Tag Archives: bacterium

Rafts! a game for your inner genetic engineer

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Earlier this week, RaftsTheGame (@TheRaftsGame) popped up on my twitter feed, which was excellent timing since it’s getting close to Christmas in a year (2020) when I imagine a lot of people may be home and inclined to play games.

The people (rafts4biotech) who produced Rafts The Game (also called Rafts!) are involved in a research project funded by the European Union’s Horizon 2020 programme,

RAFTS!
Create the bacterium of your dreams

Have you ever wondered what it would be like to be a genetic engineer? Now’s your chance to find out! Rafts! is a card game in which your aim is to design a bacterium while trying to overcome the challenges of research work.

If you are a researcher, look no further – Rafts! enables you to finally share your academic struggles with those friends who don’t have a clue of what you do!

THE GAME

In Rafts! you race to become the first scientist to create a bacterium that can do incredible things: cleaning an oil spill, detecting toxic compounds, producing blood for donations… Sounds like science fiction? More like a regular day at the lab!

But don’t get carried away – nobody said conducting research was easy! Hard work alone isn’t enough if you don’t have the right genetic instructions as well as a combination of money, time as well as food for your bacterium. You’ll have to collect all of these resources to finish the masterpiece that is your bacterium.

In this laboratory people play dirty, so don’t forget to keep an eye on your colleagues – they are all trying to achieve their objectives, and sometimes you will compete for the same resources. Don’t hesitate to strike back!

THE CARDS

There are three types of cards in Rafts!: action cards help you gather the resource cards that you will need to achieve the goal in your objective card. Bring your mouse on top of a card to know what it can do!

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GET YOURS

Ready to become the biotech wizard you’ve always wanted to be? You’re just a click away from building the bacterium of a lifetime!

Download Rafts! for free and print it yourself – or let your local print shop do it for you:

DOWNLOAD

DESCARGA

Order a ready-made Rafts! deck to your doorsteps – by clicking on the link we direct you to the card shop where you can finish your order:

ORDER

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Here’s what the cards look like,

[downloaded from http://www.raftsthegame.com/]

The rules of the game are here.

For anyone curious about the source for the game, here’s a bit about rafts4biotech, from the homepage,

Engineering bacterial lipid rafts to optimise industrial processes

Context

Bacteria are used in the biotechnology industry to produce a wide range of valuable compounds. However, the performance of these microorganisms in the demanding industrial conditions is limited by the toxicity of some compounds and the complex metabolic interactions that occur within the bacterial cells.

Challenge

Generating new synthetic microorganisms that will solve productivity hurdles and yield a great variety of economy-value compounds. These modified strains will be used as standardised microbial chassis platforms to fit industry needs.

Solution

The R4B solution relies on confining the production of compounds to specific areas of the microbe’s membrane called lipid rafts.  This recently-discovered regions present an ideal setting that will avoid interferences with bacterial metabolism and viability.

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Given that at least one of the COVID-19 vaccines (Pfizer-BioNTech?) is wrapped in lipid nanobodies and, now, with this mention of lipids, it seemed like a good idea (for me) to learn about lipids. Here’s what I found in the definition for lipid in The free Dictionary,

a group of substances comprising fatty, greasy, oily, and waxy compounds that are insoluble in water and soluble in nonpolar solvents, such as hexane, ether, and chloroform.

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Let the games begin!

Clean up oil spills (on water and/or land) with oil-eating bacterium

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Quebec’s Institut national de la recherche scientifique (INRS) announced an environmentally friendly way of cleaning up oil spills in an April 9, 2018 news item on ScienceDaily,

From pipelines to tankers, oil spills and their impact on the environment are a source of concern. These disasters occur on a regular basis, leading to messy decontamination challenges that require massive investments of time and resources. But however widespread and serious the damage may be, the solution could be microscopic — Alcanivorax borkumensis — a bacterium that feeds on hydrocarbons. Professor Satinder Kaur Brar and her team at INRS have conducted laboratory tests that show the effectiveness of enzymes produced by the bacterium in degrading petroleum products in soil and water. Their results offer hope for a simple, effective, and eco-friendly method of decontaminating water and soil at oil sites.

An April 8, 2018 INRS news release by Stephanie Thibaut, which originated the news item, expands on the theme,

In recent years, researchers have sequenced the genomes of thousands of bacteria from various sources. Research associate Dr.Tarek Rouissi poured over “technical data sheets” for many bacterial strains with the aim of finding the perfect candidate for a dirty job: cleaning up oil spills. He focused on the enzymes they produce and the conditions in which they evolve.

A. borkumensis, a non-pathogenic marine bacterium piqued his curiosity. The microorganism’s genome contains the codes of a number of interesting enzymes and it is classified as “hydrocarbonoclastic”—i.e., as a bacterium that uses hydrocarbons as a source of energy. A. borkumensis is present in all oceans and drifts with the current, multiplying rapidly in areas where the concentration of oil compounds is high, which partly explains the natural degradation observed after some spills. But its remedial potential had not been assessed.

“I had a hunch,” Rouissi said, “and the characterization of the enzymes produced by the bacterium seems to have proven me right!” A. borkumensis boasts an impressive set of tools: during its evolution, it has accumulated a range of very specific enzymes that degrade almost everything found in oil. Among these enzymes, the bacteria’shydroxylases stand out from the ones found in other species: they are far more effective, in addition to being more versatile and resistant to chemical conditions, as tested in coordination by a Ph.D. student, Ms. Tayssir Kadri.

