GLOSSARY OF RESEARCH TERMINOLOGY

Allele - one of two or more alternative forms of a gene that arise by and are found at the same place on a chromosome.

Amino acid - Amino acids, often referred to as the building blocks of proteins, are compounds that play many critical roles in your body. They’re needed for vital processes like the building of proteins and synthesis of hormones and neurotransmitters.

Angiogenesis - the development of new blood vessels.

Antibodies - a blood protein produced in response to and counteracting a specific antigen. Antibodies combine chemically with substances which the body recognizes as alien, such as , , and foreign substances in the blood.

Heavy-chain vs. Light-chain antibodies - A typical antibody is composed of two immunoglobulin (Ig) heavy chains and two Ig light chains. Several different types of heavy chain exist that define the class or isotope of an antibody. These heavy chain types vary between dif- ferent animals. All heavy chains contain a series of immunoglobulin domains, usually with one variable domain (VH) that is important for binding antigen and several constant domains (CH1, CH2, etc.). Production of a viable heavy chain is a key step in B cell maturation. If the heavy chain is able to bind to a surrogate light chain and move to the plasma membrane, then the developing B cell can begin producing its light chain.

Polyclonal antibodies - A Polyclonal Antibody represents a collection of antibodies from different B cells that recognize multiple epitopes on the same antigen. Each of these individual antibodies recognizes a unique epitope that is located on that antigen.

Antigen - a toxin or other foreign substance which induces an immune response in the body, especially the production of antibodies.

Base editors - Base editors are designed to change one , or letter, of DNA into another, without cutting the DNA. They come in two flavors: cytidine base editors, which convert a cytosine (C) nucleotide to a thymine (T), and adenine base editors, which convert an (A) to a guanosine (G).

Base pairs - a pair of complementary bases in a double-stranded , consisting of a purine in one strand linked by hydro- gen bonds to a pyrimidine in the other. Cytosine always pairs with guanine, and adenine with thymine (in DNA) or uracil (in RNA).

Cell lines - a developed from a single cell and therefore consisting of cells with a uniform genetic makeup.

Complimentary strand - either of the two chains that make up a double helix of DNA, with corresponding positions on the two chains being composed of a pair of complementary bases.

CRISPR - CRISPR is a technique that allows scientists to make precision edits to any DNA, whether bacterial or human. Scientists discovered the technique when studying a bacteria’s , which they gave the acronym CRISPR. (It stands for “clustered regularly inter- spaced short palindromic repeats.”) When a attacks one of these bacteria, the CRISPR system captures a piece of the virus’s DNA and slides it into a section of its own DNA, which lets the bacteria’s virus-fighting machinery use it like a “wanted” poster to identify and destroy the virus it came from the next time it attacks. Scientists are now able to take the CRISPR system’s ability to cut, copy, and replace pieces of DNA and use it to their own ends, applying it to virtually any DNA they want to.

Deleterious gene - An allele of a gene whose effects on the phenotype are likely to result in a reduced fitness. Such genes are often reces- sive, so that they can be transmitted through families without being detected unless two occur together in the same individual.

De Novo mutation - A genetic alteration that is present for the first time in one family member as a result of a variant (or mutation) in a germ cell (egg or sperm) of one of the parents, or a variant that arises in the fertilized egg itself during early embryogenesis.

Dephosphorlyation - the removal of a phosphate (PO43−) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, , activate and deactivate enzymes by detaching or attaching phos- phoric esters and anhydrides.

EEG - An electroencephalogram (EEG) is a test used to evaluate the electrical activity in the brain. Brain cells communicate with each other through electrical impulses. An EEG can be used to help detect potential problems associated with this activity. An EEG tracks and records brain wave patterns. Small flat metal discs called electrodes are attached to the scalp with wires. The electrodes analyze the electrical im- pulses in the brain and send signals to a computer that records the results.

www.jordansguardianangels.org @JordansGuardianAngels @JordansGAngels @JordansGuaardianAngles

1 Electrophisiological recordings - Electrophysiological techniques have been integral to our understanding of protein translocation across various membranes, and, in particular, the mitochondrial inner and outer membranes. The activity of protein import channels of native mito- chondrial inner and outer membranes can be studied by directly patch clamping mitochondria and mitoplasts (mitochondria stripped of their outer membrane by French pressing) from various genetically manipulated strains of yeast and mammalian tissue cultured cells.

Enzyme - a substance produced by a living which acts as a catalyst to bring about a specific biochemical reaction.

Eptitope - the part of an antigen molecule to which an antibody attaches itself.

Feeder cells - feeder cells and have routinely been used to support the culturing and maintenance of embryonic stem cells (ESCs) in an undif- ferentiated state without losing their pluripotency.

Fibroblasts - a cell in connective tissue which produces collagen and other fibers.

Fusion protein - proteins created through the joining of two or more genes that originally coded for separate proteins.

