Difference between revisions of "Week 11 E-notes Eyanosch"

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Week 11 Electronic Notes

1. 10 Biological terms
   • shigellosis - Shigella infection (shigellosis) is an intestinal disease caused by a family of bacteria known as shigella. The main sign of shigella infection is diarrhea, which often is bloody. (http://www.mayoclinic.org/diseases-conditions/shigella/basics/definition/con-20028418)
   • rifampin - a semisynthetic broad-spectrum antibiotic, C 4 3 H 5 8 N 4 O 1 2, used in the treatment of pulmonary tuberculosis, asymptomatic carriers of meningococcal disease, and leprosy. (http://dictionary.reference.com/browse/rifampin)
   • rifaximin - is a semisynthetic antibiotic based on rifamycin. It has poor oral bioavailability, meaning that very little of the drug will be absorbed into the blood stream when it is taken orally. Rifaximin is used in the treatment of traveler's diarrhea and hepatic encephalopathy, for which it received orphan drug status from the U.S. Food and Drug Administration in 1998. (https://en.wikipedia.org/wiki/Rifaximin)
   • pouchitis - is inflammation of the ileal pouch (an artificial rectum surgically created out of ileal gut tissue in patients who have undergone a colectomy), which is created in the management of patients with ulcerative colitis, indeterminate colitis, FAP, or, rarely, other colitides. Patients with pouchitis typically present with bloody diarrhea, urgency in passing stools, or discomfort while passing stools. The loss of blood and/or dehydration resulting from the frequent stools will frequently result in nausea. Extreme cramping and pain can occur with pouchitis. (https://en.wikipedia.org/wiki/Pouchitis)
   • putative - generally believed to be something; commonly accepted or supposed (http://www.merriam-webster.com/dictionary/putative)
   • MIC (minimal inhibitory concentration) - the smallest concentration of an antibiotic that regularly inhibits growth of a bacterium in vitro (http://www.merriam-webster.com/medical/minimal%20inhibitory%20concentration)
   • type III secretion system - Type three secretion system (often written Type III secretion system and abbreviated TTSS or T3SS, also called Injectisome or Injectosome) is a protein appendage found in several Gram-negative bacteria. In pathogenic bacteria, the needle-like structure is used as a sensory probe to detect the presence of eukaryotic organisms and secrete proteins that help the bacteria infect them. The secreted effector proteins are secreted directly from the bacterial cell into the eukaryotic (host) cell, where they exert a number of effects that help the pathogen to survive and to escape an immune response. (https://en.wikipedia.org/wiki/Type_three_secretion_system)
   • transient - lasting a very short time; of a mental act; causing effects outside the mind(http://www.vocabulary.com/dictionary/transient)
   • attenuation - reduced especially in thickness, density, or force; tapering gradually usually to a long slender point (http://www.merriam-webster.com/dictionary/attenuate)
   • nascent - beginning to exist : recently formed or developed (http://www.merriam-webster.com/dictionary/nascent)

1. Article Outline
   • What is the importance or significance of this work (i.e., your species)?

The importance of this work is to identify which genes are induced or repressed depending on the drug tested. These bactrium are responsible for shigellosis, a bacterial infection of the intestine that results in bloody diarrhea and fever. Two antibiotic compounds were studied, rifampin (RP) and rifaximin (RX), both inhibiting RNA synthesis which inhibits growth and reproduction processes of the bacteria. Due to recently increasing resistance to antibiotics in shigella strains it is imperative to see which genes are being inhibited or induced with the current market antibiotics. The expression profiles of micro arrays will provide insight into the interaction between the drugs and bacteria. By inhibiting RNA synthesis, no new proteins will be produced, any proteins still present have yet to degrade.

1. • What were the methods used in the study?

qRT-PCR is considered to be the most powerful, sensitive, and quantitative assay for the detection of RNA levels. It is frequently used in the expression analysis of single or multiple genes, and expression patterns for identifying infections and diseases.

1. • Briefly state the result shown in each of the figures and tables.

1. • How do the results of this study compare to the results of previous studies (See Discussion).

1. • For the microarray paper (GenMAPP Users only), include the following:

1. • 1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.

1. • 1. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.

1. • 1. Construct a flow chart that illustrates the above.

Notes from Dr. Dhalquist on thursday = resize graphic, genome stuff to bottom of page, links to the top