Glossary

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A

• Aggregation
  • the formation of a complex due to the adhesion between individual molecules
• Alpha helices
  • a type of secondary structure found in proteins. The carbonyl oxygen of each amino acid forms a hydrogen bond with amide hydrogen of the 4th residue toward the C-terminus of the polypeptide
• Amino acid
  • the basic building blocks of proteins. There are 20 types of amino acids; each has a different side chain
• Amplification
  • a technique that amplifies multiple copies of the product of a reaction (e.g. PrpRes of the Prion protein conversion can be amplified into multiple copies)
• Antibody
  • a glycoprotein synthesized endogenously or artificially. An antibody can be used as a marker to detect the presence of target protein via specific binding
• Antigen
  • molecules or parts of a molecule that can bind to a specific antibody which binds and recognizes different types of molecules or T-cell receptor
• Apoptosis
  • programmed cell death
• Apoptotic
  • the ability to induce apoptosis
• Ataxia
  • an abnormal condition in which the muscles fail to function in a coordinated manner during voluntary movement

C

• Cathepsin D
  • is a protein that helps regulates intracellular transport of phospholipids and cholesterol
• Cathepsin S
  • a transcript that is required for the function of macrophages
• Catheter placement
  • a tube which is inserted into a body cavity duct or vessel which allows injection of fluid
• CD68
  • transcript required for the function of macrophages
• Cell-free
  • not involving cells, lacking cells
• Chemokines
  • proteins that are active in inflammatory responses (virus textbook)
• Creutzfeldt-Jakob disease (CJD)
  • it is a Prion disease in humans
• Conversion factor
  • a molecule that is needed for the conversion of substrate to product
• Cytokines
  • secreted proteins that act on cells in the immune system to stimulate or inhibit immune functions

D

• Denaturing Agents
  • Chemicals or processes (such as heat or acid) that causes proteins to unfold from their tertiary structure. Structures and biological activities of the proteins will be lost.
• Dendritic cells
  • These cells present foreign antigen to lymphocytes in lymph nodes and other places in the body
• Densitometry
  • measurement of optical density of light sensitive material like photographic film when exposed with light
• Dicer
  • is an RNAse III nuclease present within the cytoplasm that specifically cleaves double-stranded RNAs
• DNA
  • also known as deoxyribonucleic acid, a long polymer of simple units called nucleotides and which has a double helix morphology
• DNase
  • also known as deoxyribonuclease; it is a nuclease that degrades DNA into smaller components via hydrolytic cleavage of phosphodiester linkages in DNA
• Double stranded RNA (dsRNA)
  • RNA with two strands which are hybridized together instead of one.

E

• Electron transport
  • in aerobic metabolism, a series of enzyme complexes and cofactors transport electron in through mitochondria to generate energy (ATP) for the body
• Embryonic stem cells
  • cells derived from the inner cell mass of an early embryo and hence can give rise to all differentiated cells, including germ line cells
• Endogenous
  • refers to substances that are originated within an organism
• Epitope
  • a specific site on the targe protein that is recognized by the corresponding antibody

F

• Fold (Protein folding)
  • the process involved in protein formation, in which a strand of amino acids folds into a complex three dimensional structure that gives rise to the biological activity of the protein.
• Flow cytometry
  • quantitative technique that is able to detect single cells flowing through an optical or electronic device
• FU strain
  • more virulent strain of CJD used in the inoculation of mice

G

• GAPDH
  • used as a loading control since this transcript is not affected by infection of CJD
• Gel shift assay
  • a technique used to detect DNA or RNA’s interaction with protein of interest
• GFAP
  • Glial fibrillary acidic protein is an intermediate filament protein that is specific for astrocytes. GFAP was detected in the experiments to confirm that astrocytes are not present.
• Glycoprotein
  • a protein that is covalently bound to carbohydrates

H

• Half-life
  • the time required to exponentially decay the concentration of a particular compound by a half. Typically used to measure the lifetime that a certain compound has before it is decayed or cleared from its environment
• Heat Shock protein (Hsp) 70 mRNA
  • mRNA of HSP70 protein
• Heat shock protein (HSP) 70 protein
  • molecular chaperone that prevents inappropriate protein-protein interactions and it destroys abnormal or denatured polypeptides by proteolysis.
• Heparinase
  • a enzyme that cleaves a 1-4 glycosidic linkages between residues in the heparin polymer
• Homogenate
  • a tissue mixture derived from grinding of tissue sample
• HIV
  • also known as Human Immunodeficiency Virus, is a lentivirus

