Appendix
Contents
Appendix
Review Process
Curators
• Use cover sheet to ask questions & bring up confusing issues.
• If you did something “special” explain why.
• If you do not know how to do something, you should ask before curating. Try to ask the correct senior curator-we all have our “specialties”.
• Always print a new PDF & return old PDF when asked to recurate & return to PR.
• Prioritize recurations over initial curations
Reviewers
• Answer questions that are brought up & decide if it’s a minor misunderstanding or a real unresolved issue.
• Ask other reviewers about any issue that you are not certain about before responding to the curator (communication is good!)
• Do not sign the cover sheet if you need to see the curation again
• Submit unresolved issues with all needed information to Nima by Monday for curation meeting discussion. Provide the current guideline(s), PMID, & describe what the problem is with some ideas about solutions.
• Keep review time to a minimum, if you have time off or are otherwise unable to complete a review on time, have it reassigned. If there is a delay, communicate with the curator.
• The goal is more consistent review! We must work together and share our experiences/opinions.
Metrics
For consistent metrics regarding peer review, please use the following guidelines:
• No recuration-no changes at all, corrections to typos, very minor changes that are due to problems with the system, waiting on additions to Finders, suggested subjective changes, etc.
• Minor recuration-forgotten/wrong minor fields (cell type, adjuvant, carrier etc), needs/edit comments, misunderstanding of new field, complex/confusing issue, bulking issues etc.
• Major recuration-forgotten/wrong major field (immunogen), did not curate figures/epitopes, misinterpretation of the paper, misunderstanding regarding well established rules.
Displayed Antibodies
- The cDNA of an antibody is cloned and expressed on the surface of macromolecular complexes and individual binders are subsequently selected. The cDNA is generally attached to the macromolecular complex to allow for rapid determination of the sequence of the positive clones. This technology is an alternative to the classical monoclonal antibody method using hybridoma generation from secreting clones.
- The most common library type is phage display, but other constructs, such as ribosome or yeast display, may be used.
- The antibody cDNA which is displayed may originate from either naïve or immunized individuals. Non-human libraries are usually immune and human libraries are usually from naïve or naturally exposed individuals, but there are exceptions. The Immunization field should reflect this status when provided by the reference. If the library is derived from a naive subject(s), the Immunization Category should be <Phage Display (No immunization)>. Immune libraries have increased frequency of binders and higher affinity of binding, but naïve libraries are often a source of binders of varied specificities and may be commercially available. Synthetic libraries consist of artificially generated antibody sequences and require a comment in the Comments on Immunization field to clarify what antibodies were used.
- The type of assays to be entered as contexts are those typically included in other antibody contexts, such as epitope characterization by binding of particular clones. Selection assays (immuno-panning) is not included in the database, unless that data is highly relevant to the subsequent analysis. If needed, this assay type is present under B cell response.
- The antibody displayed is typically not the entire molecule but the binding fragment. Depending on the cloning procedure, Fab, Fv, scFv or Fab’ fragments may be displayed. This information is to be entered in the Immunoglobulin Domain field. Camelids (camel, dromedary, llama, etc) have a particular IgG isotype devoid of light chains. The binding fragment (variable region of this IgG) is a unique polypeptidic chain named VHH.
- When the displayed antibody is the material assayed, the Materials Assayed field should be <Displayed Ab(s)> and Antibody Type should be <Display library>. The monoclonoal or polyclonal nature of the antibody will be entered in the Assay Comments field, while the Immunization Comments (if any) should include that the immunization was followed by display library construction.
- When a recombinant antibody is subsequently expressed in the absence of the displaying particle, the Materials Assayed field should be <Purified immunoglobulin>, the Immunoglobulin Domain field should reflect the fragment used and the Antibody Type field should be <Display library>. As before, the polyclonal or monoclonal nature will be entered in the Assay Comments field with any immunization comments including that the immunization was followed by display library construction.
3D Structural Data
The IEDB includes 3D-structural data describing complexes of epitopes with immune receptor(s): antibodies (or antibody fragments including the variable region), MHC molecules and/or the T cell receptor (or fragments including the antigen recognizing domains).
Exclusions
- Structures in which the antibody or TCR binds to the epitope outside of the variable antigen-binding region are not curated.
- Structures in which the MHC molecule binds the epitope outside of the recognition groove are not curated
3D data is captured in the IEDB by structural experts at SDSC when:
- The structure is obtained by an experimental method.
