Past Seminars & Reading Circles

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Past Seminars & Reading Circles 1 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Lab seminar (every Wednesday, from 1pm at room 306)

Nov. 19
- Yayoi Takeuchi
Nov. 14
- TBA
Nov. 12 (Evolutionary Dynamics special)
- schedule
Nov. 7
- TBA
Oct. 31
- Tetsuya Akita: with Masashi Kamo
- Varying environments favor the production of oil in microalgae through life-history evolution
  - Technological development related to the renewable energy takes on a greater sense now following the running out of fossil oil in less than fifty years, microalgae-derived oil is considered as a feasible alternative for numerous reasons. Despite experimental studies found some conditions for lipid-rich algal strains, the ecological-evolutionary basis has received little attention. We show theoretically that lipid-storage in algae might be evolved as a compensation strategy against starvation of available Carbon. As pointed out experimentally, Nutrient-limited conditions accelerate this tendency. Furthermore, the strains adapted to both Carbon-starvation and Nutrient-limited may be robust to unintentional artificial selections associated with recurrent cultivations. Together with these results, we conclude that considering evolutionary perspectives may contribute to the lipid production in algae.
Oct. 24
- cancelled
Oct. 17
- cancelled
Oct. 10 (Immunology special; seminar room 101 and 102)
- 13:00-
- Kouichi Saeki (RIKEN): with H. Doekes, R. J. De Boer
- Consideration of TCR cross-reactivity and role of regulatory T cells
  - Adaptive immunity has a large clonotype repertoire of lymphocytes characterized by a unique receptor to deal with the multitude of pathogens. Each lymphocyte receptor is estimated to have a high cross-reactivity but it may lead to autoimmune responses. For the self-non-self discrimination, lymphocytes undergo the negative selection during their development. However, it has been reported that self-reactive lymphocytes still present in the periphery. Here, we hypothesized that a subset of T cells, regulatory T cells, helps a successful immune response, Psuc, that is defined as avoiding an autoimmune response but mounting an immune response against pathogens. By means of a probabilistic model, we show that regulatory T cells make the probability of Psuc higher under some conditions. The examination of this mathematical model might predict the specificity of regulatory T cells.
- 14:00-
- Jun Nakabayashi (Yokohama city Univ.)
- Condition for the leukemic state in hematopoietic system composed of the stepwise dierentiation of intermediate progenitors
  - In the hematopoietic process, stepwise differentiation of progenitor losing the pluripotency is observed. The intermediate progenitor that maintains the capability of cell division but cannot proliferate by itself. In this study, a simple mathematical model including the stepwise differentiation of the intermediate progenitors is constructed. The population dynamics of the differentiating hematopoietic cells under the Lotka-Volterra type competition is assumed in this model. The leukemic state is defined as the autonomous proliferation of the progenitor. The condition for the leukemic state is obtained from the model. The growth rate of the progenitor exceeds a certain threshold, the progenitor can proliferate by itself. The cell count of the progenitor in the downstream step of the stepwise differentiation in hematopoiesis depends on that of the upstream progenitor. This result indicates that the propagation of the specific cell lineage observed by the laboratory examination does not always responsible for the leukemic state. All cell lineage above the proliferative progenitor is candidate cell for the leukemic state. The detailed model describing the population dynamics of the actual hematopoietic cell lineage is also proposed. The abnormal blood profile observed in knock out animal is reproduced by this detailed model. The alteration of cell count of the progenitor in K/O animal is mainly explained on the carrying capacity in the model. This result indicates that the prominent propagation of the specific cell lineage in K/O animal is caused not only by the deviation of the differentiation but also the relaxation of the restriction of the cell count regulated by the homeostatic mechanism.
