendations 1996)) on page 2218.
secondary structure of sequence macromolecule
definition: Xylene cyanol can be used as a colour marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis.
alternative term: Acid Blue 147 xylene cyanole xylene cyanol FF xylene cyanole FF
definition source: http://en.wikipedia.org/wiki/Xylene_cyanol
term imported from: Medical Subject Headings, Version 2010_2009_08_17
Definition: Compounds having one or more hydroxy groups attached to a benzene or other arene ring.
editor preferred term: plant structure harvesting
definition: the process of removing a organ or anatomical part from a plant.
Definition: Any morphological or anatomical feature of a plant.
Definition: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers.
editor preferred term: deoxyribonuclease, type II site-specific
alternative term: Deoxyribonucleases, Type II, Site Specific DNA Restriction Enzymes, Type II DNase, Site Specific, Type II DNase, Site-Specific, Type II Restriction Endonucleases, Type II Site-Specific DNase, Type II Type II Restriction Enzymes Type II Site Specific Deoxyribonucleases Type II Site Specific DNase Type II Site-Specific Deoxyribonucleases Type II Site-Specific DNase DNASE SS II Site Specific DNase, Type II Deoxyribonucleases, Type II Site Specific
alternative term: deoxy-TTP pppdT thymidine 5'-triphosphate thymidine 5'-(tetrahydrogen triphosphate) TTP deoxythymidine triphosphate deoxythymidine 5'-triphosphate C10H17N2O14P3 2'-deoxythymidine triphosphate dThd5'PPP 5'-TTP
definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H17N2O14P3.
Definition: study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
Editor Preferred Term: study subject role
Example Of Usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example people infected, then extract parasite which are then tested = observation study of the parasite 1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification.
alternative term: Gro glycyl alcohol propane-1,2,3-triol Glyzerin glycerine Oelsuess glycerolum 1,2,3-Trihydroxypropane 1,2,3-Propanetriol Glycerin C3H8O3 OCC(O)CO
Definition: An alditol compound having three carbons.
alternative term: dimethyl sulfoxide role (methanesulfinyl)methane role
definition: DMSO is probably the most commonly used enhancing agent and is frequently included as part of a standard optimization of PCR amplifications. The DMSO role, is disrupting base pairing to facilitate strand separation.
Example Of Usage: Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
Definition: a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
Definition: A 2-carbon sulfoxide in which the sulfur atom has two methyl substituents.
editor preferred term: dimethyl sulfoxide
alternative term: (methanesulfinyl)methane S(O)Me2 dimethyl sulfur oxide (CH3)2SO dimethyli sulfoxidum dimetil sulfoxido methylsulfinylmethane sulfinylbis(methane) DMSO C2H6OS
Definition: A heat function is a function that increases the internal kinetic energy of a material
Definition: A physical entity quality which exists in relation towards some other entity.
Editor Preferred Term: quality of related physical entities
Definitions: Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
editor preferred term: endoribonuclease activity, producing 5'-phosphomonoesters
definition source: http://en.wikipedia.org/wiki/Micropipette
editor preferred term: adjustable micropipette
definition: A micropipette is one instrument used in science laboratories. Micropipettes are used to accurately measure and dispense small volumes of liquid. The capacity of a micropipette can range from less than 1µl to 1000µl (1ml).
editor preferred term: ligase chain reaction
Definition: A DNA amplification technique based upon the ligation of OLIGONUCLEOTIDE PROBES. The probes are designed to exactly match two adjacent sequences of a specific target DNA. The chain reaction is repeated in three steps in the presence of excess probe: (1) heat denaturation of double-stranded DNA, (2) annealing of probes to target DNA, and (3) joining of the probes by thermostable DNA ligase. After the reaction is repeated for 20-30 cycles the production of ligated probe is measured.
definition source: Kanare, H.M., Writing the Laboratory Notebook. 1985, Washington D.C: American Chemical Society.
Definition: A lab notebook is a primary record of research. Researchers use a lab notebook to document their hypotheses, experiments and initial analysis or interpretation of these experiments. The notebook serves as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.
Definition: A concentration which relative low.
definition: these methods provide a cheap, fast, and easy way to obtain small-to-medium amounts of very high quality DNA.
editor preferred term: small-scale extraction of high quality DNA
definition source: Laboratory Protocols: CIMMYT Applied Molecular Genetics Laboratory. 2005, CIMMYT: Mexico, D.F. p. 102.
definition source: http://en.wikipedia.org/wiki/DNA_sequencing
alternative term: Automated DNA-sequencing instrument DNA sequencer
definition: Automated DNA sequencer, can sequence up to 384 DNA samples in a single batch (run) in up to 24 runs a day. DNA sequencers carry out capillary electrophoresis for size separation, detection and recording of dye fluorescence, and data output as fluorescent peak trace chromatograms. Sequencing reactions by thermocycling, cleanup and re-suspension in a buffer solution before loading onto the sequencer are performed separately. A number of commercial and non-commercial software packages can trim low-quality DNA traces automatically. These programs score the quality of each peak and remove low-quality base peaks (generally located at the ends of the sequence). The accuracy of such algorithms is below visual examination by a human operator, but sufficient for automated processing of large sequence data sets.
editor preferred term: automated_DNA_sequencer
example of usage: PhastSystem, LI-COR sequencer 4200 y ABI 377 DNA Synthesizer.
definition: A compound made from monomers linked by chemical bonds. They are produced by polymerization, and occur either naturally or synthetically.
definition source: Biology Online, Answers to all your Biology Questions. http://www.biology-online.org/dictionary/Polymer
definition source: Light Labs. http://www.lightlabsusa.com/PCR-Strip-Tubes/
definition: PCR Strip Tubes come in several different styles and colors, for example, 8-strip tubes with seperate caps, hinged attached caps, and in the snapstrip version. Also there are 12-strip tubes with seperate caps. All pcr strip tubes are RNase/DNase/Pyrogen free and made from thin-walled plastic.
editor preferred term: magnesium dichloride
definition: A magnesium halide that has formula Cl2Mg.
alternative term: Magnesium chloride MgCl2 Magnesium chloride anhydrous Magnesiumchlorid Cl2Mg [Mg++].[Cl-].[Cl-]
editor preferred term: quaternary ammonium salt
alternative term: quaternary ammonium compound
Definition: Derivatives of ammonium compounds, (NH4(+))Y(-), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually hydrocarbyl) groups.
editor preferred term: gel electrophoresis instrument
definition: gel electrophoresis instrument is used to separate macromolecules, either nucleic acids or proteins, on the basis of size, electric charge, and other physical properties. Gel electrophoresis instrument allows researchers to maintain a uniform electric field across a gel such as agarose or acrylamide gel.
definition source: Globalspec, the engineering search engine. http://www.globalspec.com/learnmore/labware_scientific_instruments/separation_techniques/gel_electrophoresis_equipment
alternative term: gel_electrophoresis_equipment
definition source: *Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples *http://www.pcrlinks.com/glossary/T.htm
editor preferred term: touchdown polymerase chain reaction
definition: Touchdown PCR is another modification of conventional PCR that may result in a reduction of nonspecific amplification. It involves the use of an annealing temperature that is higher than the target optimum in early PCR cycles. The annealing temperature is decreased by 1°C every cycle or every second cycle until a specified or 'touchdown' annealing temperature is reached. The touchdown temperature is then used for the remaining number of cycles. This allows for the enrichment of the correct product over any non-specific product.
alternative term: endonuclease G activity
Definition: Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
editor preferred term: endoribonuclease activity
definition: Gloves are excellent for handling hot objects out of the autoclave or oven. This gloves are Soft, pliant, all-cotton terry cloth. They are also excellent for use where other heat protection is needed whether in the lab, school or industry. Heat resistant up to 232°C (450°F), they replace hazardous asbestos gloves. Gloves provide wrist and forearm protection and the bright orange color offers high visibility. Machine wash, tumble dry.
definition source: Ted Pella, Inc. http://www.tedpella.com/gloves_html/gloves.htm
editor preferred term: heat resistant glove
editor preferred term: laboratory supply
example of usage: lab coats, globes, beads, bags, batteries, PCR plates and tubes, centrifuge tubes, filter paper, magnetig stir bar, parafilm, micropipettes and tips, respirators, slides, spatulas, thermometer, weighing dish, wipes, etc.
definition: refers to a variety of supplies used for scientific experiments and other work in science, especially in chemistry and biology laboratories.
definition source: http://www.labdepotinc.com/c-70-laboratory-supplies.php
Definition: An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
Editor Preferred Term: anatomical entity
Definition Editor: Bjoern Peters Philippe Rocca-Serra Tina Boussard
Example Of Usage: Tissue, organ, system, sperm, blood or body location (arm).
Editor Note: 13-02-2009: Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation. IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity' DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules. 10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species. not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion)
imported from: NCI Thesaurus, Version 10.01
editor preferred term: scientific control role
definition: Methodology that tests integrity in experiments by isolating variables as dictated by the scientific method in order to make a conclusion about such variables. In a controlled experiment, two virtually identical experiments are conducted, but the factor being tested is varied in only one of them. This serves to isolate any causal phenomena.
Alternative Term: genetic map linkage map
Definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/genetic_linkage_map.html
Definition: A genetic map, is a map of a species or experimental population that shows the position of its known genes or genetic markers relative to each other in terms of recombination frequency, rather than as specific physical distance along each chromosome. Linkage mapping is critical for identifying the location of genes that cause different types of biotic and abiotic stresses in plants.
editor preferred term: denaturing activity
definition source: A Glossary of Terms commonly used in Molecular Biology
definition: with respect to nucleic acids, refers to the conversion from double-stranded to the single-stranded state, often achieved by heating or alkaline conditions.
alternative term: C10H16N5O12P3 2'-deoxyadenosine 5'-(tetrahydrogen triphosphate) 2'-deoxyadenosine 5'-triphosphate deoxyadenosine 5'-triphosphate deoxyadenosine triphosphate
Definition: A purine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H16N5O12P3.