- 3D-structure is available in the Protein Data Bank (http://www.rcsb.org)
Each novel structure is captured only once as a context of the epitope which is bound by the immune receptor. That is if an epitope is bound by an antibody and an MHC molecule, two assays will be captured, one for each structure.
If there are different structures describing different contact residues between the epitope and a receptor, each set of differing contact residues is captured as a separate assay.
Imported Data
Data previously imported from other databases has been recurated by IEDB curators applying all curation rules as needed in order to comply with IEDB rules. This includes entering new epitopes, deleting epitopes not conforming to our criteria, and adding any new contexts as needed. References which originate from an import are labeled as such on the reference page. Each imported epitope is also labeled as originating from a data import. For example, a phrase such as "Data originally imported from the HLA Ligand Database" is entered whenever applicable.
Previously Submitted Data (Dual)
When a new publication is assigned to a curator which describes data that was previously submitted to the IEDB, a new reference id will not be created. Instead, the original submission will be moved into the curator's queue and the curator will edit the submission according to the publication. These will be identified by the document specialist and the submission curator, who will be expecting specific papers to be published. When such a paper is assigned to a curator, they will be informed of the pre-existing submission and provided with the correct reference id.
The curator will read the paper and add any missing details, epitope, or assays that are present in the manuscript and not already present in the submission. The paper will then be peer reviewed, per the standard procedure. Once approved, and prior to promotion, the submission will be converted into a "Dual" reference by Leidos, which entails adding the article information from the publication to the existing submission.
See the flow charts below:
After Curation/ External Website
Automatic Algorithms
After curation complete is accomplished, some data edits might be performed.
Response Frequency (%) is calculated and filled based upon what was entered into the Number of Subjects Tested and Number of Subjects Responded fields.
MHC Allele Name may be filled in T cell assays, if left blank by the curator, based upon Organism Name and/or Assay Information Measurement of fields. If the host is a MHC transgenic mouse strain, the MHC allele expressed by that strain will be auto filled in the MHC Allele Name field with MHC Evidence Code auto filled as T cell assay -Single MHC type present. When the host is not a MHC Tg mouse, the type of response is used to assign MHC restriction to either class I or class II. For example, if the assay type is considered to be a class I response, such as IFNg production, MHC Allele Name will be auto filled according to the host. For example, if the host is human, it will be filled as HLA class I and if the host is BALB/c, it will be filled as H2-d class I. In these cases, the MHC Evidence Code is auto filled as T cell assay -Biological process measured.
Data Aggregation
Logical Epitope
Each curated epitope will be presented aggregated with all other curated epitopes having the same exact linear sequence and Post-translational modifications. On the external website, epitopes are grouped according to a single epitope ID, for example, all curated epitopes having the linear sequence of NLVPMVATV (and no PTMs) are presented as epitope ID 44920 (https://www.iedb.org/epitope/44920), which relates to data originating from 351 separate curations/publications. When epitope data is presented on the external website, a single representative set of source protein and source organism are displayed in the results page tables. It is possible that different publications described that same sequence as originating from different proteins and organisms from what is displayed. The EPITOPE SUMMARY section of the Epitope Details page will describe the various sources for the different curated contexts. For example, see https://www.iedb.org/epitope/113645 for epitope sequence MEVGWYRSPFSRVVHLYRNGK which was curated as part of different publications describing it as being from mice, rats, and humans.
Immunome Browser
All curated epitopes originating from the same protein, across all relevant publications, can be plotted along the length of that protein using the Immunome Browser tool. There is a help article describing this tool: https://help.iedb.org/hc/en-us/articles/114094147751-Immunome-Browser-3-0 as well as a publication: https://pubmed.ncbi.nlm.nih.gov/29878047/.
Source Proteins
All epitope source proteins are presented on the external website as their reference proteome "parent" rather than by the source antigen that was selected during curation. For example, nearly 600 different isoforms of Influenza A virus Hemagglutinin have been used by curators, but all of these are presented on the external website as the single reference proteome protein Influenza A virus Hemagglutinin P03452. The use of reference proteomes is used to build the external site Protein Tree, which displays a single entry for each protein per species, presented in a hierarchical tree structure. This help article describes the protein tree in more detail: https://help.iedb.org/hc/en-us/articles/114094147251-Epitope-Source
Source Organisms
All epitope source organisms selected by curators are presented at the species level on the external website. For example, no matter what specific strain of Influenza A virus is selected by a curator, all will be displayed on the external website results tables as Influenza A virus. The Protein Tree also displays proteins at the species level. For example, the reference proteome Influenza A virus Hemagglutinin P03452 is from Influenza A virus (strain A/Puerto Rico/8/1934 H1N1), but is presented as Influenza A virus in the Protein Tree, as well as is the results page tables.
