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Meetings Calendar

Timeline
Ideas

Project Ideas

Team Newcastle iGem 2009 08-07-09 no 2.JPG

This is a list of the ideas that have been covered during the course of the first iGem meetings. Included within some of the paragraphs are links to articles which gave inspiration for that particular idea

Ideas discussed for iGEM

MAN-SCAN

Last year the Newcastle team used bacteria to detect bacteria. How about using a similar approach to detect humans? Maybe we can come up with a less androgynous title. I visualised a lawn of B. subtilis onto which you place a body part (eg hand or foot) and later an image of it appears in light.

SYNCHRO-BAC

One large colony is glowing in the dark and send a message to other colonies to do the same.

HAPPY-BACTY - general environmental monitor.

B. subtilis seems to be quite good at detecting and responding to environmental stresses (is there a thing called a stressosome?). We could ask simple questions of the colonies - is your environemnt Nice, average or poor? maybe get a three colour output (traffice lites). This kind of thing is an environmentalist dream - to detect an average of environmental stressors in theis way, such as pollutants maybe the environmental monitor uses synchro-bac to tell the others what they are "feeling" and if they were motile the other could move to a nice area, or away from a bad one.

Trapping of heavy metals then sporolate to fix them indefinatley

Metal Resistance in Acidocella Strains and Plasmid-Mediated Transfer of This Characteristic to Acidiphilium multivorum and Escherichia coli

Biological memory

Bacillus subtilis is a sporulating bacteria and can survive for years in its spore form. Also, we can make them respond to external stress such as electro-magnetic fields. Use these two features to engineer bacterias capable of storing information for years. This could become an immortal and unlimited memory. We could use bacterias in some way so that bacteria are 0 or 1 and use this to make a bacterial hardware or memory that is capable of storing octets and therefore that has memory.

Allergen detection and removal

Using bacteria as quality control and disabling of allergens by detection of peptides found to elicit allergic response in food, such as nut, shell fish, egg, dairy traces etc. Samples from batches could in theory be tested with a fluorescent output.

Calculator : Implementation of a simple calculator to add numbers

Soil Enhancer

Detection of nutritions on the soil and freeing up the minerals for the plants (Article) - maybe detect the N, P, K elements in soil and give different feedback like colour or flourescence , adjust it's metabolism system to generate a product which can be absorbed by plants easily.

Fast bacteria

Engineering the movement of bacteria with feedback systems like rockets (Article)

Inflammatory disease treatment

This idea is a little similar to the allergen detector and corrector system - it involves using Bacillus subtilis in humans to target and deal with a particular allergen particle before the immune system sets in and creates the damaging effects of inflammation. Would make use of receptors which are able to bind to 1)IgE molecules and 2) the allergen particles themselves.

Gastric Inflammation

Treatment and prevention of H. pylori(stomach ulcer) - engineer a B. subtilis that can live and grow happily in stomach acidity (pH2) - an acidophilic strain will also be needed for the heavy metal trapping.

Skin repairer

Using the production of hyaluronic acid (HA) an important glycosaminoglycan which is found in synovial fluid, extracellular matrix and very important in wound healing. It was found by Widner et al. 2005 that the HasA gene for Hyaluronan synthase could be expressed successfully in B. subtilis. It could maybe be put into a plaster or gauze used to dress wounds? (The bacteria should be friendly to the human body and generate a growth factor like HA or another product to help skin cells grow; or maybe generate skin like material which can grow together with healthy skin)

(Article)Idea came up in meeting 19/02/09- using a bacterial lawn to produce antibiotics within a plaster to protect a healing wound- OR- to produce S. aureus signal proteins which would prevent communication between S. aureus thus preventing infection.

Cosmetic bacteria

Can we use the bacteria to fill up the wounds, scratches, wrinkles etc. for a couple of hours.

Sticky bacteria

Again for filling or sticking items for example to a wound.

Hair / filament producing bacteria allied to skin repair idea - may provide scaffold.

