Prof. Masao Nagasaki will give an invited talk at 2012 Bilateral Workshop between Tohoku University and National Tsing Hua University.

・Date/Time:  December 12, 2012
・Place: Akiu Resort Hotel Sakan　http://www.sakan-net.co.jp/en/access/index.html
・Language: English
・Title: Data Management and Bioinformatics of High Throughput Sequencing Data on the Massive Parallel Supercomputer Environment and Future
http://www.smapip.is.tohoku.ac.jp/~dex-smi/2012/BW-Tohoku-TsingHua-201212/

The 18th In Silico Megabank Research Seminar will be held on Friday, November 30.

・Date/Time: November 30(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Lecturer: Yukuto Sato (National Institute of Genetics)
・Title: Evolutionary Conserved Feature of Mitochondrial Genome : a New Insight into  Functional Impairment and Disorder

・Abstract:
Although mitochondrial gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years, the functional nature of such long-term persistence has yet to be defined over the past 20 years. We analyzed mitochondrial genome by sequence comparison, focusing on translation and replication. The result showed that the tRNA genes used more frequently for translation are more likely to be located in high expression regions (r = -0.1260, p = 0.0104, n = 336), and the regions spend in the single-stranded state during replication for a longer time are richer in G and T bases in the anti-codon regions. (r = 0.4281 p = 0.0234, n = 22).
This result indicates that arrangement of genes in mitochondrial genome is rational for both efficiency of translation and prevention of loss of function of tRNA during replication, and also provides a new insight into impairment of genome function caused by de novo mutations.

The 17th In Silico Megabank Research Seminar will be held on Friday, November 16.

・Date/Time: November 16(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Title: Type 2 diabetic patients’ intestinal bacterial flora that is uncovered by the meta-genome-wide related analysis
・Lecturer: Shujiro Okuda (Ritsumeikan University)

・Abstract:
Type 2 diabetes is a kind of endocrine disease which has been rapidly increasing in the number of patients all over the world now.
In this study, I conducted a comparative study of the intestinal bacterial flora of the type 2 diabetic patients and that of the healthy persons using a new technique of meta-genome-wide related analysis. As a result, a number of markers related to type 2 diabetes were successfully identified. In addition, a possibility was suggested that type 2 diabetes could be diagnosed using these markers. From now on, a possibility of diagnosis and medical treatment with an application of the meta-genome-wide related markers to the other diseases is highly expected.
In general, meta-genome analysis generally requires high-speed sequence determination capability such as a next-generation sequencer, but it is still expensive and the process is also complicated.
I will also introduce a virtual meta-genome constructive method which does not need such a meta-genome sequence determination.

Tohoku University Graduate School of Medicine is going to hold an explanatory session of Graduate School as follows. This session will also include a talking session with graduate students, presentation of the past tests, and distribution of the application guidebook. We are really looking forward to your active participation.

Date/Time: December 1(Sat.) 13:30‐15:30
Venue: Lecture Room 1, Building #1, Tohoku University School of Medicine

・The past tests will be presented from 13:00 to 13:30 and after the end of the session until 16:00.
・The time for visiting a laboratory is allocated after the end of the session.
・Please be advised that you should make a direct contact with the field you hope to visit in advance.

・Neither prior application nor participation fee is necessary.
・Since parking lot is not available, visitors are encouraged to use public transportation.

・You can see a video clip of a part of the last session on the website.http://www.med.tohoku.ac.jp/mov/intro/index.html

“The 16th In Silico Megabank Research Seminar” will be held on Friday, November 2. The discussion will focus mainly on disease-related databases. So if you are interested, please don’t hesitate to attend the session.

・Date/Time: November 2(Fri.) 16:00‐18:00
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Lecturer: Asako Koike　(Hitachi CRL)

Title: Title: An approach of sharing information about disease-related polymorphisms/mutation information in the integrated promotion program

Abstract: In order to prevent the dissipation of recently increasing disease-related polymorphisms/mutation information as well as to share the information among the researchers, our group (The University of Tokyo Hospital, National Institute of Genetics, and Hitachi CRL) has established “Human/GWAS DB (https://gwas.biosciencedbc.jp/)” and started deposition and redistribution of GWAS/NGS variation data. In these DBs, not only GWAS data or SNV of both healthy and diseased individuals but also the insertion/deficiency of the long sequence and conformation polymorphism are the targets of collection, which aim systematization of the relation between the variations and the phenotypes (disease, medical response, and virus tolerance) of the Japanese/Asians. The presentation will outline the bias caused by experimental methods/calculation methods and the characteristics of variations of every disease, and will also introduce the originally-developed sequence analysis/genetic statistics technology.

「XiP: a computational environment to create, extend, and share workflows 」
Masao Nagasaki; Andre Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li; Satoru Miyano

Abstract:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts630?
ijkey=DXtNf2vgjT88PNG&keytype=ref

PDF:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts630?
ijkey=DXtNf2vgjT88PNG&keytype=ref

“Database Workshop for Drug Development”, the 2nd database workshop in 2012, will be held in November 3, 2012.
For more details, click here.
Please be noted that Prof. Masao Nagasaki of our institution will give a lecture in the workshop.