Standard Abbreviations
The table below (Table 7 ) shows the list of standard abbreviations consolidated from different immunological journals.
| # | Abbreviation | Expansion |
| 1 | 14C, 3H, 32P, etc. | isotopes |
| 2 | 2D/3D | two dimensional/three dimensional |
| 3 | 2-ME | 2-mercaptoethanol |
| 4 | Å | angstrom |
| 5 | A, Ado | adenosine* |
| 6 | aa | amino acid (only with numbers) |
| 7 | Ab | antibody |
| 8 | ABTS | 2,2’-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) |
| 9 | Ac | acetyl |
| 10 | ac | alternating current |
| 11 | ADCC | antibody-dependent cell-mediated cytotoxicity |
| 12 | Ade | adenine |
| 13 | af | audio frequency |
| 14 | Ag | antigen |
| 15 | AIDS | acquired immunodeficiency syndrome |
| 16 | Ala | alanine |
| 17 | AML | acute myeloid leukemia |
| 18 | AMP, ADP, ATP, dAMP, ddATP, GTP, etc. | For the respective 5’ phosphates of adenosine and other nucleosides, add 2’-, 3’-, or 5’- when needed for contrast |
| 19 | Amt | Amount |
| 20 | ANOVA | analysis of variance |
| 21 | AP-1 | activator protein 1 |
| 22 | APC | antigen-presenting cell |
| 23 | Approx | Approximately |
| 24 | Arg | arginine |
| 25 | Asn | asparagine |
| 26 | Asp | aspartic acid |
| 27 | Asx | asparagine or aspartic acid |
| 28 | at. wt. | atomic weight |
| 29 | ATP | adenosine triphosphate (also ADP, AMP, CMP, CTP, GDP, GMP, GTP, ITP, NTP, TMP, UDP and UTP) |
| 30 | ATPase, dGTPase, etc. | Adenosine triphosphatase, deoxyguanosine triophosphatase, etc |
| 31 | Avg | Average |
| 32 | AZT | 3’-azido-3-deoxythymidine |
| 33 | B.P. | before present |
| 34 | b.p. | boiling point |
| 35 | BAL | Bronchoalveolar lavage |
| 36 | BALT | bronchus-associated lymphoid tissue |
| 37 | BAPTA-AM | 1,2-bis(2-aminophenoxy)ethane-N,N,N’,N’-tetraacetic acid acetoxymethyl ester |
| 38 | bcc | body-centered-cubic |
| 39 | BCG | Bacillus Calmette Guerin |
| 40 | BCR | B cell receptor |
| 41 | BM | Bone marrow |
| 42 | bp | base pair (only with numbers) |
| 43 | BrdU | 5-bromo-2’-deoxyuridine |
| 44 | BrUra | bromouracil |
| 45 | BSA | bovine serum albumin |
| 46 | Bu | butyl |
| 47 | Bz | benzoyl |
| 48 | C | complement |
| 49 | C’ | activated complement |
| 50 | C region | constant region of Ig |
| 51 | C, Cyd | cytidine* |
| 52 | C/EBP | CCAAT/enhancer-binding protein |
| 53 | Calc., calc | calculated |
| 54 | cAMP | cyclic AMP |
| 55 | CCL | CC chemokine ligand |
| 56 | CCR | CC chemokine receptor |
| 57 | CD | circular dichroism |
| 58 | CD | cluster of differentiation |
| 59 | CD40L | CD40 ligand |
| 60 | CDC | complement-dependent cytotoxicity |
| 61 | cDNA | complementary DNA |
| 62 | CDR | complementarity determining region |
| 63 | CFA | complete Freund’s adjuvant |
| 64 | CFSE | 5- (and 6-)carboxyfluorescein diacetate succinimidyl ester |
| 65 | CFU | colony-forming unit |
| 66 | cGMP | guanosine 3’ 5’-cyclic monophosphate |
| 67 | cGy | centiGray (only with numbers) |
| 68 | CHAPS | 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate |
| 69 | CHO | Chinese hamster ovary |
| 70 | Ci | Curie (only with numbers) |
| 71 | CIITA | class II transactivator |
| 72 | CLIP | class II-associated invariant-chain peptide |
| 73 | cm | centimeter (only with numbers) |
| 74 | CM-cellulose | O-carboxymethylcellulose |
| 75 | CML | chronic myelogenous leukemia |
| 76 | CMV | cytomegalovirus |
| 77 | CNS | central nervous system |
| 78 | CoA | coenzyme A |
| 79 | Con A | concanavalin A |