Gene editing - the manipulation of the genetic material of a living organism by deleting, replacing, or inserting a DNA sequence, typically with the aim of improving a crop or farmed animal, or correcting a genetic disorder.

Gene therapy - the transplantation of normal genes into cells in place of missing or defective ones in order to correct genetic disorders.

Gene - Transcription is the first step in . It involves copying a gene’s DNA sequence to make an RNA molecule. Transcription is performed by enzymes called RNA polymerases, which link to form an RNA strand.

Genomic - relating to the haploid set of chromosomes in a gamete or microorganism, or the complete set of genes in a cell or organism.

Genotype - the genetic constitution of an individual organism.

Germline transmission - Germline transmission refers to a process where the ES derived cells of a chimera contribute to the reproductive cells of a (germ cells) and are genetically passed to its offspring.

Hematopoietic - An immature cell that can develop into all types of blood cells, including white blood cells, red blood cells, and platelets. Hematopoietic stem cells are found in the peripheral blood and the bone marrow.

Heterozygous - having two different alleles of a particular gene or genes.

Holoenzyme - a biochemically active compound formed by the combination of an enzyme with a coenzyme.

Homozygous - having two identical alleles of a particular gene or genes.

Immunotherapy - a treatment that uses certain parts of a person’s immune system to fight diseases such as

Inhibitor - a gene whose presence prevents the expression of some other gene at a different locus.

Interactomics - a discipline at the intersection of and biology that deals with studying both the interactions and the conse- quences of those interactions between and among proteins, and other within a cell.

IPSC Cells - Induced Pluripotent Stem Cells (iPS) iPSC are derived from skin or blood cells that have been reprogrammed back into an embry- onic-like pluripotent state that enables the development of an unlimited source of any type of human cell needed for therapeutic purposes.

Isoforms - any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

Isogenic Controls - Isogenic human disease models are a family of cells that are selected or engineered to accurately model the of a specific patient population, in vitro. They are provided with a genetically matched ‘normal cell’ to provide an isogenic system to research disease biology and novel therapeutic agents.

Isotope - each of two or more forms of the same element that contain equal numbers of protons but different numbers of neutrons in their nuclei, and hence differ in relative atomic mass but not in chemical properties; in particular, a radioactive form of an element.

Isotope labeling - a technique used to track the passage of an isotope (an atom with a detectable variation in neutron count) through a reac- tion, metabolic pathway, or cell. The reactant is ‘labeled’ by replacing specific atoms by their isotope. The reactant is then allowed to undergo

www.jordansguardianangels.org @JordansGuardianAngels @JordansGAngels @JordansGuaardianAngles

2 the reaction. The position of the isotopes in the products is measured to determine the sequence the isotopic atom followed in the reaction or the cell’s metabolic pathway.

Knockout cell line - A is a genetic technique in which one of an organism’s genes is made inoperative (“knocked out” of the organism). However, KO can also refer to the gene that is knocked out or the organism that carries the gene knockout. Human knockout cell lines generated using CRISPR/ -editing. This type of knockout cell line provides a complete loss-of-function phenotype from a single allele knockout and eliminates any masking of the knockout from a second allele seen in diploid cell models .

Knock-ins - In molecular cloning and biology, a knock-in refers to a method that involves the one-for-one substitution of DNA sequence information in a genetic locus or the insertion of sequence information not found within the locus.

Liposomes - a minute spherical sac of phospholipid molecules enclosing a water droplet, especially as formed artificially to carry drugs or other substances into the tissues.

Macrocephaly - An oversize head, the standard used to define macrocephaly is when the circumference of a person’s head is more than two standard deviations above average for their age. Or, their head is larger than the 98th percentile.

Malocclusion - imperfect positioning of the teeth when the jaws are closed.

Microcephaly - abnormal smallness of the head, a congenital condition associated with incomplete brain development.

MRI (Magnetic Resonance Imaging) - Magnetic resonance imaging uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from torn ligaments to tumors. MRIs are very useful for examining the brain and spinal cord. MRIs employ powerful magnets which produce a strong magnetic field that forces protons in the body to align with that field. ... When the radiofrequency field is turned off, the MRI sensors are able to detect the energy released as the protons realign with the magnetic field.

M-Tor pathway - mTOR integrates the input from upstream pathways, including insulin, growth factors, and amino acids. mTOR also sens- es cellular nutrient, oxygen, and energy levels. The mTOR pathway is a central regulator of mammalian metabolism and physiology, with important roles in the function of tissues including , muscle, white and brown adipose tissue, and the brain, and is dysregulated in human diseases, such as diabetes, obesity, depression, and certain .

Nanibodies - are a novel class of proprietary therapeutic proteins based on single-domain antibody fragments that contain the unique struc- tural and functional properties of naturally-occurring heavy chain only antibodies.

Neurogenesis - the growth and development of nervous tissue.

