The 80th In Silico Megabank Research Seminar(January 13, 2017)

The 80th In Silico Megabank Research Seminar will be held on Friday, January 13, 2017. This Time, we will be welcoming Dr. Shigehiro Kuraku, RIKEN Center for Life Science Technologies as our lecturer, and he will be speaking on “Examination on the origin of human genome using developmental control gene phylome of vertebrate as a clue”.

・Date/Time: January 13 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building 
・Title: Examination on the origin of human genome using developmental control gene phylome of vertebrate as a clue
・Lecturer: Shigehiro Kuraku(RIKEN Center for Life Science Technologies)  

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

・Abstract: Combined with the fact that the possibility of omics analysis for non-model organisms has largely expanded, genome-wide perspectives and data-driven approach have enabled discussion on the relationship between molecular evolution and phenotypic evolution in a big picture. I have conducted interspecific comparison of the developmental control gene patterns among vertebrates from the aspects of molecular phylogenetics and genome informatics. In the process, I have found some cases that have spread after becoming too simplified in basic knowledge on EvoDevo such as storability of so-called “tool kit genes.” For example, Pax6 gene which is the vertebrate ortholog of eyeless gene in drosophila has sister genes of Pax4 and Pax10 doubled through 2R genome duplication. Not much attention has pained to these genes. 
In addition to the above genes that have been “forgotten,” I have found Bmp16, Hox14, FoxG2, and FoxG3. The main reason that these genes have been “forgotten” is that these disappeared independently from multiple strains, and they possess other common characteristics such that the speed of the evolution of sequences is fast and their expression appears to be more restricted to some areas. What enabled the finding of these “forgotten” genes was the genomic information of organisms belonging to certain strains of vertebrates such as cartilaginous fishes that diverged at relatively early stage of evolution. I am currently organizing genomic information of various species at my laboratory. In this seminar, technological aspects of genomic sequencing as well as evaluation of completeness of genomic sequences of non-human vertebrates are introduced. Additionally, a new hypothesis on the evolution of human genome based on the analysis of the above “forgotten” genes is discussed.  

・Organizer: Tomoko Shibata, Kazuharu Misawa, Masao Nagasaki

The 78th In Silico Megabank Research Seminar(November 16, 2016)

The 78th In Silico Megabank Research Seminar will be held on Thursday, November 16, 2016.

This Time, we will be welcoming Dr. Masashi Mizokami, Research Institute, National Center for Global Health and Medicine as our lecturer, and he will be speaking on “Examination of host factors for Hepatitis B virus infectious disease”.

・Date/Time: November 16 (Thursday) 6:30 pm‐7:30 pm
・Venue: Conference Room(3rd Floor), Tohoku Medical Megabank Building
・Title: Examination of host factors for Hepatitis B virus infectious disease
・Lecturer: Masashi Mizokami(Research Institute, National Center for Global Health and Medicine) 

・Abstract: Liver cancer is the fourth leading cause of death from cancer in Japan, and 70% of the incidence of liver cancer is attributable to Hepatitis B virus (HBV) and Hepatitis C virus (HCV). Moreover, according of WHO, it is globally the seventh leading cause of death from cancer, meaning that it is a significant worldwide public health issue. For HCV, recent advancement of treatment has steadily decreased the number of liver cancer caused by HCV; it is expected that it will be rare disease by 2030. However, the situation with HBV-related cancers is different. Current treatment can only inhibit the growth of HBV, and the prospects for the clearance of HBV, which is the basic remedy, are still far from certain. In general, the pathology of infectious diseases is determined by the interaction of causative pathogens and infected individuals. However, only the viral factor has been examined for HBV-infected patients because there is technological difficulty to examine the interaction although it has been revealed that about 90% of HBV-infected individuals have no symptoms in their lifetime whereas about 10% of HBV-infected individuals develop liver cancer. Despite research effort, no difference has been found between the HBV-infected individuals without subjective symptoms in their lifetime and with cancer progression.
Thus, we collected genome and serum of 3500 samples whose clinical data were entered by nationwide specialized medical clinics for liver. These clinics had already completed various procedures such as IRB in the past 10 years. From the aspect of viral factors, we are currently conducting GWAS for HBVDNA sequencing and host factors. As research grant was provided to us by AMED, we would like to further reveal detailed host factors from joint research with ToMMo. Therefore, in this seminar, I would like to introduce the current situation and issues associated with HBV study and discuss the possibility for joint research with ToMMo. 

・Organizer: Masao Nagasaki

The 77th In Silico Megabank Research Seminar(November 10, 2016)

The 77th In Silico Megabank Research Seminar will be held on Thursday, November 10. This Time, we will be welcoming Dr. Koji Yahara, National Institute of Infectious Diseases as our lecturer, and he will be speaking on “Method to infer the tracemarks of recombination and population structure and its application based on genome data”.

・Date/Time: November 10 (Thursday) 5:00 pm‐6:30 pm
・Venue: Conference Room 2 (1st Floor), Building #6, Tohoku University School of Medicine
・Title: Method to infer the tracemarks of recombination and population structure and its application based on genome data
・Lecturer: Koji Yahara (National Institute of Infectious Diseases)

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

・Abstract: Mutation and recombination are the source of adaptive revolution of creatures which cause genomic diversity. Mutation rate is known to be high in certain regions within genome, and its relation with diseases is drawing attention. On the contrary, recombination is more difficult to detect than mutation. Especially, it is difficult to estimate the number of its occurrence. In the first half of this seminar, we will calculate the index of recombination rate at single nucleotide level along genome using genome data in bacterial genome and introduce new approach to infer recombination “hot regions” and its application to 11 types of pathogenic bacteria. In the latter half, the estimate of population structure which should be done at the very first of the process of population-level genome data analysis is to be discussed. Also, it is introduced that the as the first step method to detect the tracemarks of genome-wide recombination reveals the detailed population structure and also the method is useful to quantitatively understand the flow of genome information between populations.

