The Team The Team The Team Hydrogen Highly efficient energy - - PowerPoint PPT Presentation

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The Team The Team The Team Hydrogen Highly efficient energy - - PowerPoint PPT Presentation

Sep 17, 2023 222 likes •984 views

The Team The Team The Team Hydrogen Highly efficient energy carrier Production requires hypoxygenic conditions And consumes redox potentials, and protons Nitrogen Fixation Vital Process Its also COSTLY Requires

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The Team

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The Team

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The Team

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Hydrogen

  • Highly efficient energy carrier
  • Production requires

– hypoxygenic conditions – And consumes redox potentials, and protons

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Nitrogen Fixation

  • Vital Process
  • It’s also COSTLY
  • Requires hypoxygenic conditions too
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PROJECT

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Phaseolus vulgaris nodule

Ray Dixon & Daniel Kahn. Nat. Rev. 2004

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Nutrient Supply

  • Phaseolus vulgaris (bean plant) provides

Rhizobium etli (natural nitrogen fixator), carbon sources in exchange for nitrous compounds.

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Nutrient Supply

Osbaldo Resendis-Antonio. PloS Com. Biol. 2007

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Constrains

  • 1. Couple with Rhizobium physiology.

– Codon usage. – High hydrogenase production – Cross-talk with redox potentials

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Constrains

  • 2. Express system when microaerobic

enviroment is present (nodulating stage).

  • 3. Lack of standardized parts for Rhizobials,

including vectors and promoter

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Avoiding translational cross-talk

  • Codon Adaptation

Index (CAI).

– Nodulating Vs Constitutively Expressed genes

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  • Optimization of the 5' UTR

– Lower DG for 5’UTR avoiding complex structures in RBS

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Construction

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Construction

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Construction

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Low oxygen inducible promoter in Rhizobia

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Activity

  • Submitted and works as expected in low oxygen

concentration

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Activity

  • Submitted and works as expected in low oxygen

concentration

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How to introduce in R. etli?

  • Standardization pBBRMCS-5, a useful

plasmid in free living and nodulating Rhizobium.

  • Standard region for plasmid made from

pSB1T3

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  • ~4:1 ratio

with pSB1T3.

  • DH5a
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  • ~4:1 ratio

with pSB1T3.

  • DH5a
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WT

  • E. Coli
  • R. etli
  • R. etli
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Bioparts in progress

  • High stable plasmid with region repC-ctRNA.
  • Anderson´s collection in Rhizobia.
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Multi-Scale Model

Niche Cell Metabolism

  • Game Theory
  • Cellular

Automaton

  • Markov Model
  • C vs N: Cellular

Automaton

  • Flux Balance

Analysis

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METABOLIC SCALE

Flux Balance Analysis & Extreme Pathways

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Metabolism: FBA

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Electron Transport Carbon

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FBA

  • Less effective C metabolism (130%)
  • Nitrogen Fixation unaffected, or enhanced
  • Increased flow in Redox potentials

(antioxidants!!)

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CELL SCALE

Markov Model & Cellular Automaton

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Cell: Plasmid Stability

  • Given:

Hour Colonies in Antibiotic-Free Medium Colonies in Antibiotic-Present Medium Ratio 100 100 1 12 100 100 1 24 97 96 0.989690722 36 68 65 0.955882353 48 100 98 0.98 60 100 99 0.99 72 100 99 0.99

The initial inoculation at t=0 is of first daughter cells, i.e. second generation Doubling time is of 40 minutes, conservative estimate for M9 glucose medium There are no Gain-Of-Function mutations that generate phenotipe without plasmid The Total count is given by the number of colonies in AB-free medium, i.e. the positive control

Plasmid Stability P(x)=0.999774369 Markov Chain Framework

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Cell: N fixation comparison

WildType: 50 plants TransGenic: 70 plants

Cellular Automaton in Kappa

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NICHE SCALE

Game Theory & Cellular Automaton

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Niche: Game Theory

  • Payoff Matrix:

– Snowdrift Game – WT: only N fixation, no H production – TG: only produces H, no N fixation

WildType Stasis Reproduce Trans Genic Stasis 0/0 0/+ Reproduce +/0

  • /-
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Niche: Game Theory

3 Nash Equilibria

  • 1. TransGenic Fixation

Unfeasible: no one fixates N

  • 2. WildType Fixation

Unfeasible: TG is more efficient

  • 3. Mixed State

Feasible!