Neurons - a specialized cell transmitting nerve impulses; a nerve cell.

Neuroprogenitor cells - cells that are capable of dividing a limited number of times and have the capacity to differentiate into a restricted repertoire of neuronal and glial cell types.

Nucleotides - a compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA.

Organoids - an artificially grown mass of cells or tissue that resembles an organ.

Pathogenicity - the property of causing disease.

Pathology - the of the causes and effects of diseases, especially the branch of that deals with the laboratory examination of samples of body tissue for diagnostic or forensic purposes.

PBMCs - A peripheral blood mononuclear cell is any peripheral blood cell having a round nucleus. These cells consist of lymphocytes (T cells, B cells, NK cells) and monocytes, whereas erythrocytes and platelets have no nuclei, and granulocytes (neutrophils, basophils, and eosino- phils) have multi-lobed nuclei.

Peptides - a compound consisting of two or more amino acids linked in a chain, the carboxyl group of each acid being joined to the amino group of the next by a bond of the type -OC-NH-.

Periplasm - a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria.

www.jordansguardianangels.org @JordansGuardianAngels @JordansGAngels @JordansGuaardianAngles

3 Phage display - a technique for the production and screening of novel proteins and polypeptides by inserting a gene fragment into a gene responsible for the surface protein of a bacteriophage. The new protein appears in the surface coating of the phage, in which it can be ma- nipulated and tested for biological activity.

Phenotype - the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

Phosphopeptides - Any peptide that incorporates a phosphate group as a result of phosphorylation.

Phosphoproteomics - a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a post- translational modification.

Phosphorylation - the process of phosphorylating a chemical compound either by reaction with inorganic phosphate or by transfer of phosphate from another organic phosphate especially : the enzymatic conversion of carbohydrates into their phosphoric esters in metabolic processes.

Phosphotase - an enzyme that catalyzes the hydrolysis of organic phosphates in a specified (acid or alkaline) environment.

Progenitors - a person or thing from which a person, animal, or plant is descended or originates.

Promiscuous activity - a non-native activity the enzyme did not evolve to do, but arises due to an accommodating conformation of the active site.

Proteomics - the large-scale study of proteomes. A proteome is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver).

Regenerative medicine - the branch of medicine that develops methods to regrow, repair or replace damaged or diseased cells, organs or tissues. Regenerative medicine includes the generation and use of therapeutic stem cells, tissue engineering and the production of artificial organs.

RNA interference - a biological process in which RNA molecules inhibit gene expression or , by neutralizing targeted mRNA mole- cules. The term RNA interference (RNAi) was coined to describe a cellular mechanism that use the gene’s own DNA sequence of gene to turn it off, a process that researchers call silencing. RNAi is widely used by researchers to silence genes in order to learn something about their function.

Serum - includes all proteins not used in blood clotting and all the electrolytes, antibodies, antigens, hormones, and any exogenous sub- stances (e.g., drugs and microorganisms).

Serum starvation - brings all cells to phase of growth arrest thereby equalising all cells into the same phase of . This enables pro- nounced effect following treatment with growth signals.

Sib-selection - an isolation process that can be used in conjunction with any assay system. In particular, it may be used to isolate a gene from a library where there is an assay for the , but no selection or sequence information available.

Stop-code - a nucleotide triplet within messenger RNA that signals a termination of translation into proteins.

Substrates - a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). In the case of a single substrate, the substrate bonds with the enzyme active site, and an enzyme-substrate complex is formed.

Synaptic transmission - the process by which one neuron communicates with another. It must cross over the synaptic gap between the presynaptic neuron and post-synaptic neuron.

Target proteins - are functional biomolecules that are addressed and controlled by biologically active compounds. They are used in the processes of transduction, transformation and conjugation. ... Target proteins control the action and the kinetic behavior of drugs within the organism.

Translation - the process in which ribosomes in the or ER synthesize proteins after the process of transcription of DNA to RNA in the cell’s nucleus.

Variant - a group of within a species that differ in trivial ways from similar groups; a new strain of microorganisms.

Variation - is a term used to describe the variation in the DNA sequence in each of our . ... Individuals of a species have similar char- acteristics but they are rarely identical, the difference between them is called variation.

www.jordansguardianangels.org @JordansGuardianAngels @JordansGAngels @JordansGuaardianAngles

4 Missense variation - A genetic alteration in which a single substitution alters the genetic code in a way that produces an amino acid that is different from the usual amino acid at that position.

Vector - In molecular cloning, a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell, where it can be replicated and/or expressed.

Wild type - The allele that encodes the phenotype most common in a particular natural population is known as the allele. It is often designated, in genetic shorthand, as “+”. Any form of that allele other than the wild type is known as a mutant form of that allele.

www.jordansguardianangels.org @JordansGuardianAngels @JordansGAngels @JordansGuaardianAngles

5