Genspace experiment proposal

As a continuation of my temporary expert assignment in which I researched Bioremediation and different ways of using metaphors in order to explain how it works, I want to expand my research in Genspace by conducting an experiment that will allow me to visualize and understand bioremediation.

By doing some research on how to perform bioremediation without toxic waste involved, I came across a simple exercise that consists on a sugar spill, by using yeast (as a bacteria) to consume the sugar when it’s mixed with water in test tubes, and collecting the generated gases with a balloon, I would be able to replicate the way that bacteria and toxic waste interact during the bioremediation process.

Yeast consuming sugar spill experiment

Yeast consuming sugar spill experiment

The sugar spill experiment is a simple and very visual way to represent bioremediation, however, I’m 100% interested in doing something similar but using the resources and the scientific method at Genspace. This simple experiment might not be enough to provide a clear way to quantify the good performance of bacteria and at the same time, it doesn’t provide a way to understand if the bacteria are having the appropriate conditions to “eat more”, which is the basis of my research and hopefully the element that I would like to use for my final project.

I would like to find substances that will require me going to do the experiment in Genspace and hopefully be able to quantify how much gas is produced, or in a more broad way, be able to determine when the bacteria are in ideal condition to be able to “eat more” and therefore clean more the environment (consuming more toxic waste in a real-life application of bioremediation).

Later in my research I came across a more detailed experiment that involves (I believe) toxic waste: Measuring the concentration of BAC in lake water samples. BAC = benzalkonium chloride.

Measuring the concentration of BAC in lake water samples

Measuring the concentration of BAC in lake water samples

I would like to find a middle point between these two experiments to be able to do it in Genspace, in which I can measure results (concentration of the “simulated toxic substance” (nontoxic in case of the experiment in Genspace).

Final Proposal for Genspace

My final proposal involves using mycelium to digest cigarette but. Ideally I will collect them from the street, I could quantify the amount and the location from where I collect them (maybe generate a story out of it once I have done the experiment) and then be able to connect it to the science.

As my experiment I want to be able to digest cigarette buts by using some kind of mycelium. The concept that I am pursuing is how to go from something “dirty or toxic” to something clean, and how to understand the conditions that the mushrooms need in order to “eat more” and therefore clean more.

Digest cigarette but

Digest cigarette but

Gene Drive: The Pangolin

The role of advance genomics in conservation biology of endangered species

For my Gene Drive assignment I was very conflicted with the idea of changing something on a species for “selfish” reasons, while trying to come up with an idea of a gene drive that wouldn’t affect their environment or other species in a negative way, I attended to the event: Existential Medicine #5: CRISPR - Edited Humanity in New Lab, in this even I met one of the participants, a Bio Geneticist who works for a pharmaceutical company in Cambridge and before the event started we started talking about the potential of CRISPR, our different backgrounds and how important it was to be able to be part of the conversation, no matter our daily job or education.

During the talk one of the panelists talked about a famous case of CRISPR (famous for other people but it was totally new for me) in which scientists are trying to edit the Cavendish’s (the most consumed species of banana) genome with CRISPR to boost its resilience to TR4 (a deadly fungus), instead of inserting foreign genes. This was fascinating to me, because saving an already existing species, and leaving it the way they are meant that I wouldn’t do any damage to the environment or other plants or animals, however I would be saving the species, in this case, the banana. The conversation in the panel at this point changed to discuss whether or not they would eat a genetically modified banana, and the guest that I have just met in the conference turned to me and said, I believe it would be better to eat a genetically modified banana instead of a banana that has a lot of chemicals and/or contains foreign genes instead of a modification of its own gene (interesting enough, all the panelists agreed that they would 100% eat a banana genetically modified with CRISPR).

At this point I was decided that my Gene Drive assignment was going to be focussed on saving a species in danger of extinction, the only remaining part was to find which species and decide how to use CRISPR to modify one of the alleles in order to be passed with more frequency and be able to propagate the new species in their environment.

Gene Drive: The Pangolin

According to pangolinsg.org Pangolins, or scaly anteaters as they are otherwise known, are unique mammals covered in hard scales, comprised of keratin. They predate almost exclusively on ants and termites and are predominantly nocturnal and elusive, secretive mammals.