Definition: the use of enzymes to increase the number of molecules of a biomaterial
Example Of Usage: the use of a polymerase chain reaction to amplify a fragment of DNA
Editor Preferred Term: enzymatic amplification
definition: A dye used to make DNA or RNA bands visible for agarose gel electrophoresis is SYBR Safe. SYBR Safe is a variant of SYBR Green that has been shown to have low enough levels of mutagenicity and toxicity to be deemed nonhazardous waste under U.S. Federal regulations. It has similar sensitivity levels to EtBr, but, like SYBR Green, is significantly more expensive. DNA or RNA bands stained with SYBR® Safe can be detected using a standard UV transilluminator, a visible-light transilluminator, or a laser-based scanner.
definition source: Invitrogen. SYBR Safe DNA Gel Stain.
definition source: Favorgen, biotech corp. http://www.favorgen.com/products_for_res_plastics_non-skirted_PCR_plate.htm
definition: PCR plates are constructed of thin-wall polypropylene. Thin wall design delivers uniform, accurate, and rapid thermal transfer to each sample, improving cycle times and product specificity.
Definition: A protein that has catalytic activity.
definition source: PCR Down Under. http://www.uq.edu.au/vdu/PDU_PCR.htm
definition: the process is then repeated by cycling through the temperatures over and over again (35 to 55 times). Each cycle results in a new DNA duplex, each strand acting as a potential template for one or other primer.
editor preferred term: exponential template duplication
editor preferred term: secondary structure of RNA macromolecule
definition: the secondary structure of biological RNA's can often be uniquely decomposed into stems and loops. Frequently these elements, or combinations of them, can be further classified, for example, tetraloops, pseudoknots and stem-loops. There are many secondary structure elements of functional importance to biological RNA's; some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf.
definition source: Westhof , E. and P. Aufﬁnger, RNA Tertiary Structure, in Encyclopedia of Analytical Chemistry, R.A. Meyers, Editor. 2000, John Wiley & Sons Ltd: Chichester. p. 5222 – 5232.
Definition Editor: Frank Gibson Daniel Schober Melanie Courtot
Definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
definition source: Wu, D.Y., et al., The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol, 1991. 10(3): p. 233-8.
definition: the effect of temperature, is a important factor in the specificity of PCR, because, the amplification of DNA occurs by repeated cycles of three temperature dependent steps: denaturing, annealing, and extention.
definition source: http://en.wikipedia.org/wiki/LB_buffer
definition: Lithium Borate buffer is a buffer solution used in agarose electrophoresis, typically for the separation of nucleic acids such as DNA and RNA. It is made up of Lithium borate (lithium hydroxide monohydrate and boric acid).
editor preferred term: polyacrylamide_gel_loading_buffer
definition: This solution is used for loading DNA samples onto denaturing polyacrylamide gels. In a 4% (19:1 crosslinking ratio) denaturing polyacrylamide gel, the bromophenol blue migrates at approximately 40 bases and the xylene cyanol migrates at approximately 170 bases. In a 6% (19:1 crosslinking ratio) denaturing polyacrylamide gel, the bromophenol blue migrates at approximately 25 bases and the xylene cyanol FF component at approximately 105 bases.
definition source: Promega, http://www.promega.com/enotes/faqspeak/0003/fq0019.htm
alternative term: bacteriophage T7 induced RNA polymerase T7 RNA polymerase
definition source: BioLabs. http://www.neb.com/nebecomm/products/productM0251.asp
definition: T7 RNA Polymerase catalyzes the synthesis of RNA in the 5´→ 3´ direction in the presence of a DNA template containing a T7 phage promoter. T7 RNA Polymerase can be used to generate high specific activity labeled RNA probes, RNA for in vitro translation, biologically active mRNA, and/or preparative quantities of defined length RNA by the run off transcription method.
editor preferred term: bacteriophage T7 RNA polymerase
Definitions: A compound that contains three or more hydroxyl groups.
Definition Editor: person:Allyson person:Chris Stoeckert person:Alan Ruttenberg
Definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
Definition Source: group:OBI OBI_0000030
Example Of Usage: Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
Definition: supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
alternative term: Kaliumsalze Kaliumsalz
definition source: Food-dictionary.com. http://www.food-dictionary.com/definition/potassium-salt.html
definition: a crystalline compound formed from the neutralisation of an acid solution containing potassium.
definition: gloves of natural latex is a product most trusted material and first choice for healthcare settings worldwide. Latex is a material that offer a consistent fit, flexibility, and resilience ( fits the best). Also, reliable performance and barrier protection against infection and contamination, but cause an allergic reaction for some users.
editor preferred term: reverse transcriptase polymerase chain reaction
Definition: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
definition source: *http://www.ppsk.usm.my/lecturers/mravi/PDF_FIles/Group_3_2002.pdf *http://www.pcrlinks.com/glossary/A.htm
definition: Annealing is a molecular function, where the forward and reverse primers anneal to separated DNA template strand.
editor preferred term: annealing activity
definition source: http://www.image2output.com/user_resources/TextFiles/pdfs/Deionised_Water.pdf
alternative term: demineralized water DI water DIW de-ionized water
definition: Deionized water, also known as demineralized water, is water that has had its mineral ions removed, such as cations from sodium, calcium, iron, copper and anions such as chloride and bromide.
editor preferred term: laboratory power supply
example of usage: Bio Rad: PowerPac Basic power supply
definition: Power supplies are used for electrophoresis and blotting applications and it function is provide consistent voltage and current for a chosen application.
definition source: BIO RAD power supplies. http://www3.bio-rad.com/B2B/vanity/gexp/product.do?language=English?language=English&ccatoid=-35457&pcatoid=-35440&com.broadvision.session.new=Yes&root=%2fProduct+Family%2fGX%2fHome&country=US&BV_SessionID=@@@@2062474633.1279054646@@@@&BV_EngineID=ccccadekmddhkeecfngcfkmdhkkdfll.0
definition source: Sample processing and separation techniques, Version 1.070708
Definition: A gel is a compund substance which is a colloid in a more solid form than a solution.
Definition: An oxoacid containing a single carboxy group.
editor preferred term: monocarboxylic_acid
editor preferred term: endodeoxyribonuclease
Definition: A group of enzymes catalyzing the endonucleolytic cleavage of DNA.
Note that the EC recommended name for this enzyme activity is 'calf thymus ribonuclease H', even though it is found in many species.
alternative term: endoribonuclease H (calf thymus) endoribonuclease0 H activity hybrid nuclease activity hybrid ribonuclease activity hybridase (ribonuclease H) hybridase activity ribonuclease H1 activity ribonuclease H2 activity ribonuclease H3 activity RNA*DNA hybrid ribonucleotidohydrolase activity RNase H activity RNase H1 activity RNase H2 activity RNase H3 activity calf thymus ribonuclease H activity endoribonuclease H
Definition: Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
editor preferred term: ribonuclease H activity
alternative term: B Pertussis Restriction Enzyme I BpeI Endonuclease DNA Restriction Enzyme HindIII Endonuclease BstFI Endonuclease EcoVIII Endonuclease HindIII HINDIII LlaCI, Endonuclease Deoxyribonuclease BstFI Deoxyribonuclease EcoVIII Endodeoxyribonuclease BpeI Endonuclease Asp52I Endonuclease BbrI Endonuclease BpeI Endonuclease Cfr32I Endonuclease ChuI Endonuclease Eco65I Endonuclease Eco98I Endonuclease Hin1076III Endonuclease Hin173I Endonuclease HinbIII Endonuclease HinfII Endonuclease HinJCII Endonuclease HsuI Endonuclease MkiI Endonuclease LlaCI
Definition: One of the Type II site-specific deoxyribonucleases. It recognizes and cleaves the sequence A/AGCTT at the slash. HindIII is from Haemophilus influenzae R(d). Numerous isoschizomers have been identified.
editor preferred term: deoxyribonuclease HindIII
Definition: The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
Editor Preferred Term: primary structure of RNA molecule
A material continuant that is described chiefly with respect to its chemical composition.
editor preferred term: Pfu DNA polymerase
Definition: A polymer composed of repeating ethyleneoxy units.
alternative term: alpha-hydro-omega-hydroxypoly(oxyethylene) ethylene glycol homopolymer Macrogol alpha,omega-hydroxypoly(ethylene oxide) ethylene glycol polymer polyethylene glycol Polyaethylenglykol Glycols, polyethylene polyoxyethylene poly(ethyleneoxide) PEG PEO poly(oxyethylene) polyethylene oxide POE (C2H4O)n alpha-hydro-omega-hydroxypoly(oxy-1,2-ethanediyl) 1,2-ethanediol homopolymer Polyaethylenglykole
definition source: *Axygen. http://www.axygen.com/categories/pcr *http://bioteknik.tradeindia.com/Exporters_Suppliers/Exporter16966.261147/Micro-Centrifuge-Tubes-PCR-Tubes.html
definition: PCR Tubes are specifically designed for use in thermal cyclers. The tube walls are ultra thin and consistent, to ensure a fast temperature exchange between heating system and sample, resulting in faster cycles. A wide variety of sizes, configurations, and colors are offered to help organize PCR processes.
editor preferred term: polymerase chain reaction
Definition: 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.
