Osaka University Global COE Program

Mutations in UVSSA cause UV-sensitive syndrome and destabilize ERCC6 in transcription-coupled DNA repair

Thu, 17 May 2012 15:27:13 +0900

Neural activity in cortical area V4 underlies fine disparity discrimination

Mon, 26 Mar 2012 15:24:04 +0900

The structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms

Tue, 28 Feb 2012 15:21:26 +0900

Coordinated Ciliary Beating Requires Odf2-Mediated Polarization of Basal Bodies via Basal Feet

Fri, 10 Feb 2012 15:18:14 +0900

11-v02:Martin Phillip Cheung

Thu, 12 Jan 2012 10:33:08 +0900

11-v01:Dr. Ariel Blocker

Thu, 12 Jan 2012 10:27:41 +0900

11-44：2012.2.15-21 Department of Bioinfomatic Engineering / Leo iijima

Wed, 11 Jan 2012 13:14:10 +0900

Study meetings

Leo Iijima
Symbiotic network design laboratory,
Graduate School of Frontier Bioscience
Osaka University

I visited NASA Ames research center located in the U.S. San Francisco state from Feb. 19 to Feb 26, 2012. The purpose of this business trip was to give a seminar on my research and to have a study meeting for further research.
At first, I gave a presentation about my research to scientists at NASA AMES research center. My research focuses on adaptive evolution. The title of my presentation was "Laboratory evolution of thermal adaptive Escherichia coli". I introduced background and question of my research field, methods of laboratory evolution, and results of genome analysis of thermal adaptive Escherichia coli step by step. The audience included researchers using bacteria in extreme environment such as high-temperature and excess radiation and pH, so that they took strongly interest in the adaptation as a result of laboratory experiment. In addition, we discussed from wide viewpoint, which was very useful for me to discuss the results of my research. After presentation, I　also proposed the further research. We exchanged opinion about direction and significance of new studies.
Another thing that I have done was to hear a project in NASA. Dr. Lynn Rothschild, I visited in this trip, had started the new project in the field of synthetic biology last year. She explained overview of the project and introduced some themes, creation of bacteria in extreme environment. She also plans to start a laboratory evolution. We discussed about the further research and examined the collaboration.
Furthermore, I visited two laboratories in Stanford University and UC Berkeley, which studies are related to my future research. I got to know about research in each laboratory. In addition, I proposed the further studies and we could discuss about that, which brought to get comprehension of current development in research field.
At last, I deeply appreciate Osaka University and GCOE program to give me an opportunity to go abroad.

11-43：2012.2.7-15 Developmental Genetics Group / Rieko Ajima

Tue, 20 Dec 2011 11:11:18 +0900

Title: Visiting collaborators at National Cancer Institute-Frederick, NIH
Name: Rieko Ajima
Affiliation: Developmental Genetics Group (Hamada-lab)
Destination: National Cancer Institute-Frederick, NIH (Frederick, Maryland, USA)
Report:
　I joined Dr. Hamada's lab about one year ago as a GCOE postdoctoral fellow. Dr. Hamada generously allow me to continue my projects, studying about mechanisms of mesoderm formation in mouse embryos, which were started in Dr. Yamaguchi's lab in National Cancer Institute (NCI)-Frederick. I am still collaborating with previous colleagues and collaborators in NCI-Frederick about my projects.
　I have successfully established labeling system of the mesodermal progenitors in early developmental stage mouse embryos and observed their behavior through live imaging in this year. Currently, I am trying to establish the methods to analyze the data with my collaborators. But, it is really difficult to explain and discuss about live imaging data over e-mails.
The main purposes of this trip were to discuss about future direction of my projects including how to wrap up my data into paper(s) with my previous boss, Dr. Terry Yamaguchi in the Cancer and Developmental Biology Lab in NCI-Frederick, and to discuss about the methods to analyze the live imaging data with my collaborators, Dr. Stephen Lockett and Dr. Prabhakar Gudla in the Optical Microscopy and Analysis Lab in NCI-Frederick, and Dr. Yanling Liu in the Imaging and Visualization Group, ABCC,  SAIC-Frederick.

