Scientific Calendar Event



Description An ICTP meeting in person

Microbes are found all over our planet, across an enormous variety of environmental conditions. Their physiological capacities reflect the characteristics of their various niches, including competition, randomness, dynamics, nutrient availability, and stresses. Despite their behavioral diversity, microbes share the same underlying biochemical and physical principles.
 
In the last two decades systems biology and biophysics have made substantial advances in predicting the emergent physiological capacities of microbes from basic principles, making use of genomic information, massive data collection, and mathematical models. A key insight has been that the global protein expression profile of the cell is determined by the allocation of limited biosynthetic resources. Current research aims at understanding how cells modulate resource allocation to improve biological fitness and how the resulting cell states reflect niche characteristics.

In our meeting, we gather systems biologists and physicists to discuss questions at the frontier of resource allocation approaches in cell physiology to explore their general applicability and limitations. The main challenge is to better understand the role of interactions and cell-to-cell variability across multiple scales, with the hope of bridging the gap between cell physiology and microbial ecology. The aim is to map the contours of a general theory for predicting emergent cell-physiological properties from genomic information and basic physicochemical principles.
 
Call for Contributed Abstracts: All applicants are encouraged to submit an abstract for a poster presentation or a contributed talk.

Speakers:
V. BALDAZZI, INRAE, France
F. BRUGGEMAN, Free University of Amsterdam, Netherlands
L. CIANDRINI, University of Montpellier, France
O. CORDERO, MIT, USA
M. COSENTINO LAGOMARSINO, Ifom, Milan
M. DAL BELLO, MIT, USA
A. DE MARTINO, Politecnico di Torino, Italy
A. FUENTES, UNAM, Mexico
T. HWA, UCSD, USA
S. JAIN, University of Delhi, India
W. LIEBERMEISTER, INRAE, France
J. LENNON, Indiana University, USA
S. MASLOV, University of Illinois, USA
S. MCGLYNN, Tokyo Institute of Technology, Japan
I. MIZRAHI, Ben Gurion University, Israel
R. MULET GENICIO, University of Havana, Cuba
M. RIVAS-ASTROZA, Universidad Tecnologica Metropolitana, Chile
D. SEGRE, Boston University, USA
E. VAN NIMWEGEN, University of Basel, Switzerland
V. VENTURI, ICGEB, Italy
A. WEISSE, University of Edinburgh, UK

Grants: A limited number of grants are available to support the attendance of selected participants, with priority given to participants from developing countries. There is no registration fee.



Go to day
  • Monday, 2 October 2023
    • 08:30 - 09:30
      • 08:30 Registration Formalities 1h0'
        Upon arrival, Visitors not staying in the ICTP Guest Houses, are kindly requested to complete registration formalities at the Leonardo Building (Lobby). The Registration Desk will be open from 8.30 to 9.30.
        
