2022/08/17 更新

写真a

キガ ダイスケ
木賀 大介
所属
理工学術院 先進理工学部
職名
教授
ホームページ

兼担

  • 理工学術院   大学院先進理工学研究科

学内研究所等

  • 2020年
    -
    2022年

    理工学術院総合研究所   兼任研究員

学位

  • 東京大学   博士(理学)

経歴

  • 2016年04月
    -
    継続中

    早稲田大学   理工学術院   教授

  • 2005年04月
    -
    2016年03月

    東京工業大学   大学院総合理工学研究科   准教授

  • 2004年09月
    -
    2005年03月

    東京大学   大学院総合文化研究科   助手(陶山研究室)

 

研究分野

  • 生命、健康、医療情報学   生命情報

  • 生物物理学

  • システムゲノム科学

研究キーワード

  • 合成生物学

  • 人工遺伝子回路

  • 遺伝暗号

  • 人工進化

  • タンパク質合成

論文

  • 遺伝暗号による制約を突破する翻訳システムの改変と非標準アミノ酸 遺伝暗号改変を活用した人工進化からみるmagic20の意味

    木賀大介

    生化学   93 ( 3 )  2021年

    J-GLOBAL

  • A highly bioactive Lys-deficient IFN leads to a site-specific di-PEGylated IFN with equivalent bioactivity to that of unmodified IFN-α2b.

    Imada T, Moriya K, Uchiyama M, Inukai N, Hitotsuyanagi M, Masuda A, Suzuki T, Ayukawa S, Tagawa YI, Dohmae N, Kohara M, Yamamura M, Kiga D

    ACS synthetic biology   7 ( 11 ) 2537 - 2546  2018年11月  [査読有り]  [国際誌]

    DOI PubMed

  • 生命の暗号を書き換える

    木賀大介

    現代化学     35 - 40  2018年09月  [招待有り]

    担当区分:筆頭著者, 最終著者, 責任著者

  • General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming.

    Kana Ishimatsu, Takashi Hata, Atsushi Mochizuki, Ryoji Sekine, Masayuki Yamamura, Daisuke Kiga

    ACS synthetic biology   3 ( 9 ) 638 - 44  2014年09月  [査読有り]  [国際誌]

     概要を見る

    Control of the cell-type ratio in multistable systems requires wide-range control of the initial states of cells. Here, using a synthetic circuit in E. coli, we describe the use of a simple gene-overexpression system combined with a bistable toggle switch, for the purposes of enabling the wide-range control of cellular states and thus generating arbitrary cell-type ratios. Theoretically, overexpression induction temporarily alters the bistable system to a monostable system, in which the location of the single steady state of cells can be manipulated over a wide range by regulating the overexpression levels. This induced cellular state becomes the initial state of the basal bistable system upon overexpression cessation, which restores the original bistable system. We experimentally demonstrated that the overexpression induced a monomodal cell distribution, and subsequent overexpression withdrawal generated a bimodal distribution. Furthermore, as designed theoretically, regulating the overexpression levels by adjusting the concentrations of small molecules generated arbitrary cell-type ratios.

    DOI PubMed

  • Experimental evolution of a green fluorescent protein composed of 19 unique amino acids without tryptophan.

    Akio Kawahara-Kobayashi, Mitsuhiro Hitotsuyanagi, Kazuaki Amikura, Daisuke Kiga

    Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life   44 ( 2 ) 75 - 86  2014年04月  [査読有り]  [国際誌]

     概要を見る

    At some stage of evolution, genes of organisms may have encoded proteins that were synthesized using fewer than 20 unique amino acids. Similar to evolution of the natural 19-amino-acid proteins GroEL/ES, proteins composed of 19 unique amino acids would have been able to evolve by accumulating beneficial mutations within the 19-amino-acid repertoire encoded in an ancestral genetic code. Because Trp is thought to be the last amino acid included in the canonical 20-amino-acid repertoire, this late stage of protein evolution could be mimicked by experimental evolution of 19-amino-acid proteins without tryptophan (Trp). To further understand the evolution of proteins, we tried to mimic the evolution of a 19-amino-acid protein involving the accumulation of beneficial mutations using directed evolution by random mutagenesis on the whole targeted gene sequence. We created active 19-amino-acid green fluorescent proteins (GFPs) without Trp from a poorly fluorescent 19-amino-acid mutant, S1-W57F, by using directed evolution with two rounds of mutagenesis and selection. The N105I and S205T mutations showed beneficial effects on the S1-W57F mutant. When these two mutations were combined on S1-W57F, we observed an additive effect on the fluorescence intensity. In contrast, these mutations showed no clear improvement individually or in combination on GFPS1, which is the parental GFP mutant composed of 20 amino acids. Our results provide an additional example for the experimental evolution of 19-amino-acid proteins without Trp, and would help understand the mechanisms underlying the evolution of 19-amino-acid proteins. (236 words).

    DOI PubMed

  • 生物をつくることで生命を理解する (特集 生命とは何だろう?) -- (人工生命を作ることは可能か?)

    木賀 大介

    Kotoba : 多様性を考える言論誌   ( 16 ) 78 - 81  2014年

    CiNii

  • Effects of downstream genes on synthetic genetic circuits.

    Takefumi Moriya, Masayuki Yamamura, Daisuke Kiga

    BMC systems biology   8 Suppl 4 ( 4 ) S4  2014年  [査読有り]  [国際誌]

     概要を見る

    BACKGROUND: In order to understand and regulate complex genetic networks in living cells, it is important to build simple and well-defined genetic circuits. We designed such circuits using a synthetic biology approach that included mathematical modeling and simulation, with a focus on the effects by which downstream reporter genes are involved in the regulation of synthetic genetic circuits. RESULTS: Our results indicated that downstream genes exert two main effects on genes involved in the regulation of synthetic genetic circuits: (1) competition for regulatory proteins and (2) protein degradation in the cell. CONCLUSIONS: Our findings regarding the effects of downstream genes on regulatory genes and the role of impedance in driving large-scale and complex genetic circuits may facilitate the design of more accurate genetic circuits. This design will have wide applications in future studies of systems and synthetic biology.

    DOI PubMed

  • The number of amino acids in a genetic code

    Kazuaki Amikura, Daisuke Kiga

    RSC Advances   3 ( 31 ) 12512 - 12517  2013年08月  [査読有り]

     概要を見る

    It is generally accepted that the universal genetic code evolved from a simpler form that employed fewer amino acids. We have recently developed a 'simplified genetic code' only using 19 amino acids. Simplified codes will provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals. In this review, we describe the evolution of the number of amino acids in a genetic code. We also discuss the utility of engineered genetic codes having a different number of amino acids from that of the universal code. © The Royal Society of Chemistry 2013.

    DOI

  • Simplification of the genetic code: restricted diversity of genetically encoded amino acids.

    Akio Kawahara-Kobayashi, Akiko Masuda, Yuhei Araiso, Yoko Sakai, Atsushi Kohda, Masahiko Uchiyama, Shun Asami, Takayoshi Matsuda, Ryuichiro Ishitani, Naoshi Dohmae, Shigeyuki Yokoyama, Takanori Kigawa, Osamu Nureki, Daisuke Kiga

    Nucleic acids research   40 ( 20 ) 10576 - 84  2012年11月  [査読有り]  [国際誌]

     概要を見る

    At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used. Although this notion is supported by a wide range of data, the actual existence and function of the genetic codes with a limited set of canonical amino acids have not been addressed experimentally, in contrast to the successful development of the expanded codes. Here, we constructed artificial genetic codes involving a reduced alphabet. In one of the codes, a tRNAAla variant with the Trp anticodon reassigns alanine to an unassigned UGG codon in the Escherichia coli S30 cell-free translation system lacking tryptophan. We confirmed that the efficiency and accuracy of protein synthesis by this Trp-lacking code were comparable to those by the universal genetic code, by an amino acid composition analysis, green fluorescent protein fluorescence measurements and the crystal structure determination. We also showed that another code, in which UGU/UGC codons are assigned to Ser, synthesizes an active enzyme. This method will provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals.

    DOI PubMed

  • An aptazyme-based molecular device that converts a small-molecule input into an RNA output.

    Shotaro Ayukawa, Yoko Sakai, Daisuke Kiga

    Chemical communications (Cambridge, England)   48 ( 61 ) 7556 - 8  2012年08月  [査読有り]  [国際誌]

     概要を見る

    We describe the construction of an aptazyme-based molecular device that converts, through a cascade of reactions, a small-molecule input into output RNA strands. This device is applicable as an interface between a small molecule and a molecular system that accepts only nucleic acid input.

    DOI PubMed

  • Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling.

    Ryoji Sekine, Masayuki Yamamura, Shotaro Ayukawa, Kana Ishimatsu, Satoru Akama, Masahiro Takinoue, Masami Hagiya, Daisuke Kiga

    Proceedings of the National Academy of Sciences of the United States of America   108 ( 44 ) 17969 - 73  2011年11月  [査読有り]  [国際誌]

     概要を見る

    Phenotypic diversification of cells is crucial for developmental and regenerative processes in multicellular organisms. The diversification concept is described as the motion of marbles rolling down Waddington's landscape, in which the number of stable states changes as development proceeds. In contrast to this simple concept, the complexity of natural biomolecular processes prevents comprehension of their design principles. We have constructed, in Escherichia coli, a synthetic circuit with just four genes, which programs cells to autonomously diversify as the motion on the landscape through cell-cell communication. The circuit design was based on the combination of a bistable toggle switch with an intercellular signaling system. The cells with the circuit diversified into two distinct cell states, "high" and "low," in vivo and in silico, when all of the cells started from the low state. The synthetic diversification was affected by not only the shape of the landscape determined by the circuit design, which includes the synthesis rate of the signaling molecule, but also the number of cells in the experiments. This cell-number dependency is reminiscent of the "community effect": The fates of developing cells are determined by their number. Our synthetic circuit could be a model system for studying diversification and differentiation in higher organisms. Prospectively, further integrations of our circuit with different cellular functions will provide unique tools for directing cell fates on the population level in tissue engineering.

    DOI PubMed

  • 生物版国際ロボコンiGEM

    木賀 大介

    バイオサイエンスとインダストリー = Bioscience & industry   69 ( 3 ) 245 - 247  2011年05月

    CiNii

  • "ありえた生物"から生命を探る合成生物学

    木賀 大介

    日経サイエンス   37 ( 7 ) 56 - 64  2007年07月

     概要を見る

    あの時こうしていれば──。自分の人生を振り返って「if」を考えるのは,ほとんどの場合あまり建設的ではない。

    CiNii

  • An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system.

    Daisuke Kiga, Kensaku Sakamoto, Koichiro Kodama, Takanori Kigawa, Takayoshi Matsuda, Takashi Yabuki, Mikako Shirouzu, Yoko Harada, Hiroshi Nakayama, Koji Takio, Yoshinori Hasegawa, Yaeta Endo, Ichiro Hirao, Shigeyuki Yokoyama

    Proceedings of the National Academy of Sciences of the United States of America   99 ( 15 ) 9715 - 20  2002年07月  [査読有り]  [国際誌]

     概要を見る

    Tyrosyl-tRNA synthetase (TyrRS) from Escherichia coli was engineered to preferentially recognize 3-iodo-L-tyrosine rather than L-tyrosine for the site-specific incorporation of 3-iodo-L-tyrosine into proteins in eukaryotic translation systems. The wild-type TyrRS does not recognize 3-iodo-L-tyrosine, because of the bulky iodine substitution. On the basis of the reported crystal structure of Bacillus stearothermophilus TyrRS, three residues, Y37, Q179, and Q195, in the L-tyrosine-binding site were chosen for mutagenesis. Thirty-four single amino acid replacements and 16 of their combinations were screened by in vitro biochemical assays. A combination of the Y37V and Q195C mutations changed the amino acid specificity in such a way that the variant TyrRS activates 3-iodo-L-tyrosine 10-fold more efficiently than L-tyrosine. This engineered enzyme, TyrRS(V37C195), was tested for use in the wheat germ cell-free translation system, which has recently been significantly improved, and is now as productive as conventional recombinant systems. During the translation in the wheat germ system, an E. coli suppressor tRNA(Tyr) was not aminoacylated by the wheat germ enzymes, but was aminoacylated by the E. coli TyrRS(V37C195) variant with 3-iodo-l-tyrosine. After the use of the 3-iodotyrosyl-tRNA in translation, the resultant uncharged tRNA could be aminoacylated again in the system. A mass spectrometric analysis of the produced protein revealed that more than 95% of the amino acids incorporated for an amber codon were iodotyrosine, whose concentration was only twice that of L-tyrosine in the translation. Therefore, the variant enzyme, 3-iodo-L-tyrosine, and the suppressor tRNA can serve as an additional set orthogonal to the 20 endogenous sets in eukaryotic in vitro translation systems.