Definition Editor: PERSON: Jonathan Rees PERSON: Chris Stoeckert PERSON: Alan Ruttenberg
Editor Note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
Definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
Example Of Usage: Data items include counts of things, analyte concentrations, and statistical summaries.
Definition: An organic sodium salt that has formula C2H3NaO2.
alternative term: acetic acid, sodium salt C2H3NaO2 Natriumazetat sodium acetate anhydrous anhydrous sodium acetate
editor preferred term: organoammonium salt
definition source: http://www.encyclopedia.com/doc/107-chloroplastDNA.html
editor preferred term: chloroplast deoxyribonucleic acid
definition: chloroplast DNA (cpDNA) is a circular DNA, like that of mitochondria but several times larger, which is found in chloroplasts and other plastids and contains genes involved in the photosynthetic pathway. It is independent of a nuclear DNA and is maternally inherited. Between 40 and 80 DNA molecules occur in each organelle.
definition source: Withers, P.C., Reclosable plastic bags 2010, International Consolidated Bussiness Pty Ltd., Windsor (AU): Australia. p. 5.
definition: reclosable plastic bag, is a plastic bag which can be repeatedly opened and closed to receive or retrieve contents, and sometimes known as "zipper bags".
alternative term: zip lock bag zipper bag
Definition: Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.
Definition: 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.
alternative term: DNA Restriction Enzyme Endonuclease, Restriction Enzymes, DNA Restriction Restriction Endonuclease Restriction Enzyme, DNA
editor preferred term: DNA restriction enzyme
definition: PCR plates that can contain up to 96 samples. PCR plates, can be easily cut with scissors into 16, 24, 32, or 48-well pieces. The plate can be used in all 0.2ml V-bottom thermal cyclers and Real-Time thermal cyclers. finally, each plate is guaranteed RNase and DNase free.
editor preferred term: 96 well PCR plate
Definition: A molecular entity that contains carbon.
alternative term: 2'-deoxyuridine 5'-(tetrahydrogen triphosphate) deoxyuridine triphosphate 2'-deoxyuridine 5'-triphosphate C9H15N2O14P3
Definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C9H15N2O14P3.
Definitions: A member of the ethanols that has formula C2H6O.
alternative term: 1-hydroxyethane alcool ethylique Aethylalkohol spiritus vini Alkohol C2H5OH Aethanol Dehydrated ethanol alcohol alcohol etilico hydroxyethane EtOH Ethyl alcohol Methylcarbinol C2H6O CCO
definition source: http://www.qimr.edu.au/qimr_glossary.html
Definition: a macromolecule composed of one or several polypeptides. Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds.
Example Of Usage: A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3?) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
Definition: is a role which inheres in some molecular entity realized during the process of buffering
Definition Editor: Person:Helen Parkinson Philippe Rocca-Serra
editor preferred term: portable ice chest
definition: in chemistry and biology laboratories, the portable ice chest, is used for cooling samples (e.g. plant material, biological macromolecules), reagents, etc., during short time.
definition source: *Woods, E.A. and G. Worsham, Quick- Chill Ice Chest. 1989: United States of America. p. 5. *Lexic.us. http://www.lexic.us/definition-of/ice_chest#1
definition source: Weising, K., DNA fingerprinting in plants: principles, methods, and applications. Second Edition ed. 2005, Boca Raton, FL: Taylor & Francis Group.
editor preferred term: 5M potassium acetate solution
definition: in a plant DNA isolation protocol, the 5M potassium acetate solution is used to precipitated proteins and polysaccharides, leaving the nucleic acids in solution.
definition: Magnesium is a required cofactor for thermostable DNA polymerases, and magnesium concentration is a crucial factor that can affect the success of the amplification.
definition source: *http://www.promega.com/paguide/chap1.htm *http://www.pcrlinks.com/glossary/M.htm
editor preferred term: 25mM magnesium chloride
Definitions: A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it.
editor preferred term: nitrogen molecular entity
definition: mechanical pulverization of plant material, is a type of material processing. The plant materials are subjected to previous freezing with liquid nitrogen or dehydration. The purpose of the mechanical pulverization, is obtain a superfine powder to facilitate disruption of the cell wall of the plant cells.
editor preferred term: mechanical pulverization of plant material
definition source: Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples.
alterantive term: real-time PCR Instrument real-time PCR system real-time PCR cycler
definition: real-time PCR detection systems is an upgrade that adds real-time PCR capabilities to a base thermal cycler. The detection systems incorporate optical modules that enable detection of target sequences labeled with fluorescent probes. Sample quantitation by real-time PCR increases reliability of gene expression analyses, improves viral load assessment, and accelerates throughput in screening applications.
example ofo usage: DNA Engine Opticon 2 Real-Time Cycler
editor preferred term: real-time PCR thermal cycler
Definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
Definition Editor: PERSON:Melanie Courtot PERSON:James Malone PERSON:Chris Stoeckert
Definition Source: WEB: http://www.graphpad.com/www/book/survive.htm
definition: the harvest of plant material include the cutting of whole plant or only a anatomical structure of the plant. Harvesting includes an immediate post-harvest handling, for example, cooling of plant material, sorting, cleaning and packing.
definition source: http://en.wikipedia.org/wiki/Harvest
example of usage: the harvest of plant material is particularly important for plant breeding studies such as evaluation of phenotypic features, biochemical studies such as enzyme purification, for biomolecular studies such as nucleic acid extraction.
editor preferred term: harvest_of_plant_material
editor preferred term: laboratory glassware
example of usage: beakers, conical flask or erlenmeyer flask, graduated cylinder, volumetric flask, test tube, thermometer, glass microArray slides, micro filter holder assembly.
definition source: http://en.wikipedia.org/wiki/Laboratory_glassware
definition: Laboratory glassware refers to a variety of equipment or item, traditionally made of glass, used for scientific experiments and other work in science, especially in chemistry and biology laboratories. Some of the equipment or item is now made of plastic for cost, ruggedness, and convenience reasons, but glass is still used for some applications because it is relatively inert, transparent, more heat-resistant than some plastics up to a point, and relatively easy to customize. Between the functions of the laboratory glassware items include volumetric measuring, holding or storing chemicals or samples, mixing or preparing solutions or other mixtures, containing lab processes like chemical reactions, heating, cooling, distillation, separations including chromatography, synthesis, growing biological organisms, spectrophotometry, and containing a full or partial vacuum.
definition source: tools.invitrogen.com/content/sfs/manuals/10816015.pdf
definition: components necessary for easy loading and tracking of DNA samples in agarose or polyacrylamide gels.
Definition Editor: Bill Bug Frank Gibson Daniel Schober Melanie Courtot
Definition: A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
definition: A device or instrument that projects light, ultraviolet radiation, etc. Optimized for use with nucleic acid and protein stains such SYBR Green, SYBR Safe, ethidium bromide, etc.
definition source: http://en.wiktionary.org/wiki/transilluminator
definition: Nested PCR is a conventional PCR with a second round of amplification using a different set of primers. This second set of primers is specific to a sequence found within the DNA of the initial conventional PCR amplicon. The use of a second amplification step with the "nested" primer set results in a reduced background from products amplified during the initial PCR due to the nested primers’ additional specificity to the region. The amount of amplicon produced is increased as a result of the second round of amplification and due to a reduction in any inhibitor concentrations.
alternative term: nested PCR nested amplification
definition source: *Quality Assurance/Quality Control Guidance for Laboratories Performing PCR Analyses on Environmental Samples *http://www.pcrlinks.com/glossary/N.htm
editor preferred term: nested polymerase chain reaction
editor preferred term: nucleic acid stain role
definition: nucleic acid stain is an intercalating agent commonly used to visualize and quantify nucleic acids.
editor preferred term: deoxyribonuclease
definition(1): a deoxyribonuclease (DNase, for short) is any enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone. Deoxyribonucleases are thus one type of nuclease. A wide variety of deoxyribonucleases are known, which differ in their substrate specificities, chemical mechanisms, and biological functions. Definition(2): Enzymes which catalyze the hydrolases of ester bonds within DNA.
definition source: *http://en.wikipedia.org/wiki/Deoxyribonuclease *Medical Subject Headings, Version 2010_2009_08_17
alternative term: DNA Nucleases DNAase DNase DNase, Acid DNase, Alkaline Nucleases, DNA Acid DNase Alkaline DNase
Example Of Usage: nucleic acid extraction using phenol chloroform
Definition: A material separation in which a desired component of an input material is separated from the remainder
Definition Editor: Philippe Rocca-Serra Person:Bjoern Peters
Definition: Enzymes that catalyze the template-directed stepwise addition of ribonucleotides to the 3' end of a growing RNA chain using a single-stranded DNA template. The reaction is important in the flow of information from DNA to proteins. Three different forms of the polymerase have been identified and characterized.
alternative term: DNA-dependent RNA polymerase
editor preferred term: DNA-directed RNA polymerase
Definition: An enzyme that catalyses the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA/or RNA template or primer.
definition source: GO:0003887 DNA-directed DNA polymerase activity GO:0003964 RNA-directed DNA polymerase activity
alternative term: C2H3O2.K C2H3KO2 Kaliumazetat
Definition: A potassium salt that has formula C2H3O2.K.
definition: a crystalline compound formed from the neutralisation of an acid solution containing sodium.
definition source: Food-dictionary. http://www.food-dictionary.com/definition/sodium-salt.html
alternative term: Natriumsalze Natriumsalz
definition source: GMI, Inc. http://www.gmi-inc.com/Applied-Biosystems-ABI-377-DNA-Synthesizer.html
definition: ABI PRISM 377 DNA Sequencer automatically analyzes DNA molecules labeled with multiple fluorescent dyes. After samples are loaded onto the system's vertical gel- they undergo electrophoresis- laser detection- and computer analysis. Electrophoretic separation can be viewed on-screen in real-time- and final data can be output in a variety of formats. The 377 system accepts gel plates in four different lengths for flexibility in sample analysis.
example of usage: The human genome was sequenced with this instrument.
editor preferred term: ABI PRISM 377 DNA sequencer
alternative term: complementary DNA cDNA
definition: complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase.
editor preferred term: complementary_deoxyribonucleic_acid
imported from: Ontology for Genetic Interval, Version 0.15
Editor Preferred Term: sample preparation for assay
Definition Editor: PlanAndPlannedProcess Branch
Definition: A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
Definition Source: http://en.wikipedia.org/wiki/Vortex_mixer
Definition: A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
editor preferred term: reverse primer role
definition: reverse primer is the primer located at the 3'-end of the target sequence. the reverse primer has to be the reverse complement of the given cDNA sequence.
alternative term: downstream primer role antisense primer role
definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29
Definitions: Role played by a molecule or compound used to produce a chemical reaction to detect, measure, or produce other substances.
