gene ontology

Examples of gene ontology in the following topics:

• Gene Families

  • Gene families are groups of functionally related genes arising from a duplicated gene.
  • A gene family is a set of several similar genes, formed by duplication of a single original gene, that generally have similar biochemical functions .
  • If the genes of a gene family encode proteins, the term protein family is often used in an analogous manner to gene family.
  • In contrast, gene complexes are simply tightly linked groups of genes, often created via gene duplication (sometimes called segmental duplication if the duplicates remain side-by-side).
  • Unequal crossing over generates gene families.

• Sorting Out Variations on the Terms "Constructionism" and Constructivism"

  • One important point to note is the distinction between epistemology, a set of beliefs about knowing, and ontology, a set of beliefs about what exists or what is real.
  • However, usually this may be taken as an epistemological statement, not an ontological statement.

• Epistasis

  • The B gene controls black (B_) vs. brown (bb) color, while the E gene controls yellow (ee) color.
  • Genes may also oppose each other with one gene modifying the expression of another.
  • Often the biochemical basis of epistasis is a gene pathway in which the expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway.
  • In this case, the C gene is epistatic to the A gene.
  • Thus, the C gene is epistatic to the A gene.

• Altered Gene Expression in Cancer

  • Cancer, a disease of altered gene expression, is the result of gene mutations or dramatic changes in gene regulation.
  • Cancer can be described as a disease of altered gene expression.
  • There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell.
  • This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation).
  • It can bind to sites in the promoters of genes to initiate transcription.

• Tracking Cells with Light

  • In molecular biology, researchers use a reporter gene that they attach to a regulatory gene of interest.
  • Reporter genes ideally have distinguishable properties that can be easily detected and measured.
  • To introduce a reporter gene into an organism, scientists place the reporter gene and the gene of interest in the same DNA construct to be inserted into the cell or organism.
  • It is important to use a reporter gene that is not natively expressed in the cell or organism under study, since the expression of the reporter is being used as a marker for successful uptake of the gene of interest.
  • Reporter gene used as an indication of the regulatory sequence expression in the cell.

• Epigenetic Alterations in Cancer

  • Silencing genes through epigenetic mechanisms is very common in cancer cells and include modifications to histone proteins and DNA that are associated with silenced genes.
  • When these modifications occur, the gene present in that chromosomal region is silenced.
  • In cancer cells, silencing genes through epigenetic mechanisms is a common occurrence.
  • Mechanisms can include modifications to histone proteins and DNA associated with these silencing genes.
  • Describe the role played by epigenetic alterations to gene expression in the development of cancer

• Gene Duplications and Divergence

  • Gene duplication is the process by which a region of DNA coding for a gene is copied.
  • Duplicate genes are often immune to the selective pressure under which genes normally exist.
  • Many retrogenes display changes in gene regulation in comparison to their parental gene sequences, which sometimes results in novel functions.
  • This can apply to genes and proteins, such as nucleotide sequences or protein sequences that are derived from two or more homologous genes.
  • Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication within a population) can be said to display divergent evolution.

• Reporter Fusions

  • A reporter fusion is the hybrid of a gene or portion of a gene with a tractable marker.
  • In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals, or plants .
  • To introduce a reporter gene into an organism, scientists place the reporter gene and the gene of interest in the same DNA construct to be inserted into the cell or organism.
  • In these cases the reporter is directly attached to the gene of interest to create a gene fusion.
  • In molecular biology, a reporter gene (often simply reporter) is a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals, or plants

• Variations in Size and Number of Genes

  • Nucleotide variation is measured for discrete sections of the chromosomes, called genes.
  • In humans, more proteins are encoded per gene than in other species.
  • M.leprae has lost many once-functional genes over time due to the formation of pseudogenes.
  • The repeat-rich regions contain genes coding for host interaction proteins.
  • This figure represents the human genome, categorized by function of each gene product, given both as number of genes and as percentage of all genes.

• Genetics and Regulation of N2 Fixation

  • These genes are found in nitrogen fixing bacteria and cyanobacteria.
  • The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen.
  • Nif genes have both positive and negative regulators.
  • Some of nif genes are: Nif A, D, L,K, F,H S,U,Y,W,Z .
  • The nif genes can be found on bacteria's chromosomes, but many times they are found on bacteria's plasmids with other genes related to nitrogen fixation, such as the genes needed for the bacteria to communicate with the plant host.