Wiki/Team:Imperial College London/Notebook/July 6

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Revision as of 22:16, 6 July 2011

Rebekka Bauer
Action points:
-bios on the wiki
-sci-fi meeting
-characterisation talk
-come up with more ideas
-do more research on anti-venom and prodigiosin

Sci-Fi prodigiosin ideas (developed with Nick Kral and CJ from the RCA):
-use prodigiosin (red pigment) as the new "colour of health" (know something is sterile rather than assume it is)
-possible future uses: in decontamination/ as a "panic room"/ sterile hospice
-possible future products: hand gel, clothing (e.g. protective suits in bioreactor plants), decontamination paint (in hospitals etc)
-actual uses: anti-cancer (could be in a red drip, red pill?), anti-malarial (drug verification because pigment colour is hard to fake)
Eventually, this idea was scratched because optimising the production pathway does not contain enough synthetic biology. In addition, the compound is immunosuppressive (http://pubs.rsc.org/en/Content/ArticleHtml/2008/CC/b719353j) and would therefore be disadvantageous to normal people. Many of the envisaged applications would only work with less problematic analogues of prodigiosin.

Brainstorming:
Venom and BAS ideas to be presented on Friday!
-desertification (overdone already)
-thermophiles (make them express melanin so they can be heated up by the sun, saving energy)
-cell-cell signal transduction (can be used as inhibition or activation)
-desalination (commercial membranes are probably more efficient)
-data storage in bacteria (use DNA to encode information has already been done but it might be useful to come up with a new way of retrieving the information. Storing data in RNA might be more efficient)
-ocean metals (retrieving valuable materials from sea water, main problem: materials are only present at really low concentration and might be hard to retrieve) -cross-linking of hair to something useful
-dictostylium
-using melanin for heat production from sound in bacteria. The heat could then be converted into an output, producing sound sensitive bacteria. Is melanin really able to detect sound??
-modifying silk worms?
-radiotrophic fungi (fungi that use gamma radiation to produce ATP - the pathway could be used in E. coli to absorb radioactivity but the exact pathway does not seem to be known (Wikipedia))
-serum bile acid as a biomarker of liver problems in pregnancy

Research for venom:
organise slides into problem, specifications needed to tackle problem, how to achieve specifications
-venom chosen: Asian cobra (one of the most common ones)
-Ming: summarise problem and specifications needed
-Chris: look at shark antibodies
-Nikki: look at in vivo mutagenesis (PCR mutagenesis would be too tedious)
-Frank: selection (FACS with GFP?)
-Rebekka: genetic circuit (detection mechanism - two component system?, suicide mechanism for cells that do not detect venom)

Si, Nina, Nick and Yuanwei

- morning:

brain storming:

- meeting with RCA people

- presenting the DNA hard drive idea

1. use DNA sequence as a medium to store information

DNA base - quaternary bit - original text

2. put “tag in” information (i.e some specific base pairs as “prototypes”) to classify the information

3. writing functions in programming language with DNA sequences, use DNA as the function variables

- Sci-Fi:

a. in the future, a bacteria charm/necklace can be made to store and carry the information, such as exam syllabus, genetic disease history, family photos, etc

b. different coding methods and types of bacteria can be chosen by the clients for different levels of security needs ,(some high risky information can be store in Bacillus anthraci for military use)

c. data can also be stored in E.coli in the human digestive system, it can be erased by intaking antibiotics

- practical problem:

we need a bacteria platform to carry out the operation of the data

(I.e: bio-compiler? bio-CPU?)

a compiler consists of sets of programs and logic relations, it is theoretically workable, but obviously too difficult to do as a ten-week project

- afternoon:

brain storming:

- since the bio-compiler idea is abandoned, we thought about other ways to store data:

- ROM memory

8x8 gird to store 64 bits of data

the bacteria interaction can be modified to give to outputs, which indicates the two binary states (0 or 1)

- JK flip-flop or synchronized counter

- 7-segment display

one bacterium -four input channels-each channel with two states (0 or 1)-nine outputs to give nine numbers (0 to 9)- control the corresponding segments to display the number

- bacterial minesweeper

an inhibitor can be considered as a ”mine”

the main problem is that secondary diffusion is very difficult to control. a mass transfer equation must be modeled for each individual square