Definition: A quality inhering in a bearer by virtue of being kept below its freezing point. A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
editor preferred term: organonitrogen_compound
Definition: A compound containing at least one carbon-nitrogen bond.
definition: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial genome is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins (MSH).
alternative term: Mitochondrial DNA mtDNA
alternative term: C9H16N3O13P3 2'-deoxycytidine 5'-(tetrahydrogen triphosphate) 2'-deoxycytidine 5'-triphosphate deoxycytidine 5'-triphosphate deoxycytidine triphosphate
editor preferred term: Chemical entities of biological interest, Version 1.69
Definition: A pyrimidine 2'-deoxyribonucleoside 5'-triphosphate that has formula C9H16N3O13P3.
editor preferred term: 3′→5′ exonuclease (nonproofreading) activity
example of usage: Taq DNApolymerase. When a simple detection of an amplification product is the goal, Taq DNA polymerase is the most commonly used enzyme because yields tend to be higher with a nonproofreading DNA polymerase.
definition: Nonproofreading DNA polymerases can't remove a misincorporated nucleotide from a growing DNA chain. Amplification with nonproofreading DNA polymerases results in the template-independent addition of a single nucleotide to the 3′-end of the PCR product.
alternative term: nonproofreading DNA polymerase
definition source: Invitrogen. http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Nucleic-Acid-Purification-and-Analysis/Nucleic-Acid-Gel-Electrophoresis/nucleic_acid_gel_electrophoresis/Transillumination.html?CID=fl-safeimager
definition: This type of transiluminator, use pure visible blue light as the excitation source and there is NO damaging and dangerous ultra-violet radiation to worry about. Blue light transilluminators can be used for viewing a wide range of fluorescent samples including SYBR Green, SYBR Safe, GelStar, GelGreen, SYPRO Ruby, ProQ Diamond, fluorescein and various GFPs.
editor preferred term: blue light transilluminator
editor preferred term: electrophoresis buffer
definition: the buffer system in electrophoresis controls the pH of the gel, preventing damage to sample molecules and, in certain cases, controlling the ionization state of the molecules. A second, though no less significant function derives from the fact that the vast majority of current flowing through the electrophoresis gel is carried by the buffer ions.
definition source: National diagnostics. http://nationaldiagnostics.com/article_info.php/articles_id/8
editor preferred term: blue juice, agarose gel loading buffer
definition: Blue juice agarose gel loading buffer, is a liquid containing all of the components necessary for easy loading and tracking of DNA samples in agarose.
editor preferred term: elemental_nitrogen
Definition: Commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud.
editor preferred term: 2'-deoxyribonucleoside_triphosphate
Definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
Editor Note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
Definition Editor: PERSON: Chris Stoeckert
Example Of Usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
Editor Preferred Term: information content entity
Definition: A collection of information content entities intended to be understood together as a whole
Definition Editor: PERSON: Lawrence Hunter
Example Of Usage: A journal article, patent application, laboratory notebook, or a book.
editor preferred term: minus 20 degree Celsius freezer
definition: suitable for life science, clinical and industrial applications, these freezers maintain a uniform cabinet temperature of -20 degree C to -40 degree C, and are designed to provide rapid temperature recovery following door openings, many with frost-free operation.
definition source: Mandel. http://www.mandel.ca/products/General_Lab_Equipment/Freezers_Refrigerators/-20C_Freezers/index.html
definition: Nitrile is a synthetic Polymer that exhibits rubber-like characteristics. Nitrile is a material, protein and allergy free, offer the same flexibility, tensile strength, and durability as latex. the quality is superior to latex gloves in providing protection but are more expensive to produce than latex.
Definition: centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
Example Of Usage: PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
Definition Source: adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
editor preferred term: laboratory equipment
definition source: http://en.wikipedia.org/wiki/Laboratory_equipment
definition: laboratory equipment refers to machine, apparatus or device used by scientists working in a laboratory. Laboratory equipment is generally used to either perform an experiment or to take measurements and gather data.
example of usage: laboratory equipment include: DNA sequencer, microscopes, electrophoresis instrument, incubator, temperature control bath, microarray instrument, freezer, refrigerator, thermocycler, etc.
definition: PCR cycle role, is to produce a new DNA duplex, each strand acting as a potential template for one or other primer.
definition source: PCR glossary. http://www.pcrlinks.com/index.html
Definition Source: http://en.wikipedia.org/wiki/Mechanical_work
Definition: A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force.
Editor Preferred Term: mechanical function
definition source: * NiniScience. http://catalog.miniscience.com/catalog/Glassware/Test_Tube.html * Thomas Scott (transl., 1996), Concise Encyclopedia: Biology. Walter de Gruyter. ISBN 3110106612, 9783110106619. 1287 pages.
alternative term: culture tube sample tube
definition: A test tube, also known as a culture tube or sample tube, is a common piece of laboratory glassware consisting of a finger-like length of glass or clear plastic tubing, open at the top, usually with a rounded U-shaped bottom. Test tubes are available in a multitude of lengths and widths, typically from 10 to 20 mm wide and 50 to 200 mm long. The top often features a flared lip to aid pouring out the contents; some sources consider that the presence of a lip is what distinguishes a test tube from a culture tube. Some test tubes have a flat bottom; some are made so as to accept a ground glass stopper or a screw cap. They are often provided with a small ground glass or white glaze area near the top for labeling with a pencil.
definition source: http://en.wikipedia.org/wiki/Experiment
example of usage: negative control samples would contain all of the reagents for the PCR assay but no DNA.
editor preferred term: negative control role
definition: a negative control is known to give a negative result. The negative control demonstrates the base-line result obtained when a test does not produce a measurable positive result; often the value of the negative control is treated as a "background" value to be subtracted from the test sample results.
editor preferred term: LI-COR 4200 sequencer
definition source: Hilary G. Morrison and Mitchell L. Sogin. Random Genomics Using LI-COR's Model 4200 IR2 System. http://www.licor.com/bio/posters/App_491/App491.jsp
definition: LI-COR sequencers can routinely provide 800-1100 nucleotide, one-pass reads with accuracy levels better than 99% on single and double-stranded DNA templates. These instruments produce long nucleotide reads through the use of a focusing microscope mounted on a scanning laser to detect near-infrared fluorescence labeled products from DNA sequencing reactions.
Definition: A region (DNA) to which RNA polymerase binds, to begin transcription.
editor preferred term: RNA polymerase promoter activity
definition source: Navaneetham, D. and B.M. Conti-Fine, Augmented PCR amplification by thermally activated DNA polymerase -AmpliTaq Gold, in the presence of densifying agents. 1998.
definition: an alditol compound having three carbons. Glycerol is reported to improve the PCR process. The activity of DNA polymerase is influenced by densifying agents like glycerol. Glycerol concentrations between 12% and 18% have positive influence, in terms of PCR product intensity on agarose gel. Therefore, inclusion of glycerol in PCR mixture, increase the PCR product band intensity.
definition: A shaker is a device used in chemistry and biology laboratories to stir liquids. A typical shaker has a table board that oscillates horizontally, powered by an electric motor. The liquids to be stirred are held in beakers or Erlenmeyer flasks that are placed over the table; or, sometimes, in test tubes or vials that are nested into holes in the plate.
definition source: http://en.wikipedia.org/wiki/Shaker_%28laboratory%29
Definitions: Catalysis of the hydrolysis of any ester bond.
editor preferred term: hydrolase activity, acting on ester bonds
editor preferred term: oxoacid_derivative
definition source: Camlab. http://www.camlab.co.uk/item.asp?itemid=20614&categoryid=208&key=&letter=&browsecategoryid=0
editor preferred term: individual PCR tube
definition: individual PCR tubes are manufactured from polypropylene, these tubes feature dimensional uniformity and conical bottom. Offered in 0.2 and 0.5ml sizes and with choice of dome or flat cap style.
Definition: Amides of carboxylic acids, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
definition source: Beltrán, J., et al., Quantitative analysis of transgenes in cassava plants using real-time PCR technology. In Vitro Cellular & Developmental Biology - Plant, 2008. 45(1): p. 48-56.
definition: SYBR green is used as a dye for the quantification of double stranded DNA in some methods of real time PCR. It is also used to visualise DNA in gel electrophoresis.
Definition: Enzymes that catalyze the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides.
definition source: http://www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html#p
Example Of Usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
alternative term: ~#en scientific observation ~#en measuring
Definition: A planned process with the objective to produce information about some evaluant
definition source: http://en.wikipedia.org/wiki/Rubber_glove
definition: The most common material used for making gloves, is the latex, a form of rubber. Its primary purpose is protection of the hands while performing tasks involving chemicals.