Terry and I spent a good deal of time to discuss about my projects. Terry was really excited about my recent data and gave me great amount of advises. We planned when and how we will finish up the projects as papers. I also discussed with him about the projects, which are currently on going in Terry's lab. Furthermore, he had arranged for me to give a talk at the Cancer Developmental Biology Lab Meeting. There were a lot of great developmental biologists including Dr. Alan Perantoni, Dr. Mark Lewandoski, and Dr. Susan Mackem, participated to the meeting. So, it was great opportunity for me to give talk in front of them and got feedback from. My talk brought active discussions, and was taken very positively. I had opportunity to meet with Mark in person later and we exchanged opinions about mesoderm specification.
The discussion about the live imaging data analysis also went well. Dr. Gudla already tried several programs for me and selected software for the cell tracking. Furthermore Dr. Gudla and Dr. Liu are planning to establish automated 4D image alignment and cell tracking program using my data. We discussed how to proceed data analysis and decided division of roles for the analysis.
I took advantage of this trip to collect samples using a valuable mouse line, which is only available in Terry's lab. With my previous colleagues' help, I succeeded to collect embryos at several different stages, which I can use for my future experiments in Japan. The samples were arranged to ship here soon.

Overall my trip was fruitful and I accomplished a lot during my stay in NCI-Frederick. Especially the efficient discussion about live imaging data with Terry, Dr. Lockett, Dr. Gudla, and Dr. Liu could not be done without visiting and talking directly with them. I believe that this trip would make the further collaboration very productive.
　I sincerely appreciate GCOE program and Dr. Hamada giving me this opportunity and financial supports for this trip.

11-42：2012.1.7-19 Cellular and Molecular Neurobiology Group / Olga Malyshevskaya

Fri, 18 Nov 2011 10:10:04 +0900

(Name) Olga Malyshevskaya

(Name of laboratory) Cellular and Molecular Neurobiology laboratory (Yamamoto laboratory)

(Destination) Obergurgl, Austria

(Purpose) To participate in the FENS/IBRO Hertie winter school. Poster presentations in this meeting.

(Result)
The main reasons why I decided to participate in this winter school were to get feedback on my project and to broaden my knowledge in neuroscience. It was mainly focused on computational neuroscience, together with discussing advantages from using new methods in neuroscience or combining them (multichannel recordings in-vitro and in-vivo, new neuro-imaging techniques, optogenetics). The challenge for today's systems neuroscience is to understand how populations of neurons process sensory information. Phd students together with Postdocs and senior scientists discussed similarities and differences in neural architectures between species and brain areas. Every participant had a chance to present his poster and get fruitful discussion. I presented my science poster on "Study of activity-dependent cortical axon growth during development using Channelrhodopsin-2 photostimulation". My study was met with approval and interest, I`ve got useful advices and suggestions.

The tradition to hold this school kept for last 12 years. Unfortunately, Japanese young scientists almost do not participate in these European schools. I think it's a great opportunity to discuss with European colleagues about research in neuroscience. Many European countries made huge impact into neuroscience (for instance, Ramon y Cajal from Spain, Sackman from Germany) and participating in these kind of meetings is a great chance to meet successors of great neuroscientists and if you are lucky to present your project to them. That's why I would like to recommend Japanese students to apply for this kind of meetings more often.

In the end I want to say that meeting was organized on very high level. I want to thank FENS/IBRO, Hertie foundation for organizing this event and inviting me. And I want to express my deep gratitude to Global COE program for financial support.

11-41：2012.2.24-3.2 Soft Biosystem Group / Takamitu Morikawa

Mon, 14 Nov 2011 15:17:02 +0900

(Title) Report on The Biophysical Society's 56th annual meeting

(Name) Takamitsu Morikawa
(Name of Laboratory) Graduate School Of Bioscience, Soft Biosystem Laboratory (Prof. Yanagida)
(Destination) San Diego convention center
(Purpose) To participated in The Biophysical Society's 56th annual meeting at San Diego convention center
(Report)
I attended The Biophysical Society's 56th annual meeting, held during February 25th to February 29th, 2012, San Diego. This meeting is the largest meeting of biophysicists. Many biophysicists, more than 6,500 participants, around the world gathered this meeting. In the annual meeting, I attend many workshops, minisymposia, platform sessions and poster presentations. I collected a lot of cutting edge researches.
In February 26th, I presented a poster titled as "Enhancing temperature and pressure sensitivity of various fluorescent proteins". I enhanced temperature and pressure sensitivity of CFP, GFP and YFP, which were inserted several glycines at -strand 7, nearest -strand of barrel structure. The insertion of glysines changed the conformation of barrel structure and made pole at -strand 7. The pole make the chromophore be easy to interact with water molecules. At my presentation, many of researchers came to see my poster and I discussed with them. Especially, I had good discussion with experts of chemistry and crystal structure.