B. subtilis produces flagella. can we engineer it to produce large filaments of eg keratin which will stabilise a wound dressing?

Bacterial microscopy

Can they magnify very small objects for us?

MVC

Implemantation of model view controller software pattern to bacteria. One group of colony is responsible only for the view,via fluorescent proteins etc, one gives commands to model poulation. At some point we may decide to add another command type population without breaking the whole pattern because all the command type bacteria have the same interface. This could also be implemented in a different way as service oriented bacteria having bacteria population that only does one job at a time. Another colony uses the services to do a certain task. (Article 1) (Article 2)

Timed Germination

Can we engineer bacteria to start germination at a specific time. They correspond to signals to start or stop germination without the nutrition
(Article 1) (Article 2)

Path finding

Simulating the ant colony (Article). Bacteria will move intelligently tracking the pheromenes that are left by the others (Article).

Or safe walk. Others will tell if it is safe to continue in a direction

King bacteria. Other bacteria will guide king bacteria on a safe path

Chaperone producer

Depending on the conditions, some chaperiones like Hsp70, Hsp60 will be secreted. It might be used to cure Alzheimer disease (Article).

Glucose sensing bacteria

Bacteria capable of sensing the level of glucose in a blood sample. This could be a cheap way of testing for glucose level in blood sample.

Freezer

To store nutrients using sporulation depending on the input functions and release them when needed upon a forced germination

SPOT THE ROT

Spores go red on germination when conditions go from v. cold to warm to indicate spoilage on food or medical product packaging.

Bacterial automation

Using electronic sensors to connect computer directly to start a process for the bacteria. E.g Start DNA uptaking. The output function of electronic circuit should match to the input of the bacteria

Bacterial tattos

Using bacteria to have temporary tattos.

Bacterial compass

Can we use bacteria to find our direction? Can we use magnetosomes for this purpose? (Article)

Bacterial sensor which tells you how it "feels" by the rate of flashing. Maybe responding to environmental stress.

It would be much easier to use than having to measure the intensity of fluroescence. Or maybe we could have a traffic light effect.

Back in the days when I did ecotoxicology (late 80's early 90's) our dream was for a fish on a stick, you just dip it in the water and it tells you how it feels!

The closest we had then was a system called Microtox based on a phosphorescent marine bacterium Vibrio fischeri. There are tons of data relating the response of Microtox to environmental factors.

Cleaner bacteria

Eco-friendly, producing enzymes,proteins for cleaning purposes (toothpaste???)(Article)

Eco-friendly bacteria produce celullase in large quantities to aid bio-fuel production see

Cloning of the Thermostable Cellulase Gene from Newly Isolated Bacillus subtilis and its Expression in Escherichia coli

Journal: Molecular Biotechnology Publisher Humana Press Inc. ISSN 1073-6085 (Print) 1559-0305 (Online) Issue Volume 40, Number 2 / October, 2008

Bacteria gum

It is a little bit like bacteria toothpaste, to prevent decay of teeth, it can generate sweet material when we chew it.

Rock bacteria

Bacteria can sense sound and use sound to communicate with others, can we make bacteria change it's color or other behaviour according to the different sound (Article).

Finger sensor

Using the pressure sensitivity, perhaps a fingerprint impression could be made in a bacterial lawn, with varying pressures from the grooves of the fingerprint giving different responses.

World with bacterial communities as the countries

Bacteria populations that can speak to each other but also have interactions with other populations. Each population trade with others and live in a world.

Fractal design

Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment. by: E. Ben-Jacob Philos Transact A Math Phys Eng Sci, Vol. 361, No. 1807. (15 June 2003), pp. 1283-1312.

Distributed computing applications?

Could not find a practical applciation yet!