To test the microscopic cleaner, the research team purified a few of the enzymes and used them to treat samples of contaminated soil. “The degradation of hydrocarbons using the crude enzyme extract is really encouraging and reached over 80% for various compounds,” said Brar. The process is effective in removing benzene, toluene, and xylene, and has been tested under a number of different conditions to show that it is a powerful way to clean up polluted land and marine environments.”

The next steps for Brar’s team are to find out more about how these bacteria metabolize hydrocarbons and explore their potential for decontaminating sites. One of the advantages of the approach developed at INRS is its application in difficult-to-access environments, which present a major challenge during oil spill cleanup efforts.

Here’s a link to and a citation for the paper,

Ex-situ biodegradation of petroleum hydrocarbons using Alcanivorax borkumensis enzymes by Tayssir Kadri, Sara Magdouli, Tarek Rouissi, Satinder Kaur Brar. Biochemical Engineering Journal Volume 132, 15 April 2018, Pages 279-287 DOI: https://doi.org/10.1016/j.bej.2018.01.014

This paper is behind a paywall.

In light of this research, it seems remiss not to mention the recent setback for Canada’s Trans Mountain pipeline expansion. Canada’s Federal Court of Appeal quashed the approval as per this August 30, 2018 news item on canadanews.org. There were two reasons for the quashing (1) a failure to properly consult with indigenous people and (2) a failure to adequately assess environmental impacts on marine life. Interestingly, no one ever mentions environmental cleanups and remediation, which could be very important if my current suspicions regarding the outcome for the next federal election are correct.

Regardless of which party forms the Canadian government after the 2019 federal election, I believe that either Liberals or Conservatives would be equally dedicated to bringing this pipeline to the West Coast. The only possibility I can see of a change lies in a potential minority government is formed by a coalition including the NDP (New Democratic Party) and/or the Green Party; an outcome that seems improbable at this juncture.

Given what I believe to be the political will regarding the Trans Mountain pipeline, I would dearly love to see more support for better cleanup and remediation measures.

Training your bacterium to perform photosynthesis

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A Jan. 4, 2016 news item on Nanotechnology Now announces a rather distinctive approach to artificial photosynthesis,

Trainers of dogs, horses, and other animal performers take note: a bacterium named Moorella thermoacetica has been induced to perform only a single trick, but it’s a doozy. Berkeley Lab researchers are using M. thermoacetica to perform photosynthesis – despite being non-photosynthetic – and also to synthesize semiconductor nanoparticles in a hybrid artificial photosynthesis system for converting sunlight into valuable chemical products.

“We’ve demonstrated the first self-photosensitization of a non-photosynthetic bacterium, M. thermoacetica, with cadmium sulfide nanoparticles to produce acetic acid from carbon dioxide at efficiencies and yield that are comparable to or may even exceed the capabilities of natural photosynthesis,” says Peidong Yang, a chemist with Berkeley Lab’s Materials Sciences Division, who led this work.

“The bacteria/inorganic-semiconductor hybrid artificial photosynthesis system we’ve created is self-replicating through the bio-precipitation of cadmium sulfide nanoparticles, which serve as the light harvester to sustain cellular metabolism,” Yang says. “Demonstrating this cyborgian ability to self-augment the functionality of biological systems through inorganic chemistry opens up the integration of biotic and abiotic components for the next generation of advanced solar-to-chemical conversion technologies.”

A Jan. 1, 2016 Berkeley Lab news release, which originated the news item, provides a little more detail,

Photosynthesis is the process by which nature harvests sunlight and uses the solar energy to synthesize carbohydrates from carbon dioxide and water. Artificial versions of photosynthesis are being explored for the clean, green and sustainable production of chemical products now made from petroleum, primarily fuels and plastics. Yang and his research group have been at the forefront of developing artificial photosynthetic technologies that can realize the full potential of solar-to-chemical synthesis.

“In our latest study, we combined the highly efficient light harvesting of an inorganic semiconductor with the high specificity, low cost, and self-replication and self-repair of a biocatalyst,” Yang says. “By inducing the self-photosensitization of M. thermoacetica with cadmium sulfide nanoparticles, we enabled the photosynthesis of acetic acid from carbon dioxide over several days of light-dark cycles at relatively high quantum yields, demonstrating a self-replicating route toward solar-to-chemical carbon dioxide reduction.”

Cadmium sulfide is a well-studied semiconductor with a band structure and that is well-suited for photosynthesis. As both an “electrograph” (meaning it can undergo direct electron transfers from an electrode), and an “acetogen” (meaning it can direct nearly 90-percent of its photosynthetic products towards acetic acid), M. thermoacetica serves as the ideal model organism for demonstrating the capabilities of this hybrid artificial photosynthesis system.

“Our hybrid system combines the best of both worlds: the light-harvesting capabilities of semiconductors with the catalytic power of biology,” Yang says. “In this study, we’ve demonstrated not only that biomaterials can be of sufficient quality to carry out useful photochemistry, but that in some ways they may be even more advantageous in biological applications.”

Here’s a link to and a citation for the paper,

Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production by Kelsey K. Sakimoto, Andrew Barnabas Wong, Peidong Yang. Science 1 January 2016: Vol. 351 no. 6268 pp. 74-77 DOI: 10.1126/science.aad3317

This paper is behind a paywall.