    DOI PubMed

  • Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase

    D Kiga, K Sakamoto, S Sato, Hirao, I, S Yokoyama

    EUROPEAN JOURNAL OF BIOCHEMISTRY   268 ( 23 ) 6207 - 6213  2001年12月  [査読有り]

     概要を見る

    Cytidine in the anticodon second position (position 35) and G or U in position 36 of tRNA(Arg) are required for aminoacylation by arginyl-tRNA synthetase (ArgRS) from Escherichia coli. Nevertheless, an arginine-accepting amber suppressor tRNA with a CUA anticodon (FTOR1 Delta 26) exhibits suppression activity in vivo [McClain, W.H. & Foss, K. (1988) Science, 241, 1804-1807]. By an in vitro kinetic study with mutagenized tRNAs, we showed that the arginylation of FTOR1 Delta 26 involves C34 and U35, and that U35 can be replaced by G without affecting the activity. Thus, the positioning of the essential nucleotides for the arginylation is shifted to the 5' side, by one residue, in the suppressor tRNA(Arg). We found that the shifted positioning does not depend on the tRNA sequence outside the anticodon. Furthermore, by a genetic method, we isolated a mutant ArgRS that aminoacylates FTOR1 Delta 26 more efficiently than the wild-type ArgRS. The isolated mutant has mutations at two nonsurface amino-acid residues that interact with each other near the anticodon-binding site.

    DOI

  • Molecular computation by DNA hairpin formation

    K Sakamoto, H Gouzu, K Komiya, D Kiga, S Yokoyama, T Yokomori, M Hagiya

    SCIENCE   288 ( 5469 ) 1223 - 1226  2000年05月  [査読有り]

     概要を見る

    Hairpin formation by single-stranded DNA molecules was exploited in a DNA-based computation in order to explore the feasibility of autonomous molecular computing. An instance of the satisfiability problem, a famous hard combinatorial problem, was solved by using molecular biology techniques. The satisfiability of a given Boolean formula was examined autonomously, on the basis of hairpin formation by the molecules that represent the formula. This computation algorithm can test several clauses in the given formula simultaneously, which could reduce the number of Laboratory steps required for computation.

    DOI PubMed

  • State transitions by molecules

    K Sakamoto, D Kiga, K Komiya, H Gouzu, S Yokoyama, S Ikeda, H Sugiyama, M Hagiya

    BIOSYSTEMS   52 ( 1-3 ) 81 - 91  1999年10月  [査読有り]

     概要を見る

    In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3'-end sequence encodes the current state of the machine. Successive state transitions are performed in such a way that the current state is annealed onto an appropriate portion of DNA encoding the transition table of the state machine and the next state is copied to the 3'-end by extension with polymerase. In this paper, we first show that combined with parallel overlap assembly, a single series of successive transitions can solve NP-complete problems. This means that the number of necessary laboratory steps is independent from the problem size. We then report the results of two experiments concerning the implementation of our method. One is on isothermal reactions which greatly increase the efficiency of state transitions compared with reactions controlled by thermal cycles. The other is on the use of unnatural bases for avoiding out-of-frame annealing. The latter result can also be applied to many DNA-based computing paradigms. (C) 1999 Elsevier Science Ireland Ltd. All rights reserved.

    DOI

  • An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition

    D Kiga, Y Futamura, K Sakamoto, S Yokoyama

    NUCLEIC ACIDS RESEARCH   26 ( 7 ) 1755 - 1760  1998年04月  [査読有り]

     概要を見る

    RNAs that bind to xanthine (2,6-dioxypurine) were isolated from a population of 10(12) random sequences by in vitro selection. These xanthine-binding RNAs were found to have a 10 nt consensus sequence at an internal loop in the most probable secondary structure. By trimming one of the xanthine-binding RNAs, a representative xanthine-binding RNA (designated as XBA) of 32 nt residues was prepared. The dissociation constant of this RNA for xanthine was determined to be 3.3 mu M by equilibrium filtration experiments. The XBA RNA can bind to guanine as well, whereas it hardly accommodates adenine,cytosine or uracil. The ltd values for various xanthine/guanine analogues were determined, and revealed that the N1H, N7 and O6 moieties of the ligand are involved in the binding with the XBA RNA. The ribonuclease sensitivities of some internal-loop residues changed upon the addition of xanthine, suggesting that the internal loop of the XBA RNA is involved in the ligand binding. Interestingly, the consensus sequence of the xanthine/guanine-binding RNAs is the same as a sequence in one of the internal loops of the hairpin ribozyme, except for a substitution that is neutral with respect to xanthine/guanine binding.

    DOI PubMed

  • Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs

    Jacob Beal, Geoff S. Baldwin, Natalie G. Farny, Markus Gershater, Traci Haddock-Angelli, Russell Buckley-Taylor, Ari Dwijayanti, Daisuke Kiga, Meagan Lizarazo, John Marken, Kim de Mora, Randy Rettberg, Vishal Sanchania, Vinoo Selvarajah, Abigail Sison, Marko Storch, Christopher T. Workman

    PLOS ONE   16 ( 6 ) e0252263 - e0252263  2021年06月

     概要を見る

    Reproducibility is a key challenge of synthetic biology, but the foundation of reproducibility is only as solid as the reference materials it is built upon. Here we focus on the reproducibility of fluorescence measurements from bacteria transformed with engineered genetic constructs. This comparative analysis comprises three large interlaboratory studies using flow cytometry and plate readers, identical genetic constructs, and compatible unit calibration protocols. Across all three studies, we find similarly high precision in the calibrants used for plate readers. We also find that fluorescence measurements agree closely across the flow cytometry results and two years of plate reader results, with an average standard deviation of 1.52-fold, while the third year of plate reader results are consistently shifted by more than an order of magnitude, with an average shift of 28.9-fold. Analyzing possible sources of error indicates this shift is due to incorrect preparation of the fluorescein calibrant. These findings suggest that measuring fluorescence from engineered constructs is highly reproducible, but also that there is a critical need for access to quality controlled fluorescent calibrants for plate readers.

    DOI

  • Robust estimation of bacterial cell count from optical density

    Jacob Beal, Natalie G. Farny, Traci Haddock-Angelli, Vinoo Selvarajah, Geoff S. Baldwin, Russell Buckley-Taylor, Markus Gershater, Daisuke Kiga, John Marken, Vishal Sanchania, Abigail Sison, Christopher T. Workman

    Communications Biology   3 ( 1 )  2020年12月  [査読有り]

     概要を見る

    <title>Abstract</title>
    Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing <italic>E. coli</italic>. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals  &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.

    DOI

  • The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?

    Jacob Beal, Angel Goñi-Moreno, Chris Myers, Ariel Hecht, María del Carmen de Vicente, Maria Parco, Markus Schmidt, Kenneth Timmis, Geoff Baldwin, Steffi Friedrichs, Paul Freemont, Daisuke Kiga, Elena Ordozgoiti, Maja Rennig, Leonardo Rios, Kristie Tanner, Víctor de Lorenzo, Manuel Porcar

    EMBO Reports   21 ( 5 ) e50521  2020年05月  [査読有り]  [国際誌]

     概要を見る

    Synthetic biology needs to adopt sound scientific and industry-like standards in order to achieve its ambitious goals of efficient and accurate engineering of biological systems.

    DOI PubMed

  • Enhancement of binding affinity of folate to its receptor by peptide conjugation

    Roopa Dharmatti, Hideyuki Miyatake, Avanashiappan Nandakumar, Motoki Ueda, Kenya Kobayashi, Daisuke Kiga, Masayuki Yamamura, Yoshihiro Ito

    International Journal of Molecular Sciences   20 ( 9 )  2019年05月  [査読有り]  [国際誌]

     概要を見る

    © 2019 by the authors. Licensee MDPI, Basel, Switzerland. (1) Background: The folate receptor (FR) is a target for cancer treatment and detection. Expression of the FR is restricted in normal cells but overexpressed in many types of tumors. Folate was conjugated with peptides for enhancing binding affinity to the FR. (2) Materials and Methods: For conjugation, folate was coupled with propargyl or dibenzocyclooctyne, and 4-azidophenylalanine was introduced in peptides for “click” reactions. We measured binding kinetics including the rate constants of association (ka) and dissociation (kd) of folate-peptide conjugates with purified FR by biolayer interferometry. After optimization of the conditions for the click reaction, we successfully conjugated folate with designed peptides. (3) Results: The binding affinity, indicated by the equilibrium dissociation constant (KD), of folate toward the FR was enhanced by peptide conjugation. The enhanced FR binding affinity by peptide conjugation is a result of an increase in the number of interaction sites. (4) Conclusion: Such peptide-ligand conjugates will be important in the design of ligands with higher affinity. These high affinity ligands can be useful for targeted drug delivery system.

    DOI PubMed

  • Comparison between effects of retroactivity and resource competition upon change in downstream reporter genes of synthetic genetic circuits

    Takefumi Moriya, Tomohiro Yamaoka, Yuki Wakayama, Shotaro Ayukawa, Zicong Zhang, Masayuki Yamamura, Shinji Wakao, Daisuke Kiga

    Life   9 ( 1 )  2019年03月  [査読有り]  [国際誌]

     概要を見る

    © 2019 by the authors. Reporter genes have contributed to advancements in molecular biology. Binding of an upstream regulatory protein to a downstream reporter promoter allows quantification of the activity of the upstream protein produced from the corresponding gene. In studies of synthetic biology, analyses of reporter gene activities ensure control of the cell with synthetic genetic circuits, as achieved using a combination of in silico and in vivo experiments. However, unexpected effects of downstream reporter genes on upstream regulatory genes may interfere with in vivo observations. This phenomenon is termed as retroactivity. Using in silico and in vivo experiments, we found that a different copy number of regulatory protein-binding sites in a downstream gene altered the upstream dynamics, suggesting retroactivity of reporters in this synthetic genetic oscillator. Furthermore, by separating the two sources of retroactivity (titration of the component and competition for degradation), we showed that, in the dual-feedback oscillator, the level of the fluorescent protein reporter competing for degradation with the circuits’ components is important for the stability of the oscillations. Altogether, our results indicate that the selection of reporter promoters using a combination of in silico and in vivo experiments is essential for the advanced design of genetic circuits.

    DOI PubMed

  • RNA world

    Shotaro Ayukawa, Toshihiko Enomoto, Daisuke Kiga

    Astrobiology: From the Origins of Life to the Search for Extraterrestrial Intelligence     77 - 90  2019年01月  [査読有り]

     概要を見る

    © Springer Nature Singapore Pte Ltd. 2019. In the RNA world, which is a hypothetical idea to explain the origin of life, RNA molecules were considered to have roles in both information storage and as a catalyst. This chapter reviews RNA world studies from its birth to recent advancements. Natural ribozymes and coenzymes containing nucleotide moieties support the hypothesis. For maintenance and evolution of the RNA world, ribozymes that have self-replicating activity had to emerge. Although such a ribozyme has not been discovered in the natural world, in vitro evolution experiments have created ribozymes that have replicative ability, essentially. After the emergence of the replicative ribozyme, ribozymes might have gradually improved its activity by incorporating other biomolecules especially peptides, which could be synthesized spontaneously in the prebiotic world. The RNA-protein (RNP) world may have emerged through the interaction between the RNA world and peptide/protein world. Proteins with higher enzymatic activities could have appeared through Darwinian evolution in the RNP world, and the peptide/protein must have replaced the role of ribozymes as catalysts. Further interactions with other molecular worlds such as the lipid or metabolic worlds accelerated the evolution of the self-replicating system. Finally, DNA, which is chemically more stable than RNA, has taken over the role as the storage of genetic information.

    DOI

  • Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent

    Tom Froese, Jorge I. Campos, Kosuke Fujishima, Daisuke Kiga, Nathaniel Virgo

    Scientific Reports   8 ( 1 ) 3532 - 3532  2018年12月  [査読有り]  [国際誌]

     概要を見る

    © 2018 The Author(s). Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. Woese's solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells ("progenotes"), rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese's conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone.

    DOI PubMed

  • Escherichia coli expression, purification, and refolding of human folate receptor α (hFRα) and β (hFRβ).

    Dharmatti R, Miyatake H, Zhang C, Ren X, Yumoto A, Kiga D, Yamamura M, Ito Y

    Protein expression and purification   149   17 - 22  2018年09月  [査読有り]  [国際誌]

    DOI PubMed

  • Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model.

