User:Eruhi

VGEM

VGEM

http://sgp.dna.affrc.go.jp/images/top01.png http://blog-msb.embo.org/blog/img/thumb070607.jpg

Papers, References, Resources

Article Title: Molecular components of the mammalian circadian clock Author: Ko, CH Journal: Human molecular genetics ISSN: 0964-6906 Date: 2006 Volume: 15 Issue:review issue 2 Page: R271

Collection of Ideas from Idea Exchange and Other Teams

McGill

http://parts.mit.edu/igem07/index.php/McGill/Lab_Protocols

Team 1 - Fluorescence Complimentation

Team 2 – Repressilator

From IGEM07

We have two projects for the summer:

1) A biological timer

2) A biological breathalyzer

http://openwetware.org/wiki/IGEM

http://openwetware.org/wiki/IGEM:PennState

PSU 2007 iGEM team is currently developing projects radiation detection and ethanol production

http://openwetware.org/wiki/IGEM:Idea_exchange

Square bacteria

Crescentin is believed to cause Caulobacter to form a helical shape. Disrupting the CreS gene causes the bacteria to revert to a rod shape (necessity). Could importing the gene into E. coli produce the reverse effect (sufficiency)?

   * FimE inverts a specific stretch of DNA, defined by a pair of sequence elements (IRR and IRL), forming a DNA loop between the two elements[3]. If we add multiple copies of one of these elements (one IRR, two IRL), would FimE randomly choose one of the sites (one IRL out of the pair) to invert between? Either choose one of several promoters to attach to a given gene, or one of several genes to attach to a given promoter.
   * Then, can we tune the probability (from, say, 60:40 to 80:20 to 20:80)? Ideally do this dynamically (based on some small molecule) - use proteins that bend DNA to affect the probability of loop formation.

Marine biotechnology: Marine natural products represent a largely untapped and promising resource for drug development.

The marine environment may contain over 80% of the world's plant and animal species, and during the past decade over 5000 novel compounds have been isolated from marine organisms. The diversity of chemical compounds in the marine environment may be due in part to the extreme competition among organisms for space and resources … It is hypothesized that sessile marine organisms (for example, sponges, octocorals, tunicates and algae), have developed a diverse array of chemical compounds known as "secondary metabolites" or natural products for defense and competition.

http://www.rsc.org/Publishing/Journals/

Fluid approach to 3D microstructures

Used light from a microscope to polymerise specific areas of a fluid inside a microfluidic channel. This process, which causes the fluid to harden and stick to the surface of the channel, is known as photocuring. The unpolymerised material was then washed away and a second material was injected into the channel to be photocured.

Sorting bacterias

Harvard:

   * air conditioners" --> these tend to add body to the hair shaft by using bonding polymers; I was thinking that bacteria could be the new line of "bonding polyproteinecious entities" etc etc

textiles

   * silk
   * wool
   * polyester
   * nylon fibres
   * Could use the MIT idea to clone E coli that secrete pleasant smells and similarly bind to these fibers -- a living deodorant!

http://openwetware.org/wiki/IGEM:MIT/2007/Ideas

http://del.icio.us/MITiGEM

. Bacteria with squid reflecting protein (reflectin)

Magnetic alignment of bacteria

   * comments:
         o Brian: surface display of peptide which binds magnetic nanoparticles (iron oxide, cobalt oxide)

Bacteria which synthesize vitamins

   * comments: Major vitamin deficiencies
         o Brian: One of the most serious vitamin deficiencies in the current world is that of vitamin D (described as an epidemic in the USA). Although it can be produced by humans, the synthesis requires sunlight and many people do not receive sufficient UV radiation to produce the minimum daily requirement. Vitamin D is required for efficient calcium absorption in the gut, and deficiency leads to many bone disorders (rickets, osteoporosis, etc) as well as increasing the risk of autoimmune disease, diabetes, cancer, and cardiovascular disease. Current methods to synthesize vitamin D use extraction from sheep's wool. For more info on vitamin D, see wikipedia page epidemic cancer
         o Brian: Another option is Vitamin B12, which is the main vitamin lacking in vegan diets (deficiency causes pernicious anemia). It is produced ONLY in prokaryotic organisms...
         o Brian: Beriberi is caused by deficiency in thiamine (vitamin B1). It is very prevalent in Asian countries where many people rely entirely on white rice for their diet.

Plastic binding bacteria

   * comments: credit to Reshma
         o Brian: bacteria bind to polymer plastic via surface display peptides

Luciferase Lava Lamp

Organic Transister?

RNA oligo synthesizing bacteria

   * bacteria that produce and secrete RNA (mRNA, siRNA, RNAi, microRNA, etc)
   * could be used to mass produce RNA-based therapies
   * benefit from high-fidelity biological production (no error-prone commercial synthesis)
   * commercial synthesis is limited to <20 bp (maybe 50 bp max)
   * purification by HPLC later (and analyze by MS)
   * protect RNA (chemicals protect 2'OH, could secrete as dsRNA)
   * F factor secretion?

Stick-to-everything proteins from mussels

adhesive peptides which specifically bind common plastic/polymer surfaces.

Emre Ruhi

Emre is an undergraduate student at the University of Virginia and is the biologist for the Virginia Genetically Engineered Machine (VGEM) Team. He is a third-year biology major and philosophy minor and thus spends most of his time in laboratories conducting science experiments and then thinking, "Why?"

School

• University of Virginia
  • Department of Biology

Activities

• Resident Advisor in first-year residential dorms
• Brother of Phi Society Fraternity
• Echols Scholar
• Teaching Assistant for a course in Emergency Clinical Medicine
• His independent research is focused on understanding circadian behavior in the female hypothalamo-pituitary-gonadal axis. It incorporates a range of fields from cellular biology, neuroscience/surgery, genetics, and immunocytochemistry.
• Years of tutoring and teaching, from one on one interaction to large classes.
• Emergency Medicine Academic Associate. Direct contact with patients and real patient care by shadowing the attending physician’s and residents in the University of Virginia Hospital Emergency Department. Additionally, he collects research data on topics including patient satisfaction, IV insertion, and dental pain.
• Alternative Spring Break participant. Specifically, volunteering in an orphanage and local schools in the Dominican Republic.

Contact

Emre's email