Team:Groningen/Brainstorm

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Hydrophobofilm
pushing coatings into a greener future

IGEM Meeting(04.03.2010)

Synthetic amino acids: ask the researcher that had an article in the UK whether we could do something with this.

Biofilms:

-Anti-fowling coat

-Heat/cold insulation

-UV-sensitive coating which turns dark with high light intensity. For (sun)glasses and wind shields

-Paint for buildings: Make bacteria produce a certain compound (like a pigment) which you'll want to apply to a surface of some sort. Let them first produce it cytosolic and then let them secrete it by a light sensitive channel. These channels are the MscL (Mechanoselective channels of Large conductance) and have been modified to be light and pH sensitive in stead (A. Koçer, 2007). If we can get them to respond to different wavelengths of light we might be able to have a biofilm of two different mutants (e.g. MscL400nm and MscL500nm) producing different colours we can paint patterns on the building by exposing the building with different wavelengths. (Algae)

-Malaria repellent

Decolourisation of effluent from the textile industry by a microbial consortium:

A microbial consortium, PDW, was isolated capable of the rapid decolourisation of commercially important textile dyes under anaerobic conditions. Decolourisation was dependent upon the presence of a carbon and energy source in addition to the textile dyes. PDW was capable of dye decolourisation when utilising cheap and readily available carbon sources such lactose, starch and distillery waste. PDW removed 76% of colour from textile plant effluent after 3 days.(david)

Air refreshener

Ideal situation: the bacterium would take up CO2 (just so that problem will also become less :P) and release some nice smelling, non-toxic compound (maybe vanilla) -geeske

Fingerprint detecting detective bacteria.

Line detecting bacteria

Bacterial solar cells

Using Photosynthesis to produce energy in the form of electrons or pH gradient of some sort to transport the energy out of the cell to a curcuit (http://adsabs.harvard.edu/abs/1980ises.conf....2S , http://www.ks.uiuc.edu/Highlights/?section=2002&highlight=2002-08) (Jorrit)

Bacteria which could function as solar cells or produce electricity because that sounds cool and is probably useful for something. They just found a deep sea consortium which does something like this. (Remember the paper I send: Nature, Vol 463, 25 February 2010). Martijn also mailed us al lot of info on this and the 2008 Harvard team made an bacterial battery. (Djoke)

Deacidifying bacteria (pH sensitive channels): see story on MscL. In stead of a pigment we could let them make a base (hoping it will not screw with their householding)

Bacteria that do not produce methane to replace methanogen bacteria in cow's rumen: isolated microbes in the animal's stomach which allows them to eat grass and plants but without producing the flatulence common to European livestock. Even though kangaroos have a similar system for utilising plants to sheep and cattle, they have evolved independently over many millions of years and so the microbes are extremely different. Rather than produce methane, kangaroos produce acetate which aids digestion. (David)

Make E. coli smell like roses. Or bananas. Or vanilla. Or something else that does not smell like poo.

Gut bacteria that produce vitamins

Bacteria that produce insulin and that can somehow be implemented in our body

Sound producing bacteria:

Synthetic communities:Most bacteria on earth live in heterogeneous surface-bound congregations called biofilms, and vast reaches of the earth are coated in these living films. In many cases, the microorganisms comprising this ubiquitous coating form complex, interactive communities called consortia. Microbial consortia are implicated in processes of great importance to humans, from environmental remediation and wastewater treatment to assistance in food digestion. Synthetic biologists are honing their ability to program the behavior of individual microbial populations, forcing the microbes to focus on specific applications, such as the production of drugs and fuels. Given that microbial consortia can perform even more complicated tasks and endure more changeable environments than monocultures can, they represent an important new frontier for synthetic biology. (David)

Bacterial lamp:

There are these bacteria found on fish that have luminescence. During a practical course some people had to acquire a pure culture of this bacterium from fish bought at the market. There was something about that if you put a culture of these bacteria in a large tube and flip it upside down (thus making oxygen bubbles) making the bacteria illuminate. Maybe we could make this into some kind of biological ambilight (Maarten)