    Shun Asami, Daisuke Kiga, Akihiko Konagaya

    BMC systems biology   11 ( Suppl 7 ) 129 - 129  2017年12月  [査読有り]  [国際誌]

     概要を見る

    BACKGROUND: Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and correlations among drug characteristics and individual varieties, recently, whole-body physiologically based pharmacokinetic (WB- PBPK) models are getting more attention. WB-PBPK models generally have a lot of drug-related parameters that need to be estimated, and the estimations are difficult because the observed data are limited. Furthermore, parameter estimation in WB-PBPK models may cause overfitting when applying to individual clinical data such as urine/feces drug excretion for each patient in which Cluster Newton Method (CNM) is applicable for parameter estimation. In order to solve this issue, we came up with the idea of constraint-based perturbation analysis of the CNM. The effectiveness of our approach is demonstrated in the case of irinotecan WB-PBPK model using common organ-specific tissue-plasma partition coefficients (Kp) among the patients as constraints in WB-PBPK parameter estimation. RESULTS: We find strong correlations between age, renal clearance and liver functions in irinotecan WB-PBPK model with personalized physiological parameters by observing the distributions of optimized values of strong convergence drug-related parameters using constraint-based perturbation analysis on CNM. The constraint-based perturbation analysis consists of the following three steps: (1) Estimation of all drug-related parameters for each patient; the parameters include organ-specific Kp. (2) Fixing suitable values of Kp for each organ among all patients identically. (3) Re-estimation of all drug-related parameters other than Kp by using the fixed values of Kp as constraints of CNM. CONCLUSIONS: Constraint-based perturbation analysis could yield new findings when using CNM with appropriate constraints. This method is a new technique to find suitable values and important insights that are masked by CNM without constraints.

    DOI PubMed

  • High-frequency noise attenuation of a two-component system responding to short-pulse input

    Akifumi Nishida, Ryoji Sekine, Daisuke Kiga, Masayuki Yamamura

    ACM International Conference Proceeding Series     28 - 35  2016年12月  [査読有り]

     概要を見る

    Among the various biological devices developed and characterized in synthetic biology, light-sensing biological devices can serve as an input-output system owing to their light modulation property. The well-characterized devices in living systems are useful for modulating cellular sensing and transducing information. In this study, we examined short pulse responsiveness of a light-sensing two-component system (TCS), Cph8-OmpR, which was generated by replacing the sensor domain of the EnvZ-OmpR osmoregulatory system with the light sensor Cph1. We varied the input pulse width of the Cph8-OmpR system and found that an input width of &lt
    1 s was sufficient to alter the accumulation of a reporter gene upregulated by Cph8 phosphorylation of OmpR. Based on this result and the mathematical model showing that the timescale for the upstream Cph8-activity transition was much faster than that of downstream gene expression, we evaluated the merit of a TCS with such an unbalanced cascade. Our mathematical simulation of a cascade TCS suggests that high-frequency noise arising from fast transitions in kinase activity was attenuated throughout the cascade reaction. In terms of noise attenuation, these results can contribute to analyze biological cascade systems with the balance of reaction rates in each process.

    DOI

  • Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli (vol 11, e0150182, 2016)

    Jacob Beal, Traci Haddock-Angelli, Markus Gershater, Kim de Mora, Meagan Lizarazo, Jim Hollenhorst, Randy Rettberg

    PLOS ONE   11 ( 6 )  2016年06月  [査読有り]

    DOI

  • A Bacterial Continuous Culture System Based on a Microfluidic Droplet Open Reactor

    Manami Ito, Haruka Sugiura, Shotaro Ayukawa, Daisuke Kiga, Masahiro Takinoue

    ANALYTICAL SCIENCES   32 ( 1 ) 61 - 66  2016年01月  [査読有り]

     概要を見る

    Recently, micrometer-sized bacterial culture systems have attracted attention as useful tools for synthetic biology studies. Here, we present the development of a bacterial continuous culture system based on a microdroplet open reactor consisting of two types of water-in-oil microdroplets with diameters of several hundred micrometers. A continuous culture was realized the through supply of nutrient substrates and the removal of waste and excess bacterial cells based on repeated fusion and fission of droplets. The growth dynamics was controlled by the interval of fusion. We constructed a microfluidic system and quantitatively assessed the dynamics of the bacterial growth using a mathematical model. This system will facilitate the study of synthetic biology and metabolic engineering in the future.

  • RNAワールドの成立・維持と発展的解消 (特集 アストロバイオロジーとの遭遇 : 生命のルーツを探る旅)

    木賀 大介

    細胞工学   35 ( 2 ) 111 - 115  2016年

    CiNii

  • A Bacterial Continuous Culture System Based on a Microfluidic Droplet Open Reactor.

    Manami Ito, Haruka Sugiura, Shotaro Ayukawa, Daisuke Kiga, Masahiro Takinoue

    Analytical sciences : the international journal of the Japan Society for Analytical Chemistry   32 ( 1 ) 61 - 6  2016年  [査読有り]  [国内誌]

     概要を見る

    Recently, micrometer-sized bacterial culture systems have attracted attention as useful tools for synthetic biology studies. Here, we present the development of a bacterial continuous culture system based on a microdroplet open reactor consisting of two types of water-in-oil microdroplets with diameters of several hundred micrometers. A continuous culture was realized the through supply of nutrient substrates and the removal of waste and excess bacterial cells based on repeated fusion and fission of droplets. The growth dynamics was controlled by the interval of fusion. We constructed a microfluidic system and quantitatively assessed the dynamics of the bacterial growth using a mathematical model. This system will facilitate the study of synthetic biology and metabolic engineering in the future.

    DOI PubMed

  • 生命の文字に着目した進化分子工学 (特集 生命の起源と進化)

    網蔵 和晃, 木賀 大介

    理大科学フォーラム   32 ( 11 ) 14 - 17  2015年11月

    CiNii

  • 特集によせて(<特集>「細胞を創る」研究とその展開)

    木賀 大介

    生物工学会誌   93 ( 10 ) 603 - 606  2015年10月

  • Two site genetic incorporation of varying length polyethylene glycol into the backbone of one peptide.

    Qingmin Zang, Seiichi Tada, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, Yoshihiro Ito

    Chemical communications (Cambridge, England)   51 ( 76 ) 14385 - 8  2015年10月  [査読有り]  [国際誌]

     概要を見る

    Polyethylene glycol (PEG) of different lengths was genetically incorporated into the backbone of a polypeptide using stop-anticodon and frameshift anticodon-containing tRNAs, which were acylated with PEG-containing amino acids.

    DOI PubMed

  • In vitro selection of a photoresponsive peptide aptamer to glutathione-immobilized microbeads

    Seiichi Tada, Qingmin Zang, Wei Wang, Masuki Kawamoto, Mingzhe Liu, Michiru Iwashita, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, Yoshihiro Ito

    JOURNAL OF BIOSCIENCE AND BIOENGINEERING   119 ( 2 ) 137 - 139  2015年02月  [査読有り]

     概要を見る

    Photoresponsive peptide aptamer to glutathione-immobilized microbeads was in vitro selected using ribosome display incorporated with tRNA carrying an amino acid coupled with an azobenzene. (C) 2014, The Society for Biotechnology, Japan. All rights reserved.

    DOI

  • In vitro selection of a photoresponsive peptide aptamer to glutathione-immobilized microbeads.

    Seiichi Tada, Qingmin Zang, Wei Wang, Masuki Kawamoto, Mingzhe Liu, Michiru Iwashita, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, Yoshihiro Ito

    Journal of bioscience and bioengineering   119 ( 2 ) 137 - 9  2015年02月  [査読有り]  [国内誌]

     概要を見る

    Photoresponsive peptide aptamer to glutathione-immobilized microbeads was in vitro selected using ribosome display incorporated with tRNA carrying an amino acid coupled with an azobenzene.

    DOI PubMed

  • Two site genetic incorporation of varying length polyethylene glycol into the backbone of one peptide

    Qingmin Zang, Seiichi Tada, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, Yoshihiro Ito

    CHEMICAL COMMUNICATIONS   51 ( 76 ) 14385 - 14388  2015年  [査読有り]

     概要を見る

    Polyethylene glycol (PEG) of different lengths was genetically incorporated into the backbone of a polypeptide using stop-anticodon and frameshift anticodon-containing tRNAs, which were acylated with PEG-containing amino acids.

    DOI PubMed

  • Experimental Evolution of a Green Fluorescent Protein Composed of 19 Unique Amino Acids without Tryptophan

    Akio Kawahara-Kobayashi, Mitsuhiro Hitotsuyanagi, Kazuaki Amikura, Daisuke Kiga

    ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES   44 ( 2 ) 75 - 86  2014年04月  [査読有り]

     概要を見る

    At some stage of evolution, genes of organisms may have encoded proteins that were synthesized using fewer than 20 unique amino acids. Similar to evolution of the natural 19-amino-acid proteins GroEL/ES, proteins composed of 19 unique amino acids would have been able to evolve by accumulating beneficial mutations within the 19-amino-acid repertoire encoded in an ancestral genetic code. Because Trp is thought to be the last amino acid included in the canonical 20-amino-acid repertoire, this late stage of protein evolution could be mimicked by experimental evolution of 19-amino-acid proteins without tryptophan (Trp). To further understand the evolution of proteins, we tried to mimic the evolution of a 19-amino-acid protein involving the accumulation of beneficial mutations using directed evolution by random mutagenesis on the whole targeted gene sequence. We created active 19-amino-acid green fluorescent proteins (GFPs) without Trp from a poorly fluorescent 19-amino-acid mutant, S1-W57F, by using directed evolution with two rounds of mutagenesis and selection. The N105I and S205T mutations showed beneficial effects on the S1-W57F mutant. When these two mutations were combined on S1-W57F, we observed an additive effect on the fluorescence intensity. In contrast, these mutations showed no clear improvement individually or in combination on GFPS1, which is the parental GFP mutant composed of 20 amino acids. Our results provide an additional example for the experimental evolution of 19-amino-acid proteins without Trp, and would help understand the mechanisms underlying the evolution of 19-amino-acid proteins. (236 words).

    DOI

  • [Construction and control of synthetic genetic circuits].

    Ryoji Sekine, Daisuke Kiga

    Seikagaku. The Journal of Japanese Biochemical Society   86 ( 2 ) 201 - 8  2014年04月  [査読有り]  [国内誌]

    PubMed CiNii

  • Multiple amino acid-excluded genetic codes for protein engineering using multiple sets of tRNA variants.

    Kazuaki Amikura, Yoko Sakai, Shun Asami, Daisuke Kiga

    ACS synthetic biology   3 ( 3 ) 140 - 4  2014年03月  [査読有り]  [国際誌]

     概要を見る

    A "simplified genetic code", with only 19 amino acids assigned to the sense codons, was recently developed. In this study, we describe novel simplified codes in which multiple amino acids are simultaneously excluded from the universal code. In the simplest code, tryptophan, cysteine, tyrosine, and asparagine codons are assigned to serine by using four kinds of tRNA (Ser) variants. The results revealed that various sets of amino acids can easily be excluded from the universal code, using our strategy for genetic code simplification. A simplified genetic code is useful as an engineering tool for the improvement of industrial enzymes and pharmaceuticals, and also provides new insights into the assessment of protein evolution. Simplified codes in which multiple amino acids are simultaneously excluded from the code can be more effective tools than codes excluding only one amino acid.

    DOI PubMed

  • Construction and control of synthetic genetic circuits

    Sekine R, Kiga D

    Seikagaku   86 ( 2 ) 201 - 208  2014年  [査読有り]

  • An observation method for autonomous signaling-mediated synthetic diversification in Escherichia coli.

    Ryoji Sekine, Shotaro Ayukawa, Daisuke Kiga

    Methods in molecular biology (Clifton, N.J.)   1151   69 - 74  2014年  [査読有り]  [国際誌]

     概要を見る

    Phenotypic diversification of cells in development and regeneration is conceptually modeled by the motion of marbles rolling down valleys on the Waddington landscape, the main feature of which is bifurcations of the valleys. We have experimentally shown that this feature is sufficient to achieve phenotypic diversification by the construction of a synthetic phenotypic diversification system in Escherichia coli. Cells containing the synthetic phenotypic diversification system were diversified into two distinct cell states, high and low, through autonomous signaling-mediated bifurcation, when all cells were initialized to the low state. In this chapter, we illustrate the detailed experimental procedures involved in the initialization of cells and the observation of the phenotypic diversification.

    DOI PubMed

  • Why 20 amino acids?

    Amikura K, Kiga D

    Kobunshi   63 ( 6 ) 392 - 393  2014年  [査読有り]

  • Waddington地形に沿った細胞種多様化のモデル実験

    関根 亮二, 木賀 大介

    生物物理   53 ( 6 ) 319 - 320  2013年11月

    DOI CiNii

  • BIO R&D 小分子人力を検出する分子デバイスのアプタザイムを利用した開発

    鮎川 翔太郎, 木賀 大介

    Bio industry   30 ( 5 ) 39 - 46  2013年05月

    CiNii

  • Reassignment of codons from Arg to Ala by multiple tRNAAla variants.