| 80 | conc. | concentration |
| 81 | Concn | Concentration |
| 82 | const | constant |
| 83 | COSY | correlated spectroscopy |
| 84 | CP | chemically pure |
| 85 | CpG | cytosine guanine dinucleotide |
| 86 | cpm | counts per minute (only with numbers) |
| 87 | CR | Complement receptor |
| 88 | CREB | cAMP response element binding protein |
| 89 | cRNA | complementary RNA |
| 90 | CSF | colony-stimulating factor |
| 91 | CTL | cytotoxic T lymphocyte |
| 92 | CTLA | cytolytic T lymphocyte-associated Ag |
| 93 | CXCL | CXC chemokine ligand |
| 94 | CXCR | CXC chemokine receptor |
| 95 | Cys | cysteine or half-cystine |
| 96 | Cyt | cytosine |
| 97 | d | deoxy; distilled (as in dH2O) |
| 98 | d | deoxy (carbohydrates and nucleotides) |
| 99 | d | day (only with numbers) |
| 100 | D region | diversity region of Ig or T cell receptor for Ag |
| 101 | Da | dalton (only with numbers) |
| 102 | DAPI | 4’ 6-diamidino-2-phenylindole |
| 103 | dATP | 2’-deoxyadenosine triphosphate |
| 104 | dc | direct current |
| 105 | DC | dendritic cell |
| 106 | DEAE | diethylaminoethyl |
| 107 | DEAE-cellulose | diethylaminoethylcellulose |
| 108 | df | degrees of freedom |
| 109 | DHFR | dihydrofolate reductase |
| 110 | Diam | Diameter |
| 111 | DMEM | Dulbecco’s modified Eagle’s medium |
| 112 | DMSO | dimethylsulfoxide |
| 113 | DNA | deoxyribonucleic acid |
| 114 | DNase | deoxyribonuclease |
| 115 | DNP | dinitrophenyl |
| 116 | dNTP | 2’-deoxynucleoside 5’-triphosphate |
| 117 | dpm | disintegrations per minute |
| 118 | ds | double-stranded (as dsDNA) |
| 119 | dT or dThd | thymidine (2'-deoxyribosylthymine)* |
| 120 | DTH | delayed-type hypersensitivity |
| 121 | dThd | Thymidine |
| 122 | DTT | dithiothreitol |
| 123 | dUrd | Deoxyuridine |
| 124 | E | erythrocyte |
| 125 | E. coli | Escherichia coli |
| 126 | E/T | Effector-to-target cell (ratio) |
| 127 | E/T ratio | effector to target cell ratio |
| 128 | E:T ratio | effector to target ratio |
| 129 | EAE | Experimental autoimmune encephalomyelitis |
| 130 | EBV | Epstein-Barr virus |
| 131 | EC50 | 50% effective concentration |
| 132 | ECG | electrocardiogram |
| 133 | ECL | enhanced chemiluminescence |
| 134 | ED50 | 50% effective dose |
| 135 | EDTA | ethylenediaminetetraacetic acid |
| 136 | EGFP | enhanced green fluorescent protein |
| 137 | EGTA | ethylene glycol-bis(b-aminoethyl ester)-N,N,N’,N’-tetraacetic acid |
| 138 | ELISA | enzyme-linked immunosorbent assay |
| 139 | ELISPOT | enzyme-linked immunospot |
| 140 | EM | electron microscopy |
| 141 | EMBL | European Molecular Biology Laboratory |
| 142 | emf | electromotive force |
| 143 | EMSA | electrophoretic mobility shift assay |
| 144 | EPR | electron paramagnetic resonance |
| 145 | equiv. wt. | equivalent weight |
| 146 | ER | endoplasmic reticulum |
| 147 | ERK | extracellular signal-regulated kinase |
| 148 | ESR | electron spin resonance |
| 149 | EST | expressed sequence tag |
| 150 | Et | ethyl |
| 151 | Etd | ethidium |
| 152 | Exp., exp | experiment(al) |
| 153 | Expt | Experiment |
| 154 | Exptl | Experimental |
| 155 | f.p. | freezing point |
| 156 | Fab | Ag-binding fragment |
| 157 | FACS | fluorescence-activated cell sorter |
| 158 | F-actin | filamentous actin |
| 159 | FAD | flavin-adenine dinucleotide |
| 160 | FAM | 6-carboxyfluorescein |
| 161 | FBS | fetal bovine serum |
| 162 | FBS | Fetal bovine serum |
| 163 | Fc | IgG fragment crystallizable |