One marine bacterium that is luminescent is Vibrio fischeri. It is present on some squid. Five genes encoded by the Lux operon are involved in creating the luminescence. When making a bacterial lamp we could regulate the luminescence so that it is only 'on' when it is dark. The EPF-Lausanne team from last year worked on a light-induced gene switch that we could use to regulate the luminescence. (Arend Jan)

IGEM Meeting(12.03.2010)

Food: loose weight consumes fat and chlorestorial

We could design probiotic bacteria (Like that useless Actimel crap but useful!! Imagine that!!1!) which are destined to waste a certain amount of calories. They would be eaten added to yoghurt or the like (In contrast to Actimel we could even make it tasty). So lets say for some reason you feel like not becoming a diabetic or a heart attack victim, you just compensate all the extra calories by munching our genetically modified never tested on animals or the like bacteria which we only have a vague idea of what they might do and TARAAA! Technology beats nature… again. The easiest would be to get the bacteria to produce something that can’t be digested in the intestines like fat or even better, a substance that smells good (for obvious reasons) After a while the indigenous bacteria will outcompete our sissy lab bacteria and everything is back to normal –Ramon Sieber

Biodegradable fabric: good & green

Fertilizing Gounds: cactus, nitrogen fixing compatible to all plants

Bacteria -> Colon Cancer DETECTION

MscL (Mechanoselective channels of Large conductance) have been modified to be light and pH sensitive (A. Koçer, 2007). I think we can use this mechanism for the detection of cancerous cells, which have a lower pH in their microenvironment when compared to normal cells. The bacteria (for cancer in the GI tract) could then secrete some sort of detectable marker. Lipid bodies could be used for detection in the rest of the body.

Laundry machine -> bacteria producing enzymes for washing machines

Sponge - ISOLATION

Biological Anti freeze so it can detect temperature change and unfreeze for example the car window.

Bacteria to reduce air pollution

Biological Computer

The area of research in biological computing is increasing and opens waves of new possibilities into the miniaturization of computers. All research in the area shares the same basic idea: DNA is a perfect carrier of data and the expression of genes into proteins provides enormous possibilities for calculation (as life itself demonstrates). Two kinds of research can be discriminated (superficially): The utilization of bacterial colonies which perform calculations by setting in motion signaling processes(Conway's Game of Life being an example of the more general principle of Cellular Automata) and the utilization of signals cells as computers by designing mechanisms to store and retrieve data in the form of proteins or other molecules. While not a 'readymade' project, with sufficient interest in the subject this can be a very exciting summer! (Joël)

(Conway's Game of Life seems like a interesting thing to do, even though we probably won't be able to raise the dead, systems that simulate this behaviour might be possible, does anyone know if there is cells that organize in a strict patern that can be grown in a dish? (We probably won't toy with tissues even though any honest scientist has to admit that a brain in a jar would be ultimate victory, especialy if it was wondering if it might just be a brain in a jar:) I know that fungi have very definitive structures, maybee this could be thinkered with -Ramon Sieber)

Oil spill responce - Baceria cleaning it up.

After oil spills the oil which is not removed mechanically is mostly degraded by bacteria (bioremediation) so far only adding fertilizer seems to help, the addition of living bacteria has mostly not shown any effect. I can think of three ways to use bacteria in order to improve bioremediation, 1: Nitrogen fixing bacteria could be added instead of fertilizer, Nitrogen fixing bacteria already exist, but I don’t know if they can life in oily environements. 2. Bacteria which can metabolize the compounds which so far can not be degraded by bacteria 3. Bacteria which are actually better at degrading oil than existing ones ( I have however no clue how that could be achived) 1&3 would enhance speed, 2 would improve endpiont which has so far not been attempted (at least not from what I have read) -Marine microorganisms make a meal out of oil, nature reviews 2006 -Field evaluation of marine oil spill bioremediation, microbial reviews 1996 (Very long but also very complete review about the topic) -Ramon Sieber

