群集解析リンク
総合データベース
National Center for Biotechnology Information (NCBI) Nucleotide
http://www.ncbi.nlm.nih.gov/nucleotide/
DNA Data Bank of Japan (DDBJ)
http://www.ddbj.nig.ac.jp/index-j.html
16S rRNA遺伝子関連
Silva
http://www.arb-silva.de/
Ribosomal Database Project (RDP)
http://rdp.cme.msu.edu/
Greengenes
http://greengenes.lbl.gov/cgi-bin/nph-index.cgi
機能遺伝子関連
Functional Gene Pipeline/Repository (FGPR)
プローブ、プライマー設計
probeCheck
probeBase
アライメント、系統樹作成ツール
ARB
ClustalW
http://www.ebi.ac.uk/Tools/msa/clustalw2/
MUSCLE
PhyML
http://www.atgc-montpellier.fr/phyml/
Mallard
群集解析ツール
mothur
http://www.mothur.org/
Fast UniFrac
http://unifrac.colorado.edu/
QIIME
抄読会；河野洋ｄｒVolume and Surface of the Mastoid Cell System
Volume and Surface of the Mastoid Cell System
in Otitis Media With Effusion in Children:
A Case-Control Study by Three-Dimensional
Reconstruction of Computed Tomographic Images
抄読会；保富ｄｒHost and bacterial factors contributing to the c
Host and bacterial factors contributing to the clearance of colonization by Streptococcus pneumoniae in a murine model.
http://www.ncbi.nlm.nih.gov/pubmed/16239576
carriage(animal model)とcolonization(human?)
無莢膜型肺炎球菌、莢膜変化
Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster
http://www.nature.com/ncomms/2014/141112/ncomms6411/full/ncomms6411.html#genesandproteins
A random six-phase switch regulates
pneumococcal virulence via global
epigenetic changes
http://www.nature.com/ncomms/2014/140930/ncomms6055/full/ncomms6055.html
抄読会；Factors associated with hearing loss in a normal-hearing guinea pig model of hybrid cochlear implants
Factors associated with hearing loss in a normal-hearing guinea pig
model of hybrid cochlear implants
http://ac.els-cdn.com/S0378595514001294/1-s2.0-S0378595514001294-main.pdf?_tid=cdadf970-6eb1-11e4-bb1a-00000aab0f27&acdnat=1416267246_48e9452393ddbeed27b0cd7bb644156b
ELISA
ELISAの話；
ELISA Starter Accessory Kit
http://www.bethyl.com/product/pdf/E101.pdf
R&Dでは
以下のキット
http://www.funakoshi.co.jp/contents/717
マニュアルらしきもの；
http://www.dojindo.co.jp/technical/beginner/imuno.pdf
遊びで抗原抗体反応をどんどんやっていけばいいとおもうけどなあ。
MLSTによる株の同一性検討；
これからの細菌のゲノムタイピングとしてのMLST 法
New genomic typing method MLST
http://www.eiken.co.jp/modern_media/backnumber/pdf/MM0607-01.pdf
「clonal populationからnonclonal populationへ」
水平伝搬を捉えることができるのか。
理論的背景；
How clonal are bacteria?
J M Smith, N H Smith, M O'Rourke, and B G Spratt
http://www.pnas.org/content/90/10/4384.abstract
検索すると比較的最初の方にでてくるソフト
CLC bio Bioinformatics Solution
CLC MLST Module
http://www.filgen.jp/Product/BioScience21-software/index11-mlst.htm
標準の解析ツール；
BioNumerics
http://www.applied-maths.com/
肺炎球菌の全世界的なサーベイランス；
Systematic Evaluation of Serotypes Causing Invasive
Pneumococcal Disease among Children Under Five: The
Pneumococcal Global Serotype Project
http://www.plosmedicine.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pmed.1000348&representation=PDF
無莢膜型肺炎球菌のMLST結果；
http://mbio.asm.org/content/3/3/e00035-12/F1.expansion.html
ST: sequence typeの同定と、株の同一性
同じくUABでのMLST報告；
http://jb.asm.org/content/187/17/6223.full.pdf+html
やはり機能遺伝子は7つ使うべきであろう。
housekeeping gene以外を用いる方法も可能であろう。
Multi-Virulence-Locus Sequence Typing of Listeria monocytogenes
http://aem.asm.org/content/70/2/913.short