    Amikura Kazuaki, Kiga Daisuke

    Viva Origino   3   20 - 23  2013年  [査読有り]

  • Cultivation of synthetic biology with the iGEM competition

    Thiprampai Thamamongood, Nathaniel Z. L. Lim, Trevor Y.H. Ho, Shotaro Ayukawa, Daisuke Kiga, King L. Chow

    Journal of Advanced Computational Intelligence and Intelligent Informatics   17 ( 2 ) 161 - 166  2013年  [査読有り]

     概要を見る

    The main goal of synthetic biology is to create new biological modules that augment or modify the behavior of living organisms in performing different tasks. These modules are useful in a wide range of applications, such as medicine, agriculture, energy and environmental remediation. The concept is simple, but a paradigm shift needs to be in place among future life scientists and engineers to embrace this new direction. The international Genetically Engineered Machine (iGEM) competition fits this purpose well as a synthetic biology competition mainly for undergraduate students. Participants design and construct biological devices using standardized and customized biological parts that are then characterized and submitted to an existing and ever expanding library. Overall, iGEM is an eye-opening learning experience for undergraduate students. It has made a strong educational impact on participating students and cultivated a future cohort of synthetic biology practitioners and ambassadors.

    DOI

  • Synthetic biology and dual use

    Daisuke Kiga

    Journal of Disaster Research   8 ( 4 ) 698 - 704  2013年  [査読有り]

     概要を見る

    Synthetic biology is science or technology concerning layers of life such as individuals, organs, cells. In this field, components of a layer are combined to construct a system in the upper layer. This paper focuses on studies, at a layer related to gene recombinant experiments, modifying genes and combining multiple genes. By introducing research accomplishments in synthetic biology such as gene networks and synthesis of the whole genome, this paper explains how synthetic biology is an extension of conventional gene engineering and the field of interdisciplinary open innovation. The risks of synthetic biology and risk reduction methods are also introduced.

    DOI

  • Tunability of the ratio of cell states after the synthetic diversification by the diversity generator.

    Ryoji Sekine, Masayuki Yamamura, Masami Hagiya, Daisuke Kiga

    Communicative & integrative biology   5 ( 4 ) 393 - 4  2012年07月  [査読有り]  [国際誌]

     概要を見る

    The autonomous generation of phenotypic diversity in embryonic cell populations can be explained by Waddington's landscape. The landscape proposes that intra- and inter-cellular interactions mediate the generation of cellular diversity. Recently, we implemented, in a population of Escherichia coli, a synthetic diversification, which is governed by inter-cellular signaling mediated by acyl-homoserine lactone (AHL). The cells with the diversity generator diversified into two distinct cell states, "high" and "low," if all of the cells started from the low state. The ratio of the states after the diversification was affected by the velocity of autonomous signal accumulation, which depends on the cell density and the AHL production rate of individual cells. The dependency of the ratio on the initial cell density is reminiscent of the community effect, which is observed in animal development and is important for ES-cell differentiation. Therefore, it is worthwhile reviewing the roles of natural animal gene networks with similar topologies to the diversity generator design. The diversity generator design will also be the basis for a tool to direct cell fates on the population level in tissue engineering. Here, we discuss the tunability of the ratio of cell states by our synthetic circuit design.

    DOI PubMed

  • 生命をつくる

    ジョーンズ リチャード, 木賀 大介

    パリティ   27 ( 2 ) 22 - 26  2012年02月

    CiNii

  • 細胞の初期状態に依存しない多様化を実現する人工遺伝子回路の設計戦略

    関根 亮二, 木賀 大介, 山村 雅幸

    Chem-Bio Informatics Journal   12 ( 0 ) 39 - 49  2012年

     概要を見る

    細胞の初期状態に依存しない細胞種多様化を実現する人工遺伝子回路は,複数の細胞種への分化誘導のツールとしての利用が期待できる.本研究では,多様化後の二つの細胞種比率が初期状態に依存しない細胞種多様化を実現するための人工遺伝子回路,Symmetric Diversity Generator (SDG)を設計した.SDGは,二つのリプレッサーによる相互抑制と,二つの拡散性アクチベーターによるリプレッサー生産・拡散性アクチベーター生産のアンバランス補正との二つの機構からなる.多様化後の細胞種比率の初期状態依存性の計算機解析から,SDG設計には改善の余地があることが分かったため,二つのアプローチで設計の改善を行った.一つ目は,拡散性アクチベーターの分解速度を上げるアプローチ,二つ目は,拡散性アクチベーターやリプレッサーに対するリプレッサー生産の感度を下げるアプローチである.SDGと同様の計算機解析から,二つ目のアプローチによって細胞種比率の初期状態依存性が

    DOI CiNii

  • RTRACS: a modularized RNA-dependent RNA transcription system with high programmability.

    Shotaro Ayukawa, Masahiro Takinoue, Daisuke Kiga

    Accounts of chemical research   44 ( 12 ) 1369 - 79  2011年12月  [査読有り]  [国際誌]

     概要を見る

    Creating artificial biological systems is an important research endeavor. Each success contributes to synthetic biology and adds to our understanding of the functioning of the biomachinery of life. In the construction of large, complex systems, a modular approach simplifies the design process: a multilayered system can be prepared by integrating simple modules. With the concept of modularity, a variety of synthetic biological systems have been constructed, both in vivo and in vitro. But to properly develop systems with desired functions that integrate multiple modules, researchers need accurate mathematical models. In this Account, we review the development of a modularized artificial biological system known as RTRACS (reverse transcription and transcription-based autonomous computing system). In addition to modularity, model-guided predictability is an important feature of RTRACS. RTRACS has been developed as an in vitro artificial biological system through the assembly of RNA, DNA, and enzymes. A fundamental module of RTRACS receives an input RNA with a specific sequence and returns an output RNA with another specific sequence programmed in the main body, which is composed of DNA and enzymes. The conversion of the input RNA to the output RNA is achieved through a series of programmed reactions performed by the components assembled in the module. Through the substitution of a subset of components, a module that performs the AND operation was constructed. Other logical operations could be constructed with RTRACS modules. An integration of RTRACS modules has allowed the theoretical design of more complex functions, such as oscillation. The operations of these RTRACS modules were readily predicted with a numerical simulation based on a mathematical model using realistic parameters. RTRACS has the potential to model highly complex systems that function like a living cell. RTRACS was designed to be integrated with other molecules or molecular devices, for example, aptazymes, cell-free expression systems, and liposomes. For the integration of these new modules, the quantitative controls of each module based on the numerical simulation will be instructive. The capabilities of RTRACS promise to provide models of complex biomolecular systems that are able to detect the environment, assess the situation, and react to overcome the situation. Such a smart biomolecular system could be useful in many applications, such as drug delivery systems.

    DOI PubMed

  • Tunable synthetic phenotypic diversification on Waddington&apos;s landscape through autonomous signaling

    Ryoji Sekine, Masayuki Yamamura, Shotaro Ayukawa, Kana Ishimatsu, Satoru Akama, Masahiro Takinoue, Masami Hagiya, Daisuke Kiga

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   108 ( 44 ) 17969 - 17973  2011年11月  [査読有り]

     概要を見る

    Phenotypic diversification of cells is crucial for developmental and regenerative processes in multicellular organisms. The diversification concept is described as the motion of marbles rolling down Waddington&apos;s landscape, in which the number of stable states changes as development proceeds. In contrast to this simple concept, the complexity of natural biomolecular processes prevents comprehension of their design principles. We have constructed, in Escherichia coli, a synthetic circuit with just four genes, which programs cells to autonomously diversify as the motion on the landscape through cell-cell communication. The circuit design was based on the combination of a bistable toggle switch with an intercellular signaling system. The cells with the circuit diversified into two distinct cell states, "high" and "low," in vivo and in silico, when all of the cells started from the low state. The synthetic diversification was affected by not only the shape of the landscape determined by the circuit design, which includes the synthesis rate of the signaling molecule, but also the number of cells in the experiments. This cell-number dependency is reminiscent of the " community effect": The fates of developing cells are determined by their number. Our synthetic circuit could be a model system for studying diversification and differentiation in higher organisms. Prospectively, further integrations of our circuit with different cellular functions will provide unique tools for directing cell fates on the population level in tissue engineering.

    DOI

  • iGEMを通した合成生物学研究者の育成(第63回大会シンポジウム・ワークショップ報告)

    早出 広司, 上田 卓也, 木賀 大介

    生物工学会誌 : seibutsu-kogaku kaishi   89 ( 11 ) 677 - 677  2011年11月

    CiNii

  • 2SL-04 Waddington地形上において自律的な細胞間シグナリングによって表現系を多様化する調節可能なシステムの細胞内における構築(2SL 生命システムの情報処理,日本生物物理学会第49回年会(2011年度))

    Sekine Ryoji, Yamamura Masayuki, Ayukawa Shotaro, Ishimatsu Kana, Akama Satoru, Takinoue Masahiro, Hagiya Masami, 木賀 大介

    生物物理   51   S25  2011年

    DOI CiNii

  • Construction of a genetic AND gate under a new standard for assembly of genetic parts.

    Shotaro Ayukawa, Akio Kobayashi, Yusaku Nakashima, Hidemasa Takagi, Shogo Hamada, Masahiko Uchiyama, Katsuyuki Yugi, Satoshi Murata, Yasubumi Sakakibara, Masami Hagiya, Masayuki Yamamura, Daisuke Kiga

    BMC genomics   11 Suppl 4 ( SUPPL. 4 ) S16  2010年12月  [査読有り]  [国際誌]

     概要を見る

    BACKGROUND: Appropriate regulation of respective gene expressions is a bottleneck for the realization of artificial biological systems inside living cells. The modification of several promoter sequences is required to achieve appropriate regulation of the systems. However, a time-consuming process is required for the insertion of an operator, a binding site of a protein for gene expression, to the gene regulatory region of a plasmid. Thus, a standardized method for integrating operator sequences to the regulatory region of a plasmid is required. RESULTS: We developed a standardized method for integrating operator sequences to the regulatory region of a plasmid and constructed a synthetic promoter that functions as a genetic AND gate. By standardizing the regulatory region of a plasmid and the operator parts, we established a platform for modular assembly of the operator parts. Moreover, by assembling two different operator parts on the regulatory region, we constructed a regulatory device with an AND gate function. CONCLUSIONS: We implemented a new standard to assemble operator parts for construction of functional genetic logic gates. The logic gates at the molecular scale have important implications for reprogramming cellular behavior.

    DOI PubMed

  • DNAナノストラクチャー--ナノ構造の構築から機能構築の段階へ (2009年の成果の総まとめ 特集:物理科学,この1年) -- (生物物理)

    木賀 大介

    パリティ   25 ( 1 ) 71 - 73  2010年01月

    CiNii

  • ウェット実験に基づく人工遺伝子回路の設計と制御(システムバイオロジー,システムバイオロジー,一般)

    関根 亮二, 中谷 元, 木賀 大介, 山村 雅幸

    電子情報通信学会技術研究報告. CST, コンカレント工学   109 ( 165 ) 19 - 24  2009年07月

     概要を見る

    合成生物学とは,遺伝子を電子回路の部品のように組み合わせて,所望の機能を持つ遺伝子ネットワーク(人工遺伝子回路)の設計・実装をする分野である.人工遺伝子回路の設計・実装は以下の3ステップで行われる.(1)人工遺伝子回路を設計し,その挙動をシミュレーションしながら各部品の最適なパラメータ値を事前に予測する.(2)人工遺伝子回路を実装した細胞を用いたウェット実験を行うことで,各部品の実際のパラメータ値を知る.(3)実際のパラメータ値と最適なパラメータ値を比較して,適切な部品に取り換えて,所望の機能を持つ人工遺伝子回路を構築する.このシステマティックな方法によって,従来は試行錯誤を要していた複雑な人工生命システムの開発が素早くできる.ところで,生命システムには&quot;ゆらぎ&quot;が付き物であり,人工生命システムにおいても同様である.ゆらぎがシステムの挙動に少なからず影響を与えるので,設計を困難にしている.本論文では,ゆらぎを考慮して生命システムの解

  • RNA Oscillator: Limit Cycle Oscillations based on Artificial Biomolecular Reactions

    Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, Akira Suyama

    NEW GENERATION COMPUTING   27 ( 2 ) 107 - 127  2009年02月  [査読有り]

     概要を見る

    In recent years, various DNA nanomachines driven by DNA hybridizations have been developed as a remarkable application of DNA computers for nanotechnology. Here, we propose an oscillatory reaction system as a nano-sized nucleic acid engine to control the nanomachines. It utilizes DNA/RNA and their molecular reactions, and is modeled after the circadian rhythm in life systems. The molecular reactions consist of nucleic acid hybridization, RNA transcription, DNA extension, RNA degradation, and uracil-containing DNA degradation. Numerical analyses of rate equations for the reactions demonstrate that oscillatory conditions of the reaction system are determined by the balance between RNA influx into the system and RNA degradation out of the system. The analytical results will provide important information when the oscillator is constructed in in vitro experiments.