Date/Time： November 3, 2012 10:00-17:00
Venue：IT Educational Facilities (6F), Building #4, Tohoku University School of Medicine

Prof. Masao Nagasaki will give a special lecture on Network Medicine.
Please don’t hesitate to join the heated discussion regardless of whether you are student or not.

・Date/Time: October 19(Fri.) 17:30‐
・Venue: Room #201 (2F), Building #5, Tohoku University School of Medicine
・Title: Present situation and issues of bioinformatics analysis of high performance sequence data

・Abstract:
10 years after the age when researchers all over the world focused on a target human genome, the big advances in sequencing technique allow us to face a new age when one can easily read a gigantic genome from a blood sample using handy sequencer, namely the age of gigantic genome data.
This lecture presents an overview of the basic single nucleotide polymorphism of the next generation sequence data, the flow of human genome re-sequencing bioinformatics analysis such as structural mutation analysis, and the issues in the current re-sequencing data. Regarding the data computed by the international cancer genome consortium (ICGC) which is the international joint research with which the lecturer has been concerned, the lecture also outlines on what kind of scale and how the data has been processed/managed on the supercomputer and on what kind of time scale the data has been analyzed, sharing the experiences of Mr. Nakagawa, the team leader of the biomarker research and development team of ICGC, and Dr. Seishi Ogawa of University of Tokyo Medical School regarding the calculation resources used in the entire genome analysis and the exome analysis.

“The 15th In Silico Megabank Research Seminar” will be held on Friday, October 19.

・Date/Time: October 19(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Lecturer: Masanao Sato (National Institute for Basic Biology)
・Title: Title: Baculovirus as a New Model of the Next-Generation Biology:Strategy and the Present Status to Explore the “Current” Gene Networks

・Abstract:
Baculovirus is widely used for recombination protein expression using eucaryotic cells and on the other hand, it is one of the main tools of insect biotechnology which is utilized as biological pesticide (insecticide). While the comprehensive analysis by the next-generation sequencer and the feature extraction/system abstraction (modelization) from the extensive data based on statistics/mathematical modeling are currently available, I am working on the study of not only understanding the molecule basis of the useful traits of these baculoviruses but also the possible models of network biology and synthetic biology research.

Unlike the other many RNA viruses which pose clinical problems, baculovirus is a large-sized DNA virus. It is a system that viral genome DNA invades into the host cell nucleus and instigates all the transcription of infections, and can collect the firstly important information on viral-gene functional exercise using transcriptomes. Also, I am working on a research with an eye on the synthetic approach that designs a viral genome sequence, which is firstly because maintenance/modification of the viral genome within coliform bacillus is possible by introducing the origin of replication of coliform bacillus into the DNA genome, secondly because a genome can be modified so freely as to make a genetic approach easy and thirdly because the size of genome is “synthesizable” at about 130 kb. Furthermore, an evolution experiment in a short period of time is also possible due to the nature of virus, and it is also possible to take on a new challenge in experimental biology in terms of evolution of gene networks.

In this seminar, we will introduce a topic about the presumption of a viral gene network. Of the 141 genes in the BmNPV-T3 system that can affect a silk worm, we have built a viral gene network having 40 genes as components which play an important role in viral infections, utilizing an approach combined with genetics, the transcriptome by RNA-seq and network modeling.

Although we are still at the stage of vilification of the model, we would like to have a detailed discussion on what we are seeking in the transcriptome represented by RNA-seq and how we are dealing with it.

Reference literature
Modeling: Sato et al. (2010) PLoS Pathogens 6(7): e100101
Baculovirus reverse genetics: Ono et al. (2012) Virus Research 165(2) 197-206.

Prof. Masao Nagasaki will take the rostrum at Joint Conference on Informatics in Biology, Medicine and Pharmacology.
Joint Conference on Informatics in Biology, Medicine and Pharmacology will be exhibited at Tower Hall Funabori, in which Prof. Masao Nagasaki will take the rostrum in the session “Tohoku Medical Megabank Project: A challenge to the next generation genome biology by large scale genome cohort studies” .  Anyone can participate in the session free of charge and pre-registration.

*Session program
・Date/Time: October 16 Tue, 2012, 3:30 to 5:00 p.m.
・Venue: Tower Hall Funabori (4-1-1 Funabori, Edogawa-ku, Tokyo)
・Session: S-5
・Room: Training Room(4F), 84 seats

・Session Title:
Tohoku Medical Megabank Project: A challenge to the next generation genome biology by large scale genome cohort studies
・Organizer: Prof. Kengo Kinoshita (Department of Integrative Genomics, Tohoku Medical Megabank Organization)

・Lecturer:
*Prof. Shinichi Kuriyama (Department of Biobank, Tohoku Medical Megabank Organization)
Title:Genome cohort study and biobank

*Prof. Masao Nagasaki (Department of Integrative Genomics, Tohoku Medical Megabank Organization)
Title:Genome cohort, super computer, and strategies of in silico analysis

*Prof. Jun Yasuda (Department of Integrative Genomics, Tohoku Medical Megabank Organization)
Title:Perspective of genome-omics analysis at Tohoku Medical Megabank Project

Joint Conference on Informatics in Biology, Medicine and Pharmacology