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7 June 2019, Charlottesville: Mid-Atlantic Synthetic Biology Symposium #568

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Daniel-Mietchen opened this issue Jun 7, 2019 · 15 comments

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commented Jun 7, 2019

The agenda is in this Gdoc, and there is this overview page.

Organized by SynBio@UVA

No slides shared, nobody seems to be tweeting on this

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commented Jun 7, 2019

Steven Zeichner, UVA: Synthetic Biology Approach to Novel Vaccine Development
https://tools.wmflabs.org/scholia/author/Q64447346

  • collaborates with Peter Kwong (NIH) around structural context of Membrane Proximal External Region (MPER) of immunogenic proteins with potential to be used in vaccination
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commented Jun 7, 2019

Myriam Cotten, William & Mary: Identifying Principles in Peptide Engineering: Lessons Learned from the Amazing World of Host-Defense Peptides
https://tools.wmflabs.org/scholia/author/Q64447649

  • plug for solid-state NMR facility at W&M, inviting collaboration
  • peptide antibiotics in mast cells of fish
  • piscidines
  • copper as mediator of antimicrobial action via p3 binding of DNA backbone; collaborated with Ruth Nussinov at NCI
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commented Jun 7, 2019

Fengbin "Jerry" Wang, Egelman Lab, UVA: CryoEM: A Powerful Tool for Understanding Biological and Synthetic Polymers

  • PDB on first slide as the end point of their protein structure determination workflow
  • "if you can do high-resolution Cryo-EM, you d not need to much prior knowledge to determine protein structure"
  • type IV pili in bacteria and arachaea
  • Geobacter nanowires
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commented Jun 7, 2019

Mike Timko, UVA: Metabolic Engineering for Plant Based Human Therapeutics

Hai Liu (not on the program): Smart Metabolic Engineering of Plants for the Production of Human Nutraceuticals and Therapeutics

  • looking at primary and secondary metabolism in plants as the source of molecules of interest to humans
  • astaxanthin is one of the most antioxidants found in nature but supply can currently not really meet demand
  • cloning some genes from astaxanthin-producing organisms (Adonis aestivalis) into easily culturable organisms like tobacco, hemp, bacteria or yeast
  • similar approach to producing human milk oligosaccharides (derived from lactose) in plants for women who cannot breastfeed (enough)
  • question from audience: "given the range of synbio you are engaged with, is there a company that does this at scale, similar to what Ginkgo Bioworks does?" response from audience: "It used to be called Monsanto, which is now Bayer"
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commented Jun 7, 2019

Deyu Xie, NC State: Gene Design-based Alteration of the Terpenoid Pathway Increases Plant Growth and Biomass

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commented Jun 7, 2019

Ameer Shakeel, CSO of Agrospheres: Synthetically Engineered Solutions for Bio-Controls in Agriculture

  • more time lost switching computer
  • working on degrading pesticides, since pesticide is an issue both worldwide and locally (e.g. in vineyard)
  • small-scale tests showed that pesticides can be degraded within hours
  • much of pesticides is not reaching the plants anyway
  • encapsulate pesticides into "AgriCells" which allow for controlled release
  • AgriCells are engineered by tweaking bacterial division such that the centromer as at the apex, not the center, which gives nice spherical variants of rod-shaped bacteria
    • about 1 in two bacterial divisions creates such a minicell
    • they have issues harvesting the minicells from dishes, so now working on flow-based techniques
  • trying to replace synthetic pesticides with biologicals
  • currently field testing with ADAMA
  • greenhouse testing facilities
  • Mark Kester (one of the symposium organizers) is an early investor in the technology
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commented Jun 7, 2019

Ed Eisenstein, UMD: Systems, Structural and Synthetic Biology to Develop Next-Gen Plants for Biofuel

  • https://tools.wmflabs.org/scholia/author/Q28359814
  • cellulose and lignin are
    • some of the most common polymers on the planet
    • closely intertwined in plant structures, but
      • humans have a strong interest in cellulose (chiefly for biofuel) but low interest in lignin
  • idea: can the metabolic pathways that produce lignin/ cellulose be (re-)engineered such that cellulose can be more easily harvested (and ideally more of it)?
  • promising preliminary results, details to be worked out
  • multiple shout outs (by him and previous speakers) to iGEM
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commented Jun 7, 2019

Keynote Speaker: Dr. Pam Silver, Harvard University Wyss Institute of Biologically Inspired Engineering