Detecting clusters of bacteria

Synthetic biomolecules on synthetic biomolecules

Radiowave bacteria

Using magnetized components, like Neodynium an earth indigenous magnetic substance, and some sort of rotary mechanism attached (possibly like the bacterial flagellum) it can be possible to rotate a magnet around another magnetized pole. By modulating the frequency(by controlling the rotation speed) this effectively creates an FM signal.(Joël)

Bacteria changing the taste of yogurt

Bacteria that can change the taste of yoghurt (over a period of time) so that you don't know which taste that yoghurt has at the moment. Or that the bacteria change it per period of the the day, so that you have "breakfast" yoghurt in the morning and "dessert" yoghurt in the evening (Jorrit)

Making a bacterial community( to mimic the interaction between bacteia in real world)

Bacterial camera

If bacteria with photosensitive receptors are properly laid out in a grid it can be possible to create a rudimentary camera. If the photoreceptors trigger a signal which sets in motion a cascade to a measurable effect. Measurable effects can be increased expression of a specific gene (slow), the opening of certain membrane gates (through second messenger systems) or the activation of certain proteins. (Joël)

UV detecting bacteria

Bacteria that are capable of altering one type of aa to another or producing essential amino acid

Molecular fishing rod

Using the Biotin – Avidin connection bacterias could maybee ( I don’t know how strong that connection really is, but it is the strongest at hand) be bound to a surface or the like. The bacteria could express biotin or avidin to the surface (the bricks exist) at a certain metabolic state, on command, as long as they are allive, when you flash them with light or whatever… and then be fished out of the solution with a device coated with Biotin or avidin. -Ramon Sieber

Detection of movement

A system consisting of two organisms, a) Bacteria and b) a creature able to move over solid surface (Amoeba, nematode, snail…) . The bacteria would cover the ground (agar plate) completely and would detect the organism moving over them, either by a chemical which this organism releases or by pressure, depending on size of the moving agent pressure might not work, and start to produce a fluorescent or colour signal hence leaving a mark of the organisms way (I know snails do that anyway but…) Using chemotaxis the organisms could be sent through a maze or be steered in order to gain world domination.

The tron version of movement detection

In addition to a colour or fluorescence marker the bacteria also produce a repellent for the used organism. This will hinder the organism of crossing its own path or the path of another “Player”. Which basically is what Tron does. For all sorry souls who have never played it: http://gamepuma.com/action-games/Tron.html -Ramon Sieber (Dyctiostelium)

restore gulf stream pump once it breakes down

We could try to construct a bacterial pump. This is how it looks in my head: bacteria or something the like which float (sinking could also be possible) change the density of the sourounding media by metabolism of oily substances to sugar or somethinng (Someone who knows chemistry is welcome to help) the now denser media would then sink, sucking fresh media as it goes. Maybee this wont safe the gulf stream but in a bioreactor it might work –Ramon Sieber

Anti-rust bacteria

Anti-anxiety bacteria

Anti-acidification bacteria for ocean

Smelling (coffee) of circadian rythm bacteria

Cells which react to a long period of darkness (night) followed by light (the sensors for light exist so this should be possible) produce either smell of coffe or caffein (your blanket is a biofilm so you absorbe it) to assure a gentle awakening –Ramon Sieber

Timer bacteria

A simple protein clock (can be done using positive (auto-receptive) feedback loops). Can be useful for a lot of things. Like self-destruction or the smell of coffee in the morning.(Joël) (If one would repress the expression of a gen essential for cell growth with a substance that is degraded by the cell itself, you could tell your cells when to start growing. This would prevent me from coming to the lab tonight for example. If a second similiar clock existed to start the expression of another gene after the cells grew for some time (or before they start, or switches off after some time or wathever you want), you could could set up whole protein expression experiments and the like at once. I would have killed for such an organism during my bachelorthesis - (Ramon Sieber)