Final Three Ideas

Trapping of Heavy Metals using Bacillus subtilis
BioMemory
Skin Repairer

FINALISED IDEA

Trapping of Heavy Metals using Bacillus subtilis

20 – 21 June 2009 - Europe workshop (London)
23 – 24 June 2009 - UK iGEM meetup (Edinburgh)
23 October Practice Presentation (Newcastle)
23 October T-shirts are ready
27 October Practice Presentation (Sunderland)
27 October Poster is ready
30 October – 2 November 2009 - Jamboree (Boston)

@@ Line 2: / Line 2: @@
 {{:Team:Newcastle/Header}}
 {{:Team:Newcastle/Left}}
-This is a list of the ideas that have been covered during the course of the first iGem meetings (MORE EDITING TO COME!)
+__NOTOC__
+=Project Ideas=
-== Final Three Ideas ==
+[[Image:Team Newcastle iGem 2009 08-07-09 no 2.JPG|350px|center]]
-=== Trapping of Heavy Metals using ''Bacillus subtilis'' ===
-=== BioMemory ===
-=== Skin Repairer ===
+This is a list of the ideas that have been covered during the course of the first iGem meetings. Included within some of the paragraphs are links to articles which gave inspiration for that particular idea
 == Ideas discussed for iGEM ==
-=== MAN-SCAN ===
+==== MAN-SCAN ====
-Last year the newcastle team used bacteria to detect bacteria. How about using a similar approach to detect humans? Maybe we can come up with a less androgynous title. I visualised a lawn of B. subtilis onto which you place a body part (eg hand or foot) and later an image of it appears in light.
+Last year the Newcastle team used bacteria to detect bacteria. How about using a similar approach to detect humans? Maybe we can come up with a less androgynous title. I visualised a lawn of ''B. subtilis'' onto which you place a body part (eg hand or foot) and later an image of it appears in light.
-=== SYNCHRO-BAC ===
+==== SYNCHRO-BAC ====
 One large colony is glowing in the dark and send a message to other colonies to do the same.
-=== HAPPY-BACTY - general environmental monitor. ===
+==== HAPPY-BACTY - general environmental monitor. ====
-B. subtilis seems to be quite good at detecting and reponding to environmental stresses (is there a thing called a stressosome?). We could ask simple questions of the colonies - is your environemnt Nice, average or poor? maybe get a three colour output (traffice lites). This kind of thing is an environmentalist dream - to detect an average of environmental stressors in theis way, such as pollutants
+''B. subtilis'' seems to be quite good at detecting and responding to environmental stresses (is there a thing called a stressosome?). We could ask simple questions of the colonies - is your environemnt Nice, average or poor? maybe get a three colour output (traffice lites). This kind of thing is an environmentalist dream - to detect an average of environmental stressors in theis way, such as pollutants
 maybe the environmental monitor uses synchro-bac to tell the others what they are "feeling" and if they were motile the other could move to a nice area, or away from a bad one.
-=== Trapping of heavy metals then sporolate to fix them indefinatley ===
+==== Trapping of heavy metals then sporolate to fix them indefinatley ====
-Metal Resistance in Acidocella Strains and Plasmid-Mediated
+Metal Resistance in ''Acidocella'' Strains and Plasmid-Mediated
-Transfer of This Characteristic to Acidiphilium multivorum
+Transfer of This Characteristic to ''Acidiphilium multivorum''
-and Escherichia coli
+and ''Escherichia coli''
-=== Biological memory ===
+==== Biological memory ====
 ''Bacillus subtilis'' is a sporulating bacteria and can survive for years in its spore form. Also, we can make them respond to external stress such as electro-magnetic fields. Use these two features to engineer bacterias capable of storing information for years. This could become an immortal and unlimited memory. We could use bacterias in some way so that bacteria are 0 or 1 and use this to make a bacterial hardware or memory that is capable of storing octets and therefore that has memory.
-=== Allergen detection and removal ===
+==== Allergen detection and removal ====
 Using bacteria as quality control and disabling of allergens by detection of peptides found to elicit allergic response in food, such as nut, shell fish, egg, dairy traces etc. Samples from batches could in theory be tested with a fluorescent output.