Example Of Usage: Dendrograms are often used in computational biology to illustrate the clustering of genes.
Definition: A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
Definition Source: WEB: http://en.wikipedia.org/wiki/Dendrogram
editor preferred term: phosphoric acid derivative
definition source: Edvotek. http://www.edvotek.com/636.html
definition: these tips are blue color and are designed for dispensing volumes between 200µl and 1000µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
editor preferred term: micropipette tip(200-1000ul)
Definition: A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Definition: A family of enzymes that catalyze the exonucleolytic cleavage of RNA.
editor preferred term: ethidium bromide role
definition: Ethidium bromide is commonly used to detect nucleic acids in molecular biology laboratories. In the case of DNA this is usually double-stranded DNA from PCRs, restriction digests, etc. Single-stranded RNA can also be detected, since it usually folds back onto itself and thus provides local base pairing for the dye to intercalate. Detection typically involves a gel containing nucleic acids placed on or under a UV lamp.
alternative term: ethobromide role EtBr role dromilac role homidium Bromide role
definition source: *Bensaude, O. Ethidium Bromide and Safety- Readers Suggest Alternative Solutions. Trends Genet. 4:89; 1988. *Lunn, G.; Sansone, E.B. Decontamination of Ethidium Bromide Spills. Appl. Ind. Hyg. 4: 234-237; 1989.
editor preferred term: organic phosphate
Definition Source: http://en.wikipedia.org/wiki/Centrifuge
Example Of Usage: Eppendorf Multipurpose Centrifuge
Definition: A centrifuge is an instrument, generally driven by a motor, that puts an object in rotation around a fixed axis, applying force perpendicular to the axis. The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density.
Definition: An ethylenediamine derivative that has formula C10H16N2O8.
alternative term: edetic acid Acide ethylenediaminetetracetique acido edetico acidum edeticum acide edetique (ethane-1,2-diyldinitrilo)tetraacetic acid N,N'-1,2-Ethane diylbis-(N-(carboxymethyl)glycine) H4edta Edetic acid EDTA C10H16N2O8
dfinition source: Gene Ontology, Version 1.946. GO:0003899 DNA-directed RNA polymerase activity GO:0003968 RNA-directed RNA polymerase activity
Definition: An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template.
editor preferred term: hydrolase activity
Definitions: Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
definition source: *http://www.invitrogen.com/Content/benchtopics/Benchtopics_Amplification_Volume1_Number_3.pdf *http://www.pcrlinks.com/glossary/P.htm
editor preferred term: PCR additive role
definition: PCR additives, including formamide, DMSO, glycerol, betaine, and PCRx Enhancer Solution can enhance amplification. Their proposed mechanism is to lower the melting temperature, thereby aiding primer annealing and helping the DNA polymerase extend through regions of secondary structure.
definition: Forward primer is the primer located at the 5'-end of the target sequence. The forward primer has the same sequence as the "sense" strand (that produces the mRNA).
alternative term: upstream primer role sense primer role
definition source: http://www.scientific.org/tutorials/articles/riley/riley.html
editor preferred term: forward primer role
editor preferred term: tertiary structure of sequence macromolecule
definition: In biochemistry and molecular biology, the tertiary structure of a protein, nucleic acid or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.
definition source: *PAC, 1996, 68, 2193 (Basic terminology of stereochemistry (IUPAC Recomendations 1996)) on page 2220. *White book, p. 80.
Editor Preferred Term: primary structure of sequence macromolecule
Editor Note: These are all placeholders and should be replaced by SO terms
Definition: A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
editor preferred term: template quality role
definition source: QIAGEN, Sample & Assay Technologies. http://www.qiagen.com/faq/faqview.aspx?faqid=74&SearchText=&FaqCategoryId=0&MenuItemId=0&catalog=1&ProductLineId=1000222
definition: the quality of nucleic acid starting template affect PCR, in particular the sensitivity and efficiency of amplification. PCR sensitivity and efficiency can be reduced by the presence of impurities in nucleic acid preparations or in biological samples.
definition: a positive control is a procedure that is very similar to the actual experimental test but which is known from previous experience to give a positive result. The positive control confirms that the basic conditions of the experiment were able to produce a positive result, even if none of the actual experimental samples produce a positive result.
example of usage: in a PCR assay, the investigators could make several positive control samples containing various dilutions of the taq polymerase enzyme.
editor preferred term: positive control role
Definition Source: Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
Definition: A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
Example Of Usage: the phosphate concentration should be 0.1M
Editor Note: This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed. OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known. Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist.
Editor Preferred Term: molecular concentration
editor preferred term: secondary_structure_of_DNA_macromolecule
definition: the secondary structure of DNA macromolecule, refers to the basepairing interactions within a single molecule or set of interacting molecules.
Alternative term: DNA secondary structure
definition source: http://en.wikipedia.org/wiki/Biomolecular_structure#Secondary_structure
definition source: http://www.molecularstation.com/wiki/Pcr_master_mix
definition: a PCR master mix, is a mix of all most of the ingredients or factors necessary for PCR to occur. The goal of a PCR master mix is to decrease time spent pipetting.
editor preferred term: PCR master mix role
Definition: Quantitative PCR: a method to measure very small amounts of RNA transcripts as cDNA targets. There are two strategies currently used, one is called Competitive RTPCR and the other is called Real-Time PCR.
alternative term: qRTPCR quantitative RTPCR
editor preferred term: quantitative reverse transcriptase PCR
definition source: *Weising, K., DNA fingerprinting in plants: principles, methods, and applications. Second Edition ed. 2005, Boca Raton, FL: Taylor & Francis Group. *"There are many disinfectants available". www.umsl.edu/~microbes/pdf/disinfectants.pdf
definition: 70% ethanol in plant DNA isolation protocols, is used to wash pellet DNA. Ethanol is effective against a wide variety of pathogens if soaked for sufficient time (20-30 min). 70% ethanol is considered most effective disinfectant.
editor preferred term: 70 percentage ethanol
Definition: A list of plant material can be seeds, part of a plant or whole plants used as a subject of study.
Definitions: A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
Definition: Cyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.
alternative term: Zyaninfarbstoff Cyaninfarbstoff
definition: these tips are yellow color and are designed for dispensing volumes between 2µl and 200µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
editor preferred term: micropipette tip(2-200ul)
editor preferred term: micropipette tip(0.5-10ul)
definition: these tips are white color and are designed for dispensing volumes between 0.2µl and 10µl. Tips are available in bags of 1000 pieces non-sterile and in rack 96 pieces sterile, pyrogen-free. Material: polypropylene. Autoclavable.
alternative term: downstream primer antisense primer
editor preferred term: nuclear deoxyribonucleic acid
definition source: http://en.wikipedia.org/wiki/Nuclear_DNA
definition: Nuclear DNA (nDNA), is DNA contained within a nucleus of eukaryotic organisms.
alternative term: NUCLEIC ACID SEQ BASED AMPLIFICATION SELF SUSTAINED SEQ REPLICATION Analysis, NASBA NASBA Analysis Nucleic Acid Sequence Based Amplification Nucleic Acid Sequence-Based Amplification Replication, Self-Sustained Sequence Self Sustained Sequence Replication Sequence Replication, Self-Sustained NASBA
definition: An isothermal in-vitro nucleotide amplification process. The process involves the concomitant action of a RNA-DIRECTED DNA POLYMERASE, a ribonuclease (RIBONUCLEASES), and DNA-DIRECTED RNA POLYMERASES to synthesize large quantities of sequence-specific RNA and DNA molecules.
editor preferred term: self-sustained sequence replication
Definition: A boron oxoacid that has formula BH3O3.
alternative term: boron trihydroxide trihydroxidoboron B(OH)3 orthoboric acid H3BO3 BH3O3 [H]OB(O[H])O[H]
Editor Preferred Term: temperature control bath
Example Of Usage: VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
Definition: A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
Definition Editor: Alan Ruttenburg Frank Gibson Daniel Schober
Definition Source: OBI Instrument branch
alternative term: aminotris(hydroxymethyl)methane Tris base Tris amino Tris buffer Trometamol tris(hydroxymethyl)aminomethane THAM Tris-base Tromethamine 2-amino-2-(hydroxymethyl)propane-1,3-diol 2-Amino-2-(hydroxymethyl)-1,3-propanediol C4H11NO3 NC(CO)(CO)CO 1,1,1-tris(hydroxymethyl)methanamine
Definitions: A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
Definition: Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
editor preferred term: ribonuclease activity
definition source: http://www.biochem.northwestern.edu/holmgren/Glossary/Dedinitions/Def-N/nuclease.html
definition: one of the several classes of enzymes that degrade nucleic acid. An enzyme that can degrade DNA or RNA by breaking phosphodiester bonds.
definition source: Ehr, T.G.J., Transilluminator. 1994, Fotodyne Incorporated: United States. p. 7.
editor preferred term: UV transilluminator
definition: One apparatus used to illuminate electrophoresis gels produces ultraviolet light in a closed box. A light source within the box transmits UV light through a horizontal window provided in the top of the box. A gel is positioned over the window for illumination by the UV light, which passes through the gel from the window below. Such an apparatus is referred to as a transilluminator.
editor preferred term: temperature extension role
definition: the optimum extension temperature depends on the enzyme used but is usually between 68-72 degree C. In this phase of PCR cycle, the taq polymerase synthesizes a strand of DNA.