I

• Inflammatory
  • immune system response when there is an infection in the body
• Immunoflourescence Microscopy
  • when an antibody is labeled with fluorescent dye and it is used to target molecules in tissues
• Immunoprotected Proteins
  • Proteins that are not subject to the immune system. Typically proteins of the host of the immune sytem that are not target by antibodies for destruction. These proteins are typically problematic to generate antibodies against.
• Interferon-inducible protein 10 (IP-10)
  • chemokine that is expressed when an infection is present. It acts as a chemoattractant for various types of leukocytes
• Interleukin (IL) - 1a
  • produced from macrophages and epithelial cells. Upregulation leads to T cell activation and macrophage activation
• In vitro-
  • Experiments that are done in isolated cell cultures
• In vivo
  • Experiments that are done in an intact cell or organism
• Ischemia
  • Lack of or insufficient blood supply and thus oxygen to an organ or tissue. The associated deficiency of oxygen and nutrients may lead to necrosis in areas of the affected tissue
• Isoform
  • a protein isoform has different biochemical or structural properties than the normal protein

J

K

L

• L-selectin
  • cell adhesion molecule found on leukocytes that are specific to carbohydrate groups
• Lentivectors
  • vectors made from lentiviruses which have been modified and contain the gene going to be inserted into the genome of an organism
• Lentivirus
  • a subgroup of RNA viruses from the Retroviridae family who have the ability to deliver a significant amount of genetic information into the DNA of the dividing and non-dividing host cells and hence is by long periods of clinical latency after infection
• Ligand
  • a molecule that binds to another molecule

M

• MCP1
  • small inducible gene that recruits monocytes to sites of injury and infection
• MIP-1a
  • Macrophage inflammatory proteins which causes the synthesis and release of pro-inflammatory cytokines like IL-1. Produced when there is an infection.
• MIP-1 ß
  • Macrophage inflammatory proteins which causes the synthesis and release of pro-inflammatory cytokines like IL-1. These are produced when there is an infection
• Marker
  • a trait that is associated to detecting or understanding a disease
• Messenger RNA (mRNA)
  • A form of RNA which is able to be transported from the nucleus to ribosomes within the cytoplasm and serve as a template for protein synthesis
• Microglia
  • A type of glia cells that act as the immune cells in the central nervous system. They are closely related to macrophages and dendritic cells
• Mononuclear blood cells (MBCs) –
  • blood cell that has only one nucleus
• Myeloid cells
  • are cells derived from the bone marrow that give rise to cells that are important for the immune system

N

• Necrosis
  • referred to as a type of tissue death due to the lack of blood supply
• Neurodegenerative Disease
  • Class of diseases that are caused by loss/deterioration of neurons (cells of the brain, which cannot be regenerated). This devastating effect results in loss of memory (dementia) or the ability to move.
• Northern blot
  • technique used to detect gene expression of RNA
• Nucleases
  • an enzyme that breaks the phosphodiester bonds between subunits of nucleic acids

O

• Oligomer
  • a multisubunit compound molecule composed via the chemical bonding among subunit molecules known as monomers
• Ovine
  • of sheep

P

• Protein
  • a biopolymer consisting of one or more polypeptide chains, which is in turn composed of amino acids
• Proteolysis
  • degradation of proteins using enzymes called proteases.
• PrpC
  • normal form of Prion protein that is protease sensitive. Its secondary conformation that is dominated by alpha helices structure and is protease sensitive
• PrpRes
  • Prion protein produced in vitro that has the same biochemical and structural properties as PrpSC (i.e. protease resistant, dominated by beta sheets)
• PrpSC
  • an abnormal, protease resistance form of Prion protein associated with prion disease. Its secondary conformation is dominated by beat-sheets structure
• PrPC mRNA
  • a messenger RNA that gives rise to the PrPC protein
• Pyrimidines
  • group of heterocyclic aromatic compounds that consists of adenine and guanine which are used in DNA/RNA base pairing