-=== Calculator : Implementation of a simple calculator to add numbers ===
+==== Calculator : Implementation of a simple calculator to add numbers ====
-=== Soil Enhancer ===
+==== Soil Enhancer ====
-Detection of nutritions on the soil and freeing up the minerals for the plants '''([http://www.bcmicrobials.com/products_biostart.php?PHPSESSID=6e2f9df3e98e0bec71c2aa406a9f0ef0 Article]) '''- maybe detect the N, P, K elements in soil and give different feedback like colour or flourescence , adjust it's metabolisim system to generate product which can be absorbed by plants easily
+Detection of nutritions on the soil and freeing up the minerals for the plants '''([http://www.bcmicrobials.com/products_biostart.php?PHPSESSID=6e2f9df3e98e0bec71c2aa406a9f0ef0 Article]) '''- maybe detect the N, P, K elements in soil and give different feedback like colour or flourescence , adjust it's metabolism system to generate a product which can be absorbed by plants easily.
-=== Fast bacteria ====
+==== Fast bacteria ====
 Engineering the movement of bacteria with feedback systems like rockets '''([http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=193742 Article])'''
-=== Inflammatory disease treatment ====
+==== Inflammatory disease treatment ====
 This idea is a little similar to the allergen detector and corrector system - it involves using ''Bacillus subtilis'' in humans to target and deal with a particular allergen particle before the immune system sets in and creates the damaging effects of inflammation. Would make use of receptors which are able to bind to 1)IgE molecules and 2) the allergen particles themselves.
-=== Gastric Inflammation ===
+==== Gastric Inflammation ====
-Treatment and prevention of H. pylori (stomach ulcer) - engineer a B. subtilis than can live and grow happily in stomach acidity (pH2) - an acidophilic strain will also be needed for the heavy metal trapping.
+Treatment and prevention of ''H. pylori''(stomach ulcer) - engineer a ''B. subtilis'' that can live and grow happily in stomach acidity (pH2) - an acidophilic strain will also be needed for the heavy metal trapping.
-=== Skin repairer ===
+==== Skin repairer ====
-Using the production of hyaluronic acid (HA) an important glycosaminoglycan which is found in synovial fluid, extracellular matrix and very important in wound healing. It was found by Widner et al. 2005 that the HasA gene for Hyaluronan synthase could be expressed successfully in B. subtilis. It could maybe be put into a plaster or gauze used to dress wounds?
+Using the production of hyaluronic acid (HA) an important glycosaminoglycan which is found in synovial fluid, extracellular matrix and very important in wound healing. It was found by Widner et al. 2005 that the ''HasA'' gene for Hyaluronan synthase could be expressed successfully in ''B. subtilis''. It could maybe be put into a plaster or gauze used to dress wounds?
-(bacteria should be friendly to human body and generate grow factor like HA or other production to help skin cell grow; or maybe generate skin like material which can grow together with heathy skin )
+(The bacteria should be friendly to the human body and generate a growth factor like HA or another product to help skin cells grow; or maybe generate skin like material which can grow together with healthy skin)
-'''([http://www3.interscience.wiley.com/journal/121633568/abstract?CRETRY=1&SRETRY=0 Article])'''Idea came up in meeting 19/02/09- using a bacterial lawn to produce antibiotics within a plaster to protect a healing wound- OR- to produce S. aureus signal proteins which would prevent communication between S. aureus thus preventing infection.
+'''([http://www3.interscience.wiley.com/journal/121633568/abstract?CRETRY=1&SRETRY=0 Article])'''Idea came up in meeting 19/02/09- using a bacterial lawn to produce antibiotics within a plaster to protect a healing wound- OR- to produce ''S. aureus'' signal proteins which would prevent communication between ''S. aureus'' thus preventing infection.
-=== Cosmetic bacteria ===
+==== Cosmetic bacteria ====