| 164 | Fc-gamma R | Receptor for the Fc-gamma part of the IgG molecule |
| 165 | FCM | Flow cytometry |
| 166 | FcR | Fc receptors (e.g., FcgRI) |
| 167 | FCS | fetal calf serum |
| 168 | FISH | fluorescence in situ hybridization |
| 169 | FITC | fluorescein isothiocyanate |
| 170 | FLICE | Fas-associated death domain-like IL-1b-converting enzyme |
| 171 | FLIP | FLICE inhibitory protein |
| 172 | fMet | formylmethionine |
| 173 | fMLP or FMLP | formyl-methionyl-leucyl-phenylalanine |
| 174 | FMN | flavin mononucleotide |
| 175 | FPLC | fast protein liquid chromatography |
| 176 | Fru | fructose |
| 177 | Fuc | fucose |
| 178 | Fura 2-AM | fura 2-acetoxymethyl ester |
| 179 | Fv | IgG fragment variable |
| 180 | g | gram (only with numbers) |
| 181 | G, Guo | guanosine* |
| 182 | Gal | galactose |
| 183 | GalN | galactosamine |
| 184 | GALT | gut-associated lymphoid tissue |
| 185 | GAPDH or G3PDH | glyceraldehyde-3-phosphate dehydrogenase |
| 186 | GC, GLC | gas chromatography, gas/liquid chromatography |
| 187 | G-CSF | granulocyte CSF |
| 188 | GFP | green fluorescent protein |
| 189 | Glc | glucose |
| 190 | GlcA | gluconic acid |
| 191 | GlcA, GlcUA | glucuronic acid |
| 192 | GlcN | glucosamine |
| 193 | GlcNAc | N-acetylglucosamine |
| 194 | Gln | glutamine |
| 195 | Glu | glutamic acid |
| 196 | Glx | glutamic acid or glutamine |
| 197 | Gly | glycine |
| 198 | GM-CSF | granulocyte-macrophage colony stimulating factor |
| 199 | gp | glycoprotein (e.g., gp100) |
| 200 | GPI | glycosylphosphatidylinositol |
| 201 | GST | glutathione S-transferase |
| 202 | Gua | guanine |
| 203 | GVH | Graft-vs.-host (reaction) |
| 204 | h | hour (only with numbers) |
| 205 | H chain | heavy chain |
| 206 | H&E | hematoxylin and eosin |
| 207 | HACA | human anti-chimeric antibodies |
| 208 | HAHA | human anti-human antibodies |
| 209 | HAMA | human anti-mouse antibodies |
| 210 | Hb | hemoglobin |
| 211 | HbCO | carbon monoxide hemoglobin |
| 212 | HbO2 | oxyhemoglobin |
| 213 | HBSS | Hanks’ balanced salt solution |
| 214 | Hepes or HEPES | N-2-hydroxyethylpiperazine-N’-2-ethanesulfonic acid |
| 215 | hf | high frequency |
| 216 | hfs | hyperfine structure |
| 217 | HHV | human herpes virus |
| 218 | His | histidine |
| 219 | HIV | human immunodeficiency virus |
| 220 | HLA | human leukocyte antigen |
| 221 | HPLC | high-pressure or high-performance liquid chromatography |
| 222 | HPV | human papillomavirus |
| 223 | HRP | horseradish peroxidase |
| 224 | HSP | Heat shock protein |
| 225 | HSV | herpes simplex virus |
| 226 | Ht | Height |
| 227 | HUVEC | human umbilical vein endothelial cells |
| 228 | I, Ino | inosine* |
| 229 | i.d. | intradermal |
| 230 | i.d., o.d. | diameter, inside or outside |
| 231 | i.m. | intramuscular |
| 232 | i.p. | intraperitoneal |
| 233 | i.v. | intravenous |
| 234 | IC50 | 50% inhibition/inhibitory concentration |
| 235 | ICAM | intercellular adhesion molecule |
| 236 | ICOS | inducible costimulator |
| 237 | Id | idiotope, idiotype |
| 238 | ID50 | 50% infective dose or 50% inhibiting dose |
| 239 | IDO | indoleamine 2, 3-dioxygenase |
| 240 | IFA | incomplete Freund’s adjuvant |
| 241 | IFN | interferon (e.g., IFN-g) |
| 242 | Ig | immunoglobulin |
| 243 | IgG, IgM, etc. | immunoglobulin G, M, etc. |
| 244 | IgH | Ig heavy chain |
| 245 | IkB | inhibitory NF-kB |
| 246 | IL | interleukin (e.g., IL-2) |
| 247 | Ile | isoleucine |
| 248 | IMDM | Iscove’s modified Dulbecco’s medium |