    • 09:30 - 19:00
      • 09:30 Welcome Remarks 15'
      • 09:45 Growth-dependent proteome allocation in E. coli: from phenomena to control strategy and dynamics 1h0'
        Speaker: Terence HWA (University of California At San Diego, USA)
        Material: Video
      • 10:45 Coffee Break 30'
      • 11:15 Resource allocation strategies behind rate-yield phenotypes in E.coli 50'
        Speaker: Valentina BALDAZZI (INRAE, France)
        Material: Slides Video
      • 12:05 Single-cell mass growth: the interplay of volume and dry mass 30'
        Speaker: Alexander Dieter BAUMGARTNER (ETH Zurich, Switzerland)
      • 12:35 Lunch Break 1h25'
      • 14:00 Individualistic behavior of growing cells 50'
        Speaker: Marco COSENTINO LAGOMARSINO (IFOM, Italy)
        Material: Video
      • 14:50 Introduction on group work on book 30'
        Speaker: Wolfram LIEBERMEISTER (French National Research Institute for Agriculture, Food and Environment (INRAE), France)
        Material: Video
      • 15:20 Group work on book 1h30'
      • 15:20 Consumer-Resource models and ecological dynamics 1h30'
        Tutors: Leonardo PACCIANI-MORI (University of California, USA) and
        Will SHOEMAKER (ICTP, Italy)
      • 16:50 Break 10'
      • 17:00 Poster session 2h0'
        Material: Booklet with poster abstracts
      • 18:45 Get to know each other 15'
    • 19:00 - 20:00
      • 19:00 Welcome Reception 1h0' ( Leonardo Building - Terrace )
        All participants are cordially invited to a Welcome reception.
  • Tuesday, 3 October 2023
    • 09:30 - 18:30
      Location: Budinich Lecture Hall (Leonardo Building)
      • 09:30 Simple rules governing proteome allocation for fast- and slow-growing species across bacterial phylogeny 1h0'
        Speaker: Terence HWA (University of California At San Diego, USA)
      • 10:30 A model of RNA repair to study antibiotic tolerance 30'
        Speaker: Hollie HINDLEY (University of Edinburgh, UK)
        Material: Video
      • 11:00 Group photo 5'
      • 11:05 Coffee Break 25'
      • 11:30 From environmental responses at the organismal level to community properties - Part I 1h0'
        Speaker: Martina DAL BELLO (Massachusetts Institute of Technology Department of Physics, USA)
        Material: Video
      • 12:30 PCI a community-organised review of preprints and a diamond open access journal 30'
      • 13:00 Lunch Break 1h30'
      • 14:30 Phase transitions in biosynthesis fluxes determine bacterial growth regimes 30'
        Speaker: Philippe FUCHS (CNRS UMR, France)
        Material: Video
      • 15:00 Extending the Shadow Price-Based Definition of Nutrient Limitation to Genome-Scaled Metabolic Networks in Complex Medium 30'
        Speaker: Antonio Jose PEREIRO MOREJON (University of Havana, Cuba)
        Material: Video
      • 15:30 Growth laws and proteome allocation models in- and out- of steady state 1h30'
        Tutors: Rossana DROGHETTI (IFOM ETS - The AIRC Institute of Molecular Oncology, Italy) and 
        Ludovico CALABRESE (IFOM ETS - The AIRC Institute of Molecular Oncology, Italy)
      • 15:30 Group work on book 1h30'
      • 17:00 Break 30'
      • 17:30 Forum session: discussion (in presence and online) 1h0'
  • Wednesday, 4 October 2023
    • 09:30 - 14:00
      Location: Budinich Lecture Hall (Leonardo Building)
      • 09:30 Inverse modeling metabolism and metabolic crosstalk in cell populations 50'
        Speaker: Andrea DE MARTINO (Politecnico of Tourin, Italy)
        Material: Slides Video
      • 10:20 Microbial community assembly and competition in boom and bust environments 50'
        Speaker: Sergei MASLOV (University of Illinois Urbana Champaign, USA)
        Material: Slides Video
      • 11:10 Coffee Break 20'
      • 11:30 Coarse-grained descriptions of microbial community composition and metabolism 50'
        Speaker: Otto CORDERO (MIT, USA)
        Material: Video
      • 12:20 Lunch break 1h40'
  • Thursday, 5 October 2023
    • 09:30 - 17:00
      Location: Budinich Lecture Hall (Leonardo Building)
      • 09:30 Importance of environmental fluctuation and physiological adaptation for coexistence in microbial communities 1h0'
        Speaker: Terence HWA (University of California At San Diego, USA)