 Can we use the bacteria to fill up the wounds, scratches, wrinkles etc. for a couple of hours.
-=== Sticky bacteria ===
+==== Sticky bacteria ====
-Again for filling or sticking items eg to a wound ?
+Again for filling or sticking items for example to a wound.
-=== Hair / filament producing bacteria allied to skin repair idea - may provide scaffold. ===
+==== Hair / filament producing bacteria allied to skin repair idea - may provide scaffold. ====
-B. subtilis  produces flagella. can we engineer it to produce large filaments of eg keratin which will stabilise a wound dressing?
+''B. subtilis''  produces flagella. can we engineer it to produce large filaments of eg keratin which will stabilise a wound dressing?
-=== Treatment of Hemophilia ===
+==== Bacterial microscopy ====
+Can they magnify  very small objects for us?
-=== Bacterial microscopy ===
+==== MVC ====
-Can they magnify  very small objects for us.
-=== MVC ===
 Implemantation of model view controller software pattern to bacteria. One group of colony is responsible only for the view,via fluorescent proteins etc, one gives commands to model poulation. At some point we may decide to add another command type population without breaking the whole pattern because all the command type bacteria have the same interface. This could also be implemented in a different way as service oriented bacteria having bacteria population that only does one job at a time. Another colony uses the services to do a certain task.
 '''([http://www.pnas.org/content/104/5/1456.full Article 1])'''
 '''([http://www.ncbi.nlm.nih.gov/pubmed/18675483 Article 2])'''
-=== Timed Germination ===
+==== Timed Germination ====
-Can we engineer bacteria to start germination at a specific time .
+Can we engineer bacteria to start germination at a specific time.
-They correspond to signals to start or stop germination without the nutritions
+They correspond to signals to start or stop germination without the nutrition
 <br>'''([http://www.nature.com/nrmicro/journal/v7/n1/full/nrmicro2060.html Article 1])'''
 '''([http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4TT8K22-J&_user=224739&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000014659&_version=1&_urlVersion=0&_userid=224739&md5=3c2b44fd89005cb37a6ed55b08ef230a Article 2])'''
-=== Path finding ===
+==== Path finding ====
 Simulating the ant colony '''([http://en.wikipedia.org/wiki/Ant_colony_optimization Article])'''. Bacteria will move intelligently tracking the pheromenes that are left by the others '''([http://portal.acm.org/citation.cfm?id=1389095.1389115 Article])'''.
-Or safe walk. Other will tell if it is safe to continue in a direction
+Or safe walk. Others will tell if it is safe to continue in a direction
 King bacteria. Other bacteria will guide king bacteria on a safe path
-=== Chaperone producer ===
+==== Chaperone producer ====
 Depending on the conditions, some chaperiones like Hsp70, Hsp60 will be secreted.  It might be used to cure Alzheimer disease '''([http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2533148 Article])'''.
-=== Glucose sensing bacteria ===
+==== Glucose sensing bacteria ====
-Bacteria capable of sensing the level of glucose in a blood sample. this will be the cheapest way of testing for glucose level in blood sample.
+Bacteria capable of sensing the level of glucose in a blood sample. This could be a cheap way of testing for glucose level in blood sample.
-=== Freezer ===
+==== Freezer ====
-To store nutritions using sporulation depending on the input functions and release them when needed upon a forced germination
+To store nutrients using sporulation depending on the input functions and release them when needed upon a forced germination
-=== SPOT THE ROT ===
+==== SPOT THE ROT ====
 Spores go red on germination when conditions go from v. cold to warm to indicate spoilage on food or medical product packaging.
-=== Bacterial automation ===
+==== Bacterial automation ====
 Using electronic sensors to connect computer directly to start a process for the bacteria. E.g Start DNA uptaking. The output function of electronic circuit should match to the input of the bacteria
-=== Bacterial tattos ===
+==== Bacterial tattos ====