- 15:30-
- 吉田弘氏（国立感染症研究所・ウイルス第二部）
- ポリオ根絶と抗原進化
Oct. 3
- Shun Kurokawa (Univ. of Tokyo)
- 有限集団における社会行動の進化と互恵性による大きいグループでの協力行動の進化の説明
  - 社会行動は2者間での相互作用だけでなく、2個体以上が関与する社会の相互作用においても観察される。従来の生物の社会行動の進化の理論研究は、主として無限集団を仮定していて、遺伝的浮動の効果を考慮してこなかったが、最近の研究では、無限集団という仮定を取り除き、遺伝的浮動の効果を考慮したものがある。本稿第1章では、有限集団における社会行動の進化について考察して、固定確率の比、及び、ハミルトン則の一般化を与え、本稿第2章では社会行動の中でも協力行動に的を絞り、情報が不完全の時の、大きいグループにおける協力行動の互恵性による説明の可否を調べる。
Sep. 24
- Maisa Sekizawa & Kaori Mizuno
  - Final presentation
Sep. 13
- Maisa Sekizawa & Kaori Mizuno
Sep. 5
- Maisa Sekizawa & Kaori Mizuno
Aug. 29
- Maisa Sekizawa & Kaori Mizuno
Aug. 22
- cancelled (Evolution meeting)
Aug. 15
- cancelled (summer break)
Aug. 8
- Maisa Sekizawa & Kaori Mizuno
Jul 4.
- Hiroshi Ito : with Ulf Dieckmann (Evolution and Ecology Program, IIASA)
- Evolutionary branching of populations. by ecological interaction .in multidimensional trait spaces.
  - Evolutionary branching is the process by which ecological interactions induce evolutionary diversification. A necessary and sufficient condition for evolutionary branching of univariate traits is the existence of a convergence stable trait value at which selection is locally disruptive. Real populations, however, undergo simultaneous evolution in multiple traits. Here we extend conditions for evolutionary branching to bivariate trait spaces in which the response to disruptive selection on one trait can be suppressed by directional selection on another trait. To obtain analytical results, we study trait-substitution sequences formed by invasions that pos-sess maximum likelihood. By deriving a sufficient condition for evolutionary branching of bivariate traits along such maximum-likelihood invasion paths (MLIPs), we demonstrate the existence of a threshold ratio specifying how much disruptive selection in one trait direction is needed to overcome the obstruction of evolutionary branching caused by directional selection in the other trait direction. Generalizing this finding, we show that evolutionary branching of bivariate traits can occur along evolutionary-branching lines on which residual directional selection is sufficiently weak. We then present numerical analyses showing that our generalized condition for evolutionary branching is a good indicator of branching likelihood even when trait-substitution sequences do not follow MLIPs and when mutations are not rare. Finally, we extend the derived conditions for evolutionary branching to multivariate trait spaces.
Jun 27.
- cancelled
Jun. 20
- cancelled
Jun. 13
- Akira Sasaki：佐々木顕（総研大・先導研），八島健太（明治大・現象数理），中林潤（横浜市立大・免疫学）
- アルツハイマー病の数理モデル
  - 認知症の中で最も発症数の多いタイプであるアルツハイマー病(Altzheimer's disease, AD)の原因として，脳内でのベータアミロイド繊維の凝集が挙げられる．ベータアミロイド前駆体タンパク質（膜貫通型糖タンパク質）は，複数の部位で複数の酵素による競合的切断を受け，このうちベータセクレターゼによる切断を受けると，ベータアミロイドが細胞外に放出される．このベータアミロイドモノマー（正常型）が，まれに生じる異常型を核として重合することにより，難溶性のアミロイド繊維が脳内に爆発的に凝集すると考えられる．ここではアルツハイマー病の動態を２つの部分に分けて解析する．（１）まず，ベータアミロイド前駆体の競合的切断反応を，細胞膜上の複数酵素の（異常）拡散と反応のプロセスとして数理モデル化し，競合する切断酵素濃度とその拡散性・異常拡散性がベータアミロイド生産速度にどのように影響するかを調べる．（２）次に，ベータアミロイドモノマーが異常型を核として重合し繊維状になる「ベータアミロイド凝集」の過程を数理モデル化し，異常型重合の連鎖反応の進行スピードや，重合体のサイズ分布などを明らかにする．
Jun. 6
- cancelled (progress)
May. 30
- Tetsuya Akita
May. 23
- Hisashi Ohtsuki
May. 16
- cancelled (health check-up)
May. 9
- Emmanuel A. Mpolya
May. 2
- cancelled (holiday break)
Apr. 25
- Hiroshi Ito
Apr. 18
- Susumu Kato (Hongo lab., the Graduate University for Advanced Studies)
- Analysis of relationship between archaeological site distribution and multiple environmental factors in the Jomon Period of Japan using GIS
  - The purpose of the present study is to form an integrative account for a number of environmental factors, to investigate what kind of factors influenced the decision making for choosing location of land used in prehistoric times. In previous studies, the relationship between the selection of location and a single factor, such as access to topography and coast line transformation, and shell heap distribution has usually been considered. However, the relationship between multiple environmental agents and location of archeological site has not been considered. In the present study, I consider multiple environmental factors by using GIS to understand the factors determining the location of archeological sites.