Designing Biology for Health and Sustainability

  • lots of accolades, including co-founder of iGEM
  • https://tools.wmflabs.org/scholia/author/Q7129257
  • How can we identify [engineering] problems that biology can help solve?
    • sounds like molecular bionics to me
  • introduction about phage lambda
  • bionic leaf
  • "the gut is an amazing place"
  • over US$ 10 billion are used each year on colonoscopies in the US
  • probiotic pill to diagnose diarrhea using gut microbiome
  • tetrathionate as an indicator of inflammation
  • Sedlmayer and Fussenegger 2017, USB stick with multiple bacterial biosensors
  • criticizes the non-GMO movement and plans to open an "All-GMO" restaurant
  • "bug in a pill"
  • total genome resynthesis
  • book "the informer" on infection
  • microbial kill switch
  • artificial chromosome
    • key challenge: how to build a synthetic centromere
    • human artificial chromosomes can be delivered (along with proteins) to mammalian cells through yeast cells
    • big idea: for extreme use cases (e.g. severe injuries), it would be great if there were mechanisms to help, e.g. proteins from extremophiles
  • imagine cells that had 10 fluoresence markers or that were to express a 1000 antigens on their cell surface
  • "anticipatory therapeutics" - sounds to me like prophylaxis
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commented Jun 7, 2019

iGEM 2019 is Oct 31- Nov 4 in Boston: https://2019.igem.org/ .
UVA has a team participating.

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commented Jun 7, 2019

Steven Fong, VCU: Engineering Non-Model Organisms for Biochemical Production

  • self-described "microbial chauvinist"
  • likes to think of the ca. 8.7 million (or whatever) species and consider their diversity and how it can be leveraged in different contexts
  • high hopes for microbes in this regard
  • Thermobifida fusca: to turn cellulose into propanol
  • barriers for working with non-model systems
    • how to build genetic workflows to transform it
  • used enzymes that could handle several steps of a metabolic pathway
  • Serratia marcescens
    • breaks down chitin
    • naturally resistant to some typical antibiotics
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commented Jun 7, 2019

Bryan Berger, UVA: Biomanufacturing of Advanced, Functional Nanomaterials

  • introduces quantum dots as being
    • interesting in a number of contexts
    • expensive to manufacture
      • $1k-10k per gram
  • then introduces Stenotrophomonas maltophilia as a potential system to manufacture quantum dots, i.e. size-controlled conductive nanomaterials
  • engineering proteins that could in principle catalyze all steps of a given pathway
  • artificial photosynthesis
  • next candidate: silicatein alpha - can this be synthesized bottom-up?
    • PDB 2VHS
  • nanoceria catalysts (used in catalysts in cars)
  • got production costs down to about $10-$100 per gram using biosyntheis
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commented Jun 7, 2019

Preetam Ghosh, VCU: Information Theory Models of Molecular Communication and Cellular Signaling

  • running fast-forward loops around the Lac operon by the thousands
  • sounds like metabolic control theory at scale
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commented Jun 7, 2019

Hannes Schniepp, William & Mary: Unlocking the Mysteries of a Biogenic Wonder Material: Understanding Spider Silk from the Molecular to the Meter Scales

  • https://tools.wmflabs.org/scholia/author/Q47986821
  • touts silkworm silk a "7000 year-old synbio success story", and until about WW2, the best material of its kind
  • then introduces spider silk, which is even more amazing, e.g. compared to steel and kevlar
  • interested in use cases like bullet-prove vests
  • considers biotechnological workflows to produce spider silk
  • structure of spider silks not well known
  • model system: Loxosceles laeta
    • ribbon structure
    • consists to 100% of nanofibrils
  • Nephila clavipes
  • "We can make spider silk from protein!"
  • comment from audience: someone from Tufts has determined that spider protein is "intrinsically disordered", with folding patterns thus depending much on context
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commented Jun 7, 2019

Mark Styczynski, GA Tech: Low-Resource, Low-Cost Diagnostics Via Synthetic Biology

  • bacteria-based tests for micronutrient deficiencies (zinc specifically, which kills about 100k kids under 5 each year) in low-cost settings
  • coupled Lac operon with Zinc-responsive elements in cell-free system produced in E. coli that were then lyzed
  • key issue is calibration
  • need standards
  • "saturate the biomarker and vary the regulator"
  • generalizing from Zinc to other micronutrients
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commented Jun 7, 2019

Key take-aways:

  • lots of exciting science
  • lots of things relevant to protein structure
  • not much openness
  • would benefit from interaction with data science
  • iGEM is an interesting model to look at in terms of engaging the next generation
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