Spore eating bacteria

Detect bad milk bacteria

bad milk turns sour, so all you would need is a bacterium that would show us that the pH of the milk has gone below a certain value. it could show this by perhaps turning red/blue whatever. have the feeling though that this has already been done (geeske)

Biofilm insulating bacteria (bacteria cover the building)

I found an article which states that biofims are a hugh problem on buildings. The detoriaton is accelerated by the micro-organisms. Did not read the paper completely, but maybe we can find the cause of the problem and solve that. Deteriogenic Biofilms on Buildings and their Control: a Review – C.C. Gaylarde et al., Biofouling, 1999, Vol 14(1), pp 59-74 (Laura)

Two component gene made by bacteria stolling factor

Vitamine rich food , nice tasting food

Bacteria that import vitamins or minerals and inject them into plant cells to make them more nutritional. I don't know how to, would need to look into that further... Maybe we could have them inject vanilla flavour to dull tasting, but otherwise very nutritional foods (like coli flower). (Maarten)

IGEM Meeting(15.03.2010)

anti-hangover bacteria

quit smoking bacteria

plactic degrading bacteria(microplastic degrading bacteria)

Plastic degrading bacteria(microplastic degrading bacteria) Several bacteria and fungi are involved in degrading natural and synthetic plastics. First, polymers are broken down to monomers, these monomers are mineralized further (to CO2, H2O and CH4). This review shows a table with all known micro-organisms and the plastics that they can degrade with references. Biological degradation of plastics: A comprehensive review - Aamer Ali Shah, et al., Biotechnology Advances 26 (2008) 246–265. (Laura)

On the other hand, plastic (PHA) producing bacteria can be very interesting for medical applications (fixation and orthopaedic applications) Bacillus subtilis as potential producer for polyhydroxyalkanoates - Mamtesh Singh et al., Microbial Cell Factories 2009, 8:38 (Laura)

caffeine producing bacteria

Bacterial (gas) filter (previously gas pump). Have bacteria in some sort of rigid structure (like a platinum / magnesium plate with microscopic pores) and produce some … this is is very bad idea, now that I'm writing it. The original train of thought of thought was as follows: create vesicles susceptible to a certain gas on one side of the bacteria and having the vesicles transported through the other side and releasing them(using a re-uptake mechanism for the vesicles). Effectively creating a selectively permeable gas filter. This is however a bad idea because gas diffuses and it's next to impossible to find a structure that is both selective and non-porous to gasses. On top of that coordinating the movement of the vesicles through the dense packed inner world of a bacterium is a project in itself. Amongst other reasons (size/controlling the expressed location of the entry / exit points). (Joël)

bacteria against the skin disease

bioglue

melanin production stimulating baceria

Bacteria creating (carbon) nanotubes. While microscopic structures in cells are not uncommon (think neuronal axons and other micro tubulea) the mass production of nano tubes is still tedious. However they do play a major part in most of nanotechnology advances. Having bacteria to produce them and then being able to harvest them (without breaking the structures) would be a good idea. Also carbon nanotubes can conduct electricity (outer-layer electron movement?) which might provide chances of more tight integration of silicon-based computers and bacterial systems. (Joël)

flying and ozone producing bacteria

Alcohol content controll by apoptosis

Right now alcohol content is controlled either by sugar availability, cytotoxicity, or manual killing of the yeast at a certain alcohol level (the idea could be applied to other fermentation products as well). It would be usefull to have a system in which you could decide beforehand to which degree the yeast will grow, this could be done by getting the yeast to recognize a certain ratio between alcohol and a second substance and kill themselves once that ratio is reached. By dosing that second substance it could be determined when the yeast starts killing itself and hence the final alcohol level. - Ramon Sieber

seismo detecting bacteria(sound detecting bacteria)