WildType Stasis Reproduce Trans Genic Stasis 0/0 0/+ Reproduce +/0

  • /-
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Niche: Game Theory

Mixed State:

If Players unable to change «States», Mixed Equilibrium becomes an Evolutionary Steady State. Id est: resistant to «Mutations»

WildType Stasis Reproduce Trans Genic Stasis 0/0 0/+ Reproduce +/0

  • /-
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Niche: Cellular Automaton

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MODELING END

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Planning

Involve people

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Current Scenario

?

Planning

Involve people

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Planning

Involve people Current Scenario

?

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Some Background

Mexico Can’t rely on oil

  • r fossil fuels for much

longer Mexico is supposed to have commitments with the environmental care Relies too much on Fertilizer for agricultural activities

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Hydrobium etli in Cuatzoquitengo

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Overview

Pursued the ideal of applying our potential developments on the ground

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Hydrobium etli goes Cuatzo

  • Small community in the Sierra

Mixteca

  • Population 1,618
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Cuatzo has very few spanish speakers

Their main activity is agriculture

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Traditional cultivation of the bean plant (experience)

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Taking the energy services to communities like Cuatzo is a challenge

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Outreach Practice

Community Teachers talked to the assembly about the project We addressed the communal authorities with the details

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Outreach Practice

Feedback

“It could be a dream come true, we wouldn’t have to worry about electricity shortage anymore” “It could be truly beneficial for us if you could prove that the little plant can give us electricity” “We wouldn’t have to depend on the Federal Commission of Electricity anymore”

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“What is the distance that must be kept between the house and the plant?” “What about our original bean crops? What would happen if they mixed? “Are there special cares? Do we have to fumigate?” “The plant has a lifetime, we wouldn’t know how to mantain it living for longer, if that was the case”

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What did we learn?

  • Investigating and developing solutions for

people’s necessities is not enough.

  • We must involve them in the whole process

 They are eager to participate!

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Bio-Sintetizarte

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Bio-SintetizARTe

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Planning Bio-SintetizArte

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Finding the artists

  • Encouraged everyone’s participation
  • Small Synthetic Biology Definition
  • Invited to a talk about SynBio at our

campus

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Bio-Sintetizarte At The Museum

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September 30th: Inauguration

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Hall of fame

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The Art

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Yuria Tamayo

Over intention

“I am inspired through the

  • bservation of the cells and

nature itself”

The Uterus Insects

www.francescadallabenetta.com/ “On the one hand the scientific progress is extraordinary… …on the other hand, it’s almost a betrayal to the feminine nature of life”

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Summing up

  • Bio-Sintetizarte let us to know how are

we, and our work seen.

  • Reached people in an elegant, sensitive,

beautiful manner.

  • Called attention to Synthetic Biology
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Ma Making king ev everyone eryone a part rt of

  • f

Sy Synthetic nthetic Bio iology logy

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Project Wrap Up

  • Hydrogen Build: In progress, 20%
  • Rhizobial Kit: In progress, 50%
  • Impact Exploration: Done
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Sponsor Thanks

  • Oil Sands Leadership Initiative, Canada
  • Mr. Gene, Germany
  • Gobierno de Tamaulipas, Mexico
  • Centro de Ciencias Genómicas, Mexico
  • Licenciatura en Ciencias Genómicas, Mexico
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Special Thanks

  • Dr. Maria Lourdes Guirard
  • Dr. Esperanza Martínez
  • Dr. David Romero & his Lab
  • Dr. Rafael Palacios
  • Dr. Guillermo Dávila & his Lab

Our Instructors Our Advisors Our Team