Laboratory for Systems Biology
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circadian transcription circuits

Toward the realization of experimental systems biology at the organism level

With our members from different backgrounds, we would like to realize experimental systems biology at the organism level. To this end, we are using the mammalian circadian clock as a model system, and planning multi-scale research activities covering a series of length scales; molecule-to-cell, cell-to-tissue, and tissue-to-organism. On each layer, we would like to solve at least one fundamental question.
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What's New

2021/1/11 Our theoretical paper "A design principle for posttranslational chaoticoscillators" was published. It may underlie spontaneous activity of cells. It completes our biochemical trilogy over 8yrs (oscillator in 2012, Turing in 2017, chaos).
2020/9/4 Nature Reviews Neuroscience published the viewpoint by 18 experts to overview the past and future of neuroscience. I introduced organism-level systems biology based on whole-organ cell profiling & next-generation genetics, and future human systems biology.
2020/5/14 Our review on whole-brain profiling of cells and circuits was published on Neuron.
2020/5/14 Our new paper on CUBIC-HistoVIsion, a versatile whole-organ/body tissue staining and imaging methods are now published on Nature Communciation.
2020/1/9 Our review "tissue clearing and its applications" has been published in Nature Reviews Neuroscience.
2019/11/27 Our new paper on whole-organ profiling of cells was just published in Nature protocols. We also developed "MOVIE" method to speed up the imaging by LSFM.
2018/12/14 Our tissue clearing (TC) reagents CUBICs were featured in Nature by Eisenstein.
2018/10/01 Ms. Harada was awarded a poster prize in RIKEN summer school 2018
2018/08/29 Publishing research results concerning "Two genes that regulate how much we dream"
The preview by Dr. Hayashi and Kashiwagi of International Institute for Integrative Sleep Medicine (WPI-IIIS) is here.
2018/08/21 Our paper on chemical principle on tissue clearing was published.
2018/03/26 Dr. Shinohara was awarded an encouraging prize in the 18th annual meeting of the protein science society of Japan
2017/11/30 New paper with Hideki Ukai (RIKEN QBiC) and Hiroshi Kiyonari (RIKEN CLST) on "production of knock-in mice in a single generation from ES cells" was published in Nature Protocols. Next-generation mammalian genetics w/o crossing has been published.
2017/10/30 Dr. Shinohara was awarded an outstanding poster prize at the 24th annual meeting of Japanese Society for Chronobiology
2017/09/07 Our new paper on molecular mechanisms for temperature compensation of circadian clocks is published in Mol Cell
2017/08/30 A new article on CUBIC pathology was out. We applied tissue-clearing and imaging to clinical pathology.
2017/07/05 Our new paper with Miyazono lab on whole-body clearing and imaging of cancer metastasis is just out.
2017/03/22 Ms. Shoko Harada received a student presentation prize at 90th annual meeting of the Japanese pharmacological society
2016/12/27 Our ms "KO-Rescue ES Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1" came out in Mol Cell. Surprisingly, we could double circadian period of mammalian cells from 19 h to 38 h with the change of only two amino acids in CRY1 protein.
2016/06/17 Mass spectrometry-based absolute quantification of mouse circadian clock proteins is now online.
2016/03/23 We know calcium is good for our bones, but it might also be the key to a good night sleep. Our research group have unveiled a new theory for how sleep works. Published in the journal Neuron, the work shows how slow-wave sleep depends on the activity of calcium inside neurons.
2016/01/23 Cell Chemical Biology has launched with our review on whole-body cell analysis for organism-level systems biology.
2016/01/12 Publishing research results concerning“Snappy Sleep Stager system identifies gene related to shorter sleep”
[PDF]   [Supplemental 1] [Supplemental 2] [Supplemental 3] [Supplemental 4]
2015/10/10 The advanced CUBIC protocols for clearing/imaging/informatics are now on line.  [PDF]   [Supplement movie (nature protocol)]
2015/09/29 Dr.Hiroki R. Ueda was awarded 15th (2015) Yamazaki-Teiichi Prize.
2015/02/24 Dr.Hiroki R. Ueda was elected as Young Academy (1st term), Chair of SCIENCE COUNCIL OF JAPAN.
2014/12/30 Dr. Hiroki R. Ueda talked on his hopes in 2015 on Nature.
2014/12/30 Tissue-clearing techniques such as CUBIC were selected as Methods of the year 2014 ("Methods to watch") by Nature Method.
The interview of Dr. Hiroki R. Ueda was here.
The article on Methods of the year 2014 was here.
2014/12/17 “Transparent mouse” by CUBIC technology from our lab (published on Cell, November 6th) was selected as “Images of the year 2014”.
2014/11/7 Publishing research results concerning“Whole-body imaging with single-cell resolution by tissue-decolorization”
2014/09/16 Publishing research results concerning“A Mammalian Circadian Clock Model Incorporating Daytime Expression Elements”
2014/08/21 ALS Ice Bucket Challenge
2014/08/8 “Tokyo Translational Therapeutics Meeting: Homeodynamics in Clocks, Sleep and Metabolism” will be held on September 24, 2014.”
2014/04/18 Publishing research results concerning“Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis”
2014/03/20 Publishing research results concerning“Non-Enzymatic DNA Cleavage Reaction Induced by 5-Ethynyluracil in Methylamine Aqueous Solution and Application to DNA Concatenation”
2013/07/04 Publishing research results concerning a robust and reproducible approach for surveying the mRNA content of individual cells.
2012/10/19 Publishing research results concerning a generic mathematical model for post-translational biochemical oscillations.
2012/08/28 Publishing research results concerning a convenient, non-invasive method for calculating body time in humans
2011/08/12 Publishing research results concerning comprehensive gene expression data of the adult mouse brain
2011/08/05 Publishing research results concerning perturbation analyses of intermolecular interactions
2011/05/10 Project Leader Hiroki R. Ueda has recently published a review in Nature Reviews Genetics.
2011/03/10 Rikuhiro Yamada (Special Postdoctoral Researcher) and Maki Ukai-Tadenuma (Technical Staff) are awarded RIKEN Research and Technology Incentive Awards respectively for their achievement in elucidation of a design principle in the circadian transcriptional network.
2011/02/04 Project Leader Hiroki R. Ueda wins JSPS Prize
2009/11/10 Team Leader Wins The 23rd Japan IBM Science Prize.
2009/10/28 Dr. Yoichi Minami Wins poster awards for the 16th Annual Meeting of Japanese Society for Chronobiology.
2009/09/01 Announcement of research results concerning “Central gears of the mammalian circadian clock exposed ”
2008/10/25 Announcement of research results concerning “PEPCA”
2008/09/30 Announcement of research results concerning “Principles proven: Transcriptional logic of the mammalian biological clock”
2008/09/24 Announcement of research results concerning “New-found control principles for biological clocks”
2008/06/25 The 17th CDB Meeting “Towards Synthesis of Cells”
2008/04/30 Notification of FPR Recruitment
2008/03/26 Announcement of research results concerning “spring hormone”
2007/12/11 Our laboratory is introduced by the TV program of NHK in 11th December.
2007/11/07 Team Leader Wins Chronobiology Prize
2007/10/21 Announcement of research results concerning ”singularity behavior”
Center for Developmental Biology Laboratory for Systems Biology 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Tel: 078-306-3195 / Fax: 078-306-3194 E-mail: Osaka University Mammalian Promoter Enhancer Database
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