Reading Circles

Essential Mathematical Biology / Britton, N. F. / Springer / 2003
- every Monday from 1pm

Past Seminars & Reading Circles 2 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Lab seminar

2011
- Aug. 17 (Shonan seminar)
  - Kazuhiro Bessho (Kyushu Univ.)
    - HETEROMORPHIC AND ISOMORPHIC ALTERNATIONS OF GENERATIONS IN MACROALGAE, AS ADAPTATIONS TO A SEASONAL ENVIRONMENT
    - Macroalgea (seaweeds) show diverse life cycles. Especially notable is the difference between heteromorphic cycle and isomorphic cycle. Species with heteromorphic life cycle have a large multicellular body in one generation but have a very small body in the other generation of a year. This alternation of life forms is linked with the alternation of the genome: one generation is diploid (2n), and the other is haploid (n). In contrast, isomorphic species have both diploid and haploid life forms with very similar morphology, having more than two generations in a year. Here we examine a hypothesis that the diversity of life cycle observed among macroalgae might be adaptations to seasonally changing environments. We develop mathematical models for the optimal life cycle in the environment where productivity changes seasonally. Then we discuss the condition in which hetermorphic or isomorphic species are more advantageous than the other. We first discuss the optimal reproductive schedule for a heteromorphic species that achieves the maximum population growth rate. It is to have the generation with a large body size in the productive season and the generation with a small body size in the unproductive season. In the optimal reproductive schedule of isomorphic species, algae of different generations mature when the body size reaches a common value, but the length of a generation greatly varies between seasons. In a strongly seasonal environment, the heteromorphic species is more profitable than isomorphic species, which is consistent with the observed latitudinal distribution.
- Aug. 3
  - Hyeong-Chai Jeong (Sejong Univ., Korea)
    - Emergence of cooperation with self-organized criticality
    - Cooperation and self-organized criticality are two main keywords in current studies of evolution. We propose a generalized Bak-Sneppen model and provide a natural mechanism which accounts for both phenomena simultaneously. We use the prisoner's dilemma games to mimic the interactions among the members in the population. Each member is identified by its cooperation probability and its fitness is given by the payoffs from the neighbors. The least fit member with the minimum payoff is replaced by a new member with a random cooperation probability. When the neighbors of the least fit one are also replaced with a non-zero probability, a strong cooperation emerges. Bak-Sneppen process builds a self-organized structure so that the cooperation can emerge even in the parameter region where a uniform or random population decreases the number of cooperators. The emergence of cooperation is due to the same dynamical correlation which leads to self-organized criticality in replacement activities.
- May. 18
  - Ryosuke Omori
    - The effect of school closure and holiday to epidemic peak
    - The understanding of epidemic peak is important for controlling epidemic. We solved standard SIR model and got analytic solution of i) timing of epidemic peak ii) number of infectious people on epidemic peak. Then we compared two cases, with/without temporal reduction of transmission rate. Key result is temporal reduction of transmission rate decreases infectious people on epidemic peak and delay peak timing.
- May. 9
  - Kenta Yashima
    - Epidemic dynamics on the commute network in Tokyo metropolitan area
