User:Jonathan Cline/Notebook/Melaminometer/Brainstorming

Related Works and News

• DEVELOPMENT OF BIOSENSORS FOR DETECTING HAZARDOUS CHEMICALS (Natalie Sarange Omattage, 2008 Intel International Science and Engineering Fair)
  • Food additives contaminated with cyanuricacid and melamine were responsible for recent deaths of many pets. Food imports are currently beingscreened using chromatographic and mass spectrometric methods (e.g. HPLC & GC-MS/MS). Although these methods are very sensitive, the instruments as well as the reagents are expensive and require highly trained personnel to operate.
  • A recombinant M13 bacteriophage library was screened to identify peptide sequences with high affinity to cyanuric acid and melamine. Amino acid sequences STNFFYQTFAFH and RNSNHTAYGEEP were identified as the consensus sequences specific to cyanuric acid and melamine, respectively. Quartz crystal microbalance (QCM) based biosensors were developed using these peptides.
  • Although cyanuric acid binding peptide demonstrated better mass accumulation rates than the melamine binding peptide, both peptides were capable of detecting their respective ligands at concentrations as low as 1.25 parts per billion (ppb) during the first five minutes of the experiment.
  • Cyanuric acid and Melamine binding peptides coupled to a gold binding peptide sequence are currently being developed to increase the peptide density and sensitivity of the assay. Biosensors with synthetic peptides could decrease the detection limit to pico-molarconcentrations of the ligands. QCM instruments are portable, cost much less than GC-MS setups, and do not require highly trained personnel to operate. Therefore, QCM based biosensors may be used at ports and warehouses to more thoroughly screen food additives imported into the United States. In addition to food contaminants, the QCM based biosensors may also be employed to detect other harmful chemicals.
  • see ISEF (International Science and Engineering Fair) photos
  • Intel Announces Winners of World's Largest Pre-College Science Fair (2008)

• Amateurs are trying genetic engineering at home (U.S. News, Thursday December 25, 2008, 6:16 PM)

• Meredith L. Patterson, Switch to thumbnail view Industrial technologies Photos

• Amateurs are trying genetic engineering at home (Yahoo News, Thu Dec 25, 6:49 pm ET)

• New Scientist, Rise of the garage genome hackers

Dry Lab Design Method

1. Project definition
   1. Iteratively (re-)define project
   2. Verify theoretical feasibility
   3. Repeat from above
2. Project Feasibility
   1. Research existing metabolism/catabolism/enzymatic activity
   2. Research existing microbe structure
   3. Verify theoretical feasibility of inserting metabolic path into desired microbe
      1. Need a suitable vector -- not all plasmids are appropriate for all gut bacteria
      2. Must be stable, i.e., reproduce from generation to generation
   4. Verify theoretical compatibility of biological components
      1. Find possible promoters, repressors = regulators for gene expression
      2. Design decision: in vivo microbial system, or in vitro cell free system?
   5. Repeat from above
3. Project Testability
   1. Research method for testing microbe
   2. Research required controls, blanks, positives, samples
   3. Repeat from above for design of test method, as necessary
4. Project Modeling
   1. Model theoretical operation of microbe
      1. Pathways + membrane + multi-cell
      2. Gene regulation
   2. Model theoretical compatibility of components
   3. Model testing method
   4. Obtain expert assistance/advice on design & models
   5. Repeat from above
5. Project Implementation Scoping
   1. Scope building organism (cost, labor, designer)
   2. Funding source
   3. Materials source
   4. Proceed to wet lab phase

Wet Lab Implementation Method

1. Verify Prior Research
   1. Obtain close analogues to original microbes & plasmids
      1. Culture control & target
   2. Modify strain
   3. Verify strain
      1. Compare growth & products
      2. Measure against control
      3. Compare to model
      4. Improve model
   4. Repeat as necessary for validation of original & current protocols
2. Optimize for Desired Function
   1. TBD
   2. Isolate to enzymes
   3. Switch strains or microbes

Designing the Melamine Sensing System

Design of a Sensor

• Definition of a sensor: A sensor is a device that measures a physical quantity and converts it into a signal which can be read by an observer or by an instrument.
• Concerns about a sensor
  • Specificity
  • Sensitivity
  • Measurement Error Control

General Architecture of Molecular Sensor

1. Signal Recognition
2. Signal Transduction
3. Signal Reporting

• (Bio)sensors for measurement of analytes implicated in food safety: a review (P. D. Patel,TrAC Trends in Analytical Chemistry 2002)

Type of Currently Available Melamine Sensors

• Recognized by physical properties (charge, mass)
  • LC/MS/MS
  • GC/MS
  • HPLC
• Recognized by chemical topology/structure
  • antibody (ELISA) and improved version of ELISA: one-step ELISA, protein array
  • nano-sensor, MEMS, electronic nose

Design of GMO-based Subcellular Biological Sensors

Strategies

• indirect method
  • detect the byproduct(s) after metabolizing melamine
• direct method
  • detect the melamine by specific antibody (inspired by ELISA method)

