Glossary Terms for BEECM Spring 2007

Shoda et al. paper (Collagens LBL):

1. Pulmonary Fibrosis

Pulmonary Fibrosis involves scarring of the lung. Scarring from deposition of collagen thickens the alveolar sacks, inhibiting the tissue's ability to transfer oxygen into the bloodstream.

2. Reverse Transcriptase-Polymerase Chain Reaction

A highly sensitive technique for the detection and quantization of mRNA. The technique consists of two parts:

The synthesis of cDNA from RNA by reverse transcription and the amplification of a specific cDNA by PCR.

3. Fibroblasts

Specialized cells whose role is to organize structures and remodel tissues.

4. Interferon Type II (IFN- γ)

Produced by Helper T cells. Its main role is to inhibit virus replication when cells are infected. Responsible for inflammation and controlling other helper cells.

5. Cytokines

Small secreted proteins which mediate and regulate immunity, inflammation, and hematopoiesis. Their main role is the regulation of gene transcription resulting in altered gene expression. Responses include proliferation, migration, and secretion.

6. Signal Transducers and Activator of Transcription (STAT)

Proteins that regulate many aspects of cell growth, survival, and differentiation. Involved with interferons to directly effect gene expression.

Langen et al. paper (Other ECMs paper):

1. Matrigel – a product that contains extracellular matrix proteins like collagen IV, laminin, heparan sulfate proteoglycans and entactin, simulating the endomysium

2. Creatine kinase – an enzyme produced by muscle to aid in energy production

3. Endomysium – the extracellular matrix of skeletal muscle tissue, modeled accurately by Matrigel

4. Myotube – fully differentiated myoblasts, have a “tube-like” structure and are multinucleated

5. Myosin heavy chain – a protein inherent to muscle cells, involved in contraction and relaxation

6. Troponin I – a part of a three-protein complex involved in muscle contraction and relaxation, blocks or allows the myosin binding site on actin filaments

Edwards et al. paper (ECM Signaling):

Prolactin: The most important function of is to stimulate the mammary glands to enlarge and also to produce milk.

Electrophoretic Mobility Shift Assay (EMSA): a common technique used to study protein-DNA or protein-RNA interactions. Determine if a protein or mixture of proteins binds to given DNA or RNA sequence.

Basement membrane: a thin membrane upon which a single layer of cells laid upon. It is made up of proteins and held together by type IV collagen. The epithelial cells are anchored with hemidesmosomes to the basement membrane.

Lactogenic: hormones are secreted by the anterior pituitary. In females they stimulate growth of the mammary glands and lactation after parturition. Promote the production of milk and feedback at the hypothalamus to inhibit PRL release.

Stat5b: is a member of the STAT family of transcription factors, that are phosphorylated by the receptor associated kinases in response to cytokines and growth factors. They translocate to the cell nucleus where they act as transcription activators.

Protein-Tyrosine Phosphatases (PTP): are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins.

Together with tyrosine kinases, PTPs regulate the phosphorylation state of many important signalling molecules, such as the MAP kinase family.

Bergland et al. Paper (Mechanics LBL) Glossary Terms

1. Viscoelasticity – the concept that describes a material which demonstrates both viscous and elastic characteristics. The combination of these properties produces a material which exhibits a time-dependent strain response.

2. Stress Relaxation – a time-dependent decay of stress when a constant strain is applied to a material.

3. Creep – an increase in strain over time when a material is subjected to a constant stress.

4. Yield Energy – the energy required to bring a material to the point of yielding. This is measured as the area under the stress-strain profile from the start of the test to the yield point (the stress at which a material begins to plastically deform).

5. Ultimate Tensile Stress (UTS) – the highest stress a material can withstand. This is observed as the peak on a stress/strain curve. The UTS does not always correspond to the failure/breaking stress.

6. Failure Energy – the energy required to bring a material to the point of failure. This is measured as the area under the stress-strain profile from the start of the test to the failure point (defined in this paper as the point where the stress had dropped to 50% of the UTS).

Mok et al. Paper (ECM Pathology)

Cerebral Amyloid Angiopathy:

(CAA) is a neurological condition in which amyloid protein is deposited onto the walls of the arteries of the brain. CAA increases the risk of bleeding into the brain (hemorrhagic stroke).

Beta-Amyloid Protein:

An amyloid that circulates in human blood and in cerebrospinal fluid and is deposited into plaques found in the brains of patients with Alzheimer's disease.

ERK:

A second messenger kinase (an enzyme adding phosphate groups from ATP), ERK belongs to the MAPK family and is responsible for transmitting signals from the cellular surface to the nucleus by the activation of transcription factors

Atomic Force Microscopy (AFM):

A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical position is recorded as a spring attached to the probe rises and falls in response to peaks and valleys on the surface. These deflections produce a topographic map of the sample.

MAP Kinase (MAPK):

MAPKs are a family of enzymes that form an integrated network influencing cellular functions such as differentiation, proliferation, and cell death. These cytoplasmic proteins modulate the activities of other intracellular proteins by adding phosphate groups to their serine/threonine amino acids.

Perlecan:

a large multidomain proteoglycan that binds to and cross-links many extracellular matrix (ECM) components and cell-surface molecules.

Heparin:

A naturally occurring mucopolysaccharide that acts in the body as an antithrombin factor to prevent intravascular clotting. Heparin is used therapeutically as an anticoagulant.

Beniash et al paper (Nanobiotech)

Amphiphilic: having distinct hydrophobic and hydrophilic regions

Oscillating Rheometry: measurement of viscoelastic properties of a material, from forced harmonic oscillatory input

Fourier Transform Infrared (FTIR) Spectroscopy: a technique for measuring a material’s absorbance of infrared radiation, accomplished by exposing the material to a high intensity flash of light and measuring its response

Complex Viscosity: a complex valued function of frequency which distinctly represents elasticity and resistance to flow

Transmission Electron Microscopy (TEM): imaging technique which consists of passing electrons through extremely thin samples and studying the “shadow”

Cho et al. paper (Tissue Engineering)

Willhauk et al. paper (Recent Advances)

Vascular Endothelial Growth Factor (VEGF) – A growth factor which stimulates angiogenesis (the growth of new capillaries from existing vascular structures) via promoting endothelial cell migration and mitosis

Complementary DNA (cDNA) – DNA synthesized from an mRNA template (thus not containing introns) that is used in in situ hybridization in order to localize specific DNA in a section of a tissue

in situ – in terms of cancer, a stationary tumor that is contained and not invasive

Tumor Stroma/microenvironment – includes the extracellular matrix and non-tumor cell types that have been recruited to participate in communicating with the tumor cells