“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

The Symposium titled “Challenge for Information Sciences to Non-Virtual Big Data” will be held, and Professor Nagasaki give a talk in the session titled “Creation of Infrastructure for Life Information Science in the Age of Life Information Big Bang”.
At the symposium, anyone is welcome and can attend free of charge.

Date/Time  April 26, (Thu) 10:00-17:00
Place  Tohoku University Kawauchi Hagi Hall
*2012 Graduate school of Information Sciences Symposium
“Challenge for Information Sciences To Non-Virtual Big Data”
http://www.tohoku.ac.jp/japanese/2012/04/event20120412-01.html

“Creation of Infrastructure for Life Information Science in the Age of Life Information Big Bang”.
11:40-12:00 Professor Nagasaki

We are searching for a secretary.

Check this page
http://nagasakilab.csml.org/en/researcher