Mechanical pressure sensitive bacteria. Two ideas: colony sensing bacteria, if most of them die in a certain area the pressure must be great. This can be done by having all bacteria release a simple chemical, if concentration drops beyond a certain threshold trigger a signal (production of GFP/RFP maybe). Other idea, completely different scale: use the fact that bacteria can change shape (to some extend). Position a specific receptor on the outer membrane, position a donor at a known distance from the receptor. This creates an auto-receptive system with known concentrations (taking into account diffusion) in the loop. If the distance between the receptor and the donor changes (due to changes in the bacteria shape) the concentration changes which can be used in a cascade towards other signals. Effectively creating a mechanical pressure sensor. (Joël)

glitter bacteria

sparkling bacteria

caffeine biobrick

cake degrading bacteria

Anti-body binding bacteria: for numerous functions, targeted that is

@Home ideas

(Maarten):

Bacteria that import vitamins or minerals and inject them into plant cells to make them more nutritional.

(Djoke):

I also found a paper on magnetic bacteria (Nature nanotechnology, online 14 march 2010) which seemed really cool to me. As I got it, they overexpressed ironoxide in the cells and could then fish these cells out with a magnet. Cool selection tool right?
I recently saw this article and movie of a oil droplet which moves through a maze due to a acid-base gradient. Watch the cool movie at http://news.sciencemag.org/sciencenow/2010/01/13-04.html Maybe this something to consider when we are going to work with hydrophobic bacteria or surfaces.

(Jorrit):

Hairstyling bacteria:

Bacteria that produce gel or wax so that you don't have to do your hair every morning

(Arend Jan): Chemotaxis and bacterial conjugation

Many bacteria use chemotaxis to move toward, or away from, chemoattractants and chemorepellents.

If we could invert this system in pathogenic bacteria it would decrease their ability to infect their host. To spread this inversion mechanism through a population of bacteria we could make use of conjugation plasmids. These plasmids facilitate their own transfer form one bacteria to another and can also carry resistance genes spreading antibiotic resistance. We could create a conjugation plasmid that also carries genes that somehow cause this inversion.

Also involving chemotaxis and bacterial conjugation, a conjugation plasmid that disrupts chamotaxis by inducing a constant tumble (no linear movement).

At the same time this plasmid could carry a gene for a chemoattractant that would attract more bacteria to the immobilized bacteria. The plasmid is then transferred to these bacteria, starting a chain reaction.

8 April

Minutes iGem-meeting April 8th

• Anouncements: o Laura has been added to Y-drive o Ezgi should put the minutes on the Y-drive • Calendar: o upcoming meetings  16 April: 17.00 biological centre G105  22 April: 17.00 biological centre G105  28 April: 17.00 biological centre G105 • Wiki iGEM'10: o Most people have changed their personal pages, it looks good • ...@iGEMgroningen.com o People should really use this, check whether they can use it. o Mails should be marked "unread" when they have been read. • Finances: o There's a brochure but it's not good, the team is making a brochure now o The financial subteam will start sending letters in two weeks o They're having contact with "De chemische binding" about possibilities to prit logos on shirts • PR: o Group picture postponed once again till the weather improves. • Info scouting: o No news. • Participation: o Tugce quit because of internship she has to do in order to graduate. o Ezgi will be here until August and can't be here from September (available July 9th till end of August), we concluded it's no problem. • Next meeting: o April 16th

Minutes iGEM meeting 16/04/2010

Short presentations. On the timer mechanisms: Usefull as a technique, we don’t have a project an sich. For a project you could think of all sorts of things, Oscar proposed for example a timer for the in situ production of medicin. On the hydrophobic film: Very interesting, novel: Yet again, you’d need a good project to use it in and make sure that it’s not just about the production of hydrophobic proteins. You’ll have to make sure synthetic biology is applied as wel.

It might even be used in last year’s project, for floating. You could use it to coat a surface of some kind, maybe in medical appliances: in tubes for example. Or to strengthen a biofilm, in paint.