Idea #1: Take advantage of Melamine Degradation Pathway

Single Melamine Sensor + pH sensor

Comments

• Idea #1 is OK, however need to address cyanuric acid as well. it is not necessary to distinguish between the two, only to detect both. Also, this adds the complexity of the pH sensor (would it have any compatibility problems with the new enzymes?) -- JC

• About the Entrance Gateway of Melamine into Cellular System:
  • Does melamine channel exist? Where we can get melamine channel? -- blent
  • Does E.coli intake melamine? Which bacteria can intake melamine? -- blent

• About the pH sensor
  • Does the scale of our pH sensor fit to our scale in melamine detection? -- blent

• About the ammonia exporting
  • How E.coli deal with the ammonia? Can E.coli export the ammonia outside as expected? -- chc

• Possibility of Dual Sensor
  • Does it mean we have to create TWO different method to detect melamine and cyanuric acid? -- blent

Dual Sensor for Melamine and Cyanuric Acid + Ammonia Sensor + Carbon Dioxide Sensor

Idea #2: Re-writing the Signal Transduction in Bacteria

Fusion HPK-based Melamine Sensor	The most common TCS module: EnvZ+OmpR
	Caren Chang and Richard C. Stewart (Plant Physiol., 1998)

How to rewrite TCS in E. coli
Rewriting TCS module	available TCS modules in KEGG
Skerker, J. M. and et. al. (Cell 2008, June 13) Michael A. Kohanski and James J. Collins (Cell 2008, June 13) Protein Domains DHp (Dimerization and Histidine phosphotrasfer) CA (Catalytic and ATP-binding)

Related Works
Re-engineer E.coli to sense light	Re-engineer E.coli to sense another bacteria
Christopher A. Voigt and et. al. (Nature 2005, Nov 24) fused Histidine Protein Kinase (HPK) light sensing module PCB (cyanobacteria) transmitter module of EnvZ (E.coli) WT Response Regulator (RR) receiver module of OmpR (E.coli) DNA-binding module of OmpR (E.coli)	University of Sheffield, iGEM 2008 move a set of signaling pathway from one bacteria to another not prove to work properly yet

Comments

• About Melamine sensing
  • How to identify Melamine Binding Peptide? And then we can create a new HPK for melamine sensing ^^ --blent
  • Is it possible to infer Melamine Binding Peptide from Melamine Deaminase? --blent

Search by TriA sequence	Search by Melamine structure
42 ligand hits were found by TriA sequence search in PDB. The ligands similar to melamine structure are:	one protein hit (3BMM) were found by EXACT melamine structure search in PDB There are 4 identical protein chains (A, B, C and D) in this structure 3D snapshot of 3BMM structure in jmol TriA and chains in 3BMM are locally similar in sequence (TriA vs. Chain C in 3BMM)

Which enzymes should we produce?

Per the second bullet point at User:Jonathan_Cline/Notebook/Melaminometer/Toxicology_Details, it sounds like melamine and cyanuric acid aren't that harmful in isolation, but when combined they produce renal toxicity by forming the melamine cyanurate salt. Should we think about developing multiple strains of test bacteria, one which reports the presence of melamine and one which reports the presence of cyanuric acid? Or should we develop a plasmid which carries reporters for both melamine and cyanuric acid (with different colours, e.g. yellow and blue?)

Pros:

• More realistic determination of risk
• Single strain has a simple detection protocol -- if the sample turns yellow there's melamine, if it turns blue there's cyanuric acid, if it turns green (yellow+blue), there's both!

Cons:

• Two strains of bacteria = more complicated process (blent says: we can have one plasmid with both melamine and cyanuric acid detection and put it in one single host/chassis)
• Cyanuric acid is a product of melamine degradation, so if the test organism contains the full melamine degradation pathway, the whole sample will start out yellow, shift to green, and finally turn blue as melamine is deaminated into cyanuric acid.
  • Could solve this problem by only including melamine deaminase and cyanurate amidohydrolase, i.e., the first step of each pathway. Melamine deaminase will deaminate the melamine twice, but the third deamination never takes place if there's no ammelide aminohydrolase. Thus, the sample will only turn green if both melamine and cyanuric acid are present.
    • Another benefit of including just the first step of each pathway: the first step for both pathways is present in A. acidovorax subsp. citrulli. Should it turn out to be more cost-effective, practical, whatever, to clone our genes of interest from a living organism rather than synthesizing them de novo, we'll only have to work with one organism -- and it's an organism that isn't pathogenic to humans, unlike Pseudomonas.