| 249 | IMEM | Iscove’s minimal essential medium |
| 250 | IPTG | isopropyl b-d-thiogalactoside |
| 251 | IR | infrared |
| 252 | ITAM | immunoreceptor tyrosine-based activation motif |
| 253 | ITIM | immunoreceptor tyrosine-based inhibitory motif |
| 254 | IU | international unit (only with numbers) |
| 255 | J region | joining region of Ig or T cell receptor for Ag |
| 256 | JAK or Jak | Janus kinase |
| 257 | JNK | c-Jun N-terminal kinase |
| 258 | Ka | association constant |
| 259 | kb | kilobase (only with numbers) |
| 260 | kbp | kilobase pair (only with numbers) |
| 261 | Kd | distribution coefficient; dissociation constant |
| 262 | KD | affinity constant |
| 263 | kDa | kilodalton (only with numbers) |
| 264 | KIR | Killer cell Ig-like receptor |
| 265 | L | ligand |
| 266 | L chain | light chain; light |
| 267 | LAK | lymphokine-activated killer (cells) |
| 268 | LB | Luria-Bertani or Lenox broth |
| 269 | LC | Langerhans cell |
| 270 | LCMV | Lymphocytic choriomeningitis virus |
| 271 | LD50 | 50% lethal dose |
| 272 | Leu | leucine |
| 273 | LFA | leukocyte (lymphocyte) function-associated Ag |
| 274 | LIF | leukemia inhibitory factor |
| 275 | lim | limit |
| 276 | LN | Lymph node |
| 277 | LPS | lipopolysaccharide |
| 278 | LTR | long terminal repeat |
| 279 | LU | lytic unit |
| 280 | Lys | lysine |
| 281 | M | molar (only with numbers) |
| 282 | m.p. | melting point |
| 283 | m.w. | molecular weight |
| 284 | mAb | monoclonal antibody |
| 285 | MACS | magnetic-activated cell sorting |
| 286 | MALDI | matrix-assisted laser desorption ionization |
| 287 | MALDI-TOF | matrix-assisted laser desorption ionization-time of flight |
| 288 | MALT | mucosa-associated lymphoid tissue |
| 289 | Man | mannose |
| 290 | MAPK | mitogen-activated protein kinase |
| 291 | Mb | myoglobin |
| 292 | MbCO | carbon monoxide myoglobin |
| 293 | MCP-1 | monocyte chemoattractant protein-1 |
| 294 | M-CSF | macrophage CSF |
| 295 | Me | methyl |
| 296 | MEK | mitogen-activated protein kinase kinase |
| 297 | MEM | minimum essential medium |
| 298 | MES | 2-(N-morpholino)ethanesulfonic acid |
| 299 | Met | methionine |
| 300 | mg | milligram (only with numbers) |
| 301 | MHC | major histocompatibility complex |
| 302 | MIC | Minimal inhibitory concentration |
| 303 | min | minute (only with numbers) |
| 304 | MIP | macrophage-inflammatory protein |
| 305 | ml | milliliter (only with numbers) |
| 306 | MLC | mixed lymphocyte culture |
| 307 | MLR | mixed leukocyte reaction |
| 308 | mM | millimolar (only with numbers) |
| 309 | mo | month(s) (only with numbers) |
| 310 | mol | mole |
| 311 | Mol wt | Molecular weight |
| 312 | MOPS | 4-morpholinepropanesulfonic acid |
| 313 | Mr | relative molecular mass |
| 314 | MRI | magnetic resonance imaging |
| 315 | mRNA | messenger RNA |
| 316 | MS | mass spectrometry or spectroscopy |
| 317 | mtDNA | mitochondrial DNA |
| 318 | MTT | 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide |
| 319 | MU | Macrophage |
| 320 | MyD88 | myeloid differentiating factor 88 |
| 321 | n | number in study or group |
| 322 | N, Nuc | nucleoside (unknown)* |
| 323 | NAD | nicotinamide adenine dinucleotide |
| 324 | NAD+ | Nicotinamide adenine dinucleotide, oxidized |
| 325 | NADH | Nicotinamide adenine dinucleotide, reduced |
| 326 | NaDodSO4 | sodium dodecyl sulfate |
| 327 | NADP | NAD phosphate |
| 328 | NADP+, NADPH | nicotinamide-adenine dinucleotide phosphate |
