Med term 2

colectomy

Whipple

Limb salvage surgery

transsphenoidal resection

wedge resection

radical

steriotactic radiosurgery

bracytherapy

• pneumon/o -ectomy
• meanings: lung excision, surgical removal
• term meaning: excision of the lung

• col/o -ectomy
• colon excision, surgical removal
• excision of (all or part of) colon

• cyst/o -ectomy
• bladdar excision, surgical removal of
• excision of the bladder

• thyroid/o -ectomy
• thyroid gland

• laryng/o -ectomy
• larynx
• excision of (all or part of) larynx

• irid/o
• iris
• excision of (part of) the iris

• crani/o
• skull
• excision of (part of) the cranium

Gastrointestinal stromal tumor

Ductal carcinoma in situ

Transurethral resection of prostate

Hepatobiliary iminodiacetic acit

bone marrow transplant

Radiofrequency ablation

transrectal ultrasound

epidermal growth factor receptors

Magnetic resonance cholangiopancreatography

endoscopic ultrasound

A) melanoma-mastectomy

nonmalignant

gastrectomy

retina

TURP

nephroma

children

reconstructive surgery

adjuvant

gynecologic oncologist

abnormal chromosomal number. For example, a loss of chromosome 4 and an extra copy of chromosome 21 could both be described as aneuploidy. Aneuploidy is also applied to portions of chromosomes.

• Annotated-a gene is annotated when it has been recognized
• from a large segment of genome sequence and often we know something about its cellular role. Genomes can also be described as annotated once they have been analyzed for gene content.

• Accession number-identification number given to every DNA
• and protein sequence submitted to NCBI or equivalent database. For example, the human leptin receptor SwissProt accession number is P48357.

• Autocatalytic-an enzyme capable of stimulating its own
• (auto) activity (catalyst).

• Antigen-any molecule that stimulates an immune response in
• the form of an antibody. Pollen and vaccines are both antigens.

Array-an orderly pattern of objects. In genomic studies, there are micro arrays and macro arrays. Microarrays are small spots of DNA or protein, and the identity of the spotted material is known. Macroarrays are bacterial, yeast, or similar colonies on plates used to determine functional consequences of genomic manipulations.

Aquaporin-protein that forms a channel (pore) across a membrane to allow the flow of water ( aqua ) molecules. Arabidopsis a flowering plant about 15 cm tall that reproduces very quickly; sometimes referred to as the plant equivalent of the fruit fly. First plant to have its genome fully sequenced.

a normal function for many cells, apoptosis is agenetically encoded sequence of cellular actions that leads to the cell’s death; often referred to as "programmed cell death."

• Anthrax-( Bacillus anthracis ) rod-shaped Eubacteria that
• can infect skin or lungs; may be used as a biological weapon.

• Bioinformatics-a field of study that extracts biological
• information from large data sets such as sequences, protein interactions, microarrays, etc. This field also includes the area of data visualization.

Blast-the protein and nucleic acid sequence search engine developed at NCBI that allows you to search sequence databases. BLASTn searches for nucleotide sequences; BLASTp searches for amino acid sequences; BLAST2 compares two sequences.

• Contiguous-overlapping DNA segments that as a collection form a longer and gapless
• segment of DNA.

Cox-Cox converts arachidonic acid into prostaglandins, which are lipid-signaling molecules that trigger the sensation of pain, inflammation, and fever. Humans have two Cox genes called Cox-1 and Cox-2. Cox-1 is expressed in every cell, with the highest levels in the stomach and kidneys. Cox 2 is expressed primarily in the brain, lung, kidney, and white blood cells

Dideoxy sequencing-invented by Fred Sanger, a method for sequencing DNA that utilizes ddNTPs.

Dendrogram-a branching diagram that shows the relative sequence similarity between many different proteins or genes. Typically, horizontal lines indicate the degree of differences in sequences, but vertical lines are used for clarity to separate the branches. A scale bar should be included with each dendrogram.

Domain-(1) the highest level of taxonomic organization. All life is divided into three domains: Archaea, Eubacteria, and Eukaryota. (2) a region within a protein that has a particular shape and function

Epistatic-Gene A is said to be epistatic to gene B if an allele of gene A masks the encoded effects of gene B.

control of gene activity without altering DNA sequence. One example of epigenetic regulation is imprinting, which is affected in part by methyltransferases adding a methyl group (–CH3) to cytosine bases in DNA.

Extremophie-organisms that live in extreme environments, members of the domain Archaea . For example, Archaea can live in boiling water, extremely acidic water, or at the bottom of the ocean near hot vents.

Founder effect-a population genetics term that explains a lack of genetic diversity in a population. For example, when a small number of adults land on a small island, all subsequent children typically contain no more variability than was present in the original inhabitants.

Gene therapy-correcting a defective gene by inserting a wt allele. Gene therapy can only work to correct recessive alleles unless the defective dominant allele is replaced by a knockout deletion.

GenBank-developed and housed at NCBI, GenBank is the U.S. repository for all DNA and protein sequences.