    DOI

  • Design and Numerical Analysis of RNA Oscillator

    Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, Akira Suyama

    NATURAL COMPUTING, PROCEEDINGS   1   201 - +  2009年  [査読有り]

     概要を見る

    In recent years, various types of DNA nanomachines driven by DNA hybridizations have been developed as one of remarkable applications of DNA computer for nanotechnology. Here, we propose all oscillator as a nanosystem to control the nanomachines. It was modeled after a circadian rhythm in life systems and utilized DNA/RNA and their molecular reactions. The molecular reactions were composed of nucleic-acid hybridization, RNA transcription, DNA extension, RNA degradation, and uracil-containing DNA degradation. Results of numerical analyses of rate equations for the reactions demonstrated that oscillatory condition of the system was decided by balance between RNA influx into the system and RNA degradation out of the system. The analytical results will provide much important information when the oscillator is constructed in in vitro experiments.

  • Experiments and simulation models of a basic computation element of an autonomous molecular computing system.

    Masahiro Takinoue, Daisuke Kiga, Koh-Ichiroh Shohda, Akira Suyama

    Physical review. E, Statistical, nonlinear, and soft matter physics   78 ( 4 Pt 1 ) 041921 - 041921  2008年10月  [査読有り]  [国際誌]

     概要を見る

    Autonomous DNA computers have been attracting much attention because of their ability to integrate into living cells. Autonomous DNA computers can process information through DNA molecules and their molecular reactions. We have already proposed an idea of an autonomous molecular computer with high computational ability, which is now named Reverse-transcription-and-TRanscription-based Autonomous Computing System (RTRACS). In this study, we first report an experimental demonstration of a basic computation element of RTRACS and a mathematical modeling method for RTRACS. We focus on an AND gate, which produces an output RNA molecule only when two input RNA molecules exist, because it is one of the most basic computation elements in RTRACS. Experimental results demonstrated that the basic computation element worked as designed. In addition, its behaviors were analyzed using a mathematical model describing the molecular reactions of the RTRACS computation elements. A comparison between experiments and simulations confirmed the validity of the mathematical modeling method. This study will accelerate construction of various kinds of computation elements and computational circuits of RTRACS, and thus advance the research on autonomous DNA computers.

    DOI PubMed

  • A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme

    Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga, Masayuki Yamamura

    Natural Computing   7 ( 3 ) 303 - 315  2008年09月  [査読有り]

     概要を見る

    In this paper, we propose an autonomous molecular walking machine using DNA. This molecular machine follows a track of DNA equipped with many single-strand DNA stators arranged in a certain pattern. The molecular machine achieves autonomous walk by using a restriction enzyme as source of power. With a proposed machine we can control its moving direction and we can easily extend walking patterns in two or three dimensions. Combination of multiple legs and ssDNA stators can control the walking pattern. We designed and performed a series of feasibility study with computer simulation and molecular biology experiments. © Springer Science+Business Media B.V. 2008.

    DOI

  • Synthetic biology

    Daisuke Kiga, Masayuki Yamamura

    New Generation Computing   26 ( 4 ) 347 - 364  2008年08月  [査読有り]

     概要を見る

    Recent progress in various related fields has engendered a new style of biology, named Synthetic Biology, which utilizes concepts from modern engineering to emulate specific cellular functions and their functional combinations. This paper presents an introduction to Synthetic Biology from various viewpoints. First, we survey the concepts and tools from Systems Science along with several issues on social impact. Then, we discuss the recent progress in Molecular Biology that supports Synthetic Biology. © 2008 Ohmsha, Ltd.

    DOI

  • 細胞ウェアの物質的・生物学的側面 (第21回 回路とシステム軽井沢ワークショップ論文集) -- ("システムバイオロジー"から合成生物学へ)

    木賀 大介

    回路とシステム軽井沢ワークショップ論文集   21   295 - 297  2008年04月

    CiNii

  • Realization of DNA molecular machine that walks autonomously by using a restriction enzyme

    Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga, Masayuki Yamamura

    DNA COMPUTING   4848   54 - +  2008年  [査読有り]

     概要を見る

    In this paper, we propose an autonomous molecular walking machine using DNA. This molecular machine follows a track of DNA equipped with many single-strand DNA stators arranged in a certain pattern. The molecular machine achieves autonomous walk by using a restriction enzyme as source of power. With a proposed machine we can control its moving direction and we can easily extend walking patterns in two or three dimensions. Combination of multiple legs and ssDNA stators can control the walking pattern. We designed and per-formed a series of feasibility study with molecular biology experiments.

    DOI

  • 合成生物学 (Synthetic Biology) とは何か

    木賀 大介

    バイオサイエンスとインダストリー = Bioscience & industry   65 ( 2 ) 92 - 96  2007年02月

    CiNii

  • Oscillator for self-assembled DNA nanomachines

    Takinoue M, Kiga D, Shohda K.-I, Suyama A

    4th Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices, FNANO 2007     104 - 106  2007年  [査読有り]

  • SYANAC: SYnthetic biological Automaton for Noughts and Crosses

    S. Ayukawa, A. Kobayashi, Y. Nakashima, H. Takagi, S. Hamada, M. Uchiyama, K. Yugi, S. Murata, Y. Sakakibara, M. Hagiya, M. Yamamura, D. Kiga

    IET Synthetic Biology   1 ( 1-2 ) 64 - 67  2007年  [査読有り]

     概要を見る

    The project of Tokyo Alliance was to construct a bacterial system which plays 'noughts and crosses' against a human player. We named it SYANAC, SYnthetic biological Automaton for Noughts And Crosses. An unbeaten strategy of the game could be written in a simple state transition diagram with at most three turns. Based on the diagram, we tried to construct a set of in vivo logic gates which determines a move of SYANAC against that of the human player. For the logic gates, inputs are chemicals that regulate protein bindings to corresponding DNA sequences in reporter genes. In order to implement the logic gates efficiently, we standardised the protein-binding sequences and designed a systematic construction method. With the method, it is practical to combine some of these standardised sequences together to construct transcriptional regulatory regions. Since these protein-binding sites are short, we can use chemically synthesised DNA as a part. A regulatable gene was constructed by insertion of a -35/-10 promoter part and LacI-binding-site parts into a promoterless reporter plasmid which can also accommodate canonical Biobricks. This new method, thus, will allow us to construct a set of logic gates by combining standardised protein-binding parts and Biobricks and to realise the game. © 2007 The Institution of Engineering and Technology.

    DOI

  • Cation-pi interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase.

    Noriko Morikubo, Yoriyuki Fukuda, Kazumasa Ohtake, Naoko Shinya, Daisuke Kiga, Kensaku Sakamoto, Miwako Asanuma, Hiroshi Hirota, Shigeyuki Yokoyama, Tsutomu Hoshino

    Journal of the American Chemical Society   128 ( 40 ) 13184 - 94  2006年10月  [査読有り]  [国際誌]

     概要を見る

    It has been assumed that the pi-electrons of aromatic residues in the catalytic sites of triterpene cyclases stabilize the cationic intermediates formed during the polycyclization cascade of squalene or oxidosqualene, but no definitive experimental evidence has been given. To validate this cation-pi interaction, natural and unnatural aromatic amino acids were site-specifically incorporated into squalene-hopene cyclase (SHC) from Alicyclobacillus acidocaldarius and the kinetic data of the mutants were compared with that of the wild-type SHC. The catalytic sites of Phe365 and Phe605 were substituted with O-methyltyrosine, tyrosine, and tryptophan, which have higher cation-pi binding energies than phenylalanine. These replacements actually increased the SHC activity at low temperature, but decreased the activity at high temperature, as compared with the wild-type SHC. This decreased activity is due to the disorganization of the protein architecture caused by the introduction of the amino acids more bulky than phenylalanine. Then, mono-, di-, and trifluorophenylalanines were incorporated at positions 365 and 605; these amino acids reduce cation-pi binding energies but have van der Waals radii similar to that of phenylalanine. The activities of the SHC variants with fluorophenylalanines were found to be inversely proportional to the number of the fluorine atoms on the aromatic ring and clearly correlated with the cation-pi binding energies of the ring moiety. No serious structural alteration was observed for these variants even at high temperature. These results unambiguously show that the pi-electron density of residues 365 and 605 has a crucial role for the efficient polycyclization reaction by SHC. This is the first report to demonstrate experimentally the involvement of cation-pi interaction in triterpene biosynthesis.

    DOI PubMed

  • 生物科学への構成的アプローチの一つとしての人工遺伝子回路(<特集>システムと生命総合特集号)

    木賀 大介

    システム/制御/情報 : システム制御情報学会誌   50 ( 8 ) 315 - 320  2006年08月

     概要を見る

    近年、細胞内に人工的な遺伝子回路を構築することを手段とするsyntheticbiologyが興隆している。その成果として、細胞内の遺伝子回路の振る舞いについて興味深い知見も得られつつあるが、細胞というブラックボックスに対して解析を行うことの問題点は避けることができなかった。これに対し本発表では、各種生体分子を調製して混合することで人工的な遺伝子回路を試験管内に構築する我々の戦略について報告する。とくに本研究が、情報科学と生命科壜学の共同研究として始まったDNAコンピュータ開発の流れを受け、どのように進展してきたかついて紹介する。Recently, artificial genetic circuits are constructed in cells not only to produce useful compounds but also to analyze fundamental property of cellular system. However, we have not identified functions of many proteins even in E. coli though its genome sequence is known. Thus in vitro construction of artificial genetic circuits composed by known DNAs, RNAs and proteins is an effective approach to describe system behavior of li

  • 合成生物学--その概念と未来 (特集 生命をデザインする合成生物学)

    木賀 大介, 菅 裕明

    バイオニクス   3 ( 3 ) 28 - 33  2006年03月

    CiNii

  • Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli.

    Namthip Chumpolkulwong, Kensaku Sakamoto, Akiko Hayashi, Fumie Iraha, Naoko Shinya, Natsuko Matsuda, Daisuke Kiga, Akiko Urushibata, Mikako Shirouzu, Kenji Oki, Takanori Kigawa, Shigeyuki Yokoyama

    Journal of structural and functional genomics   7 ( 1 ) 31 - 6  2006年03月  [査読有り]  [国際誌]

     概要を見る

    We analyzed the effect of nine 'rare' codons (AGA, AGG, AUA, CCC, CGA, CGG, CUA, GGA, and UUA) on gene expression in an Escherichia coli coupled transcription/translation cell-free system, in comparison with a cell-based expression system. Each reporter gene contained five consecutive repeats of a rare codon, or in some experiments, three consecutive repeats. The cell-free expression of the genes bearing the codons CGA, CUA, GGA, and UUA was not affected, although these codons, except for GGA, were inefficiently translated in E. coli cells. Translation of the remaining five codons (AGA, AGG, AUA, CCC, and CGG) was severely reduced in both systems, and was remarkably facilitated in the cell-free system based on an S30 extract from the E. coli cells overproducing 'minor' tRNAs for these codons.

    DOI PubMed

  • DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing.

    Ken Komiya, Kensaku Sakamoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Daisuke Kiga, Shigeyuki Yokoyama, Masami Hagiya

    Bio Systems   83 ( 1 ) 18 - 25  2006年01月  [査読有り]  [国際誌]

     概要を見る

    Parallelism is one of the major advantages of molecular computation. A large number of data encoded in DNA molecules can be processed simultaneously by molecular biology techniques, although only a single set of instructions has been implemented in a solution. We have developed a computing machine, called the "whiplash" machine, which is made of DNA polymerase and a hairpin DNA. This machine simulates a finite state machine, executing its own instructions encoded in the DNA moiety, and would thus be applicable to multiple-instruction operation in a solution. In the present study, we explored the feasibility of this novel type of parallelism by applying the whiplash machine in a computation of the directed Hamiltonian path problem. The possible paths in a given graph were represented with different instruction sets, which were then implemented separately by whiplash machines in a test tube. After an autonomous operation of the machines, only the machine that implemented the instruction set corresponding to the Hamiltonian path was recovered from the tube. On the basis of the efficiency of machine operation, which was experimentally determined, 10(10) different instruction sets could be implemented simultaneously in a 1-ml solution.

    DOI PubMed

  • 構成的生物学 : つくることで理解する生物学

    木賀 大介, 山村 雅幸

    人工知能学会誌   20 ( 6 ) 715 - 721  2005年11月

  • 3P351 自律的核酸分子計算素子の理論的解析と応用(その他))

    瀧ノ上 正浩, 木賀 大介, 陶山 明

    生物物理   45   S291  2005年

    DOI CiNii

  • 2P301 自律的に動作する分子コンピューターによる核酸配列の変換(バイオエンジニアリング)

    木賀 大介, 持田 哲宏, 瀧ノ上 正浩, 陶山 明

    生物物理   44   S185  2004年

    DOI CiNii

  • Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells.