At last, I want to show my appreciation for financial support from the GCOE program.

11-40：2012.2.24-3.2 Soft Biosystem Group / Shinichi Yamazaki

Mon, 14 Nov 2011 14:44:41 +0900

(Title) Report on The Biophysical Society's 56th Annual Meeting
(Name) Shinichi Yamazaki
(Name of Laboratory) Graduate School of Frontier Bioscience, Laboratory for Cell Signaling Dynamics (Prof. Ueda)
(Destination) The San Diego Convention Center, San Diego, California, USA
(Schedule)
2/24: Itami -> Haneda -> Los Angeles -> San Diego
2/25-29: Biophysical Society's 56th Annual Meeting
2/29-3/2: San Diego -> Los Angeles -> Haneda -> Itami
(Report)
Purpose : To present my research poster entitled "Regulation of self-organization in chemotactic signaling system by an adhesion-related molecule, talin" and collect the latest information related to our research.
Content : I attended the Biophysical Society's 56th Annual Meeting, held in San Diego, California on February 25-29, 2012. With over 6,000 attendees, the meeting is the largest gathering of biophysicists around the world. A wide variety of research fields were represented, including molecular imaging and dynamics, biophysical simulation and cell motility. The meeting included many oral and poster presentations.
Achievement : In the oral session, I found some interesting reports and collected information relevant to my research field, such as cell motility analysis and adhesion molecule imaging techniques. On February 26, the second day of the meeting, I presented my research. In my poster presentation, I reported the relationship between the phosphatidylinositol lipids system and the adhesion system. Phosphatidylinositol lipids are key signaling mediators for cell motility. Researchers in the fields of lipids systems, cell adhesion and cell motility asked questions and we discussed my research. They gave me good suggestion for my future works. For example, a person studying inositol lipids suggested to me a new experimental idea to test my hypothesis.
Acknowledgement : I would like to show my deep gratitude to all the people who supported my research. Finally, I thank the GCOE program for giving me the opportunity to attend this meeting and for financial support.

11-39:2012.2.24-3.2 Soft Biosystem Group / Keisuke Fujita

Tue, 08 Nov 2011 15:24:35 +0900

1. Report on The Biophysical Society's 56th Annual Meeting.
2. Keisuke Fujita
3. Graduate school of Frontier Biosciences, Soft Biosystem Laboratory (Prof. Yanagida)
4. San Diego Convention Center
5.
I attended the Biophysical Society's 56th Annual Meeting, held in San Diego, California on February 25-29, 2012. Thanks to this financial support, I could have a good opportunity to present my research (the title is "Single molecule measurement of the myosin-V energy transduction process") to international researchers and know a lot of cutting-edge researches in the world.

I am currently studying the mechanical properties of myosin-V by using optical tweezers system. Myosin-V is a molecular motor, which converts chemical energy into mechanical work and functions as a vesicle transporter in a cell. Optical tweezers is one of the most popular techniques to manipulate such molecular motors at single molecule level. Our group has revealed a lot of properties of molecular motors by optical tweezers experiments in the past.

One of the most interesting themes for me is that molecular motors may generate forces and directional motion by rectifying thermal fluctuations. My recent result suggests that myosin-V can produce mechanical work by rectifying thermal fluctuation more than that by a conformational change of the lever arm domain of myosin-V. I think this mechanism is used by other many molecular motors, and in fact there were several results in the meeting, which suggested the rectifying mechanism for another motor such as RNA polymerase.

Also, in the meeting, there are many researches about how single molecular motors are integrated into complex functions such as mitosis, locomotion, intracellular transport or mechanical sensory transduction. In future, we should understand whether the rectifying mechanism is also applied to higher hierarchical level of organism.