・Organizer: Yosuke Kawai, Masao Nagasaki

 

Professor Nagasaki will give a lecture at the 23rd Annual Meeting of the Japanese Society Gene Diagnosis and Therapy on October 7

Professor Nagasaki will give a lecture at the 23rd Annual Meeting of the Japanese Society Gene Diagnosis and Therapy on October 7

・Date: October 7 (Friday)
・Venue: Iino Hall & Conference Center
・Session&Thema: Symposium3 “Basics of Genome Statistics and its Clinical Application”
・Title: 日本人2049人の全ゲノムリファレンスパネルの構築と今後

The 75th In Silico Megabank Research Seminar(September 2, 2016)

The 75th In Silico Megabank Research Seminar will be held on Friday, September 2.

This Time, we will be welcoming Dr. Makoto Shimada, Fujita Health University as our lecturer, and he will be speaking on “Explore the relationship between triplet repeat disease and human revolution through selective pressure for human STR sequence ”.

・Date/Time: September 2 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building 
・Title: Explore the relationship between triplet repeat disease and human revolution through selective pressure for human STR sequence
・Lecturer: Makoto Shimada (Institute for Comprehensive Medical Science, Fujita Health University)

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

・Abstract: In STR (Short Tandem Repeat), repeating sequences of very short base segments, the number of tandem repeats changes very frequently. Thus, there has been a hypothesis that adaptive trait and evolutionary stable state were quickly established using the high variability of the number of tandem repeat. On the contrary, human STR sequence is known to have multiple repetitive sequences which are the cause of neurodegenerative diseases. However, why such dangerous repetitive sequences are maintained among human population is not yet known well. We have identified the number of the STR repetition and repeat polymorphism within human genome by integrating information of polymorphism into H-invDB, the genetic database that we developed and released to the public. Furthermore, we evaluated the selective pressure for each STR through intercomparison. The result showed that repetitive amino-acid sequences were formed in STR in amino acid coding regions due to 2 mechanisms each of which are represented by proline repeats and glutamine repeats while keeping the repeats short at the DNA sequencing level.. Moreover, it was revealed that glutamine repeats have a tendency to have longer repeats at amino-acid level and that especially the repeat polymorphism exists in the genes related to the regulation of the generation of nervous system and brain. These results suggest the possibility that polymorphism of these repeats facilitated the diversification of the functions related to the regulation of the generation of nervous system and brain. In our article, we have further argued the relationship between the evolution of sociality throughout human evolution and the switch function for the regulation of STR neural development.

・Organizer: Yosuke Kawai, Kazuharu Misawa, Masao Nagasaki

The 73rd In Silico Megabank Research Seminar(February 12, 2016)

The73nd In Silico Megabank Research Seminar will be held on Friday, February 12, 2016. This Time, we will be welcoming Dr. Yuki Hitomi, Graduate School of Medicine, The University of Tokyo as our lecturer, and he will be speaking on “Search for Genetic Factors of Immune-related Diseases”.

・Date/Time: February 12 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Search for Genetic Factors of Immune-related Diseases
・Lecturer: Yuki Hitomi (Department of Human Genetics, Graduate School of Medicine, The University of Tokyo)

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

・Abstract: Genome-wide Association Study (GWAS) has been conducted in large scale globally especially as a statistical genetic approach that exhaustively search disease sensitive genes for multifactorial diseases. On the other hand, it is known that there is genetic risk, Missing Heritability, which is unaccountable with GAWS. Therefore, further advancement of research is currently highly anticipated for understanding of whole genetic factors for disease onset.  In this seminar, diseases that are considered to be attributable to immune system being the target, we will give an outline of genetic factors which have been revealed until today (especially HLA) as well as the pathologies. Additionally, we will introduce joint-research having been conducted with ToMMo for the purpose of exhaustive search for genetic factors in association with the development of Primary biliary cirrhosis (PBC) and Stevens-Johnson Syndrome (SJS)

・Organizer: Kaname Kojima, Masao Nagasaki

The 72nd In Silico Megabank Research Seminar(January 26, 2016)

The 72nd In Silico Megabank Research Seminar will be held on Tuesday, January 26, 2016. This Time, we will be welcoming Dr. Ryu Takeda, The Institute of Scientific and Industrial Research, Osaka University as our lecturer, and he will be speaking on “Recent Machine Learning and Component Technology for Speech Dialog System”.
・Date/Time: January 26 (Tuesday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Recent Machine Learning and Component Technology for Speech Dialog System
・Lecturer: Ryu Takeda(The Institute of Scientific and Industrial Research, Osaka University)

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

・Abstract: A speech dialog system is a system that understands and corresponds to human voice questioning to it. Such system is applied to the interface of mobile terminals (Siri), robots (Pepper), and so on. At our laboratory, we conduct studies focusing not only on the linguistic understanding of user speech but on hierarchical understanding of speech behavior and mutual adaptation between system and user. For these types of studies machine learning is an inevitable technology, and it is widely used from signal processing, and voice recognition to the core dialog strategy and user model learning.  In this seminar, challenges and necessary technologies for speech dialog system and application of machine learning technology including our study cases will be introduced. In addition, examples of the application of recent Deep Learning in component technology and my approaches and efforts are also introduced.

・Organizer: Kaname Kojima, Masao Nagasaki