    Kensaku Sakamoto, Akiko Hayashi, Ayako Sakamoto, Daisuke Kiga, Hiroshi Nakayama, Akiko Soma, Takatsugu Kobayashi, Makoto Kitabatake, Koji Takio, Kazuki Saito, Mikako Shirouzu, Ichiro Hirao, Shigeyuki Yokoyama

    Nucleic acids research   30 ( 21 ) 4692 - 9  2002年11月  [査読有り]  [国際誌]

     概要を見る

    A suppressor tRNA(Tyr) and mutant tyrosyl-tRNA synthetase (TyrRS) pair was developed to incorporate 3-iodo-L-tyrosine into proteins in mammalian cells. First, the Escherichia coli suppressor tRNA(Tyr) gene was mutated, at three positions in the D arm, to generate the internal promoter for expression. However, this tRNA, together with the cognate TyrRS, failed to exhibit suppressor activity in mammalian cells. Then, we found that amber suppression can occur with the heterologous pair of E.coli TyrRS and Bacillus stearothermophilus suppressor tRNA(Tyr), which naturally contains the promoter sequence. Furthermore, the efficiency of this suppression was significantly improved when the suppressor tRNA was expressed from a gene cluster, in which the tRNA gene was tandemly repeated nine times in the same direction. For incorporation of 3-iodo-L-tyrosine, its specific E.coli TyrRS variant, TyrRS(V37C195), which we recently created, was expressed in mammalian cells, together with the B.stearothermophilus suppressor tRNA(Tyr), while 3-iodo-L-tyrosine was supplied in the growth medium. 3-Iodo-L-tyrosine was thus incorporated into the proteins at amber positions, with an occupancy of >95%. Finally, we demonstrated conditional 3-iodo-L-tyrosine incorporation, regulated by inducible expression of the TyrRS(V37C195) gene from a tetracycline-regulated promoter.

    DOI PubMed

▼全件表示

書籍等出版物

  • 合成生物学は社会に何をもたらすか つくることで生命を知る——合成生物学とその産業応用

    木賀大介( 担当: 分担執筆)

    2022年05月 ISBN: 9784881253700

  • 自然計算へのいざない

    小林, 聡, 萩谷, 昌己, 横森, 貴, 山村, 雅幸, 木賀, 大介, 礒川, 悌次郎, Peper, Ferdinand, 西田, 泰伸, 角谷, 良彦, 本多, 健太郎, 青野, 真士

    近代科学社  2015年11月 ISBN: 9784764904880

Misc

▼全件表示

産業財産権

▼全件表示

受賞

  • 学術振興会賞

    2016年02月   学術振興会   合成生物学による人工生命システムの構築  

    受賞者: 木賀大介

  • 竹田国際貢献賞

    2015年08月   武田理化工業(株)   合成生物学と社会の関わりの調整についての国際貢献  

    受賞者: 木賀大介

     概要を見る

    日本学術会議からの付託を受けて、国際学術団体がNature誌で広報することになる合成生物学に関するコメントの策定

  • 工学教育賞

    2014年03月   日本工学教育協会   国際学生コンテストを通じた多分野共同型の次世代生物工学教育  

    受賞者: 山村雅幸, 木賀大介, 瀧ノ上正浩, 小宮健

  • ナイスステップな研究者(人材育成部門)

    2012年12月   文部科学省 科学技術・学術政策研究所   iGEM(国際遺伝子工学マシン競技会)を通して次代を担う研究者の育成を牽引  

    受賞者: 木賀大介

共同研究・競争的資金等の研究課題

  • ありえた生体高分子ネットワークを創出する BioDOS の構築

    JST  CREST

    研究期間:

    2021年05月
    -
    2027年03月
     

  • リソース競合とボトルネック効果を加味した多数分子多段システムデザイン戦略の確立

    日本学術振興会  科学研究費助成事業 学術変革領域研究(A)

    研究期間:

    2021年09月
    -
    2023年03月
     

    木賀 大介

  • アミノ酸種が限定されていた生命の共通祖先以前のタンパク質の配列推定法の開発と評価

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)

    研究期間:

    2021年07月
    -
    2023年03月
     

    木賀 大介

  • 生命に現在の20種類の標準アミノ酸は必要か:遺伝暗号改変による理工学アプローチ

    日本学術振興会  科学研究費助成事業 基盤研究(A)

    研究期間:

    2019年04月
    -
    2022年03月
     

    木賀 大介, 村田 昇

  • 遺伝暗号における正確さの向上と低下がもたらす進化上のトレードオフの理解と活用

    科研費・挑戦的研究(萌芽)

    研究期間:

    2018年
    -
    2019年
     

    木賀大介

  • 細胞集団内で遺伝子発現が空間分布により多様化されるための諸要素の相関の解明

    科研費・基盤研究(B)

    研究期間:

    2016年
    -
    2018年
     

    木賀大介

  • 動物細胞における複数人工遺伝子回路の組み合わせのシステム理論の確立と実践

    科研費・基盤研究(C)

    研究期間:

    2015年
    -
    2018年
     

    鮎川翔太郎

  • グローバルな感染症等生物学的脅威を巡る新たな紛争ランドスケープの研究

    科研費・基盤研究(B)

    研究期間:

    2015年
    -
    2018年
     

    齋藤智也

  • 平成24年度「革新的バイオマテリアル実現のための高機能化ゲノムデザイン技術開発」

    革新的バイオマテリアル実現のための高機能化ゲノムデザイン技術開発

    研究期間:

    2012年
    -
    2016年
     

    近藤昭彦

  • 2種細胞間に分担されたポジティブフィードバックによる細胞集団挙動のプログラミング

    科研費・挑戦的萌芽研究

    研究期間:

    2014年
    -
    2015年
     

    木賀大介

  • 人工遺伝子回路の機能向上のための進化分子工学による生体分子の改良

    科研費・新学術領域研究(研究領域提案型)

    研究期間:

    2011年
    -
    2015年
     

    木賀大介

  • 哺乳細胞内で動作する人工遺伝子回路によるエピジェネティック・ランドスケープの構築

    科研費・若手研究(A)

    研究期間:

    2011年
    -
    2013年
     

    木賀大介

  • 単純化遺伝暗号を併用する細胞の構築

    科研費・挑戦的萌芽研究

    研究期間:

    2011年
    -
    2012年
     

    木賀大介

  • 細胞間相互作用により双安定状態を維持する人工遺伝子回路の解析

    戦略的創造研究推進事業(さきがけ) 「生命現象の革新モデルと展開」研究領域

    研究期間:

    2008年
    -
    2011年
     

    木賀大介

  • オープンサイエンスの分析と基盤的ソフトウェアの構築

    科研費・挑戦的萌芽研究

    研究期間:

    2009年
    -
    2010年
     

    萩谷昌己

  • アミノ酸の種類が減少した生体分子システムの構築

    科研費・若手研究(A)

    研究期間:

    2009年
    -
    2010年
     

    木賀大介

  • 小分子入力インターフェイスを備えた分子コンピュータの構築

    科研費・挑戦的萌芽研究

    研究期間:

    2008年
    -
    2009年
     

    木賀大介

  • 安定性が上昇した高機能蛋白質、および、部位特異的に修飾・固定化が可能な高機能蛋白質を低コストに大量生産する手法の開発

    産業技術研究助成事業(若手研究グラント)

    研究期間:

    2008年
     
     
     

    木賀大介

  • 遺伝暗号表の起源への実験的アプローチ

    科研費・若手研究(A)

    研究期間:

    2007年
    -
    2008年
     

    木賀大介

  • 安定性が上昇した高機能蛋白質、および、部位特異的に修飾・固定化が可能な高機能蛋白質を低コストに大量生産する手法の開発

    産業技術研究助成事業(若手研究グラント)

    研究期間:

    2007年
    -
    2008年
     

    木賀大介

  • DNAエンコード技術による生体情報分析法

    先端計測分析技術・機器開発事業 要素技術プログラム(平成16年度〜平成19年度採択課題)

    研究期間:

    2007年
    -
    2008年
     

    陶山明

▼全件表示

講演・口頭発表等

  • Simplified genetic code for directed evolution of proteins without specific amino acid species

    Daisuke Kiga  [招待有り]

    BuildACell  

    発表年月: 2022年02月

  • Designing Life

    Daisuke Kiga

    Gordon Research Conference Origins of Life  

    発表年月: 2016年

  • 19 and 21 amino acid genetic codes

    Daisuke Kiga

    Gordon Research Conference  

    発表年月: 2014年

  • Keynote : Synthetic experiment of life and evolution of genome

    Daisuke Kiga

    Earth-Life Science Institute 1st International Symposium  

    発表年月: 2013年

  • 合成生物学とデュアルユース問題

    木賀 大介

    日本学術会議公開シンポジウム、デュアルユース問題とBSL4 施設シンポジウム  

    発表年月: 2012年07月

  • Synthetic Biology

    Daisuke Kiga

    Japanse-French Frontier Science Symposium (日仏先端科学シンポジウム)  

    発表年月: 2012年

  • 合成生物学-生体分子を天然には無い様式で組み合わせる-

    木賀大介

    第51回日本熱帯医学会大会  

    発表年月: 2010年

  • 19種類以下のアミノ酸で構成されるタンパク質の配列最適化

    小林晃大, 内山正彦, 木賀大介

    第82回 日本生化学会大会(優秀プレゼンテーション賞獲得)  

    発表年月: 2009年

  • 2P47 DNAコンピューティングによるブール式の並列評価

    木賀大介, 小宮健, 有田正規, 坂本健作, 横山茂之, 萩谷昌己

    生物物理   日本生物物理学会  

    発表年月: 1997年09月

    開催年月:
    1997年09月
     
     
  • Trpを持たない酵素群によって構成される解糖系の構築に向けた活性測定

    高木有隣, 橋本真奈, 西田暁史, 柘植謙爾, 木賀大介

    生物物理学会関東支部会  

    発表年月: 2022年03月

  • ありえた生命のかたちの設計と実装をDXする

    木賀大介 宮崎和光 山村雅幸

    ラボオートメーション研究会  

    発表年月: 2022年02月

  • 合成生物学とバイオセキュリティ

    木賀大介  [招待有り]

    バイオエコノミーの現状 セミナー(シリーズ) 応用編  

    発表年月: 2022年02月

  • 合成生物学に期待される役割

    木賀大介  [招待有り]

    生命倫理学会  

    発表年月: 2021年11月

  • ありえた生体高分子ネットワークを 創出するBioDOSの構築

    木賀大介  [招待有り]

    「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」キックオフシンポジウム  

    発表年月: 2021年11月

  • ありえた生体高分子ネットワークを 創出するBioDOSの構築

    木賀大介

    「細胞を創る」研究会 14.0  

    発表年月: 2021年11月

    開催年月:
    2021年11月
     
     
  • Modulation of autonomous signaling system for phenotypic diversification on Waddington’s landscape

    Masaki Takeda, Akifumi Nishida, Daisuke Daisuke Kiga

    Cell Synth14.0 meeting  

    発表年月: 2021年11月

    開催年月:
    2021年11月
     
     
  • 組換えと翻訳エラーの併⽤が進化の局所解トラップを緩和することの計算機実験に よる検証

    満冨健太, 木賀大介

    第 10回日本生物物理学会関東支部会(オンライン)  

    発表年月: 2021年03月

  • 単純化遺伝暗号を用いた 酸化耐性GFPの人工進化

    宮地亮多, 木賀大介

    第 10回日本生物物理学会関東支部会(オンライン)  

    発表年月: 2021年03月

  • 普遍遺伝暗号を用いた 人工進化の限界: 硫黄抜き酸化耐性GFPを例に

    榎本利彦, 村上泰平, 網蔵和晃, 松本航, 〇木賀大介

    第 10回日本生物物理学会関東支部会(オンライン)  

    発表年月: 2021年03月

  • シミュレーションによるコロニーパターン形成を支配する因子の解明

    北川一輝, 西田暁史, 太田裕作, 青木一洋, 木賀大介

    生物物理学会関東支部会  

    発表年月: 2020年03月

  • 細胞間通信を介して自律的に多様化を行う人工遺伝子回路の挙動拡張

    畑敬士, 中川絵理子, 橋本真奈, 西田暁史, 関根亮二, 山村雅幸, 〇木賀大介

    生物物理学会関東支部会  

    発表年月: 2020年03月

  • 種々の遺伝暗号それぞれが発揮できるより広い機能性生体高分子の進化戦略

    木賀大介  [招待有り]