 Using bacteria to have temporary tattos.
-=== Bacterial compass ===
+==== Bacterial compass ====
 Can we use bacteria to find our direction? Can we use magnetosomes for this purpose?
-http://www.scientificblogging.com/news_releases/magnetic_crystals_are_bacterial_compass_say_researchers
+'''([http://www.scientificblogging.com/news_releases/magnetic_crystals_are_bacterial_compass_say_researchers Article])'''
-=== Bacterial sensor which tells you how it "feels" by the rate of flashing. Maybe responding to environmental stress. ====
+==== Bacterial sensor which tells you how it "feels" by the rate of flashing. Maybe responding to environmental stress. ====
 It would be much easier to use than having to measure the intensity of fluroescence. Or maybe we could have a traffic light effect.
@@ Line 114: / Line 110: @@
 The closest we had then was a system called Microtox based on a phosphorescent marine bacterium ''Vibrio fischeri''. There are tons of data relating the response of Microtox to environmental factors.
-=== Cleaner bacteria ===
+==== Cleaner bacteria ====
-Eco-friendly, producing enzymes,proteins for cleaning purposes (toothpaste???)
+Eco-friendly, producing enzymes,proteins for cleaning purposes (toothpaste???)'''([http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V24-4VBM49J-3&_user=224739&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=950885605&_rerunOrigin=google&_acct=C000014659&_version=1&_urlVersion=0&_userid=224739&md5=c747408865efc0bec1a88605aa318756 Article])'''
-=== Eco-friendly bacteria produce celullase in large quantities to aid bio-fuel production see ===
+==== Eco-friendly bacteria produce celullase in large quantities to aid bio-fuel production see ====
-Cloning of the Thermostable Cellulase Gene from Newly Isolated ''Bacillus subtilis'' and its Expression in Escherichia coli
+Cloning of the Thermostable Cellulase Gene from Newly Isolated ''Bacillus subtilis'' and its Expression in ''Escherichia coli''
 Journal: Molecular Biotechnology
 Publisher  Humana Press Inc.
 ISSN  1073-6085 (Print) 1559-0305 (Online)
 Issue  Volume 40, Number 2 / October, 2008
-=== Bacteria gum ===
+==== Bacteria gum ====
-It is a little bit like bacteria toothpaste, to prevent decay of teeth, it can generate sweet materia when we chewing it.(I did not check whether some igem team have done it )
+It is a little bit like bacteria toothpaste, to prevent decay of teeth, it can generate sweet material when we chew it.
-=== Rock bacteria ====
+==== Rock bacteria ====
-bacteria can sense of sound and use sound to communicate with others, can we make bacteria change it's color or other behaviour according to the different sound.
+Bacteria can sense sound and use sound to communicate with others, can we make bacteria change it's color or other behaviour according to the different sound '''([http://www.jstage.jst.go.jp/article/jgam/44/1/44_49/_article Article])'''.
-=== Finger sensor ===
+==== Finger sensor ====
 Using the pressure sensitivity, perhaps a fingerprint impression could be made in a bacterial lawn, with varying pressures from the grooves of the fingerprint giving different responses.
-=== Nutrient generator ===
+==== World with bacterial communities as the countries ====
-=== Gene therapy using bacterial enzymes ====
-=== World with bacterial communities as the countries ===
 Bacteria populations that can speak to each other but also have interactions with other populations. Each population trade with others and live in a world.
-=== Fractal design ===
+==== Fractal design ====
+Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment.
+by: E. Ben-Jacob
+Philos Transact A Math Phys Eng Sci, Vol. 361, No. 1807. (15 June 2003), pp. 1283-1312.
-=== Distributed computing applications? ===
+==== Distributed computing applications? ====
 Could not find a practical applciation yet!
-=== Mutation detector ===
+<br>
+== Final Three Ideas ==
+* Trapping of Heavy Metals using ''Bacillus subtilis''
+* BioMemory
+* Skin Repairer
+<br>
+== FINALISED IDEA ==
+* '''[https://2009.igem.org/Team:Newcastle/Project/Overview Trapping of Heavy Metals using ''Bacillus subtilis'']'''
 {{:Team:Newcastle/Footer}}
 {{:Team:Newcastle/Right}}

Team:Newcastle/Ideas