        Material: Video
      • 10:30 How total mRNA influences cell growth through free ribosome 30'
        Speaker: Ludovico CALABRESE (FOM ETS, Italy)
        Material: Video
      • 11:00 Coffee Break 30'
      • 11:30 From environmental responses at the organismal level to community properties - Part II 1h0'
        Speaker: Martina DAL BELLO (Massachusetts Institute of Technology Department of Physics, USA)
        Material: Video
      • 12:30 Effective bet-hedging through growth rate dependent stability 30'
        Speaker: Hugo Daan DE GROOT (University of Basel, Switzerland)
        Material: Video
      • 13:00 Lunch Break 1h30'
      • 14:30 Homogeneous degree-one models of bacterial physiology: Understanding exponential trajectories, balanced growth and aspects of cell size. 50'
        Speaker: Sanjay JAIN (University of Delhi, India)
        Material: Video
      • 15:20 How do bacteria adaptively control their growth rate in fluctuating environments? 30'
        Speaker: Robert PLANQUE (VU Amsterdam, Netherlands)
      • 15:50 PCI a community-organised review of preprints and a diamond open access journal 15'
      • 16:05 Break 10'
      • 16:15 Young Scholars Forum 45'
  • Friday, 6 October 2023
    • 09:30 - 17:00
      Location: Budinich Lecture Hall (Leonardo Building)
      • 09:30 From environmental responses at the organismal level to community properties - Part III 1h0'
        Speaker: Martina DAL BELLO (Massachusetts Institute of Technology Department of Physics, USA)
        Material: Video
      • 10:30 Evolutionary adaptation of microbes to grow fast at low concentrations of nutrients 30'
        Speaker: Justus FINK (ETH Zurich, Switzerland)
        Material: Video
      • 11:00 Coffee Break 30'
      • 11:30 Mechanistic models of bacterial growth 50'
        Speaker: Andrea WEISSE (SynthSys - Synthetic & Systems Biology, University of Edinburgh, UK)
        Material: Video
      • 12:20 The collective metabolism of microbial communities is driven by proteome efficiency of individuals – a perspective 30'
        Speaker: Matthias HUELSMANN (ETH Zurich, Switzerland)
        Material: Video
      • 12:50 Lunch Break 1h40'
      • 14:30 Multiscale experimental evolution of antibiotic resistance 50'
        online
        Speaker: Ayari FUENTES-HERNANDEZ (UNAM, Mexico)
        Material: Video
      • 15:20 Optimal enzyme profiles in metabolic pathways: principles and simple solutions 30'
        Speaker: Elad NOOR (Weizmann Institute of Science, Israel)
        Material: Video
      • 15:50 Flux Balance Analysis 1h10'
        Tutor: Daan DE GROOT (University of Basel, Switzerland)
      • 15:50 Group work on book 1h10'
  • Monday, 9 October 2023
    • 08:45 - 18:45
      Location: Kastler Lecture Hall (Adriatico Guesthouse)
      • 08:45 Principles of dormancy and microbial complexity 1h0'
        Speaker: Jay LENNON (Indiana University, USA)
        Material: Video
      • 09:45 Single-cell analysis of bacterial gene expression dynamics during starvation 30'
        Speaker: Jules Luc Théo GERVAIS (University of Basel, Switzerland)
        Material: Video
      • 10:15 Coffee Break 30'
      • 10:45 Inferring metabolic flow rates by maximizing information entropy under gene expression constraints 50'
        Speaker: Marcelo RIVAS-ASTROZA (Universidad Tecnologica Metropolitana, Chile)
        Material: Slides Video
      • 11:35 Unveiling Global Patterns in Gene Expression Dynamics: Modeling and Analyzing Species Abundance Distributions and their Biological Interpretation 30'
        Speaker: Emanuele PIGANI (Anton Dohrn Zoological Station, Italy)
        Material: Video
      • 12:05 Lunch Break 2h25'
      • 14:30 Dynamics of algae-bacteria interactions in artificial plankton communities 30'
        Speaker: Marco MAURI (Jena University, Germany)
        Material: Video
      • 15:00 Exploring the effects of metabolic mutations on cell-cell interactions in spatially structured synthetic microbial communities 30'
        Speaker: Divvya RAMESH (ETH Zurich, Switzerland)
        Material: Video
      • 15:30 Group work on book 1h30'
      • 15:30 Biochemical Thermodynamics and Modeling 1h30'