Bile Acid Sensor:

- the idea came up with SI’s final year project

- a biosensor can be produced for daily home use to detect the bile acid concentration level in blood to prevent a series of liver diseases, especially the Intrahepatic cholestasis of pregnancy (ICP)

- the basic concept behind this sensor:

bile acid - enzyme binding with the acid molecules – promoter – triggering the FXR gene – production of GFP

- GFP is normally used as an indicator of the bio-sensor

the main problem is that the fluorescent intensity is very hard to quantified for a home-user

- being inspired by the cosmetic skin colour sample card , we can make a sample card of fluorescence to give the rough concentration level of bile acid

- a threshold value is required to tell the patient when their blood bile acid level is dangerous and may need a medical treatment

- therefore, we will modify the linear relationship between bile acid concentration and GFP intensity level into a Hill system using Hill equation to find the threshold value

- also, we may use colour indicator instead of GFP (light indicator)

Christopher Schoene

RCA sci-fi story ideas:
Nuclear winter leaving people without immune systems. Use external immune system to save everybody?

Synthetic life can only use certain amino acids, firewall?
Biocomputers where man and machine are converged closer together.
Floppy disk baby?
Mock news articles (Times, science article, tabloid), comic strips (simplified version of our project), documentary type video?,
Terrorist attacks

Characterization presentation by Chris:

in vivo presentation
Timer vs. switch. need to know characteristics of parts.
How to characterise
Look at individual parts. What goes in, what goes out. What function is carried out.
What specifically do you want to characterise.
Terminator, core-promoter, RBS, reporter, coding region.
Terminator requires several different characterizations.
Place promoter, coding region into an expression circuit with a reporter.
Standards are only existant for promoters. How strong promoters are.
Canton paper 2008. Base characteristics that you need to know about an inducible promoter.
How responsive (transfer function of response), dynamic? (output)
All relative to J23101.
Synthesis rate, number of cells and divide your promoter output with standard which gives you a value relative to J23101. RPU (relative promoter unit)
RBS calculator gives you a value to how strong it is. Need to debug yourself.
Hard to characterise until we know what we want to do.
Plate readers look at OD, fluorescene, luminescence.
Individual cells analyzed for GFP and RFP.
Chris works on methods to make it more high-throughput (automates to make faster).
Won't consider optimizing something unless it worked twice on the assays.
Fluorescence doesn't give use pinpoint accuracy. Can't be measured really well, only bulk events and not specific events.
Enzymatic activity more done in vitro.
You're working with factories that work depending on what they're in.
Can find Chris though James at any time.
Make sure positive and negative control will work.

Antibody research:

-Single-domain antibodies such as the nurse shark derived IgNAR and the camelid derived VHH have been used for many purposes and have recently started to gain popularity among the scientific community.
-Contain CD3 loop that gives these Ig's an advantage when looking for cryptic viral epitopes. However, contain ten epitope copies and might still infect. Solved by increasing their mass.
-Both of these Ig's are stable enough to be administered orally.
-Orally administered transformed lactobacilli were used to administer anti-TNF Ig.
-Small dimensions of VHHs allow it to be easily tagged.
-Lactobacilli have been engineered that produces VHH's at a rate fast enough to prevent infection by p2 bacteriophage. Possibly use lactobacillus for screening and E. coli for secretion?
-VHH's and IgNAR's have been effective in detecting poliovirus and inhibiting its replication in vitro, as well as preventing the assembly and secretion of hepatitis B. Possible to use VHH's as intrabodies vs. HIV-1?
-N-glycosylation increases stability.
-Studies demonstrated that pre-immune libraries can be used for rapid generation of Ig's against a large number of harmful antigens. Troublesome low sensitivity overcome by using phage-displayed instead of purified antibodies.[1]

References:

[1]Ario de Marco, “Biotechnological applications of recombinant single-domain antibody fragments,” Microbial Cell Factories 10, no. 1 (2011): 44.