definition source: *http://www.wellscenter.iupui.edu/MMIA/htm/pcr.htm#4 *http://www.pcrlinks.com/glossary/E.htm
alternative term: temperature elongation role
editor preferred term: graduated cylinder
definition source: http://en.wikipedia.org/wiki/Graduated_cylinder
definition: A graduated cylinder, also known as a measuring cylinder, is a piece of laboratory equipment used to accurately measure the volume of an object. Water displacement can be used to find out the volume of an object. Graduated cylinders are generally more accurate and precise for this purpose than flasks and beakers. Often, the largest graduated cylinders are made of polypropylene for its excellent chemical resistance or polymethylpentene for its clarity, making them lighter to ship and less fragile than glass. Polypropylene cylinders have excellent chemical high resistance and do not shatter when dropped, although one problem with this type of cylinder is that it can not be heated. Polypropylene is easy to repeatedly autoclave (sterilize); however, autoclaving of some polypropylene graduated cylinders may affect their accuracy.
definition: A DNA ladder is a solution of DNA molecules of different lengths used in agarose and polyacrylamide gel electrophoresis. It is applied to an agarose and polyacrylamide gel as a reference to estimate the size of unknown DNA molecules. In addition it can be used to approximate the mass of a band by comparison to a special mass ladder.
definition source: http://en.wikipedia.org/wiki/DNA_ladder
example of usage: a λ DNA-HindIII Digest: a common lambda DNA ladder that has band sizes (in base pairs) of 23,130; 9,416; 6,557; 4,361; 2,322; 2,027; 564; and 125 bp.
definition source: Mandel. http://www.mandel.ca/products/liquid_handling/tips/Specialty_Tips/index.htm
definition: micropipette tips have a wide tip opening that helps prevent damage to fragile cell and genomic DNA during pipetting. May also be used with viscous solutions for greater accuracy. Polypropylene tips are autoclavable. RNase, DNase, DNA free, and non-pyrogenic.
alternative term: Conical flask E-Spot flask
definition: An Erlenmeyer, commonly known as a conical or E-Spot, is a widely used type of laboratory flask which features a flat, conical body, and a cylindrical neck. It's named after the German chemist Emil Erlenmeyer, who created it in 1861. The Erlenmeyer is usually marked on the side (graduated) to indicate the approximate volume of contents, and has a spot of ground glass or enamel where it can be labeled with a pencil. It differs from the beaker in its tapered body and narrow neck. The opening usually has slight rounded lips so that the Erlenmeyer can be easily stoppered using a piece of cotton wool. Alternatively, the neck may be fitted with a female ground glass joint to accept a glass stopper. The conical shape allows the contents to be swirled or stirred during an experiment, either by hand or by a shaker; the narrow neck keeps the contents from spilling out. The smaller neck also slows evaporative loss better than a bigger neck. The flat bottom of the conical makes it unlikely to tip over and spill.
definition source: http://en.wikipedia.org/wiki/Conical_flask
editor preferred term: monocarboxylic acid amide
alternative term: upstream primer sense primer
definition: When designing primers for PCR, sequencing or mutagenesis it is often necessary to make predictions about these primers, for example melting temperature (Tm) and propensity to form dimers with itself or other primers in the reaction. Some thoughts on designing primers. 1. primers should be 17-28 bases in length; 2. base composition should be 50-60% (G+C); 3. primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; 4. Tms between 55-80oC are preferred; 5. 3'-ends of primers should not be complementary (ie. base pair), as otherwise primer dimers will be synthesised preferentially to any other product; 6. primer self-complementarity (ability to form secondary structures such as hairpins) should be avoided; 7. runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided.
editor preferred term: primer_desing_role
definition source: adapted from Innis and Gelfand,1991
Example Of Usage: A journal article or book
Definition: A document that has been accepted by a publisher
editor preferred term: phage RNA polymerase promoter activity
Definition: A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription.
editor preferred term: real time polimerase chain reaction
term adapted from: NCI Thesaurus, Version 10.01 ID: Real_Time_PCR Full Id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Real_Time_PCR
definition source: *http://en.wikipedia.org/wiki/Real-Time_PCR *http://www.pcrlinks.com/glossary/R.htm
alternative term: Real Time PCR quantitative (real-time) PCR Real-Time Quantitative PCR RTQ-PCR
definition: Real-Time PCR, also called quantitative (real-time) PCR or Real-Time Quantitative PCR (RTQ-PCR), is a method of simultaneous DNA quantification and amplification. DNA is specifically amplified by polymerase chain reaction. After each round of amplification, the DNA is quantified. Common methods of quantification include the use of fluorescent dyes that intercalate with double-strand DNA and modified DNA oligonucleotides (called probes) that fluoresce when hybridized with a complementary DNA.
definition source: *Fisher scientific. http://www.fishersci.com/wps/portal/CMSTATIC?href=Scientific/lifeScience/ProductsServices/Electrophoresis/electrophoresis_index.jsp&store=Scientific&segment=lifeScience *BIO-RAD. http://www3.bio-rad.com
definition: electrophoresis instrument is used for protein and nucleic acid separation. These instruments use gel systems or blotters.
alternative term: electrophoresis equipment
editor preferred term: electrophoresis instrument
example of usage: types of electrophoresis instruments: protein electrophoresis, nucleic acid electrophoresis, precast gel systems, 2-D systems.
Definition: Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
editor preferred term: transferase activity, transferring phosphorus-containing groups
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
Definition: A molecular entity consisting of two or more chemical elements.
editor preferred term: heteroatomic molecular entity
Definition Source: WEB: http://en.wiktionary.org/wiki/photograph
Definition Editor: PERSON:Joanne Luciano PERSON:Melanie Courtot PERSON:Alan Ruttenberg
Definition: A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
Definition: 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
alternative term: 3',3'',5',5''-tetrabromophenolsulfophthalein 4,4'-(1,1-dioxido-3H-2,1-benzoxathiole-3,3-diyl)bis(2,6-dibromophenol) bromophenol blue, sultone form 3',3'',5',5''-tetrabromophenolsulfonephthalein C19H10Br4O5S
editor preferred term: pyrimidine_deoxyribonucleoside_triphosphate
Example Of Usage: Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
Definition Editor: person:Chris Stoeckert
Definition: A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
editor preferred term: nucleoside_phosphate
Example Of Usage: Any picture, diagram or table.
Definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
definition source: http://en.wikipedia.org/wiki/Tetramethylammonium_chloride
definition: etramethylammonium chloride is a quaternary ammonium salt with the chemical formula [(CH3)4N]Cl. It is a colourless solid that is soluble in water and polar organic solvents. Tetramethylammonium chloride has few applications, unlike quaternary ammonium salts that feature more longer alkyl substituents.
editor preferred term: tetramethylammonium chloride
Definition: A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis.
editor preferred term: inorganic hydroxy compound
editor preferred term: nuclease activity
Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', does not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
Definition: Catalysis of the hydrolysis of ester linkages within nucleic acids.
definition: ultra low temperature freezer (-86 degree C to -120 degree C) offers an array of ultra low temperature freezers. Uses of ultra low temperature freezer include prolonged storage of temperature sensitive biological samples, red cell samples and blood plasma.
editor preferred term: minus 86 degree Celsius freezer
definition source: Deepee Cooling Products Pvt. Ltd. http://www.hospitals-management.com/products_services/medicalequipment_technology/deepee_cooling_products.html
editor preferred term: 3M sodium acetate solution
definition: routinely used in DNA and RNA precipitation.
definition source: Fermentas. http://www.fermentas.com/en/products/all/reagents/r118-sodium-acetate-solution
editor preferred term: polyacrylamide_gel_electrohoresis
Definition: Polyacrylamide gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of polyacrylamide.
definition: P-100 model, refer to the maximum volume in microliters. P100 is a micropipette designed for dispensing volumes between 20µl and 100µl.
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123615
editor preferred term: P-100 micropipette
Definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
editor preferred term: double-distilled water
alternative term: ddH2O Bidest. water DDW
definition source: http://en.wikipedia.org/wiki/Purified_water#Double-distillation
definition: Double-distilled water is prepared by double distillation of water. Historically, it was the de facto standard for highly purified laboratory water for biochemistry and trace analysis until combination methods of purification became widespread.
definition source: Chevet, E., G. Lemaitre, and M.D. Katinka, Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic Acids Res, 1995. 23(16): p. 3343-4.
definition: in low concentrations, it is used with polymerase chain reactions to increase yield and specificity. It has been shown to enhance yield 5-10 fold at 3M by stabilizing the AT base pairs.
editor preferred term: tetramethylammonium chloride role
editor preferred term: thermostable DNA polymerase
definition: Thermostable DNA polymerases revolutionized and popularized PCR because of their ability to withstand the high denaturation temperatures. The use of thermostable DNA polymerases also allowed higher annealing temperatures, which improved the stringency of primer annealing.
definition source: Promega, Protocols & Applications Guide. http://www.promega.com/paguide/chap1.htm
Definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
alternative term: acido nucleico Nukleinsaeuren acide nucleique NA Nukleinsaeure
alternative term: organic entity organic compound
editor preferred term: organic molecular entity
Definition: A contain function is a function to bound or constrain some quantity of material in some space
Definition: Distinct from adult leaves, being characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
Accession: PO:0006339 The first juvenile leaves are e.g. the embryonic leaves found in the grass kernel (caryopsis).