        Tutor: Elad NOOR (Weizmann Institute of Science, Israel)
        Material: Slides
      • 17:00 Poster session 1h45'
        Material: Booklet with poster abstracts
    • 19:00 - 20:30
      • 19:00 Reception 1h0' ( Adriatico Guesthouse - Terrace )
        All participants are cordially invited to a Reception.
  • Tuesday, 10 October 2023
    • 09:00 - 16:30
      Location: Kastler Lecture Hall (Adriatico Guesthouse)
      • 09:00 Bacteria-phage coevolution with a seed bank 1h0'
        Speaker: Jay LENNON (Indiana University, USA)
        Material: Video
      • 10:00 Diversity limits in an eco-evo dynamics in the presence of infinite resources 30'
        Speaker: Vitor MARQUIONI MONTEIRO (UNICAMP, Brazil)
        Material: Video
      • 10:30 Coffee Break 30'
      • 11:00 Exploring cellular budgeting with non-equilibrium traffic models 1h0'
        Speaker: Luca CIANDRINI (Université de Montpellier, France)
        Material: Video
      • 12:00 PCI a community-organised review of preprints and a diamond open access journal 30'
      • 12:30 Group Photo 5'
      • 12:35 Lunch Break 1h55'
      • 14:30 Spatio-temporal dynamics of ecosystem metabolism 50'
        online
        Speaker: Daniel SEGRE (Boston University, USA)
        Material: Video
      • 15:20 Group work on book 1h10'
      • 15:20 Environmental dependence of the target of selection 1h10'
        Tutor: Justus FINK (ETH Zurich, Switzerland)
  • Wednesday, 11 October 2023
    • 09:00 - 14:30
      Location: Kastler Lecture Hall (Adriatico Guesthouse)
      • 09:00 Interacting cells: From toy models to the industry 50'
        Speaker: Roberto MULET GENICIO (University of Havana, Cuba)
        Material: Video
      • 09:50 When noise is regulation and regulation is noise: how bacteria adapt their phenotypes to an uncertain environment 50'
        Speaker: Erik VAN NIMWEGEN (University of Basel, Switzerland)
        Material: Video
      • 10:40 Coffee Break 20'
      • 11:00 What we talk about when we talk about ... optimality, adaptation and control 50'
        Speaker: Antonio CELANI (ICTP, Italy)
        Material: Video
      • 11:50 Fluid dynamics of expanding yeast colonies 30'
        Speaker: Gabriele MANGANELLI (Cornell University, USA)
      • 12:20 Lunch Break 2h10'
  • Thursday, 12 October 2023
    • 09:00 - 17:00
      Location: Kastler Lecture Hall (Adriatico Guesthouse)
      • 09:00 Evolution of a minimal cell 1h0'
        Speaker: Jay LENNON (Indiana University, USA)
        Material: Video
      • 10:00 Analysis of mycobacterial metabolic variability using genome-scale metabolic models 30'
        Speaker: Andrea Ignacia CANCINO AGUIRRE (Centre INRIA de l'Universite Grenoble Alpes, France)
      • 10:30 Coffee Break 30'
      • 11:00 Single cell anabolic rates measured by the nanoSIMS: space, population structure, and relationships 1h0'
        Speaker: Shawn MCGLYNN (Tokyo Institute of Technology, Japan)
        Material: Video
      • 12:00 Lunch Break 2h30'
      • 14:30 Metabolic value theory 50'
        Speaker: Wolfram LIEBERMEISTER (French National Research Institute for Agriculture, Food and Environment (INRAE), France)
        Material: Slides Video
      • 15:20 Modeling the physiological and demographic consequences of recycling in closed microbial systems 30'
        Speaker: William R. SHOEMAKER (ICTP, Italy)
        Material: Video
      • 15:50 Precarity and uncertainty in academia 1h10'
  • Friday, 13 October 2023
    • 09:00 - 12:00
      Location: Kastler Lecture Hall (Adriatico Guesthouse)
      • 09:00 Cell-Cell contact independent signaling in the plant microbiome 1h0'
        Speaker: Vittorio VENTURI (ICGEB, Italy)
        Material: Video
      • 10:00 Growth Mechanics: Optimal cellular resource allocation in dynamical environments 30'
        Speaker: Hugo DOURADO (Heinrich Heine University, Germany)
        Material: Video
      • 10:30 Coffee Break 30'
      • 11:00 Oscillations naturally arise from the ppGpp-mediated incoherent feedback between amino acids and ribosomes 30'
        Speaker: Rossana DROGHETTI (IFOM ETS, Italy)
        Material: Video
      • 11:30 Traffic Slowdown by Antibiotics 30'
        Speaker: Johannes KEISERS (CBS, France)
        Material: Video