@@ Line 98: / Line 98: @@
 <P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN><FONT size=3><FONT face=Calibri><FONT color=#000000>- <SPAN style="mso-spacerun: yes">&nbsp;&nbsp;</SPAN>also, we may use colour indicator instead of GFP (light indicator) <SPAN style="mso-spacerun: yes">&nbsp;</SPAN><SPAN style="mso-spacerun: yes">&nbsp;</SPAN><SPAN style="mso-spacerun: yes">&nbsp;</SPAN><o:p></o:p></FONT></FONT></FONT></SPAN></P>
 <P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN style="COLOR: #0d0d0d; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-themecolor: text1; mso-themetint: 242" lang=EN-US><o:p><FONT color=#000000 size=3 face=Calibri>&nbsp;</FONT></o:p></SPAN></P>
+</html>
+<html><br><br><b>Christopher Schoene</b><br><br>
+RCA sci-fi story ideas: <br>
+Nuclear winter leaving people without immune systems. Use external immune system to save everybody? <br><br>
+Synthetic life can only use certain amino acids, firewall? <br>
+Biocomputers where man and machine are converged closer together. <br>
+Floppy disk baby? <br>
+Mock news articles (Times, science article, tabloid), comic strips (simplified version of our project), documentary type video?, <br>
+Terrorist attacks<br><br>
+<b>Characterization presentation by Chris:</b> <br><br>
+in vivo presentation<br>
+Timer vs. switch. need to know characteristics of parts. <br>
+How to characterise<br>
+Look at individual parts. What goes in, what goes out. What function is carried out. <br>
+What specifically do you want to characterise. <br>
+Terminator, core-promoter, RBS, reporter, coding region. <br>
+Terminator requires several different characterizations. <br>
+Place promoter, coding region into an expression circuit with a reporter. <br>
+Standards are only existant for promoters. How strong promoters are. <br>
+Canton paper 2008. Base characteristics that you need to know about an inducible promoter. <br>
+How responsive (transfer function of response), dynamic? (output) <br>
+All relative to J23101. <br>
+Synthesis rate, number of cells and divide your promoter output with standard which gives you a value relative to J23101. RPU (relative promoter unit) <br>
+RBS calculator gives you a value to how strong it is. Need to debug yourself. <br>
+Hard to characterise until we know what we want to do. <br>
+Plate readers look at OD, fluorescene, luminescence. <br>
+Individual cells analyzed for GFP and RFP. <br>
+Chris works on methods to make it more high-throughput (automates to make faster). <br>
+Won't consider optimizing something unless it worked twice on the assays. <br>
+Fluorescence doesn't give use pinpoint accuracy. Can't be measured really well, only bulk events and not specific events. <br>
+Enzymatic activity more done in vitro. <br>
+You're working with factories that work depending on what they're in. <br>
+Can find Chris though James at any time. <br>
+Make sure positive and negative control will work. <br><br>
+<b>Antibody research:</b> <br><br>
+-Single-domain antibodies such as the nurse shark derived IgNAR and the camelid derived VHH have been used for many purposes and have recently started to gain popularity among the scientific community. <br>
+-Contain CD3 loop that gives these Ig's an advantage when looking for cryptic viral epitopes. However, contain ten epitope copies and might still infect. Solved by increasing their mass. <br>
+-Both of these Ig's are stable enough to be administered orally. <br>
+-Orally administered transformed lactobacilli were used to administer anti-TNF Ig. <br>
+-Small dimensions of VHHs allow it to be easily tagged. <br>
+-Lactobacilli have been engineered that produces VHH's at a rate fast enough to prevent infection  by p2 bacteriophage. Possibly use lactobacillus for screening and E. coli for secretion? <br>
+-VHH's and IgNAR's have been effective in detecting poliovirus and inhibiting its replication in vitro, as well as preventing the assembly and secretion of hepatitis B. Possible to use VHH's as intrabodies vs. HIV-1? <br>
+-N-glycosylation increases stability. <br>
+-Studies demonstrated that pre-immune libraries can be used for rapid generation of Ig's against a large number of harmful antigens. Troublesome low sensitivity overcome by using phage-displayed instead of purified antibodies.[1] <br><br>
+<b>References:</b> <br><br>
+<a href=http://ultr23.vub.ac.be/ultr/pub/pdfs/98.pdf>[1]</a>Ario de Marco, “Biotechnological applications of recombinant single-domain antibody fragments,” Microbial Cell Factories 10, no. 1 (2011): 44.
 </html>