The Pangolin

Most pangolins in illicit, international trade end up in China and Vietnam. Here the meat of the animals is consumed as a delicacy, but it is also believed to impart health benefits such as nourishing the kidneys. Despite a lack of evidence suggesting they’re effective, pangolin scales are used as an ingredient in traditional Asian medicine to help breastfeeding women lactate milk, to cure ailments ranging from asthma and psoriasis to cancer, and to improve blood circulation.

-In this remote part of the Central African Republic, poaching for the overseas wildlife trade is not yet widespread, but pangolins are seen as food. They are easy prey; a pangolin’s defence strategy is to roll into a scaly ball (their name comes from the Malay pengguling – “something that rolls up”). This makes it difficult for most predators to eat them but all too convenient for human hands intent on scooping them up and putting them into a sack.- Post Magazine

Defense mechanism

According to the Post Magazine article in April 2019, authorities in Singapore seized nearly 13 tonnes of scales in a container en route from Nigeria to Vietnam, a haul valued at US$38 million. It is estimated 17,000 pangolins would have been killed for this shipment and scales from all four African species were identi­fied. In February, 30 tonnes of frozen pangolins were seized in Sabah, Malaysia’s biggest bust to date, and the previous month, Hong Kong authorities found eight tonnes of scales in a container from Nigeria bound for Vietnam.

One pangolin is poached from the wild every five minutes

My design question for the assignment was, how to prevent the trafficking of Pangolins by genetically modifying al allele with CRISPR? I decided to focus on the flavor factor. Pangolins are trafficked, among other reasons, for the exotic and good taste of their meat. It is sold as a delicatessen which means that people pay high amounts of money to be able to eat something delicious, exotic, that they can’t eat every day. People are willing to pay a lot of money which means that people are willing to remove the Pangolins from their environment and kill them in order for people to try their exotic meat, no matter if they are about to be extinct.

What would happen if a group of scientists using CRISPR where able to genetically modify the pangolin by changing the paste of the meat for human perception? It would have to be a subtle change so that their predators don’t get affected by this change and therefore the food chain remains the same, however it has to be a noticeable enough change so that humans stop trafficking the Pangolin for the taste of their meat.

In this assignment I have decided to use an edible metaphor to exemplify the process of a gene drive in Pangolins and how the offer and demand would change in order for humans to reduce the amount of trafficked species and hopefully save the Pangolins from extinction.

Note: details of the activity will be added after class in order to avoid spoilers!

Week 3 | Temporary Expert: Bioremediation

The in-class assignment helped me to determine which aspects of the bioremediation I would like to explore for my midterm assignment, I’m particularly interested in the fact that organisms feed from toxic waste and that waste is their fuel and energy to maintain them alive. I’m fascinated by the idea that something that is supposed to kill (for example, toxic waste is supposed to kill humans) however, this organisms somehow find a way to use that as food and by doing that it improves the conditions of their environment. I Im very interested in understanding what are the conditions that are necessary for that to happen and how everyday citizens can get involved in that process, what are the steps and the materials needed in order for this microbes to “eat more contaminants”.

From nothing to something

From nothing to something

Week 2 | Temporary Expert: Bioremediation

What Is Bioremediation?

Bioremediation is the use of microbes to clean up contaminated soil and groundwater. Microbes are very small organisms, such as bacteria, that live naturally in the environment. Bioremediation stimulates the growth of certain microbes that use contaminants as a source of food and energy. Contaminants treated using bioremediation include oil and other petroleum products, solvents, and pesticides.

How Does It Work?

Some types of microbes eat and digest contaminants, usually changing them into small amounts of water and harmless gases like carbon dioxide and ethene. If soil and groundwater do not have enough of the right microbes, they can be added in a process called “bioaugmentation.” For bioremediation to be effective, the right temperature, nutrients, and food also must be present. Proper conditions allow the right microbes to grow and multiply—and eat more contaminants. If conditions are not right, microbes grow too slowly or die, and contaminants are not cleaned up. Conditions may be improved by adding “amendments.” Amendments range from household items like molasses and vegetable oil, to air and chemicals that produce oxygen. Amendments are often pumped underground through wells to treat soil and groundwater in situ (in place).