Genomics-a vague term that encompasses the study of reference genome sequences, variations within a species’ genome, DNA microarrays, circuits, and systems biology. Some people include wider areas such as proteomics, metabolomics, etc., under the genomics umbrella. Due to its recent and changing definition, the term does not have a universally accepted meaning.

Gastrulation-a process of embryonic development when part of a blastula invaginates and forms a second layer of embryonic cells.

Genetic determinism-the idea that all human traits are encoded in DNA. Examples of genetic determinism can be found in popular media stories that tout the discovery of a "smart gene" or "worry gene."

Haplotype-(derived from haploid genotype) a collection of alleles in one individual that are located on one chromosome. Alleles within a haplotype often are inherited as a single unit from one generation to the next. In SNP studies, haplotypes refer to a group of genomic variations found repeatedly in many people within a population.

Induced-a gene with increased transcription. Typically refers to the switch from none to some transcription, but it could also refer to a switch from low to high transcription.

Iteration-when a process is repeated in an attempt to reach the ideal outcome, each repetition is called an iteration. Each iteration is slightly different from the previous one since we learn from the first and improve the second iteration.

In vitro-experimental process performed in a tube or petri dish and not in a living cell or organism. Literally translated as "in glass."

Leptin-mammalian protein hormone (encoded by the ob gene) produced by fat cells that regulate fat homeostasis (the lipostat). If you produce too much leptin, you will lose fat, but if you don’t produce enough, you will store more fat. In addition to fat homeostasis, leptin also influences sexual reproduction, immune and brain functions.

Motif-a sequence of amino acids or nucleotides that performs a particular role and is often conserved in other species or molecules.

Megabase-1,000 kilobases or 1 million bases of DNA.

Omim-a comprehensive web site that catalogs all the genetic and molecular information related to human diseases (not just male diseases).

• Phylogoenetic tree-graphic way to illustrate the evolutionary
• relatedness of genes, proteins, individuals, strains, or species.

Phagosome-internal organelles of white blood cells that engulf and kill pathogens.

Pseudogenes-segments of DNA that resemble genes by their sequence of bases but are nonfunctional. Pseudogenes often have transposons inserted in them, or they may have other mutations that led to their inability to encode a functional protein.

PCR-molecular method that allows you to mass-produce any segment of DNA as long as you have two oligos that hybridize to the two strands of target DNA with their 39 ends pointed toward each other.

Ribozyme-RNA enzymes. Contrary to the initial rule "all enzymes are proteins," some enzymatic reactions are performed by RNA.

Stationary phase-a description of cells growing in culture that have slowed down their growth rate. Stationary cells are not increasing in number, but they are not dead.

Signal transduction-conveyance of information from the outside to the inside of a cell. When a ligand binds to its receptor, this information is conveyed to the rest of the cell through a complex pathway of signal transduction that involves second messengers.

• Structural proteomics-a discipline
• within proteomics that focuses on the 3D shape of proteins.

SNPs-very similar to point mutations except SNPs are considered to represent the genetic variation present in wt genotypes. By definition, SNPs differ from the reference sequence of a species.

T-test-statistical method for determining whether a mean, or the difference between two means, is significantly different from the hypothesized value.

Tumor suppressor-protein slows down the progression of the cell cycle and prevents cancers. Typically, tumor suppressors work at checkpoints to ensure the cell is functioning properly before permitting the cell cycle or mitosis to continue. p53 and pRB are two examples.

Wild-type-allele, genotype, or phenotype that is considered to be the standard for a given strain or species. Wild-type alleles encode functional proteins and produce typical phenotypes. Italics is used if referring to genes or alleles.

• Intergenic sequence-DNA sequence
• between two genes, sometimes referred to as "junk DNA."

• COG-NCBI compilation of evolutionarily related gene sequences from several
• microbial genomes. This site allows you to search by gene or cellular role and
• produces dendrograms to show sequence similarities.

Consanguineous-synonym for incest; breeding among closely related individuals that can accumulate deleterious alleles in the offspring and thus more genetic diseases.

• Clone-noun or verb. A clone is any molecule/cell/organism present in more than
• one identical copy. To clone something means to produce more than one copy of
• the original molecule/cell/organism.

• Conserved domain-(CD) a domain that has been retained during
• evolution presumably due to its essential role within the protein’s structure.
• Conserved domain searches are a part of the BLAST search.

• Dendrogram-a branching diagram that shows the relative sequence similarity between
• many different proteins or genes. Typically, horizontal lines indicate the
• degree of differences in sequences, but vertical lines are used for clarity to
• separate the branches. A scale bar should be included with each dendrogram.

• DNA microarray-or DNA chips synonyms for gene sequences spotted on
• glass slides used to measure simultaneously the level of transcription of many
• genes.

Ectopic-a gene inserted in an unnatural location. For example, in mutant strains of T7, ectopic copies of gene 1 were inserted throughout the genome to test the positional effects of gene locations.

Exons-parts of RNA molecule spliced together to form mRNA.

