The 39th In Silico Megabank Research Seminar will be held on Friday, November 15. This Time, we will be welcoming Dr. Jun Ohashi, University of Tsukuba as our lecturer, and he will be speaking on “The specificity of the HLA gene region and HLA-related analysis”.

・Date/Time: November 15(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
・Title: The specificity of the HLA gene region and HLA-related analysis
・Lecturer: Jun Ohashi（University of Tsukuba）

＊This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: The major function of HLA (Human Leukocyte Antigen) is to present autologus and non-autologus antigen (pathogen) to T cells. Classical HLA molecules have class I molecules and class II molecules, and the HLA gene cluster encoding those HLA molecules is located in short arm region, 6p21.3, of the sixth chromosome.  Characteristics of the HLA gene region include the presentation of the most sophisticated polymorphism in human genome, actual observation of high in linkage disequilibrium for several Mbs, difference in the number of genes by Haplotypes, and existence of polymorphism related to sensitivity toward disorders. In this presentation, the roles of natural selection, which is the key to understand the linkage disequilibrium of HLA gene region, is explained using an example of recent action of positive selection on DPB1*04:01 allyl in Japanese group. Also, we would like to introduce HLA gene-related studies on patients with Plasmodium Falciparum Malaria.

・Organizer: Gen Tamiya, Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 38th In Silico Megabank Research Seminar will be held on Friday, November 8.

This Time, we will be welcoming Dr. Minae Kawashima, JST as our lecturer, and she will be speaking on “NBDC Human Database: Human Data Sharing Guideline and Provision of Private Data. Report on the User Application”.

・Date/Time: November 8(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
・Title: NBDC Human Database: Human Data Sharing Guideline and Provision of Private Data. Report on the User Application
・Lecturer: Minae Kawashima (Japan Science and Technology Agency (JST))

・Abstract: Life science data, properties of human, such as Next Generation Sequencer and image has become large in volume in accordance with the advancement of analysis techniques. Rules and systems are necessary to arrange and store such data of Next Generation Sequencer and utilize them effectively for the advancement of life science.  Japan Science and Technology Agency (JST) and National Bioscience Database Center (NBDC) created the Platform “NBDC Human Database” for sharing various database regarding human database and have promoted for disclosure of human data with cooperation of and National Institute of Genetics and DNA Data Bank of Japan (DDBJ) in order to share human data and promote its usage while considering the protection of personal information. They have also created and released the “NBDC Human Data Sharing Guideline” and “Security Guideline for handling NBDC Human Data” as operative rules (http://humandbs.biosciencedbc.jp/guidelines). In this article, we introduce the points to share data while complying with Human Data Sharing Guideline and concretely show how to submit application for data provision and data usage as well as required documents for the application.

・Organizer: Gen Tamiya、Masao Nagasaki

Access : http://www.megabank.tohoku.ac.jp/english/info/access.html

The 36th In Silico Megabank Research Seminar will be held on Friday, October 18.
This Time, we will be welcoming Dr. Kana Shimizu, The National Institute of Advanced Industrial Science and Technology as our lecturer, and she will be speaking on “Database Search with Secret （private）Computation” .

・Date/Time: October 18(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Database Search with Secret （private）Computation – Aim for its Application to Genome Database –
・Lecturer: Kana Shimizu（The National Institute of Advanced Industrial Science and Technology (AIST)）

・Abstract: In recent years the cost of DNA sequencing drastically fell, which enabled acquisition of genome data at individual level. However, the extreme difficulty still lies in the realization of both protecting privacy of genome including personal information and analyzing information with high flexibility. Although extraordinary amount of cost and effort has generated this rich store of data, such balance issue does not allow full utilization of the data at the present state. On the other hand, in the area of the Computer Science, data itself is coded, and secret computation technology is being developed where coded information is analyzed while contents of individual data are not revealed. By this lecture, we would like to introduce database search technology by the secret computation that we have developed and argue about its application to genome database.

・Organizer: Soichi Ogishima

The 35th In Silico Megabank Research Seminar will be held on Wednesday, October 16.
This Time, we will be welcoming Mr. Satoshi Hirata, Criminal Investigation Laboratory, Miyagi Prefectural Police Headquarters as our lecturer, and he will be speaking on “Duties of Criminal Investigation Laboratory: On DNA Identification”.

・Date/Time: October 16, 2013(Wed.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Duties of Criminal Investigation Laboratory: On DNA Identification
・Lecturer: Satoshi Hirata (Criminal Investigation Laboratory, Miyagi Prefectural Police Headquarters )

・Abstract: In recent years, the role of objective evidence utilizing scientific technique such as DNA identification is becoming important because it is getting harder to obtain information from the witness due to the increase of crimes of high anonymity and the collapse of the local communities and because the need for objective evidence is increasing more than before in criminal trials due to the introduction of the citizen judge system. There are quite a few cases, including retrials, in which credibility and probative value of scientific evidence become controversial. Above all, the role of such evidence is particularly important in the serious cases for which the citizen judge system might be considered. The following functions are in charge of criminal investigation: National Research Institute of Police Science set up in the National Police Agency, Criminal Investigation Laboratory and Criminal Identification Department in the Tokyo Metropolitan Police Department and the Prefectural Police Headquarters, and Identification Section in each police station. These organizations are working on the investigation of objective evidence working closely with detectives engaged in the criminal investigation or according to the request by them. Based on these circumstances, I would like to outline the duties of the criminal investigation laboratory, especially about the principles and methods of DNA identification. Finally, I would like to talk about the police measures such as body identification associated with the East Japan great earthquake disaster.

