Mpetredi Week 11

Mitchell Petredis

[[Team Name]]

References

• Week 11

Unfamiliar Biological Terms (Combination of Genome and Microarray Paper Terms

• Mb: mega base pairs, equal to 1,00,000 base pairs
  • Source: [Wikipedia]
• orphan gene: A strict definition of the term is that no homologous gene exists in any other species. A more liberal definition is that orphan genes are protein-coding regions that have no recognizable homolog in distantly related species
  • Source: [Wikipedia]
• kinase: any of various enzymes that catalyze the transfer of phosphate groups from a high-energy phosphate-containing molecule (as ATP) to a substrate
  • Source: [Merriam-Webster]
• megaplasmid: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside.
  • Source: [Springer]
• quorum sensing: A phenomenon where microorganisms communicate and coordinate their behavior by the accumulation of signaling molecules. A reaction occurs when a substance accumulates to a sufficient concentration. This is most commonly seen in bacteria.
  • Source: [Reference.md]
• nodulation: the process of forming nodules and especially root nodules containing symbiotic bacteria
  • Source: [Merriam-Webster]
• rhizophere: soil that surrounds and is influenced by the roots of a plant
  • Source: [Merriam-Webster]
• minimal medium: a medium that contains only inorganic salts, a simple carbon source (as carbon dioxide or glucose), and water
  • Source: [Merriam-Webster]
• chaperone: any of a class of proteins (as heat shock proteins) that facilitate the proper folding of proteins by binding to and stabilizing unfolded or partially folded proteins
  • Source: [Merriam-Webster]
• filamentation: the anomalous growth of certain bacteria, such as E. coli, in which cells continue to elongate but do not divide (no septa formation)
  • Source: [Wikipedia]
• chemotaxis: orientation or movement of an organism or cell in relation to chemical agents
  • Source: [Merriam-Webster]
• sigma factor: a detachable polypeptide subunit of RNA polymerase that facilitates the initiation of transcription by recognizing specific DNA promoter sites
  • Source: [Merriam-Webster]
• periplasm: the region in a gram-negative bacterium between the plasma membrane and an outer surrounding membrane that contains especially enzymes and a thin layer of peptidoglycan
  • Source: [Merriam-Webster]
• downregulation: the process of reducing or suppressing a response to a stimulus; specifically : reduction in a cellular response to a molecule (as insulin) due to a decrease in the number of receptors on the cell surface
  • Source: [Merriam-Webster]
• plasmolysis: shrinking of the cytoplasm away from the wall of a living cell due to outward osmotic flow of water
  • Source: [Merriam-Webster]
• replicon: a linear or circular section of DNA or RNA which replicates sequentially as a unit
  • Source: [Merriam-Webster]

Outline of Microarray Paper

• Real world relevance: soil salinity severely limits productivity of agricultural crops
  • An estimated 40% of Earth's land surface has salinity problems.
• Rhizobia: aerobic gram-negative soil bacteria that establish nitrogen-fixing symbioses with leguminous plants under nitrogen deprivation conditions
  • exchange of molecular signals between the 2 partners occurs here
    • forms root nodules (biological nitrogen fixation occurs here)
• Rhizobium-legume symbiosis sensitivity to salt and osmotic stress > free-living rhizobia
• Salt stress effects
  • inhibits initial steps of the symbiosis
  • depressive effect on nitrogen fixation
• rhizobial tolerance to salinity is important