Definition: A simple carboxylic acid containing two carbons; the active ingredient in vinegar. Unlike longer-chain carboxylic acids (the fatty acids), acetic acid does not occur in natural triglycerides. Reported to suppress accumulation of body fat and liver lipids in mice.
alternative term: ethoic acid HOAc Essigsaeure CH3-COOH acide acetique Ethylic acid Methanecarboxylic acid Ethanoic acid C2H4O2
Definition: A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
editor preferred term: tertiary structure of RNA macromolecule
definition: is a level of organization of RNA, in which, the secondary structure elements are associated through numerous van der Waals contacts, specific hydrogen bonds via the formation of a small number of additional Watson-Crick pairs and/or unusual pairs involving hairpin loops or internal bulges. The parsing of energy levels between secondary and tertiary structures is reasonable in large RNAs, considering the relative energies and the clear identification of the secondary structure elements. In some cases, it is even possible to cut RNA molecules into modular domains which can re-associate only through tertiary contacts. RNA tertiary structure comprises those interactions involving (a) two helices, (b) two unpaired regions, or (c) one unpaired region and a double-stranded helix.
alternative term: RNA tertiary structure
editor preferred term: purine_2'-deoxyribonucleoside_5'-triphosphate
definition: fine powder of plant material is obtained by mechanical action of grind the tissue in a mortar and pestle. This takes a fair amount of effort but it is worth it because the finer the grind, the greater the DNA yields.
editor preferred term: fine powder of plant material
definition: A beaker is a simple container for stirring, mixing and heating liquids commonly used in many laboratories. Beakers are generally cylindrical in shape, with a flat bottom and a lip for pouring. Beakers are available in a wide range of sizes, from one millilitre up to several litre.
definition source: Oxford English Dictionary 1989 edition
editor preferred term: sulfur molecular entity
definition: A PCR technique designed to amplify a limited genomic DNA sample so as to generate a new sample that is indistinguishable from the original but with a higher DNA concentration.
editor preferred term: whole genome amplification
definition source: Sarkar, G., S. Kapelner, and S.S. Sommer, Formamide Can Dramatically Improve the Specificity of Pcr. Nucleic Acids Research, 1990. 18(24): p. 7465-7465.
definition: role of formamide in the PCR, is eliminate most of the nonspecific products and increase the efficiency of the amplification.
definition source: http://en.wikipedia.org/wiki/Weighing_scale
definition: laboratory balance instrument, is a measuring instrument for determining the weight or mass of an object.
editor preferred term: laboratory balance instrument
Example Of Usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
Definition: A figure that expresses one or more propositions
editor preferred term: 384 well PCR plate
definition source: Axigen. http://www.axygen.com/categories/pcr
definition: PCR plates that can contain up to 384 samples. 384 PCR plates are designed to fit virtually all thermal cyclers available. Also, each plate is guaranteed RNase and DNase free.
definition: A freezer is a dry, cold-storage machine. In a laboratory, the freezer is used to store tissue of the plant material, nucleic acids, enzymes, reagents and other supplies that needs to be stored at temperatures below zero degrees Celsius.
Definition: a material separation to recover the nucleic acid fraction of an input material
Editor Preferred Term: nucleic acid extraction
Example Of Usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
definition: P-10 model, refer to the maximum volume in microliters. P10 is a micropipette designed for dispensing volumes between 1µl and 10µl.
editor preferred term: P-10_micropipette
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F144802
definition: Agarose gel electrophoresis is a one dimensional gel electrophoresis protocol which use the application of voltage to separate a sample along a separation medium which is a gel matrix made of agarose.
editor preferred term: agarose gel electrophoresis
Definition: An alkali metal hydroxide that has formula HLiO.
alternative term: LiOH HLiO Lithiumhydroxid lithium hydrate lithium hydroxide anhydrous
editor preferred term: lithium hydroxide
alternative term: RNA pentosenucleic acid ribose nucleic acid
Definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
Definition: A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. T7 RNA Polymerase is an RNA polymerase that catalyzes the formation of RNA in the 5'→ 3' direction. T7 polymerase is extremely promoter-specific and only transcribes bacteriophage T7 DNA or DNA cloned downstream of a T7 promoter.
definition source: *http://en.wikipedia.org/wiki/T7_RNA_polymerase * NIFSTD, Version 1.8
editor preferred term: T7 RNA polymerase promoter activity
Example Of Usage: A cell lysis, production of a cloning vector, creating a buffer.
Editor Preferred Term: material processing
alternative term: ~#en material transformation
Definition: A planned process which results in physical changes in a specified input material
Definition Editor: PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Bjoern Peters PERSON: Philippe Rocca Serra
editor preferred term: P-1000 micropipette
definition: P-1000 model, refer to the maximum volume in microliters. P1000 is a micropipette designed for dispensing volumes between 200µl and 1000µl.
definition source: Anachem, a Mettler Toledo Company. http://www.anachem.co.uk/catalogue/product/itemNo/F123602
alternative term: delta DNA polymerase activity deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (DNA-directed) activity deoxyribonucleic acid duplicase activity deoxyribonucleic duplicase activity deoxyribonucleic polymerase I DNA duplicase activity DNA nucleotidyltransferase (DNA-directed) activity DNA polymerase alpha DNA polymerase beta DNA polymerase gamma DNA polymerase I DNA polymerase II DNA polymerase III DNA polymerase V activity DNA replicase activity DNA-dependent DNA polymerase activity duplicase epsilon DNA polymerase activity eta DNA polymerase activity gamma DNA-directed DNA polymerase activity iota DNA polymerase activity kappa DNA polymerase activity Klenow fragment lambda DNA polymerase activity mu DNA polymerase activity nu DNA polymerase activity sequenase sigma DNA polymerase activity Taq DNA polymerase Taq Pol I Tca DNA polymerase theta DNA polymerase activity zeta DNA polymerase activity alpha DNA polymerase activity beta DNA polymerase activity
editor preferred term: DNA-directed DNA polymerase activity
Definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and primer.
definition: A mortar and pestle is a tool used to crush, grind, and mix solid substances (trituration). The pestle is a heavy bat-shaped object, the end of which is used for crushing and grinding. The mortar is a bowl, typically made of hard wood, marble, clay, or stone. The substance to be ground is placed in the mortar and ground, crushed or mixed with the pestle.
definition source: http://en.wikipedia.org/wiki/Mortar_and_pestle
editor preferred term: mortar and pestle
Definition: A document that has been accepted by a patent authority
editor preferred term: pyrimidine_2'-deoxyribonucleoside_5'-triphosphate
Definition: A quality inhering in a leaf (anatomical part of a plant) by virtue of being kept below its freezing point. A quality inhering in a leaf (anatomicla part of a plant) by virtue of the leaf is being kept below its freezing point.
definition source: adapted from: oboContent:PATO
Definition Editor: PERSON: Philippe Rocca-Serra
Definition: agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.
Example Of Usage: Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
Definition: Adult leaves are characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.
Accession: PO:0006340 The adult leaves are placed above the juvenile (oldest) leaves. However in some plants the juvenile leaves may go on to establish as adult leaves.
editor preferred term: agarose gel electrophoresis instrument
definition: agarose gel electrophoresis instruments are typically used for separating larger nucleic acids or protein samples. These apparatuses come in horizontal or vertical forms.
Definition: Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
definition: This is an example of the type of plate used in ELISA assays. It uses 48 or 96 well microtiter plate format, and is made of inexpensive transparent plastic material. These types of plates are sometimes used in ELISPOT assays as well. They have the advantage of being much cheaper than other plates which are commonly used in ELISPOT assays.
example of usage: This type of plate is used in Enzyme-linked immunosorbent assay (ELISA), also known as an enzyme immunoassay (EIA), is a biochemical technique used mainly in immunology to detect the presence of an antibody or an antigen in a sample. The ELISA has been used as a diagnostic tool in medicine and plant pathology, as well as a quality control check in various industries.
definition source: http://www.membrane-solutions.com/elisa_plate_products.htm
Definition: The entire plant, including roots, shoots and leaves, at any stage of its life cycle.
Accession: PO:0000003 This term is so general that it should be avoided whenever possible.
definition: the tertiary structure of a DNA is its precise three-dimensional structure, as defined by the atomic coordinates.
editor preferred term: tertiary structure of DNA macromolecule
term imported from: Chemical entities of biological interest, Version 1.69
Definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
alternative term: desoxyribose nucleic acid DNA
Definition: A camera is an image acquistion device which is used for taking photographs (usually consisting of a lightproof box with a lens at one end and light-sensitive film at the other).
definition source: Mo Bio, Laboratories, Inc. http://www.mobio.com/pcr-water/pcr-water-certified-dna-free.html
definition: Water certified by PCR to be free of all DNA, RNase, and DNase contamination.
Definition: A purine 2'-deoxyribonucleoside 5'-triphosphate that has formula C10H16N5O13P3.
alternative term: deoxyguanosine triphosphate C10H16N5O13P3 2'-deoxyguanosine 5'-(tetrahydrogen triphosphate) 2'-deoxyguanosine 5'-triphosphate deoxyguanosine 5'-triphosphate
Definition: An enzyme that catalyzes the template-directed addition of ribonucleotides to the 3' end of a growing RNA chain. The enzyme utilizes single-stranded RNA as a template.
editor preferred term: RNA-directed RNA polymerase
alternative term: RNA-dependent RNA polymerase
definition source: Biology Online, Answers to all your Biology Questions. http://www.biology-online.org/dictionary/Macromolecule.
alternative term: biological macromolecule
definition: In biology, a macromolecule is a term used to a large complex molecule, such as nucleic acids, proteins, carbohydrates and lipids, which are made up of small monomers linked together and with relatively large molecular weight.
editor preferred term: alkali metal hydroxide
Editor Preferred Term: reverse transcriptase
Definition Editor: person:Melanie Courtot
Definition: enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity).
