Revision as of 00:27, 12 November 2013

Quality Assurance Notes:
Strain IDs:
TIGR4:SPN#####
R6: spr####
G54: SP####

R6 and G54 strains were found using alternate names: R6: ATCC BAA-255, G54: serotype 19F

Individual Assignment

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources.

• beta-hemolytic: test performed on blood agar showing lysis of red blood cells. Hemolysis refers to the release of hemoglobin when red blood cells break open. (http://www.biology-online.org)
• contigs: casual term referring to overlapping parts of the genome. (http://www.biology-online.org)
• bacteriocins: antibacterial that hurts some strains within the same bacterial family as the ones who produce it. (http://medical-dictionary.thefreedictionary.com)
• sortase: "enzyme that anchors surface proteins to cell wall" of gram positive bacteria. (http://www.wikigenes.org/e/ref/e/10427003.html)
• putative: generally inferred (http://medical-dictionary.thefreedictionary.com)
• concomitant: joined together or accessoried. (http://medical-dictionary.thefreedictionary.com)
• transposase: enzymes that codes for the insertion of transposons, a utility of bacteria. (http://www.biology-online.org)
• ubiquitous: occurring in many places at once. (http://www.merriam-webster.com/dictionary)
• porins: component proteins that assemble to make a pore in a membrane. (http://www.biology-online.org)
• ortholog: gene found in one or many organisms with a common ancestor. (http://www.biology-online.org)

Genome of the Bacterium Streptococcus pneumoniae Strain R6 Article

Introduction

• S. pneumoniae infection is a top cause of death in the U.S., ~1.1 million annually worldwide
• 1/3 isolates are able to resist penicillin, antibiotic resistance is increasing
• Streptococcus can be either pathogenic or commensalists, requiring a eukaryotic host
• the experiment sequenced the genome of S. pneumoniae with hopes that it would help find new therapies
• used R6 strain, a derivative of a smooth strain, used commonly in clinical and lab settings
• this strain is malleable and safe to work with

Materials/Methods Used in the Experiment

• original R6 strain retrieved from an Alexander Tomasz
• derived from original strain D39
• R6 has ability to be converted to a strain able to resist penicillin
• Genome Sequencing:
  • brain heart infusion medium was used to grow cultures of bacteria, where DNA was extracted from
  • used a purification process including extractions, precipitations, and spoolings
  • plasmids were made using the DNA fragments
  • ~44,000 sequences in total were made
  • used PHRED, CONSED, and PHRAP to rejoin the DNA and analyze the sequences
  • an algorithm was used in order to determine repeating patterns in the sequences
  • used a process called southern blotting and PCR to analyze the plasmids and find end sequences
  • located a hypothetical protein on one ORF that they predicted would be many base pairs larger than the found repeat actually was
• Sequence Annotation/Analysis:
  • used gene prediction programs to annotate the genome
  • results were imported to database using the Microsoft SQL server
• Identification of ORFs:
  • used program called Glimmer to match potential ORF sequences within the genome
  • assigned each sequences a gene id formatted as spr####
• Gene Assignment:
  • all specified ORFs were put through a BLAST search in GenBank
  • also compared these with those found in Prosite library
  • searches allowed for gene id finalization
• RNA identification:
  • RNAs identified using subsequent ribosome sequence database
• Sequence was given an accession number in GenBank database

Results of Experiment