    - Epidemic dynamics of an infectious disease spreading over the commute network in Tokyo metropolitan area is analyzed using a simple mathematical model. The model is formulated based on the meta-population connected by railway lines where populations (train stations) are interconnected by commuter flows (commuter railway network). Here, the actual data from the Urban Transportation Census (Japanese Ministry of Land, Infrastructure, Transport and Tourism) is used to simulate the movements of commuters. The effect of infectiousness of pathogen and the structure of commute network are investigated and the following results are obtained. i) The probability of global epidemic is mainly determined by the joint distribution of home and work population sizes of commuters, but is insensitive to the geographical or topological structure of the network. ii) The first passage time of epidemic at each populations follows a power law distribution against it's population size.
- Apr. 27 (Shonan seminar)
  - Hisashi Ohtsuki (Dept. Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies, Kanagawa, Japan)
    - Evolution of cooperation by phenotypic similarity
    - Phenotypic similarity is often used as a cue of genetic kin recognition. An example is found in kin recognition in ants, where cuticular hydrocarbons work as a chemical cue in nestmate recognition. Here I develop a theoretical model to investigate the condition for evolution of altruism via phenotypic similarity. My model assumes that one's phenotype is represented by an integer number and that it increases or decreases by one in each random mutation. Results suggest that a high mutation rate in phenotype space or the use of multiple cues favors evolution of altruism.
  - Takasu Fugo (Dept. Information and Computer Sciences, Nara Women's University, Nara, Japan)
    - A spatial territory game in continuous space
    - We propose a spatial territory game in continuous space where a player fights for territory overlapped with other players. This game is basically a spatial version of snow drift/prisoner's dilemma games but differs from many of previous spatial games in that players are positioned in continuous space rather than on grids of lattice and that reproduction of players is individual-based and population dynamics of strategies in focus is explicitly implemented. Simulation study suggests that this game can be very different from spatial games played in lattice space; continuous space seems to encourage spread of "selfish" individuals and to discourage the "cooperative", which is very contrary to the widely established theory that clustering of cooperative strategists can prevent the invasion of the selfish. Some analytical treatments and the significance of the structure of space in focus will be discussed.

Reading Circles

- 2011
- 統計学入門 / 東京大学教養学部統計学教室 / 1991
- 自然科学の統計学 / 東京大学教養学部統計学教室 / 1992
  - every Thursday, from 13:00 to 15:00 at room 306
- An Introduction to Stochastic Modeling (4th edition) / Pinsky, M. A. & Karlin, S. / 2010
  - every Thursday, from 13:00 to 15:00 at room 306
- 2010
  - パーコレーションの基本原理 / Dietrich Stauffer & Amnon Aharony / 吉岡書店 / 2001（修正版）
    - (from Jan. 2009) every Thursday from 17:00 at room 311 (lounge)
  - Dynamical Processes on Complex Networks / Alain Barrat, Marc Barthlemy & Alessandro Vespignani / Cambridge Uni. / 2008
    - every Wednesday from 17:00 at room 311 (lounge)
  - Coalescent Theory: An Introduction / John Wakeley / Roberts & Co / 2008
    - (from May. 2010) every Wednesday from 10:00 at room 306
- 2009
  - Mathematical Models in Biology / Leah Edelstein-Keshet / Society for Industrial and Applied Mathematics / 2005
- 2008
  - Evolutionary Dynamics: Exploring the Equations of Life / Martin A. Nowak / Belknap Press of Harvard University Press / 2006