Q

R

• Recombinant
  • a recombinant protein involves the insertion of promoter and gene of interest into a vector, which is then incorporated into bacterial host for replication and translation into protein of interest
• Renal Clearance
  • a method for molecules to be removed from the body through kidney filtration and eventually accumulate in the bladder as urine for export outside of the body
• RT PCR
  • (reverse transcriptase PCR) technique used to amplify specific pieces of RNA
• Ribonuceloprotein
  • a complex containing ribonucleic acid and protein
• RNA
  • also known as ribonucleic acid, a polymer with its ribonucleotide subunit linked by 3’-5’ phosphodiester
• RNase
  • also known as ribonuclease; it is a nuclease that degrades RNA into smaller components via hydrolytic cleavage of phosphodiester linkages in RNA
• RNA aptamer
  • Chemically synthesised strand of RNA that folds into a 3-D structure and can bind to a target molecule with high affinity and specific binding.
• RNA-induced silencing complex (RISC)
  • is a multi protein siRNA nuclease complex, composed of proteins and siRNA which targets and destroys endogenous mRNAs complementary to the siRNA within the complex.
• RNA interference
  • is a mechanism initiated by double stranded RNA (or small interfering RNA) which induces efficient sequence-specific silencing of gene expression
• RNA polymerase
  • an enzyme complex that synthesizes RNA from DNA template
• RNA virus
  • is a virus who possesses RNA as its genetic material and does not replicate using a DNA intermediate

S

• Scrapie
  • a type of Prion disease commonly found in goats and sheep
• SELEX
  • (Systematic Evolution of Ligands by EXponential enrichment) A process in which a library of ligands(RNA or DNA) are incubated with a target molecule and the best binding ones are selected for and amplified. This is repeated many times until a family of ligands with high binding affinity to the target is achieved.
• Serum amyloid A3 (SAA3)
  • is a chemoattractant that is secreted from the body, and also stimulates T cells cytokines production
• shRNA (short hair pin RNA)
  • is a modified double stranded RNA which contains sense and antisense sequences from a target gene connected by a loop and is the target of Dicer
• shsRNA (small, highly structured, signled stranded RNA)
  • a synthetic RNA that is used to study the role of RNA in Prion protein conversion
• Slot blot
  • a precursor to microarrays, a technique that involves an array of DNA/RNA slots on a membrane which are blotted onto the membrane by a slot blot manifold. Then radioactive targets can be presented for interactions with the DNA/RNA to be quantified.
• small interfering RNA (siRNA)
  • is a short RNA duplex that can be generated from shRNA and can induce gene silencing by binding to the complementary portion of the target messenger RNA and tagging it for degradation
• Size chromatography
  • a technique that separates complexes in a mixture based on their sizes
• Sonication
  • a technique that involves the application sound energy to break intermolecular bonds within a multisubunit compound
• Spiegelmers
  • RNA/DNA that are made of L-ribose rather than D-ribose sugars. These spiegelmers are resistant to enzyme digestion.
• SY sporadic agent
  • less virulent strain of CJD

T

• T lymphocytes
  • subset of lymphocytes that are developed in the thymus
• Transmissible Spongiform Encephalopathies
  • progressive disease that results in the degernation of the brain and nervous system of humans and animals; occurs from transmission of Prion
• Tumor Neurosis Factor (TNF) a proinflammatory
  • is a cytokine produced by macrophages and T cells that function during an immune response. They associate with their TNF receptors, which signal within the cell

U

V

• Variant Creutzfeldt Jakob disease (vCJD)
  • a form of human Prion disease, which can be transmitted upon ingestion of Prion-infected livestock
• Vaccines
  • a preparation of weakened or inactivated strains of virus/bacteria. Upon injection, body’s immune system can develop immunity to specific virus/bacteria
• Viral
  • A term that refers to viruses. Viruses invade cells and take control of reproduction machinery and are thus able to reproduce and spread rapidly. Viruses consists of a protein coat which protects the nucleic acids that encode machinery and information necessary for reproduction.

W

• Western blot
  • a technique that detects proteins of interest on a gel using labelled antibody

X

Y

Z