E-Value-(E-value) when performing a BLAST search, you will obtain an E-value for each sequence that is retrieved. An E-value can be thought of as the probability that two sequences are similar to each other by chance. Therefore, E values are best when they are small (e.g., 1 3 10212) compared to larger E-values (e.g., 0.06).

• Gene therapy-correcting a defective gene by inserting a wt allele. Gene therapy can
• only work to correct recessive alleles unless the defective dominant allele is
• replaced by a knockout deletion.

• GMO-in contrast to gene therapy, GMO has a transgene inserted into the
• genomes in every cell in its body, as will all its offspring.

Homology-a term with two different meanings that are often confused. Initially, homology referred to two sequences (DNA or amino acid) that were similar due to evolutionary relatedness. The newer and less specific meaning is simply two sequences that are similar. One other usage refers to homologous chromosomes, the pair of chromosomes in diploid organisms.

Lipostat-a term to describe the integrated circuit that uses leptin and other molecules to regulate fat homeostasis. Each person’s lipostat is set for a percentage of body fat, and this set point can be increased by eating a high-fat diet or decreased by exercising.

Linkage-when two genes are located near each other on the same chromosome; quantified by the frequency of recombination between two loci and measured in map units or centiMorgans, where 1 map unit equals 1% recombination frequency.

• Leprosy-a disfiguring
• disease caused by the bacterium Mycobacterium leprae. They infect white blood cells called macrophages, which normally engulf and kill pathogenic bacteria. Later, Schwann cells surrounding the nerves become infected, which leads to the loss of myelin, nerve damage, loss of sensation, and eventually loss of extremities due to reduced blood circulation.

Metabolome-term coined to encompass the entire metabolic content of a cell or organism.

• NCI-(NCI) federally funded part of the U.S. National Institutes of Health, the NCI focuses on basic and applied research to treat and prevent cancer. Home for the Cancer Genome Anatomy Project, which intends to catalog the gene
• activity found in every type of cancer and compare this to the gene activity to wt tissues.

• Occams razor-a guiding principle; when deciding which
• explanation to accept, always start with the simplest one.

ORF-a portion of a cDNA or gene that begins with the start codon and ends with the stop codon. Synonym for coding sequence (CDS) on GenBank results.

Oncogene-mutant dominant alleles of vital genes (e.g., Ras). Oncogenes (acting like the accelerator on a car) force the cell cycle to speed up, while tumor suppressors are similar to brakes trying to slow down the cell cycle.

Pub Med-an extensive database of biomedical literature hosted by NCBI that is searchable. You can subscribe to PubCrawler and automatically search PubMed and receive email results on a schedule of your choosing.

Pharmacogenomics-very similar to pharmacogenetics, pharmacogenomics attempts to study genome-wide influences on the efficacy of medications.

PDB-database of every protein for which the 3D structure is known; it also contains a few nonprotein structures.

Protease-enzyme degrades proteins into smaller pieces. Two examples are cathepsins found in phagosomes and trypsin produced by the pancreas to help digest food.

• Prion-proteins that have two shapes, one benign and the other contagious,
• which leads to the conversion of the benign shape to the contagious shape.
• Contagious prion proteins can spread from one organism to another and cause
• neurological diseases such as scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob
• Disease (CJD) in humans.

bacterium that can harm its host

a person who disects a complex system into increasingly smaller parts in order to understand it.

an engineering term that indicates the ability to function in lest htat optimun conditions (i.e, noise) ex: southern blots and DNA sequencing

• Redundant-in the context of genomic circuits, redundant means that a critical
• process can be performed by more than one gene or individual pathway. For
• example, there are three redundant IDH genes that utilize NADP1 and consume
• isocitrate to produce NADPH and ketoglutarate.

Southern blot-named to honor its inventor, Dr. Ed Southern. A classic molecular method that allows the investigator to separate DNA by size in a gel, transfer the DNA to specialized paper (called a membrane), and hybridize the DNA with a particular probe.

• Stochastic-not exactly the same as random, stochastic refers to genes or proteins
• that can produce widely variable outcomes.

• Serotype-analogous to genotypes, serotypes describe pathogens based on the
• ability of antibodies to bind to different subsets. For example, Neisseria
• meningitides exists in several serotypes.

• Systems biology-coined to denote the new perspective for research
• in the postgenomic era. Systems biology studies whole cells/tissues/organisms
• not by a traditional reductionist’s approach but by holistic means in a
• reiterative attempt to model the complete cell/tissue/organism.

Signature genes-often cited in DNA microarray experiments; a collection of genes that are characteristic for a particular sample. For example, you would expect all green leaves to express a set of signature genes necessary to conduct photosynthesis

Teratogen-a substance such as lithium or alcohol that causes developmental abnormalities.

TB-the pathogenic bacterium Mycobacterium tuberculosis causes TB, which is a debilitating and potentially lethal respiratory infection that can be antibiotic resistant and thus difficult to treat.

Virulent pathogen-or parasite that has the potential to do serious harm to its host.

TURP

palliative