| 329 | NADPH | Nicotinamide adenine dinucleotide phosphate, reduced |
| 330 | NADPH+ | Nicotinamide adenine dinucleotide phosphate, oxidized |
| 331 | NBT | nitroblue tetrazolium |
| 332 | NCI | National Cancer Institute |
| 333 | ND | not determined |
| 334 | NDP | nucleoside 5’-diphosphate |
| 335 | NF | nuclear factor |
| 336 | NFAT or NF-AT | nuclear factor of activated T cells |
| 337 | NF-kB | nuclear factor kB |
| 338 | NIH | National Institutes of Health |
| 339 | Ni-NTA | nickel-nitrilotriacetic acid |
| 340 | NK | natural killer (cells) |
| 341 | NKT | Natural killer T (cell) |
| 342 | NMN | nicotinamide mononucleotide |
| 343 | NMP | nucleoside 5’-monophosphate |
| 344 | NMR | nuclear magnetic resonance |
| 345 | NO | nitric oxide |
| 346 | No. | Number |
| 347 | NOD | nonobese diabetic |
| 348 | NOESY | nuclear Overhauser effect/enhancement spectroscopy |
| 349 | NP40 | Nonidet-P40 |
| 350 | NS | not significant |
| 351 | nt | nucleotide (only with numbers) |
| 352 | nt | nucleotide (only with numbers) |
| 353 | OAc | acetate |
| 354 | Obs., obs | observed |
| 355 | OCT | octamer-binding factor |
| 356 | OD | optical density |
| 357 | oligo(dT), etc. | Oligodeoxythymidylic acid, etc. |
| 358 | ORD | optical rotatory dispersion |
| 359 | ORF | open reading frame |
| 360 | OVA | ovalbumin |
| 361 | p | probability |
| 362 | P | probability |
| 363 | P or p | phosphate (in compounds) |
| 364 | PAGE | polyacrylamide gel electrophoresis |
| 365 | PBL | peripheral blood lymphocyte |
| 366 | PBMC | peripheral blood mononuclear cell |
| 367 | PBS | phosphate-buffered saline |
| 368 | PCR | polymerase chain reaction |
| 369 | PCR-RFLP | PCR-restriction fragment length polymorphism |
| 370 | PE | phycoerythrin |
| 371 | PECAM-1 | platelet endothelial cell adhesion molecule-1 |
| 372 | PEG | polyethylene glycol |
| 373 | PEI-cellulose | polyethylenimine-cellulose |
| 374 | PerCP | peridinin chlorophyll protein |
| 375 | PFC | Plaque-forming cell |
| 376 | PFU or pfu | plaque-forming unit |
| 377 | PG | prostaglandin |
| 378 | Ph | phenyl |
| 379 | PHA | phytohemagglutinin |
| 380 | Phe | phenylalanine |
| 381 | pI | isoelectric point |
| 382 | Pi | phosphate (inorganic) |
| 383 | pI | isoelectric point |
| 384 | PI | propidium iodide |
| 385 | PI3K | phosphatidylinositol 3-kinase |
| 386 | PIPES | piperazine-N |
| 387 | Pipes | 1,4-piperazinediethanesulfonic acid |
| 388 | PK, PKC | protein kinase, protein kinase C |
| 389 | PKC | Protein kinase C |
| 390 | PMA | phorbol myristate acetate |
| 391 | pmf | proton-motive force |
| 392 | PMN | Polymorphonuclear (cell, leukocyte) |
| 393 | PMSF | phenylmethylsulfonyl fluoride or phenylmethanesulfonyl fluoride |
| 394 | poly(A), poly(dT), etc. | Polyadenylic acid, polydeoxythymidylic acid, etc. |
| 395 | PPD | Purified protein derivative of tuberculin |
| 396 | Pr | propyl |
| 397 | Prepn | Preparation |
| 398 | Pro | proline |
| 399 | PWM | pokeweed mitogen |
| 400 | QED | quantum electrodynamics |
| 401 | r | recombinant, (e.g., rIFN-g) |
| 402 | R | receptor (e.g., IL-2R) |
| 403 | RACE | rapid amplification of cDNA end |
| 404 | RAG | recombination-activating gene |
| 405 | RANTES | regulated upon activation |
| 406 | RBC | red blood cell |
| 407 | rDNA, rRNA | ribosomal DNA, ribosomal RNA |
| 408 | resp (mathematics) | respectively |
| 409 | rf | radio frequency |
| 410 | RFLP | restriction fragment length polymorphism |
