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

“The 14th In Silico Megabank Research Seminar” will be held on Friday, October 12.

・Date/Time: October 12 (Fri.) 15:00‐16:00
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Title: How promoters help to find new drugs Mechanisms of action of RITA compound on cancer cells
・Lecturer: Dr. Olga Kel (Director Applied Life Science Informatics geneXplain GmbH)

・Abstract:
The current study is done in collaboration between Karolinska Institute, Sweden, Institute of Biomedical Chemistry, Russia, and geneXplain GmbH, Germany, and partially funded by European commission in FP7 research project “Net2Drug”.

Background. Antineoplastic compound RITA is known to prevent p53-mdm2 interactions and thus to result in increasing levels of active p53.

High concentrations of RITA cause apoptosis in cancer cells, however small concentrations of RITA do not.

Aim of the study. To understand concentration- and time-dependent molecular  mechanisms of action of the antineoplastic compound RITA as well as to suggest novel candidate compounds to be applied in combination with small concentration of RITA, the following steps were done.

Initially, large scale gene expression and ChIP-seq studies were performed on breast cancer MCM7 cells treated with RITA in both high and small concentration.

At the next step, computational analysis with the geneXplain platform confirmed concentration- and time-dependent downregulation of pro-survival genes. Upstream analysis approach was applied to these genes. First, their promoters were analyzed and combinations of transcription factors involved in their regulation were identified. Next, topological modeling of the signal transduction network upstream of these transcription factors revealed potential master-regulators of the cell survival program that may prevent efficient apoptosis in cancer cells. We considered master regulatory proteins (e.g. PI3K subunits) as causal biomarkers as well as prospective targets for novel anticancer drug combinations.

Then, the cheminformatics program PASS was applied to the target molecules suggest at the previous step. We identified several novel prospective antineoplastic chemical compounds.

Finally, two compounds were experimentally validated in a cellular assay confirming their potential to selectively triggering apoptosis in cancer cells and act synergistically with small concentration of RITA.

“The 13th In Silico Megabank Research Seminar” will be held on Friday, September 28.

・Date/Time: September28 (Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Title: About the three intestinal types discovered from human intestinal flora
・Lecturer: Takuji Yamada (Tokyo Institute of Technology)
・Abstract:
It is said that in the human intestinal, there are 1000 species and 100 trillion bacterial groups are symbiotic. In this study, we found that it can be divided roughly into three types of intestinal bacterial compositions that do not depend on the relationship between nationalities and geographic location. With each type, its own unique intestinal flora metabolic has been built up, and the differences in their metabolic capacity are supposed to be accurately quantified in the future.

With regard to the personalized medicine in the future, genomic information, as well as diagnosis of metabolic capacity of intestinal flora should be necessary for proper choice of oral medication and diet.

“The 12th In Silico Megabank Research Seminar” will be held on Friday, September 14.

・Date/Time: September 14(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Lecturer: Itoshi Nikaido (Institute of Physical and Chemical Research )
・Title: Understanding on Characteristics of Cells – On ChIP-seq and Single-Cell RNA-seq

Abstract:
Our body comes into existence when only one cell properly differentiates into 400 kinds of cells. Fundamentally, these cells have the same genome information. In order for a cell to acquire individuality, a proper gene expression and a transcriptional network building in a cell is necessary. As embryonic stem cells (ES cells) differentiate, we have grasped how the transcriptional network would change structurally with the help of statistical modeling in terms of the time-series ChIP-seq and transfer. Moreover, since we are engaged in the development of the new protocol and the data-analysis technique of highly precise single cell RNA-seq in order to suppress the fluctuating cellular status that are said to be connected with individuality acquisition of a cell, we will update the current status of it as well.

Professor Nagasaki will give an invited talk at the 44h Autumn Meeting of The Society of Chemical Engineers, Japan (SCEJ). The 44th Autumn Meeting of SCEJ will be held at Tohoku University. Professor Nagasaki will give a talk titled “Environmental management of next-generation sequencing and its practical operation in the age of gigantic genome data” at the symposium ” Proposal from next-generation engineering for effective utilization of biological information”.

Date/Time  September 21,2012 (Fri.) 13:00-13:40
Place  Tohoku University Kawauchi Hagi Hall http://www.bureau.tohoku.ac.jp/hagihall/institution/access.html

*Summary of the Talk*
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.  A lecture will be given on how we can handle and analyze such a gigantic data based on experiences gained during International Cancer Genome Consortium and Tohoku Medical Megabank Organization.

The Society of Chemical Engineers, Japan The 44th Autumn Meeting site is here.

Professor Nagasaki will give a lecture at 16th Bioinformatics workshop.
Place : Minato-ku Commerce and Industry Hole (Minato-ku Shoko Kaikan).
http://minato-shoukou.jp/access
Text Fee : 1,000 yen (Please pay at a front desk on the day).
* If you need a receipt, please inform the address. We will make out a receipt with the address.

http://amelieff.jp/news/benkyokai/benkyokai-16

Tohoku Medical Megabank Organization will hold a laboratory orientation session where acceptable laboratories will be introduced and details about recruitment of student will be given. Our laboratory will attend the session. We look forward to seeing you there.
Eligible person : a person who is interested in aending our graduate school. A student under 4th grade is also welcome.

Professor Nagasaki will give an invited talk at Agilent Genomics Forum.
Date/Time  May 30, 2012, (Wen.)
Place  KFC building, Tokyo
Title  “About resources of supercompuer calculation and analytical techniques that are necessary for exome, transcriptome and entire genome sequencing.”
http://www.chem-agilent.com/contents.php?id=1002303