    第42回日本分子生物学会年会(福岡)  

    発表年月: 2019年12月

  • 適切な翻訳エラーは進化が局所解で止まってしまわないようにする

    榎本 利彦, 〇木賀 大介

    無細胞生命科学研究会(三浦市)  

    発表年月: 2019年11月

  • Cell-cell communication dependent bifurcation of stability in genetic circuit

    Daisuke Kiga  [招待有り]

    Asian Synthetic Biology Association  

    発表年月: 2019年10月

  • Influence Analysis of Amino Acid Residues on Protein Functions using Attention-based Neural Networks

    Chem-Bio Informatics Society(CBI) Annual Meeting 2019  

    発表年月: 2019年10月

  • 合成生物学・遺伝子工学と デュアルユース 大規模遺伝子工学が普及した際のリスク

    木賀大介  [招待有り]

    第19回日本バイオセーフティ学会  

    発表年月: 2019年10月

  • Directed Evolution under genetic codes with reduced-size alphabet or with low fidelity

    Daisuke Kiga  [招待有り]

    OIST  

    発表年月: 2019年10月

  • Simulation and regulation of E.coli which has autonomous diversification ability

    第57回日本生物物理学会年会(宮崎)  

    発表年月: 2019年09月

  • 細胞間通信を介した細胞集団の遺伝子発現における 計算機実験と培養実験でのフィードバック効果の一致

    橋本 真奈, 鮎川 翔太郎, 木賀 大介

    第92回日本生化学会(横浜)  

    開催年月:
    2019年09月
     
     
  • 遺伝暗号の改変による調節可能な 翻訳エラーが適応度地形の局所解への トラップを回避する

    榎本 利彦, 〇木賀 大介

    第21回日本進化学会  

    発表年月: 2019年08月

  • 原始生命の誕生

    木賀大介  [招待有り]

    武田セミナー (第16回)  

    発表年月: 2019年07月

  • 生命の部品を組み合わせることによる理学と工学

    木賀大介  [招待有り]

    都立医学研セミナー  

    発表年月: 2019年07月

  • 意図的に翻訳エラーを増大させる ことによる進化の加速

    榎本 利彦, 〇木賀 大介

    タンパク質科学会2019  

    発表年月: 2019年06月

  • Novel Directed Evolution Using Engineered Genetic Code

    Daisuke Kiga

    5 th Core-to-Core International Symposium "3D Lab-Exchange Program"  

    発表年月: 2019年02月

    開催年月:
    2019年02月
     
     
  • 合成生物学・遺伝子工学とデュアルユース

    木賀大介  [招待有り]

    第6回バイオセキュリティ研究会 次世代のバイオセキュリティ  

    発表年月: 2019年01月

  • 在の生命に普遍な4塩基20アミノ酸の制約から外れた進化を探る(ワークショップ企画)

    木賀大介, 赤沼哲史

    第41回日本分子生物学会年会(MBSJ2018)  

    発表年月: 2018年11月

  • Directed Evolution under genetic codes with reduced-size alphabet

    Daisuke Kiga

    The 1st Asian Synthetic Biology Association (ASBA 2018)  

    発表年月: 2018年11月

    開催年月:
    2018年11月
     
     
  • Artificial cell-cell communication and symbiosis designed by synthetic biology

    Daisuke Kiga  [招待有り]

    ADVANCED TECHNIQUES TO STUDY AND EXPLOIT THE SPONGE AND CORAL MICROBIOMES WORKSHOP  

    発表年月: 2018年11月

    開催年月:
    2018年11月
     
     
  • Biological containment through engineering of genetic code

    Daisuke Kiga  [招待有り]

    The 2nd International Conference on Molecular Robot Ethics  

    発表年月: 2018年10月

  • Programmable misincorporation of amino acids increases probability of protein evolution

    Toshihiko Enomoto, 〇Daisuke Kiga

    27th tRNA conference  

    発表年月: 2018年09月

    開催年月:
    2018年09月
     
     
  • ゲノムスケールDNA合成技術による セーフティとセキュリティの向上

    木賀大介  [招待有り]

    第5回バイオセキュリティ研究会  

    発表年月: 2018年07月

  • 人工遺伝子回路設計における下流レポーター遺伝子が与える影響

    木賀大介

    デザイン生命工学会研究会  

    発表年月: 2018年

  • 設計生物学:生物工学を指数関数的に進展させる方策

    鮎川翔太郎, 木賀大介

    第69回 日本生物工学会大会  

    発表年月: 2017年

  • Repeats of diversification on Waddington landscape realized with synthetic gene circuit

    Takashi Hata, Shotaro Ayukawa, Zicong Zhang, Yochiku Shi, Akifumi Nishida, Masayuki Yamamura, Daisuke Kiga

    SB 7.0, The Seventh International Meeting on Synthetic Biology  

    発表年月: 2017年

  • 設計生物学 ― 博物学ではない生物学の構築

    木賀大介

    第2回 デザイン生命工学研究会  

    発表年月: 2017年

  • Effects of downstream genes on synthetic genetic circuits

    Takefumi Moriya, Zicong Zhang, ○Shotaro Ayukawa, Masayuki Yamamura, Daisuke Kiga

    Effects of downstream genes on synthetic genetic circuits  

    発表年月: 2017年

  • Systems biology : Synthetic biology = Systems chemistry : ???

    Daisuke Kiga

    ELSI symposium  

    発表年月: 2017年

  • 設計生物学と進化工学のあいだ(セッションオーガナイズ)

    木賀大介

    第39回日本分子生物学会年会  

    発表年月: 2016年

  • 多細胞合成生物学(セッション オーガナイズ)

    木賀大介

    第54回日本生物物理学会年会  

    発表年月: 2016年

  • サブシステムの組み合わせによる人工遺伝子回路の設計と構築

    鮎川翔太郎, 木賀大介

    「細胞を創る」研究会9.0  

    発表年月: 2016年

  • 合成生物学についての大学教育

    木賀大介

    日本遺伝学会第88回大会  

    発表年月: 2016年

  • 合成生物学による人工生命システムの創生における理論に基づく実装の重要性

    木賀大介

    日本農芸化学会 2016年度 大会  

    発表年月: 2016年

  • RNAワールドとオリゴペプチドワールドから翻訳系の出現へ

    木賀大介

    生命の起源および進化学会年回  

    発表年月: 2016年

  • 2種類のリボザイムを組み合わせた、多段階RNA自律反応システムの構築

    前島昂弥, 鮎川翔太, 清岡隆司, 木賀大介, 井川善也

    第5回日本生物物理学会関東支部会  

    発表年月: 2016年

  • Simplification of the Genetic

    K. Amikura, D. Kiga

    Pacifichem 2015, The international Chemical Congress of Pacific Basin Societies  

    発表年月: 2015年

  • 細胞間相互作用による抗生物質耐性の解析のための大腸菌コロニー擬似共培養系の高効率作製

    濱野 洋茂, 鮎川 翔太郎, 瀧ノ上 正浩, 木賀 大介

    BMB2015  

    発表年月: 2015年

  • 合成生物学と進化実験

    木賀大介

    NINS/IURIC Colloquium 2015  

    発表年月: 2015年

  • 単純化遺伝暗号表を用いた進化工学によるアミノ酸種限定タンパク質の創出

    木賀大介

    BMB2015  

    発表年月: 2015年

  • 生命の起源と初期進化における、情報と「知能」の出現

    木賀大介

    分子ロボティクスシンポジウム(CBI学会第25回大会内)  

    発表年月: 2015年

  • A genetic code without the sulfur containing amino acids

    Daisuke Kiga

    10th International Aminoacyl-tRNA Synthetase Symposium  

    発表年月: 2015年

  • Prisoner’s Dilemma

    Hiraku Tokuma, Airi Masuyama, Emi Fuse, Erinn Sim Zixuan, Jun Kawamura, Koji Abe, Misa Minegishi, Riku Shinohara, Takahiro Kashiwagi, Tomoka Koshimizu, Shuhei Yasunishi, Yuki Koura, Yuki Sasahara, Yuta Yamazaki, Shotaro Ayukawa, Nobutaka Nakashima, Masayuki Yamamura, Yasunori Aizawa, Hisakazu Mihara, Daisuke Kiga

    iGEM 2015 Jiant Jamboree  

    発表年月: 2015年

  • 高い安定性と比活性を併せ持つタンパク質製剤を開発するための遺伝暗号の改変

    木賀大介

    第80回日本インターフェロンサイトカイン学  

    発表年月: 2015年

  • 特定のアミノ酸を持たないタンパク質創出における単純化遺伝暗号の活用

    一柳光弘, 塩谷知範, 中村聡, 王勇, 宮本秀俊, 木賀大介

    第15回日本蛋白質科学会年会  

    発表年月: 2015年

  • Effects of downstream genes on synthetic genetic circuits in living bacteria

    Takefumi Moriya, Zicong Zhang, Shotaro Ayukawa, Masayuki Yamamura, ○Daisuke Kiga

    Gordon Research conference Synthetic Biology  

    発表年月: 2015年

  • Synthetic Study to Uncover Hierarchical Ordering of Biological Systems: Introduction

    Daisuke Kiga

    第37回分子生物学会  

    発表年月: 2014年

  • A genetic code without the sulfur containing amino acids

    Kazuaki Amikura, Daisuke Kiga

    25th tRNA conference  

    発表年月: 2014年

  • 数理モデルに基づいて細胞内で人工遺伝子回路を動作させる

    木賀大介

    日本遺伝学会第86回大会  

    発表年月: 2014年

  • 現代から遡るアミノ酸の種類

    木賀大介

    進化学会第16回大会  

    発表年月: 2014年

  • Simplification of the Genetic Code

    K. Amikura, D. Kiga

    Origins 2014  

    発表年月: 2014年

  • 数理モデルに基づいて生体高分子ネットワークを実装する

    木賀大介

    総研大「生命概念の普遍化−宇宙の生命」第5回研究会  

    発表年月: 2014年

  • 原始タンパク質を創造するための単純化異伝暗号表

    網蔵和晃, 木賀大介

    生命の起原および進化学会第39回学術講演会  

    発表年月: 2014年

  • Simplification of the genetic code

    Daisuke Kiga

    Synthetic Biology 6.0  

    発表年月: 2013年

  • Simplification of genetic codes and

    Daisuke Kiga

    9th International Symposium on Aminoacyl-tRNA Synthetases  

    発表年月: 2013年

  • Implementation of artificial genetic circuits based on deformation of a nullcline

    Daisuke Kiga

    The first annual winter q-bio meeting, Honolulu  

    発表年月: 2013年

  • シンポジウム 「細胞を創る研究と社会との関わり」について、今、一度振り返る(セッションオーガナイズ)

    加藤和人, 木賀大介

    細胞を創る研究会 6.0  

    発表年月: 2013年

  • Construction of multiple amino acids excluded "simplified genetic code" by using multiple sets of tRNA variants

    Kazuaki Amikura, Akio Kawahara-Kobayashi, Yoko Sakai, Shun Asami, Masahiko Uchiyama, Daisuke Kiga

    The 65th Fujihara Seminar, International Symposium on Synthetic Biology of Unnatural Base Pairs and Amino Acids  

    発表年月: 2013年

  • 複数種類のアミノ酸が同時に除かれた単純化遺伝暗号の構築

    網蔵和晃, 酒井洋子, 浅見俊, 河原-小林晃大, 木賀大介

    第36回日本分子生物学会年会  

    発表年月: 2013年

  • アミノ酸を19種類未満しかコードしない「単純化遺伝暗号表」の構築

    木賀大介

    分子生物学会  

    発表年月: 2013年

  • Simplification of the Genetic Code: Restricted Diversity of Genetically Encoded Amino Acids

    Amikura K Kawahara-Kobayashi, A. Kiga D

    The International Astrobiology Workshop 2013  

    発表年月: 2013年

  • 複数種のtRNA変異体を用いた複数種のアミノ酸が除かれた単純化遺伝暗号表の構築

    網蔵和晃, 一柳光弘, 酒井洋子, 浅見俊, 河原-小林晃大, 木賀大介

    第8回無細胞生命科学研究会  

    発表年月: 2013年

  • Genetic codes with less than 20 amino acids

    Daisuke Kiga

    The 65th Fujihara Seminar : International Symposium on Synthetic Biology of Unnatural Base Pairs and Amino Acids  

    発表年月: 2013年

  • 原始タンパク質を創造するための単純化遺伝暗号表

    網蔵和晃, 木賀大介

    生命の起原および進化学会第38回学術講演  

    発表年月: 2013年

  • 数理モデルと定量結果とに基づいた人工遺伝子回路の改善サイクル

    木賀大介

    定量生物学の会 第五回年会  

    発表年月: 2012年

  • ヌルクラインの変形に基づく人工遺伝子回路の実装

    木賀大介

    第35回分子生物学会シンポジウム 複雑な生命システムへの理論的・構成的アプローチ  

    発表年月: 2012年

  • Conferring multipotency to the bistable system by overexpression of genes

    Daisuke Kiga

    Joint Conference on Informatics in Biology, Medicine and Pharmacology  

    発表年月: 2012年

  • Simplification of the genetic code : construction of a 19-amino acid genetic code