Bioremediation diagram

Bioremediation diagram

Why Use Bioremediation?

Bioremediation has the advantage of using natural processes to clean up sites. Because it may not require as much equipment, labor, or energy as some cleanup methods, it can be cheaper. Another advantage is that contaminated soil and groundwater are treated onsite without having to dig, pump, and transport them elsewhere for treatment. Because microbes change the harmful chemicals into small amounts of water and gases, few if any waste byproducts are created. Bioremediation has successfully cleaned up many polluted sites and has been selected or is being used at over 100 Superfund sites across the country.

Example:

Bioremediation is cleaning up groundwater contaminated with dry cleaning solvent at the Iceland Coin Laundry Superfund site in New Jersey. To improve the conditions at the site for bioremediation, amendments were added. A solution of vegetable oil and baking soda was injected into the groundwater in an area of particularly high contaminant concentrations. Bacteria also were added to increase the existing population of microbes. The treatment area is about 1800 feet long, 500 feet wide and extends 40 feet below ground. Preliminary testing of the groundwater has shown that bioremediation is working and contaminant concentrations are decreasing. The objective is to continue to reduce the concentration of contaminants from 10 or more parts per billion to less than 1 part per billion.

Transgenic Pseudomonas bacteria capable of degrading toxic compounds that contain chlorine (such as vinyl chloride).

Some ongoing developments related to microbial remediation:

  • Bacteria that can degrade some of the components of oil.

  • Powerful bacteria reduce highly toxic forms of mercury into less toxic and volatile ones.

  • Bacteria that transform soil metals (such as chromium) into less toxic or insoluble forms.

  • Aggressive microorganisms to degrade TNT, an explosive of great power and very aggressive for the environment.

  • Bacteria that can remove sulfur from fossil fuels, such as coal or oil, to allow cleaner combustion.

  • The use of the bacterium Deinococcus radiodurans to eliminate radioactive elements present in the soil and groundwater. This microorganism is an extremophile that resists radiation, sequence, oxidizing agents and various mutagenic compounds.

  • Cyanobacteria that have been activated genes of Pseudomonas bacteria capable of degrading different hydrocarbons or pesticides.

  • Transgenic bacteria that are used to extract valuable metals from factory or mine waste, or to eliminate oil spills, or the sulphide that causes acid rain produced by coal power plants.

Sources:

http://www.argenbio.org/index.php?action=novedades&note=202

https://www.nap.edu/read/2131/chapter/4

https://www.nature.com/subjects/bioremediation

https://clu-in.org/download/Citizens/a_citizens_guide_to_bioremediation.pdf

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5026719/


Week 1 | Temporary expert: Bioremediation

Assigned topic: Bioremediation

Humans have done a lot to pollute the world we live, contaminating soil and water with everything from oil to radioactive waste. Some parts of nature have evolved to survive pollution and might even be able to help clean up these contaminants.

Using living organisms to get rid of toxic waste is called bioremediation, which is a relatively safe and cost efficient process. The most common bioremediator is bacteria however certain plants and animals can help too.

Bioremediation is defined as a process that uses microorganisms or their enzymes to treat polluted sites for regaining their original condition (Glazer and Nikaido, 1995). Bioremediation approaches are generally classified as in situ or ex situ.

In situ bioremediation can be described as the process whereby pesticides are biologically degraded under natural conditions to either carbon dioxide and water or an attenuated transformation product. It is a low cost, low maintenance, environment-friendly, and sustainable approach for the clean-up of contaminated soils (Megharaj et al., 2011). For ex situ bioremediation, contaminated soils have to be excavated and moved to another site for treatment, which may result in a high cost. Therefore, considering the large scale of agricultural land, in situ bioremediation is preferred to ex situ remediation for restoration of contaminated agricultural soils.

References:

https://www.youtube.com/watch?v=c2pQ9guh27s

https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bioremediation

https://www.sciencedirect.com/topics/earth-and-planetary-sciences/bioremediation

https://www.sciencedirect.com/book/9780128161555/integrated-analytical-approaches-for-pesticide-management

https://www.sciencedirect.com/book/9780128000212/microbial-biodegradation-and-bioremediation#book-info