T Cell Receptor Genetics and Bioinformatics

Comprehensive vocabulary flashcards covering T cell receptor genetics, lymphocyte development, immunological loci, and bioinformatics data formats based on the lecture transcript.

T cell Receptors (CTR/TCR)

Antigen receptors of the T cells of the adaptive immune response.

Antigen

Any substance the immune system identifies as foreign.

Receptors

Specialized protein molecules located on the surface of a cell or in its interior.

Gnathostomata (grathostomata)

Jawed vertebrates that acquired T cell receptors.

TR Alpha Beta

Receptors that recognize processed antigens which present themselves as peptides by the highly polymorphic major histocompatibility proteins.

Peptide

A short chain of $2$ to $50$ amino acids linked by chemical bonds that regulate cellular function.

Polymorphic Major Histocompatibility Complex Proteins

Cell surface receptors that bind foreign antigens and display them to T cells triggering an adaptive immune response.

TR Gamma and Delta

T cell receptors that recognize nonpeptidic antigens.

TRA

TR Alpha locus located at $14911.2$.

TRB

TR Beta locus located at $7934$.

TRG

TR Gamma locus located at $714$.

TRD

TR Delta locus located at $14911.2$.

Orphon

Nonfunctional genes or DNA sequences located outside the main chromosomal locus.

Variable (V)

A specific sequence of DNA that encodes the N-terminal portion of an antigen receptor in B and T cells.

TR Gene Types

Four types including Variable (V), Diversity (D), Joining (J), and Constant (C) which contribute to T cell Receptor synthesis.

TR cell Inheritance

The process where a child inherits exact DNA sequences for the constant and variable regions of the TCR from parents.

Immunoglobulin Lambda Locus

A region of DNA containing genetic instructions for Lambda creation.

IGH, IGK, and IGL loci

Loci responsible for encoding antibodies (immunoglobulins) in B cells.

Immunoglobulin Heavy Chain

A major protein subunit of antibodies.

Invariant signaling chains

Components that relay signals when an antigen is successfully recognized, including CD3YE and CD38E heterodimers.

$\zeta$ (Zeta) chain homodimer

A component critical for launching the signaling cascade in T cells.

Lymphocyte Development

The process by which multipotent hematopoietic stem cells in the bone marrow differentiate into functional T and B cells.

VDJ recombination

A unique genetic process used by developing B cells and T cells to shuffle and assemble unique antigen receptor genes (variable V, Diversity D, and joining $5$ gene segments).

CDR3 (Complementarity Determining Region 3)

Generates $8$ to $20$ amino acid sequences that form T cell receptor binding sites important for contacting antigens.

Experimental Assays

Used to identify which CDR3 sequences are diverse.

VDJdb

A curated database that stores and annotates antigen-specific CDR3s and matches cancer patients to CDR3s.

Anti-Viral CDR3s

T cell receptor CDR3 sequences that specifically recognize viral peptides, defined by functional evidence.

RNA sequencing

A powerful molecular biology technique using high throughput sequencing to capture a snapshot of a cell's transcriptome.

Transcriptome

The set of all RNA molecules in a cell.

Exome File Formats

Digital datasets used by geneticists, including $1$ FASTQ, $2$ BAM, $3$ VCF, and $4$ BED.

Bioinformatics pipeline

A process used to align sequences and identify variants to find mutant amino acids in exome and RNAseq files.