・Organizer: Yukuto Sato, Masao Nagasaki

Prof. Nagasaki will be delivering a lecture at ” Fukuoka International Symposium on Genomics & Epigenomics 2013 – Kyusyu University” (September 10, 2013)

・Date/Time: September 10(Tues.) 10: 05‐10:40
・Venue: Biomedical Research Station 1F Seminar Room 105 and Science Cafe Hospital Campus, Kyushu University
・Title: Towards thousands Japanese whole genome project and its data management and bioinformatics

The 34h Silico Megabank Research Seminar will be held on Friday, August 2.
This Time, we will be welcoming Dr. Yosuke Kawai, Maebashi Institute of Technology as our lecturer, and he will be speaking on “Molecular Evolution of Natural Denatured Protein.”

・Date/Time: August 2(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization  http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Molecular Evolution of Natural Denatured Protein
・Lecturer: Yosuke Kawai (Maebashi Institute of Technology)

・Abstract: There are some proteins that include an irregular region which does not form a fixed structure under a physiological condition. They are called natural denatured proteins. It is predicted that 30% or more of human proteins are natural denatured protein, and many of which are located in a nucleus and associated with transcription control and signal transduction. Some irregular region forms a fixed structure when forming a complex with other proteins, which is considered because the polypeptide chain in an irregular state recognizes the target molecule and both binding and folding occur in a conjugated manner. The molecular recognition mechanism of this natural denatured protein has been attracting attention in recent years as the different paradigm from the molecular recognition mechanism of proteins with a structure. Natural denatured protein is hardly present in a prokaryotic organism, and the molecular recognition through the irregular region is thought to be inherent to a eukaryotic organism. In addition, the amino acid sequence in the irregular region has poor keeping quality and seems to undergo molecular evolution close to neutrally. However, it is not understood as to why such a site came to play an important role in the protein-protein interaction. This presentation will especially focus on the interaction involving the irregular region and introduce findings regarding the relationship between the structure, function, and evolutionary rate of the natural denatured protein that have not been clarified so far.

・Organizer: Masao Nagasaki

The 33rd In Silico Megabank Research Seminar will be held on Friday, July 26.
This Time, we will be welcoming Dr. Kryukov Kirill, National Institute of Genetics as our lecturer, and he will be speaking on “A tool for genomic multiple sequence alignment.”

・Date/Time: July 26(Fri.) 17:00‐18:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: MISHIMA – a tool for genomic multiple sequence alignment
・Lecturer: Kryukov Kirill (National Institute of Genetics )
・Abstract: MISHIMA is a multiple DNA sequence alignment method that uses heuristics for quickly finding regions of high similarity between sequences. MISHIMA operates by locating rare DNA fragments shared by multiple sequences and using them as alignment anchors. This technique allows aligning multiple bacterial genomes in short time. Here we present the improved version 2 of MISHIMA aligner. Sensitivity of the aligner has been improved by using only certain positions within the analyzed DNA words. Another improvement concerns the choice of the word length. In the original MISHIMA a fixed user-specified word length was used. Now it is chosen dynamically and automatically during the alignment process. Also MISHIMA can now better handle circular DNA sequences. The improved MISHIMA aligner has been tested on a range of bacterial and fungal genomes.

・Organizer: Masao Nagasaki

New address:(26.06.2013 ~)
Nagasaki Lab
8F #West, IDAC Research Building
Tohoku University
Seiryo-machi 4-1, Aoba-ku, Sendai, Miyagi, JAPAN 980-8575

The 31st In Silico Megabank Research Seminar will be held on Monday, June 10.
This Time, we will be welcoming Dr. Toshitaka Odamaki, Food Science & Technology Institute, Morinaga Milk Industry Co., Ltd. as our lecturer, and he will be speaking on “The Anti-allergic Action by Bifidobacterium Administration.”

・Date/Time: June 10(Mon.) 16:00‐17:30
・Venue: Conference Room 1(2nd Floor), Tohoku Medical Megabank Organization http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: The Anti-allergic Action by Bifidobacterium Administration
・Lecturer: Toshitaka Odamaki (Food Science & Technology Institute, Morinaga Milk Industry Co., Ltd.)

・Abstract: Bifidobacterium is a kind of dominant bacterial species in the intestine, and various physiologies of it have been reported as “probiotics” as well as lactic acid bacterium. In the seminar, we will share the basic knowledge of bifidobacterium and introduce this focusing on two clinical tests that were confirmed with the anti-allergic action, namely, “Symptom relieving action of cedar pollen allergy for adults” and “Preventative action on the development of infant allergy by administration of bifidobacterium to pregnant women/infants” along with the analysis of the intestinal flora.

・Organizer: Masao Nagasaki

「ChopSticks: High-resolution analysis of homozygous deletions by
exploiting concordant read pairs」
Tomohiro Yasuda, Shin Suzuki, Masao Nagasaki and Satoru Miyano

Detail here