University of Puerto Rico - CayeyRISE ProgramTemplate for Laboratory Summaries of Assignment 2 Biol. 4997-Biomedical TechniquesDue date April 5, 2013Reg.# 15 Name Zuleika Velázquez Ortiz Date: April 5, 2013Summary 4. Nanotechnology and Electron Microscopy February 22, 2013The workshop of Nanotechnology and Electron Microspy had the purpose ofinstructing us about the advantages and benefits of using nanoparticles in the area of research.This workshop offered by Dr. Wilfredo Otaño, also provided us the opportunity to work with theElectron Microscopy (EM). First, Dr. Otaño informed us that nanoparticles are particles at anano scale (1 x 10-9) frequently used in research because they have biomedical applicationsand can be effectively manipulated in terms of area, amount and interactions with otherparticles. After the introduction, we worked in different areas of the physics laboratory, fromwhich I worked with the Magnetrium Sputtering System. This machine works with differentmaterials. In my case we used gold in order to deposit it in a substrate. This process forms athin film that is characterized with the EM in order to know its applications in electronical devices(microchips, sensors, etc.). At the end of the workshop, we identified the surfaces of the gold’sthin film in the EM. This way we were able to know how they look and how to correctly operatethe EM.Summary 5. Column Chromatography and SDS-Page March 1, 2013The nanoparticles are materials frequently used by the researchers because of theirefficient dispersibility, high surface, and low diffusional limitations. The workshop was given byDr. Vibha Bansal. It was about how magnetic nanoparticles could create an easier method forthe separation of proteins based in affinity. The magnetic nanoparticles were synthesized withmetals and aminopropylsilane to create a colloidal solution that provides a functionalization ofthe particles. This way they can have the necessary affinity to the protein. Later, we added aPara-aminobenzamidine (PABA) binding buffer to equilibrate the solution. Next, the proteinwas incubated and bound to the magnetic nanoparticles (mnp). Subsequently, we separatedthe proteins that did not bind to the mnp through three washes. The proteins bounded to themnp were separated by an elution process that was an application of a pH shock to break thebond between the mnp and the protein. Finally, the solutions obtained were analyzed by a SDS
Page that showed us the size, bands, and confirmed the identification of the protein. In thiscase, the protein was the Plasminogen Activators.Summary 6. Protein – Protein Interactions: an In silico approach March 15, 2013Every day we know about new drugs that are released to the world for a specifictreatment. The purpose of the In-Silico Workshop offered by Dr. Hector Maldonado is to knowhow to identify the best drugs that can be used to inhibit the VIH protease. The process ofidentifying the drug was divided in four stages. In the first stage, the affinity areas of the VIHprotease were identified to later create a Pharmacophore model. This model provided thecapacity of creating a list of hundreds of drugs that can be targeted in the VIH protease. Thethird step, was to make a second screening that told us which of those drugs have the highestaffinity. At stage four, the one realized by my group, we selected the first five drugs with themost affinity to the VIH protease, and then we looked for information about them, andconstructed the 3D models. Our last step was to analyze the different amino acids thatinteracedt with the drug. The identification of the drug had the purpose to summit it to aBioAssay that at the end can provide a new certified drug for the disease.