20.109(F08):Anna YingFei Module3

Anna Simon and YingFei Li: 20.109 Module 3 Sources

We are still in the process of developing our ideas. Some ideas that we have had are management of silver nanoparticles, using engineered phage and bacteria to break down organic pollutants, and the use of phage to develop and deliver longer-lasting drugs. These are some sources we've used:

Removal of pharmaceuticals in drinking water treatment : Effect of chemical coagulation

The inhibitory effects of silver nanoparticles, silver ions, and silver chloride colloids on microbial growth

Yuan, G. “Natural and modified nanomaterials as sorbents of environmental contaminants.” Journal of Environmental Science and Health (2005). 39(10), pp 2661-2670. Only abstract is available. Compares the performance of synthetic nanomaterials with natural nanomaterials in adsorbing different kinds of pollutants: copper, napthelene, and estradiol (like synthetic estrogen). Mentions unknown risk and possible concern for human uses of nanomaterials.

Owen, R, and M Depledge. “Nanotechnology and the environment: risks and rewards.” Marine Pollution Bulletin (2005). 50(6), pp 609-612. General survey of benefits and risks of nanotechnology. Basically, nanoparticles are small enough that surfaces, with their quantum properties, become important. Nanotechnology has a lot of potential uses and values, including environmental remediation; iron nanoparticles can help remediate contaminated ecosystems. However, the environmental effects of nanoparticles are not well known. Ultrafine dust, which is natural, can be very toxic, although this doesn't necessarily mean that nanoparticles would be. Need to evaluate the presence of nanoparticles in the environment, both how much they are there and the effects. The physical behavior in water can be different than not in water, because they tend to clump together. Paper advocates a precautionary approach and further study. This seems to be the first of this kind of report; look at the papers citing it for more information.

Barnard, AS. “Nanohazards: Knowledge is our first defense.” Nature Materials(2008). 5, pp 245-248. Advocates need to assess hazards from nanotechnology. The safety of nanoparticles is not well documented, and there needs to be further study and a cautious approach. First step: identify nanomaterials that are potentially harmful. Relationship between reactivity and size; nanoparticles have properties that the bulk materials do not have, and there is a different relationship between size and phase at the nanoscale. A study (done by different authors) showed that exposure of silver nanoparticles to uv radiation changed the shape, with unknown effects on their bioreactivity.

Benn, T., and P. Westerhoff. “Nanoparticle silver released into water from commercially available sock fabrics.” Environ. Sci. Technol., 2008, 42 (11), pp 4133–4139 . More than 500 commercially available products contain nanoparticles; about 20% of these are silver nanoparticles. Nano-silver has antimicrobial properties. Ionic silver is highly toxic in the marine environment, and EPA has standards of 1.9 ppb in salt water and 3.4 ppb in fresh water. Nanoparticle silver is potentially harmful to aquatic ecosystems. Important to characterize whether silver from the environment is colloidal or ionic (could be either). Nanosilver will probably end up in wastewater treatment plants, and if it isn't removed easily, it will go into water environments and potentially be harmful there. Said that wastewater treatment plants should be able to remove silver by adsorption.

Another idea: we are thinking of having a membrane made up of phages at the bottom of a filtration column. These phages will express specific peptides that bind to certain organic compounds in water. We then flow water through the column and the organic compounds will bind. We then take this membrane out and put it in a solution/bioreactor that consists of bacteria which can degrade the organic compounds that we have collected. We thought of this because for water treatment, what people are doing now is only to collect the organic compounds and they are not doing anything further to degrade them.

1)Bioremediation: environmental clean-up through pathway engineering

Shailendra Singh1, 2, 3, Seung Hyun Kang1, 3, Ashok Mulchandani1 and Wilfred Chen1, E-mail The Corresponding Author

Given the immense risk posed by widespread environmental pollution by inorganic and organic chemicals, novel methods of decontamination and clean-up are required. Owing to the relatively high cost and the non-specificity of conventional techniques, bioremediation is a promising alternative technology for pollutant clean-up. Advances in bioremediation harness molecular, genetic, microbiology, and protein engineering tools and rely on identification of novel metal-sequestering peptides, rational and irrational pathway engineering, and enzyme design. Recent advances have been made for enhanced inorganic chemical remediation and organic chemical degradation using various pathway-engineering approaches and these are discussed in this review.

2)Microbial Bioremediation of Fuel Oil Hydrocarbons 

in Marine Environment Sapna Pavitran, C.B. Jagtap, S. Bala Subramanian, Susan Titus, Pradeep Kumar, and P.C. Deb

The last idea is that: we are thinking of incorporating phage in drug delivery. Some experiments have done to prove that phage peptides can be used to increase the specificity of the binding of drug(protein molecules) to targets(cells in body). Other articles have shown that phage peptides can be used to protein the drug from being degraded by the enzymes in body, and this way, the half life of the drug will increase and the signal will last longer. we are thinking of incorporating these ideas together, such as looking to see if there are any phages that can perform both of these tasks. Also, another option would be look into see what properties the phages need to possess in each case, and see if we can engineer such properties in a phage.

Tanaka T et al. "A novel method for selection of antimicrobial peptides from a phage display library using bacterial magnetic particles." Appl. Environ. Microbiol (2008). Magnetic particles covered with cell membrane were isolated from magnetoctactic bacteria. A phage library was used to screen against these particles to find antimicrobial peptides. The peptides that were found by the library screening were improved by increasing their hydrophobicity by adding more hydrophobic amino acids. The authors state that this approach is potentially promising for large-scale screenings for antimicrobial peptides.

Rosengren JK et al. “Twists, knots, and rings in proteins: structural definition of the cyclotide framework.” J. Biol. Chem., (2003). 278(10) 8606-8616. Cyclotides are a family of proteins with a cyclized backbone and six conserved disulfide residues in the middle, which forms a disulfide knot. They typically contain 28-37 amino acids, and have been identified from plants. There are some conserved sections, and some nonconserved sections. This paper gives a detailed structural survey of some cyclotides, and suggests that they might be good targets for drug design.