Possible solution:

• Agree that 1-step degradation of melamine is best, to eliminate crosstalk between melamine->product and cyanuric acid.
• Ratio of melamine-to-cyanuric acid may or may not be important? 10-to-1 same as 1-to-1 for crystal formation.
  • Reference 2006 igem arsenic detector for 'amplifer' circuit used.
    • http://parts.mit.edu/wiki/images/5/5d/IGEM2006-Edinburgh-Powerpoint.pdf

Sensitivity

• What's the threshold for detection? How can this threshold be modified?
  • "Melamine levels in imported Chinese candies recalled last week in California were as high as 520 parts per million, about 200 times greater than the level set Friday by the FDA for "tolerable" risk."
  • Must detect close to "2.5 ppm of melamine and its analogues"

The sensitivity of melamine detection methods

Method	Sensitivity (in ppm)
LC/MS/MS	0.05 ppm (current Taiwan standard)
GC/MS	0.5 ppm
HPLC	2.0 ppm - 2.5 ppm (previous Taiwan standard)
ELISA	Romer Labs: AgraQuant® Melamine Sensitive ELISA Test Kit Quantitation Range: 0.1 - 5.0 ppm in milk 0.5 - 25 ppm for milk powder Limit of Detection: 8 ppb in milk 150 ppb for milk powder Abraxis, Warminster, Pa. LDD (lease detectable dose) 10 ppb in their manual 9 ppb in PBS (FDA report) 1 ppm in dog food (FDA report) different dilution methods vary the performance of detection it is difficult to detect melamine in mixed sample (real sample)

• Limitation of Melamine Detection Methods (in Chinese)

25 Labs in Taiwan provide melamine detection service

Organization and Lab	Equipment and Service
SGS TAIWAN LIMITED: Ultra Trace Industrial Safety Hygiene Lab	LC/MS/MS
National Animal Industrial Foundation	LC/MS/MS
TÜV Rheinland Aimex Ltd (Taiwan)	LC/MS/MS
Intertek Taiwan	LC/MS/MS, HPLC
Wei-Chuan Corp.	GC/MS, HPLC
FSI (Food Safety Institute) International - Asia Pacific Office	LC/MS/MS, GC/MS, HPLC
FIRDI (Food Industry Research and Development Institute)	LC/MS/MS, HPLC
GSL (General Standard Laboratory)	LC/MS/MS
Sun Dream Environmental Technology Corp.	LC/MS/MS
Cheng-Shiu University: Super Micro Mass Research and Technology Center	LC/MS/MS
Sinphar Group	LC/MS/MS, LC/MS
Meiho Institute of Technology: Biotechnology Service Center	LC/MS/MS
Hwayo Tech & Lab Co., LTD.	GC/MS, HPLC
SL (Super Laboratory) in Taiwan	HPLC
Lin Family Biotech Co.	HPLC
National PingTung University of Science and Technology: CAAPIC (Center for Agriculture and Aquaculture Product Inspection and Certification)	LC/MS/MS
VCRO (Virginia Contract Research Organization) Co., Ltd.	LC/MS/MS
Taiwan Eel Farming Industry Development Foundation	LC/MS/MS
BSMI (Bureau of Standards, Metrology and Inspection), R.O.C.	LC/MS/MS
Department of Health, Taipei	LC/MS/MS
Department of Health, Kaohsiung	LC/MS/MS
BFDA (Bureau of Food and Drug Analysis): North, Central, South and Eastern Departments]	LC/MS/MS

• list from the Department of Health in Taiwan
• Food Safety Web in Taiwan

Chassis

• Desired to be non-pathogenic, wide temperature stability, non-smelly
  • "Pseudomonas sp. strain ADP is not amenable to genetic studies. [...]"
  • I'm generally in favour of Lactobacillus sp., although Gram-positive bacteria are more difficult to transform than E. coli are. There are good electroporation protocols for lactobacilli though.
    • as an uneducated opinion, I'm partial to cyanobacteria since they seem friendly (and easy to differentiate our GMO from wild type by adding salt). Dont know enough about compatibility or growing though. -JC
• How will CO2 production affect microbe? -JC
• How will diffusion into microbe affect metabolism? -JC
• How will products build up in microbe & diffuse out? -JC

Environmental

• Metabolizing melamine/etc throws off NH4+ ammonium cation with each degradation step.
  • Are you sure about that? MetaCyc says it's NH3.
    • I'm confused on this point. Some pathway diagrams show NH3. MetaCyc shows ammonium. Result graph from K. terragena shows concentration of NH4. Likely both will exist and swap back & forth to reach equilibrium depending on pH of the environment. -JC
  • Will the microbe be affected with change in pH?
    • I'm bad at chemistry: does that mean the pH goes up or down? Lactobacilli tend to like acidic environments.
      • more free H+ (or + in general) means more acidic means much lower pH. NH3 ammonia is high pH since it is more "-" thus basic. -JC
  • Can ammonium be used as a super-easy detection mechanism?
    • if user smells ammonium, then melamine is present.
      • "The average human nose can detect ammonia concentrations on the order of 50 ppm or less." [1]
      • Need to test whether it's released as a gas. If so, then it should be quite easy to detect -- though note that concentrations of 100ppm are irritating to the nasal passages!
        • Good point about the vapor. Maybe could add heat. or if chassis already requires 30C temperature, maybe vapor is already produced. -JC
    • use pH strip or drop kit, scale of red indicates melamine metabolized. What is blank pH of typical sample; infant baby formula likely very neutral; milk is very neutral. -JC
    • Depending on concentration of NH3/NH4, could measure conductivity as a measure of melamine reduction products. This would be very easy to threshold/calibrate. Maybe much easier than using gene expression for visual indicator. This could really be a key point. -JC