Editor Preferred Name: DNA-directed DNA Polymerase
definition source: (1) medical dictionary. http://www.mondofacto.com/facts/dictionary?DNA-directed+DNA+polymerase (2) IUBMB Enzyme Nomenclature
alternative term: DNA-Dependent DNA Polymerase
definition (1): During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair. Definition (2): Catalyses DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. Requires a primer, which may be DNA or RNA. (IUBMB Enzyme Nomenclature)
Example Of Usage: a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
Editor Preferred Term: nucleic acid template role
Definition: nucleic acid template role is inhering in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
definition: An incorrect concentration of deoxynucleotidetriphosphates (dNTPs) can cause problems for the PCR procedure. The usual dNTP concentration is between 40μM and 200μM of EACH of the four dNTPs. Excessive dNTP concentrations can inhibit the PCR preventing the formation of product. However, concentrations up to 400 μM each dNTP have been reported to work adequately. Low primer, target, Taq, and dNTP concentrations are preferable as these generally ensure cleaner product and lower background. For longer PCR-fragments a higher deoxynucleotidetriphosphate concentration may be required. A large change in the dNTP concentration may require a corresponding change in the concentration of MgCl2. definition: Mix consists of a solution of all four nucleotides (dATP, dCTP, dGTP, dTTP). Usually, each nucleotide at a concentration of 2.5 mM. It is neutralized to pH 8.0 with NaOH, and supplied in purified water. dNTP Mix is suitable for use in polymerase chain reaction (PCR), sequencing, fill-in, nick translation, cDNA synthesis, and TdT-tailing reactions.
definition source: PCR Troubleshooting: Inadequate dNTPs. http://www.highveld.com/pages/pcr-troubleshooting.html
definition source: Markoff, A., et al., Optimization of single-strand conformation polymorphism analysis in the presence of polyethylene glycol. Clinical Chemistry, 1997. 43(1): p. 30-33.
definition: polyethylene glycol (PEG) helps improve the differential separation of conformers (a conformation of a molecule). Therefore in PCR, the PEG is used to precipitate the PCR reaction.
editor preferred term: polyethylene glycol role
editor preferred term: RNA-directed DNA polymerase
Definition: An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements.
alternative term: DNA polymerase, RNA-dependent reverse transcriptase revertase RNA dependent DNA polymerase RNA transcriptase RNA-dependent DNA polymerase DNA polymerase, RNA directed DNA polymerase, RNA-directed deoxynucleotide-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) RNA directed DNA polymerase
definition: phase of PCR cycle following annealing of primer during which the Taq polymerase synthesizes a strand of DNA. The optimum temperature depends on the enzyme used but is usually between 68 - 72 degree C.
definition source: http://www.wellscenter.iupui.edu/MMIA/htm/pcr.htm#4
editor preferred term: extension activity
editor preferred term: multiplex polymerase chain reaction
definition: Multiplex PCR is the term used when more than one pair of primers is used in a PCR. The goal of multiplex PCR is to amplify several segments of target DNA simultaneously and thereby to conserve template DNA, save time, and minimize expense. It is a PCR strategy that enables the amplification of multiple DNA targets in one run.
definition source: *http://viroligo.okstate.edu/enterdata/PCRs.htm *http://www.pcrlinks.com/glossary/M.htm
definition source: European Aluminium Foil Association (EAFA). [cited 2010; Available from: http://www.alufoil.org/front_content.php.
definition: is aluminium prepared in thin metal leafs, with a thickness less than 0.2 mm (0.008 in), although much thinner gauges down to 0.006 mm are commonly used.
definition: Used in cryogenic atmosphere, ultra low temperature freezers, dry ice, steam autoclaves and ovens. Suitable for temperatures from -160°C (-250°F) to +148°C (300°F).
definition: Gel electrophoresis is used in forensics, molecular biology, genetics, microbiology and biochemistry. The results can be analyzed quantitatively by visualizing the gel with a transilluminator and a gel imaging device. The image is recorded with a camera, and the intensity of the band or spot of interest is measured and compared against standard or markers loaded on the same gel. Depending on the type of analysis being performed, other techniques are often implemented in conjunction with the results of gel electrophoresis, providing a wide range of field-specific applications.
definition source: http://en.wikipedia.org/wiki/Gel_electrophoresis#Applications
editor preferred term: gel-based electrophoresis
editor preferred term: temperature denaturating role
definition: denaturation temperature, plays a role in the process of splitting the complementary double strands of DNA to form single strands.
definition source: *Short Tandem Repeat DNA Internet DataBase *http://www.pcrlinks.com/glossary/D.htm
Definition: A quality inhering in a DNA by virtue of being kept below its freezing point. A quality inhering in a DNA by virtue of the DNA is being kept below its freezing point.
editor preferred term: magnesium_molecular_entity
editor preferred term: tetracarboxylic_acid
Definition: An oxoacid containing four carboxy groups.
Definitions: A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
definition source: http://www.cramster.com/reference/wiki.aspx?wiki_name=Microcentrifuge_tube
editor preferred term: microcentrifuge_tube
definition: Microcentrifuge tubes or microfuge tubes are small, cylindrical plastic containers with conical bottoms, typically with an integral snap cap. They are used in molecular biology and biochemistry to store and centrifuge small amounts of liquid. Made of polypropylene, they can be used in very low temperature (-20 °C) or with organic solvents such as chloroform. They come in many different sizes, generally ranging from 250 μL to 2.0 mL. The most common size is 1.5 mL. Disinfection is possible (1 atm, 120 °C, 20 minutes), but due to their low cost and the difficulty in cleaning the plastic surface, they are usually discarded after each use.
example of usage: Eppendorf tube has become a genericized trademark for microfuge tubes or microcentrifuge tubes. Eppendorf is a major manufacturer of this item, but by no means the only one.
Editor Preferred Term: centrifuge pellet role
Definition: pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.
Example Of Usage: Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
editor preferred term: laboratory microwave oven
definition source: http://www.microwaveresearch.com/
definition: Laboratory microwave ovens, are used in sample preparation for biological, chemical and medical applications.
example of usage: laboratory microwave oven, is used to heat chemical substances in solution, or return to liquid state to the agarose gels.
definition: nitrogen gas condensed to a liquid with a boling point of about -196 degree Celsius. Very commonly the medium in which containers of genetic material are stored.
definition source: Zaid, A., et al., Glossary of biotechnology and genetic engineering. 1999.
alternative term: LN - Liquid nitrogen Liquid nitrogen (substance)
alternative term: 2-{[3-(dimethylamino)propyl](propyl)amino}-4-[(E)-(3-methyl-1,3-benzothiazol-2(3H)-ylidene)methyl]-1-phenylquinolinium 2-{(E)-[2-{[3-(dimethylamino)propyl](propyl)amino}-1-phenylquinolin-4(1H)-ylidene]methyl}-3-methyl-1,3-benzothiazol-3-ium
Definition: SYBR Green I is a cationic unsymmetrical cyanine dye used as a nucleic acid stain in molecular biology. SYBR Green I binds to double-stranded DNA.
alternative term: aqua hydrogen hydroxide Wasser water [OH2] oxidane dihydrogen oxide dihydridooxygen HOH eau agua acqua H2O BOUND WATER [H]O[H]
Definition: An inorganic hydroxy compound that has formula H2O.
definition: the quantity of nucleic acid starting template affect PCR, in particular the sensitivity and efficiency of amplification. PCR sensitivity and efficiency can be reduced by the presence of impurities in nucleic acid preparations or in biological samples.
editor preferred term: template quantity role
definition: A naturally occurring substance of large molecular weight, responsible of genetic transmision.
Alternative term: genetically encoded biomacromolecule information macromolecule genetically encoded biopolymer information biopolymer
editor preferred term: information_biomacromolecule
definition source: http://www.biology-online.org/dictionary/Biomacromolecule
Definition: A processual entity that realizes a plan which is the concretization of a plan specification.
Editor Note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Example of usage: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
Imported From: Ontology(http://purl.obolibrary.org/obo/obi.owl)
Example Of Usage: Injecting mice with a vaccine in order to test its efficacy
editor preferred term: analytical balance instrument
definition source: http://en.wikipedia.org/wiki/Analytical_balance#Analytical_balance
definition: An analytical balance is used to measure mass to a very high degree of precision and accuracy. The measuring pan(s) of a high precision (0.1 mg or better) analytical balance are inside a transparent enclosure with doors so that dust does not collect and so any air currents in the room do not affect the balance's operation.
Definition: A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
Definition: An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
editor preferred term: amino-acid betaine
Definition: Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents.
editor preferred term: purine deoxyribonucleoside triphosphate
definition: annealing temperature is one of the most important parameters that need adjustment in the PCR reaction. Moreover, the flexibility of this parameter allows optimization of the reaction in the presence of variable amounts of other ingredients (especially template DNA and oligonucleotide primer length).
editor preferred term: temperature annealing role
Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
Example of usage: the life of an organism, the process of sleeping, the process of cell-division
Definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
Example: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxyrenated and oxygenated blood, etc.
Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
Definition: A spatial region [snap:SpatialRegion] with three dimensions.
Example of usage: a cube-shaped part of space, a sphere-shaped part of space
Definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
Example: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building.
Example of usage: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall.
Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
Example of usage: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life
alterantive term: real-time PCR Instrument real-time PCR system
Definition: A spatial region [snap:SpatialRegion] with one dimension.
Example of usage: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space.
Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
Example of usage: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space.
editor preferred term: automated electrophoresis equipment
Example of usage: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.
Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
Example of usage: the sum total of all space in the universe, parts of the sum total of all space in the universe
Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
Example of usage: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
Definition: A spatial region [snap:SpatialRegion] with no dimensions.
Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
Example of usage: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together
Example of usage: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
Example of usage: an organism, a heart, a chair, a lung, an apple
Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
Example of usage: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.
Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
Example of usage: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso.