== Individual Journal Assignment ==

===Citation===

Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., … Yu, J. (2002). Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Research, 30(20), 4432–4441.

Link: [http://nar.oxfordjournals.org/content/30/20/4432.full HERE]

=== Preparation for Journal Club on Your Species ===

Some steps are taken from [[Week 11 | here.]]

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# I made a list of 11 biological terms for which I did not know the definitions when I first read the article. I then defined each of the terms.

# I made a list of 12 biological terms for which I did not know the definitions when I first read the article. I then defined each of the terms.

##enterohemorrhagic - Based on what my teammates have told me and what I've found on [http://www.cdc.gov/ncidod/dbmd/diseaseinfo/enterohemecoli_t.htm the CDC website.] Enterohemorrhagic is used to describe a strain of ''E. coli'' that induces hemorrhagic diarrhea which is a result of bleeding into the intestines.

##plasmid - Plasmids are circular independent DNA molecules that hold a few genes and can be inserted into genomes. [https://askabiologist.asu.edu/plasmids]

##inversions - An inversion is a defect in a chromosome. Physically it occurs when a segment of the chromosome breaks off and is reinserted into the chromosome in the same spot. [http://www.biology-online.org/dictionary/Inversion Source]

##translocations - Translocation is another type of defect in a chromosome when a segment breaks off and is moved to another location within the same chromosome or to another chromosome.[http://www.biology-online.org/dictionary/Translocation Source]

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##bacteriophage - [http://www.biology-online.org/dictionary/Bacteriophage | Biology Online Dictionary] A bacteriophage is a virus that can infect a bacteria.

##bacteriophage - [http://www.biology-online.org/dictionary/Bacteriophage Biology Online Dictionary] A bacteriophage is a virus that can infect a bacteria.

##pathogenicity islands - The segment of genetic material within an organism(in this case within the bacteria) that gives the organism the ability to cause disease. [http://www.medicinenet.com/script/main/art.asp?articlekey=20705 This helped.]

##enteric - I just used the google dictionary for this: [https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=enteric] It means relating to the intestines, so it isn't really strictly a biological term.

##virulence - The severity of the disease the bacteria causes and a measure of how infectious it is.[http://www.medicinenet.com/script/main/art.asp?articlekey=6911 source]

##operons - An operon is a cluster of genes with a single promoter. [https://books.google.com/books?id=ANT8VB14oBUC&pg=PA349&hl=en#v=onepage&q&f=false source]

##serotype - Serotypes are classifications within a species of bacteria or virus. These classifications are based on distinctive surface structures on the bacteria.[http://www.cdc.gov/salmonella/reportspubs/salmonella-atlas/serotyping-importance.html CDC.gov]

# Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.

Outline:

#Introduction

##The scientists behind this paper decided to sequence the genome of Shigella flexneri serotype 2a. Shigella flexneri is responsible for causing bacillary dysentery or shigellosis and as a result an estimated 160 million and 1.1 million deaths occur from each of these diseases. This is especially a problem in developing countries. In China 10 million cases occur a year of which 50-70% is caused by the serotype 2a. With the ability to reproduce in the cytoplasm of host cells, Shigella flexneri causes an inflammatory reaction in the colon and rectum. In the 1890s Shigella was identified as the agent for bacillary dysentery. A recent study shows that Shigella emerged from multiple independent origins of E. Coli, which this paper verifies. Due to the fact that a genome for serotype 5a has become available they felt it necessary to sequence serotype 2a. The virulence plasmid from 2a diverges slightly from 5a, in this paper they have revealed the highly dynamic nature of Shigella.

#Materials and Methods

##Growth Conditions

###The strain they sequenced (Sf301) was isolated from a patient with severe clinical manifestations of shigellosis in Beijing in 1984. This instance of this sequence has been used as a reference strain for S.flexneri in China. The strain was grown at 37 degrees Celsius overnight on tryptic soy agar containing 0.01% Congo red. The colonies were inoculated into tryptic soy broth and grown to the stationary phase at 37 degrees for isolating plasmid and chromosomal DNA.

##Sequencing and Sequence Assembly

###The plasmids and chromosomes were separately constructed using a variety of programs and methods. Shotgun sequencing was the algorithm they used and their automated sequencers created 48,000 clones which gave rise to 10 times coverage.

##Open Reading Frames and identification of gene families

###Glimmer 2.0 is a program that searches for regions within DNA that code for protein. In this sequencing experiment it was used to find ORFs that possessed more than 30 consecutive codons.

##Accession of the genome sequence

###In GenBank the accession numbers for the Sf301 chromosome is AE005674 and for the plasmid pCP301 it is AF386526

#Results and Discussion

##General Features of the Genome

###The whole genome is made of 4,607,203 base pair chromosome and a 221,618 base pair virulence plasmid. About 3.9 Mb (Million base pairs) of the chromosome are shared with E.coli K12 (MG1655) and O157(EDL933), these base pairs are essentially collinear.

###However they are not entirely collinear as they are interrupted by segments of K12, O157 and Shigella DNA which the author calls “islands”. Collinearity is also broken by inversions and translocations between the two species.

##The Shigella islands

###There are 64 Shigella islands with sizes greater than 1000 base pairs (detailed in ‘linear map 1’). Among these islands they identified pathogenicity islands.

##The Pseudogenes

###Frame shifts, stop codons, and insertions in the coding regions appear to play a major part in creating Pseudogenes

##Virulence Plasmid pCP301

###Like previous virulence plasmids from serotype 5a, pCP301 has a lot of virulence related genes, IS elements, maintenance genes and functionally unknown ORFs.

#Conclusion

##Comparison of S. flexneri with E. coli shows that E. coli is closely related to S. flexneri and may turn out to belong to the same genus

##S. flexneri is more closely related to the non-pathogenic K12 E.coli strain than the pathogenic O157 strain

#* What is the importance or significance of this work (i.e., your species)?

#**This paper releases to other scientists data about Shigella flexneri. This is important because it will allow further study of this pervasive bacteria that hurts China and other third world countries by creating Shigellosis. Since this bacteria and the disease that comes with it is a leading cause of death in the world it is important that people are able to study it, and this paper enables them to do just that.

#* What were the methods used in the study?

#**This strain of S. flexneri was taken from Beijing in 1984 and has been used as a kind of standard of shigellosis in China. It was grown in a tryptic soy broth at 37 degrees Celsius, they sequenced it using shotgun sequencing. They used phred/phrap a program to automate assembly of the sequences. Using Glimmer 2.0 they figured out the open reading frames and then they compared the genome to that of E.coli using the GenomeComp software.

#* Briefly state the result shown in each of the figures and tables.

#**Figure 1 is a circular map of the sequenced S.flexneri genome compared to E.coli K12. These organisms share the same "backbone structure" which is about 3.9 million base pairs long.

#**Figure 2 is a representation of translocations, inversions, and strain‐specific islands in S.flexneri when compared to the two strains of E.coli mentioned.

#**Table 1 has general features of the Sf301 genome when compared to E.coli K12 and 0157.

#**Figure 3 the N-terminal halves of a class of protein identified in Sf301.

#**Table 2: Insertion Sequence elements identified in genomes of Sf301, MG1655 and EDL933, the virulence plasmid, and pWR501, from S.flexneri 5a

#**Figure 4 is a comparison of two regions on 3 different genomes. The regions are the rfa/waa regions that are responsible for LPS biogenesis.

#**Table 3 is a list of pseudogenes within Sf301 with a known function, the function is listed next to the pseudogene.

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

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