On the bacterial solar cell: Consists of two parts: Photosynthesis to create any kind of energy rich chemical, and then: Harvard ’08 project to convert this to electricity. We could then use nanowires to steer the current. The problem here would be that the bacteria Harvard used, would not do photosynthesis. So maybe we could use a mixed population in which two bacteria function as the mediators photosynthesis and electricity producers. Population growth control would then be necessary. On the bacterial tumble: A cool idea, which might actually be plausible to test in vitro. The use of a transfer mechanism needs to be further investigated, and we would have to see on which species, and where, you’d want to apply it. Look into the project of Impereal from last year On plastic degrading bacteria: Without a presentation not much was clear about what is and what isn’t possible, although according to the instructors this might be hard. On the tron idea: It’s feasible, likeable, yet maybe not that appealing to the outsiders. Of course tron doesn’t solve any of the great (environmental) problems of today, so it might be hard to sell it. About feasibility: some blanks need to be filled in (e.g. what secretant of the nematode would you use. On the molecular fishing rod: More of a tool than a project, feasible, yet probably not that appealing.

On all the subjects that made it through for the next meeting, those were: Tron, Solar Cell, Hydrophobic, and Tumble Bacteria (Platic). More work needs to be done. We have to come up with concrete ideas, appealing projects, and details…

Furthermore, on the meeting: David and Joël will not be there for the meeting on the 28th of April. It is important for everyone to engage in the wiebetaaltwat.nl list, you can fill in your name and email, then point out when you had dinner: At the end the site will calculate who has to pay/receive what from who.. The meeting of the 22nd will be the meeting when we’ll make a second group picture. There was a discussion about whether or not we should create a forum, we decided not to: We already have a lot of things we can use to communicate with each other. Also: we might have a BBQ next meeting.

Peter	Ask about BBQ for next meeting, work on solar cell project
David	Project hydrophobia
Maarten	Project hydrophobia
Joël	Finances: have a look into with all three involved, Work on solar cell bacteria
Geeske	Work on plastic degrading bacteria, Finances: have a look into with all three involved,
Djoke	Finances: have a look into with all three involved, work on solar cell bacteria
Arend	Dive into the wiki, arrange a password for Ezgi
Arend-Jan	Work on project of tumbling bacteria
Jorrit	work on solar cell bacteria
Ezgi	Project tron
Ramon	Work on project of tumbling bacteria, work on tron
Laura	Work on plastic degrading bacteria

Minutes iGem-meeting April 22nd

Anouncements:
1. Ezgi will not be present from May 6th till May 16th.
2. We've got a new member, Keimpe, a mathematician. Welcome!!!
Project:
1. Hydrophobic biofilm
2. Tumbling bacteria
In order to choose a number of questions need to be answered:
1. Has it been done before @iGEM?
2. Which biobricks are available?
3. How big are the genes involved?
4. What are possible applications?
5. Is there a modelling aspect?
6. How many different hydrophobins are there?

IT:

Ezgi could not find the iGEM folder on the Y-drive but it was pointed out to her and she'll try again.

Arend Jan asked whether mail was ok, because he didn't receive any mails in his ...@igemgroningen.com. It was noted that most of the e-mail get send to the igem@igemgroningen.com mail address. • Finances: o Joël gave a financial update and it appears there's a hole in the budget which we'll have to fill with sponsors from companies. Or we should get creative otherwise. We could look at more governmental funds. Chances on getting EU-funding are rather slim Oscar noted. Action points

Team-member	Action point	Status
Arend	-Answer questions on projects -Work on Wiki -Invite Keimpe to Google Groups and igemgroningen.com mail etc
Arend Jan	-Answer questions on projects
David	-Answer questions on projects -Beg for money from GLV Idun -Check some funds -Put Keimpe on Y-drive
Djoke	Answer questions on projects -Work on sponsoring
Ezgi	Answer questions on projects -Try to get on Y-drive
Geeske	Answer questions on projects -Work on sponsoring
Joël	Answer questions on projects -Work on sponsoring
Jorrit	-Answer questions on projects
Keimpe	-Answer questions on projects
Laura	Answer questions on projects
Maarten	Answer questions on projects
Peter	Answer questions on projects
Ramon	Answer questions on projects