This joining the meeting was meaningful in the sense that I found a clue to improving my research and extended my knowledge about a single molecule system. Theses experience will surely lead to a good result in my future work.

Finally, I thank everyone who helped me, and the Global COE program for financial support and for providing me this great opportunity again.

11-38:2012.2.24-3.2 Soft Biosystem Group / Masashi Omachi

Tue, 08 Nov 2011 15:14:35 +0900

(Title) Report on Biophysical Society 56th Annual Meeting

(Name) Masashi Ohmachi

(Laboratory) Yanagida laboratory

(Destination) San Diego Califolnia, USA

(Results)
I attended the Biophysical Society 56th Annual Meeting held in San Diego Febrary 24-29, 2012. San Diego has a moderate climate through a year. I gave a poster presentation and collected information about my research field. More than 6000 researchers in the multidisciplinary fields representing biophysics attend the annual meeting. This Annual Meeting is the largest meeting of biophysicists in the world with more than 4000 poster presentations, over 200 exhibits, and more than 20 symposia. The meeting has subgroup meetings, platform sessions, social activities, and poster session. What's good about Biophysical society is that researchers in different fields, such as biology, chemistry and physics, get together and talk about the subject from a different point of views. Biophysical society includes many kinds of topics in various fields. I gave a poster presentation entitled "Simultaneous observation of the three-dimensional orientation and position of a single fluorescent probe "on the last day of the annual meeting. In the presentation, I talked about the development of new microscopy to simultaneously measure three dimensional orientation and movement of a fluorescently labeled single molecule. I wanted to talk with scientists in any field, since our developed new microscopy has particular applicability for various biophysical studies interested in a wide range of dynamic processes of single molecule. Actually, I could talk with many people in different field. Some of them provided crucial comments and helpful advices. I also visited other presentations to collect new information for future research. It was exciting and rewarding for me to get the latest reports on many field and discuss with scientists from around the world. Especially, I tried to talk with people in other field in the poster and platform session because I feel that ideas and thinking in chemistry and physics is important to advance the research in biology. Biophysical meeting is one of the best places to progress multidisciplinary research. Finally, I greatly appreciate GCOE program for the financial support and giving me a chance to attend this meeting.

11-37：2012.1.3-10　Kokoro-Biology Group　/ Arikuni Uchimura

Mon, 07 Nov 2011 16:23:46 +0900

(Title) Report for visiting IGIB extension Center at Naraina

(Name) Arikuni Uchimura

(Name of Laboratory) Laboratory of Integrated Biology (Prof. Yagi)

(Destination) New Delhi, India

(Purpose) To share research and related technologies about genome science with Indian scientists

(Result)
In India, science and technology have been improved rapidly. This time, fortunately I had a chance to visit institutions of biological science in India and share information of up-to-date research. I had two purposes. One is visiting "Institute of Genomics and Integrative Biology (IGIB)", one of the best institutes for genomic science and genetics in India. The other is attending "the India-Japan Developmental Biology Workshop" and giving an oral presentation of our research. Here, I would like to report visiting IGIB.
According to the website, IGIB is a premier Institute of Council of Scientific and Industrial Research, engaged in research of national importance in the areas of genomics, molecular medicine, bioinformatics, proteomics and environmental biotechnology. I visited the IGIB Extension Centre (Naraina) with 8 other Japanese scientists majored in life science. The institute located at about 10 km west of the center of Delhi city and is in Indian traditional residential town. Building of the institute looked to be a little old. We were taken to a tour of the facility. There were a lot of latest instruments and machines for genomic science, including two sets of high-through-put sequencers (HighSeq2000 from illumina), super computer, finest microscope, cell culture system and many aquariums for breeding zebrafish. All Indian scientists who we saw there, worked hard for their studies. After the tour, a meeting was held to share information of up-to-date research between the Japanese and Indian scientists. There were many interesting talks and discussions. One of the IGIB scientists, Dr. Vinod Scaria talked about an outline of studies performed in the institution and his scientific interests. I was surprised to see they had a high-through-put sequencer because I recently started to use that sequencer for my study in Japan. I was fascinated with their strategy of scientific study, their approach making most of their ability and facility by using both new technology-based approach and traditional method. When I talked about my study, mouse evolution project, briefly in the meeting, some of Indian scientist had interests and asked me some questions. After this, I knew that the level of science in India was very high.
This visit was a quite fruitful opportunity for me to know that India has great potential to be a center of scientific research in the near future. I would like to thank the GCOE program for the financial support to give me this opportunity.