| 411 | RIA | radioimmunoassay |
| 412 | Rib | ribose |
| 413 | rms | root-mean-square |
| 414 | RNA | ribonucleic acid |
| 415 | RNase | ribonuclease |
| 416 | rpm | revolutions per minute |
| 417 | RPMI | Roswell Park Memorial Institute (culture media) |
| 418 | rRNA | ribosomal RNA |
| 419 | RT-PCR | reverse transcriptase polymerase chain reaction |
| 420 | s | second (only with numbers) |
| 421 | s.c. | subcutaneous(ly) |
| 422 | SCID | severe combined immunodeficiency |
| 423 | SD | standard deviation |
| 424 | SDS | sodium dodecyl sulfate |
| 425 | SDS-PAGE | sodium dodecyl sulfate polyacrylamide gel electrophoresis |
| 426 | SE | standard error |
| 427 | SEM | standard error of the mean |
| 428 | Ser | serine |
| 429 | SHIP | src homology 2-containing inositol 5’ phosphatase |
| 430 | sIg | Surface immunoglobulin |
| 431 | SIV | simian immunodeficiency virus |
| 432 | SLE | Systemic lupus erythematosus |
| 433 | SN | Supernatant |
| 434 | Sp gr | Specific gravity |
| 435 | sp. act. | specific activity |
| 436 | SPF | Specific pathogen free |
| 437 | SRBC | sheep red blood cells |
| 438 | ss | single-stranded (e.g., ssDNA) |
| 439 | SSC | standard saline citrate |
| 440 | STAT | signal transducer and activator of transcription |
| 441 | SV40 | simian virus 40 |
| 442 | T or Thd | ribosylthymine |
| 443 | t1/2 | half-life, half-time |
| 444 | TAMRA | 5-(and 6)-carboxytetramethylrhodamine |
| 445 | TAP | transporter associated with Ag processing |
| 446 | Tat | terminal deoxynucleotidyltransferase |
| 447 | TBS | Tris-buffered saline |
| 448 | TBST | TBS with Tween 20 |
| 449 | TCA | trichloroacetic acid |
| 450 | TCR | T cell receptor |
| 451 | TdR | thymidine deoxyribose (also UdR, AdR) |
| 452 | TdT | terminal deoxynucleotidyltransferase |
| 453 | Temp | Temperature |
| 454 | TFA | trifluoroacetic acid |
| 455 | Tg | Transgenic |
| 456 | TGF | transforming growth factor |
| 457 | Th | T helper (cell) |
| 458 | Thr | threonine |
| 459 | Thy | thymine |
| 460 | TIL | tumor-infiltrating lymphocyte |
| 461 | TLC | thin-layer chromatography |
| 462 | TLR | Toll-like receptor |
| 463 | TNF | tumor necrosis factor |
| 464 | TNP | trinitrophenyl |
| 465 | Tr | Trace |
| 466 | TRAIL | TNF-related apoptosis-inducing ligand |
| 467 | Tris | tris(hydroxymethyl)aminomethane |
| 468 | tRNA | transfer RNA |
| 469 | Trp | tryptophan |
| 470 | TUNEL | Tdt-mediated dUTP nick end labeling |
| 471 | Tyr | tyrosine |
| 472 | U | unit (only with numbers) |
| 473 | U, Urd | uridine* |
| 474 | UHF | ultrahigh frequency |
| 475 | Ura | uracil |
| 476 | UTR | untranslated region |
| 477 | UV | ultraviolet |
| 478 | V region | variable region of Ig |
| 479 | V(D)J | variable diversity joining |
| 480 | v/v | volume to volume ratio (%) |
| 481 | Val | valine |
| 482 | VCAM | vascular cell adhesion molecule |
| 483 | VLA | very late activation Ag |
| 484 | vol | volume |
| 485 | Vs | Versus |
| 486 | VSV | vesicular stomatitis virus |
| 487 | W | watt (only with numbers) |
| 488 | WBC | white blood cell |
| 489 | wk | week (only with numbers) |
| 490 | WT | wild type |
| 491 | Wt | Weight |
| 492 | Xaa | unknown or "other" amino acid |
| 493 | xid | X-linked immunodeficiency |
| 494 | yr | year (only with numbers) |
| 495 | ZAP70 | ζ-associated protein 70 (or ζ-chain-associated protein 70) |
| 496 | μg | microgram (only with numbers) |
| 497 | μl | microliter (only with numbers) |