    Daisuke Kiga

    COLD SPRING HARBOR ASIA CONFERENCES on Synthetic Biology  

    発表年月: 2012年

  • iGEMを通した合成生物学研究者の育成(第63回大会シンポジウム・ワークショップ報告)

    早出 広司, 上田 卓也, 木賀 大介

    生物工学会誌 : seibutsu-kogaku kaishi  

    発表年月: 2011年11月

    開催年月:
    2011年11月
     
     
  • Waddingtonの地形の概念を人工遺伝子回路でデザインする

    木賀大介

    第84回日本生化学会 シンポジウム「ゲノムデザインの最前線」  

    発表年月: 2011年

  • Tunable synthetic phenotypic diversification on Waddington’s landscape through autonomous signaling

    木賀大介

    第49回日本生物物理学会年会 シンポジウム「生命システムの情報処理」  

    発表年月: 2011年

  • iGEM を通した合成生物学研究者の育成

    木賀大介

    第63回日本生物工学会大会  

    発表年月: 2011年

  • Cell-Free Protein Synthesis for Biomolecular NMR

    Takanori Kigawa

    4th Asia-Pacific NMR Symposium  

    発表年月: 2011年

  • 単純化遺伝暗号表を用いたtRNAのコドン認識の検証

    網蔵和晃, 小林晃大, 木賀大介

    生命の起原および進化学会第36回学術講演会  

    発表年月: 2011年

  • 合成生物学の実験のためのトレース可能なデータベース

    川又生吹, 木賀大介, 有田正規, 田中文昭, 萩谷昌己

    細胞を創る研究会3.0  

    発表年月: 2010年

  • Reducing the amino acids alphabet : Construction of "Simplified" Genetic Codes

    Akio Kobayashi, Daisuke Kiga

    23rd tRNA workshop  

    発表年月: 2010年

  • 20種類未満のアミノ酸のみを使用する「単純化遺伝暗号」の構築

    小林晃大, 酒井洋子, 網蔵和晃, 木賀大介

    第5回 無細胞生命科学研究会  

    発表年月: 2010年

  • 人工遺伝子回路:細胞をプログラムする

    木賀大介

    分子ロボティクス研究会  

    発表年月: 2010年

  • 遺伝暗号の起源と初期進化を考察するための改変遺伝暗号の構築

    網蔵和晃, 小林晃大, 木賀大介

    日本進化学会 第12回 東京大会  

    発表年月: 2010年

  • 普遍遺伝暗号への統一と遺伝子の水平伝播

    小林晃大, 木賀大介

    生命の起原および進化学会第35回  

    発表年月: 2010年

  • Simplification of the genetic code : construction of a 19-amino acid genetic code

    Akio Kobayashi, Kazuaki Amikura, Daisuke Kiga

    23rd tRNA workshop  

    発表年月: 2010年

  • 遺伝暗号の改変とタンパク質の進化分子工学

    木賀大介

    システム・情報部門学術講演会2009  

    発表年月: 2009年

  • Synthetic biology for protein engineering

    Naoto Inukai, Masahiko Uchiyama, Daisuke Kiga

    CBI-KSBSB JOINT CONFERENCE  

    発表年月: 2009年

  • 小分子の存在に応じて活性化される試験管内の人工遺伝子回路

    木賀大介

    日本化学会 第24回生体機能関連化学シンポジウム,第12回バイオテクノロジー部会シンポジウム  

    発表年月: 2009年

  • 小分子の存在を検出して自律的に動作する生体分子コンピュータの構築

    木賀大介

    第11回日本RNA学会年会  

    発表年月: 2009年

  • 細胞内および試験管内の遺伝子発現ネットワークを数理モデルに基づいて構築する

    木賀大介

    理化学研究所第4回「バイオ医工学シンポジウム」(招待講演)  

    発表年月: 2009年

  • 遺伝暗号や遺伝子ネットワークにありえたかたち

    木賀大介

    自然科学研究機構アストロバイオロジーワークショツプ2008(口頭発表)  

    発表年月: 2008年

  • 理論を欲している実験分野としての合成生物学 : 生命のサブシステムを組み合わせて階層を登る

    木賀大介

    自然科学研究機構「自然科学における階層と全体」平成20年度シンポジウム(招待講演)  

    発表年月: 2008年

  • "単純化"遺伝暗号表を用いたタンパク質の進化分子工学

    小林晃大, 内山正彦, 木賀大介

    第31回日本分子生物学界年会・第81回日本生化学会大会合同大会  

    発表年月: 2008年

  • なぜ普遍遺伝暗号表には20種類のアミノ酸か?つくることで考えてみる

    木賀大介

    細胞を創る」研究会  

    発表年月: 2008年

  • 「合成生物学 : 『ありえた生命』のかたちを考察する」

    木賀大介

    学振151委員会ナノバイオフユージョン分科会(招待講演)  

    発表年月: 2008年

  • 「「生物」はどこまでの可能性を持つか : 生体高分子を人工的に組み合わせることによる考察

    木賀大介

    極限環境微生物学会第9回シンポジウム(招待講演)  

    発表年月: 2008年

  • 種類以下のアミノ酸のみを含む改変遺伝暗号表を使用したタンパク質の人工進化

    内山正彦, 小林晃大, 木賀大介

    第8回日本タンパク質科学会年会  

    発表年月: 2008年

  • 19種類以下のアミノ酸のみを含む改変遺伝暗号表を使用したタンパク質の人工進化

    内山正彦, 小林晃大, 木賀大介

    第8回日本蛋白質科学会年会  

    発表年月: 2008年

  • 細胞ウェアの物質的・生物学的側面

    木賀大介

    第21回回路とシステム軽井沢ワークショップ  

    発表年月: 2008年

  • 「これまでの進化史にありえた遺伝暗号表」を試験管内に再現する

    小林晃大, 内山正彦, 浅見俊, 木賀大介

    生命の起原および進化学会第33回学術講演会  

    発表年月: 2008年

  • 「ありえた生命」から生命を知る合成生物学

    小林晃大内山正彦浅見俊木賀大介

    生命の起原および進化学会第33回学術講演会  

    発表年月: 2008年

  • 2P280 細胞サイズのリボソーム中での自律型DNAコンピューティング(生体膜・人工膜(ダイナミクス),ポスター発表,第45回日本生物物理学会年会)

    庄田 耕一郎, 木賀 大介, 瀧ノ上 正浩, 豊田 太郎, 景山 義之, 菅原 正, 陶山 明

    生物物理   一般社団法人日本生物物理学会  

    発表年月: 2007年11月

    開催年月:
    2007年11月
     
     
  • 分子コンピュータと分子通信:生体分子を用いての構成的アプローチ

    木賀大介

    日本生物物理学会第45回年会(口頭発表)  

    発表年月: 2007年

  • ワークショップ遺伝暗号表の起源を知るために-翻訳系における合成生物学

    小林晃大, 内山正彦, 浅見俊, 木賀大介

    第30回日本分子生物学会年会・第80回日本生化学会大会合同大会  

    発表年月: 2007年

  • 「これまでの進化史にありえた遺伝暗号表」を試験管内に再現する

    小林晃大, 内山正彦, 浅見俊, 木賀大介

    第30回日本分子生物学会年会・第80回日本生化学会大会合同大会ワークショップ (口頭発表)  

    発表年月: 2007年

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特定課題研究

  • 原始的なエネルギー獲得系の再現

    2021年   高木有隣

     概要を見る

    本研究は、初期生命が用いるアミノ酸の種類を追及する申請者の一連の研究を拡張するための、基礎となるものである。全生物の共通祖先も、ある段階では現在の生命と同じように、20種類のアミノ酸をタンパク質合成に用いていたことは間違いない。しかし、生命の初期進化を考察するために、それ以前、20種類のアミノ酸を用いる以前の遺伝暗号について追及する必要がある。そこで、本研究では、遺伝暗号に最後に加わった可能性が高いトリプトファン(Trp)が存在せずとも動作する解糖系を再現する。この研究のために、生体内での活性、試験管内での活性、双方からアプローチを、活性予測プログラムを用いて効率化する。

  • 原始的なエネルギー獲得系の再現

    2020年  

     概要を見る

    本研究は、初期生命が用いるアミノ酸の種類を追及する申請者の一連の研究を拡張するための、基礎となるものである。全生物の共通祖先も、ある段階では現在の生命と同じように、20種類のアミノ酸をタンパク質合成に用いていたことは間違いない。しかし、生命の初期進化を考察するために、それ以前、20種類のアミノ酸を用いる以前の遺伝暗号について追及する必要がある。そこで、本研究では、遺伝暗号に最後に加わった可能性が高いトリプトファン(Trp)が存在せずとも動作する解糖系を再現する。この研究のために、生体内での活性、試験管内での活性、双方からアプローチを、活性予測プログラムを用いて効率化する。

  • 原始的なエネルギー獲得系の再現

    2019年  

     概要を見る

    本研究は、初期生命が用いるアミノ酸の種類を追及する申請者の一連の研究を拡張するための、基礎となるものである。全生物の共通祖先も、ある段階では現在の生命と同じように、20種類のアミノ酸をタンパク質合成に用いていたことは間違いない。しかし、生命の初期進化を考察するために、それ以前、20種類のアミノ酸を用いる以前の遺伝暗号について追及する必要がある。そこで、本研究では、遺伝暗号に最後に加わった可能性が高いトリプトファン(Trp)が存在せずとも動作する解糖系を再現する。この研究のために、生体内での活性、試験管内での活性、双方からアプローチを、活性予測プログラムを用いて効率化する。

  • 原始的なエネルギー獲得系の再現

    2017年  

     概要を見る

    本研究は、初期生命が用いるアミノ酸の種類を追及する申請者の一連の研究を拡張するための、基礎となるものである。全生物の共通祖先も、ある段階では現在の生命と同じように、20種類のアミノ酸をタンパク質合成に用いていたことは間違いない。しかし、生命の初期進化を考察するために、それ以前、20種類のアミノ酸を用いる以前の遺伝暗号について追及する必要がある。そこで、本研究では、遺伝暗号に最後に加わった可能性が高いトリプトファン(Trp)が存在せずとも動作する解糖系を再現する。この研究のために、生体内での活性、試験管内での活性、双方からアプローチする

  • 設計生物学:博物学ではない生物学の構築

    2017年  

     概要を見る

    合成生物学に対する過度の期待は、普遍的な理解の達成よりも、従来の生物工学を延長したにとどまる個々の生産系の構築を優先させる動機づけとなってしまった。本研究では、理工学一般にみられる多階層モデルを活用して部分システムの組み合わせを設計・評価する、という研究サイクルの適用先として、生物学としても重要な、細胞間の通信に基づく多階層系を選択した。研究代表の木賀は、合成生物学アプローチで部分システムの組み合わせを構築し、実験と数理モデルとの整合性のある理解を達成している。本研究は、これを、合成生物学で重要な社会との関わりの調査を含めた、より広い分野に拡大するものである。

  • 低分子触媒から高分子触媒への遷移による生命システムの深化の本質に迫る

    2016年  

     概要を見る

    本研究の目的は、各種反応条件による反応の進行を解析することで、低分子触媒による反応が、高分子酵素による触媒に遷移する過程を考察することにある。その過程において、(1)反応条件のバラエティ、(2)触媒となるタンパク質酵素のアミノ酸配列における少数の置換に起因するバラエティ、2つのバラエティの組み合わせについて、反応を測定する必要がある。本学における研究室立ち上げの年度となる本年度については、特に、タンパク質酵素の種々の変異体を作成しその活性を評価した。また、本研究の成果の一部を外部資金によって別方向に拡張した成果は、早稲田大の資金による特許出願につながった

  • 低分子触媒から高分子触媒への遷移による生命システムの深化の本質に迫る

    2016年  

     概要を見る

    本研究の目的は、各種反応条件による反応の進行を解析することで、低分子触媒による反応が、高分子酵素による触媒に遷移する過程を考察することにある。その過程において、(1)反応条件のバラエティ、(2)触媒となるタンパク質酵素のアミノ酸配列における少数の置換に起因するバラエティ、2つのバラエティの組み合わせについて、反応を測定する必要がある。本学における研究室立ち上げの年度となる本年度については、特に、タンパク質酵素の種々の変異体を作成しその活性を評価した。また、本研究の成果の一部を外部資金によって別方向に拡張した成果は、早稲田大の資金による特許出願につながった

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現在担当している科目

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