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(Title) Report on the India-Japan Developmental Biology Workshop at NCBS

(Name) Arikuni Uchimura

(Name of Laboratory) Laboratory of Integrated Biology (Prof. Yagi)

(Destination) Bangalore, India

(Purpose) To collect latest information and have oral presentation at the India-Japan Developmental Biology Workshop

(Result)
　After visiting IGIB extension Center in Delhi, I moved to Bangalore in order to attend "the India-Japan Developmental Biology Workshop" held at National Center for Biological Sciences (NCBS). Since Bangalore is located in 1700 km south of Delhi, the climate in Bangalore was warmer and more comfortable for my stay than in Delhi. The place where NCBS built was originally used as a villa. So, there were a lot of beautiful gardens and some ponds with green trees.
The workshop started with welcome evening reception and dinner. Beginning the next day, there were 6 sessions, including 27 oral presentations during 2 days. Most of participants in this workshop were from India or Japan, and some of them were from U.S. The content of the sessions had broad interests related to developmental biology. For example, there were talks about cell differentiation to mesoderm, various organogenesis, signaling pathway, mathematical simulation, behavioral genetics, brain development, neurobiology, and germ cells by using various model, mice, drosophila, zebrafish, discoideum cell, and plant. So, many of these sessions included unknown contents to me. My oral presentation was scheduled as a last speaker on the last day. My talk title is "Mouse Evolution Project: understanding genetic buffering system in mammalian". I had 20-min talk for my presentation. I started to talk about an introduction of our project "mouse evolution project", and then talked about experimental results we have obtained so far, including mice having singing behavior. Many audiences had interests in our study, asking many helpful questions during and after my presentation.In our project, we experimentally imitated evolutionary process by using mice in laboratory facility, one of these questions suggested that if I would perform the same experiment in the field, it might be better experiment. I would like to try it. Most of scientists, who heard my presentation, seem to have a favor to our mouse evolution project.
Honestly speaking, I was very nervous before beginning my presentation. However, when starting my talk, the attitude of the audience, which were keen on listening and understanding my presentation made me feel relaxed to talk. This experience has provided a tremendous amount of confidence for me in my future work.
Finally, I would like to thank everyone who helped me in my work and the GCOE program for the financial support to give me this great opportunity.

11-36：2012.2.24-3.2 Soft Biosystem Group / Keigo Ikezaki

Mon, 07 Nov 2011 16:14:33 +0900

１．Report on The Biophysical Society's 56th Annual Meeting

２．Keigo Ikezaki

３．Graduate school of Frontier Biosciences, Soft Biosystem Laboratory (Prof. Yanagida)

４．San Diego Convention Center, 111 W. Harbor Drive, San Diego, CA 92101

５．
I attended the Biophysical Society's 56th Annual Meeting.
The meeting held in San Diego Convention Center and thousands people from all over the world attended this meeting.
In the annual meeting, I presented a poster titled as "The adjacent binding state enables Myosin VI dual function.( Keigo Ikezaki, Tomotaka Komori, Mitsuhiro Sugawa, Yoshiyuki Arai, So Nishikawa, Atsuko H. Iwane and Toshio Yanagida) ". My research reveals that myosin VI can take two binding state; a distant and adjacent binding state and its tail domain is strongly biased toward forward direction, which ensures myosin VI's dual functions; a transporter and a cytoskeletal anchor. I argued over my poster with lots of people overseas. I attended many platform sessions and poster presentations, I collected information on cutting-edge research of molecular motor proteins and some posters and sessions struck me. In the platform about Imaging & Optical Microscopy: Superresolution Imaging & Single Molecules, a lot of researchers presented several kind of super-resolution techniques. Super-resolution techniques can overcome a diffraction limit and visualize the details of nano-scale structures. I was interested in some of presented techniques and want to learn the techniques to apply them to my interests.
Finally, I'd like to show my gratitude to all the people who gave me this opportunity and also to the GCOE's financial support.