1. University of Puerto Rico
RISE Program
Cayey, Puerto Rico
BIOL 4997 – 2013 Laboratory Summaries
Importance and Pipetting Practice
The micropipette is a laboratory instrument used to transfer a measured
volume of a liquid. It is used in different analytical techniques. There are two
types of micropipettes that are generally used: air-displacement pipettes and
positive-displacement pipettes. We used air-displacement micropipettes that are
piston-driven and dispense an adjustable volume of liquid from a disposable tip.
During this workshop we learned how to correctly use micropipettes that were
from different volumes with their correspondent tips. By using different
volumes we also had to decide, according to the amount of liquid that was
required, which micropipette was the most adequate to have a precise, or as
close as possible, sample. We were also tested on our ability to follow
instructions and to work in teams. To work in a laboratory doing research,
means to become part of a web of knowledge where everybody, as coworkers,
shares it to achieve a common goal. That is why micropipeting is a fundamental
and basic technique for biology and general research, as well as collaborative
work.
Microscopy and Photomicrography
When things are not visible to the naked eye we use microscopes. The
first microscope was made by Hans and Zacharias Janssen in 1590 and from
there many other scientists like Robert Hooke and Anton Van Leeuwenhoek have
used them to make some of the most important discoveries for humanity.
Microscopes can be separated into several classes, mostly because of what they
use to generate an image. The three most well known are optical microscopes,
electron microscopes (scanning and transmission), and scanning probe
microscopes. During this workshop we used optical microscopes with different
types of light microscopy and micro-techniques. I was assigned to observe
Tillandsia trichomes under dark field microscopy using a whole-mount micro-

2. technique. Dark field microscopy uses light from an angle where it only
illuminates the specimen and its background is completely dark. Microscope
development has abled humans to evolve and also to increase and expand our
knowledge, not being retained by size anymore. Without microscopes, humanity
wouldn’t be the same; as for they allow us to see a complete different world that
is not visible to the naked eye.
Workshop University of North Carolina (UNC) - From DNA to Protein
The principal purpose of this workshop was for us to learn and apply
techniques in molecular biology using previous biological knowledge and
combining it with hands-on-work. We refreshed our knowledge of the central
dogma, from DNA to proteins and expanded it with specific terminologies that
lead us to understand more clearly the different mechanisms of our body. On the
first day, we extracted our own DNA utilizing products that are available to the
general public like Gatorade and Contact Lens cleaning solution. During the
second day we did PCR to determine if we had samples from patients who were
infected with diabetes. Viewing the PCR results requires you to make an agarose
gel that revealed that if our patient was positive or not for diabetes. The third
day, we run an SDS-PAGE gel to determine if some samples presented a
Lysosomal Storage Disorder (LSD). After denaturing the protein and running the
gels, in the PCR machine that used an electricity current to separate de particles,
we found out that our patient was positive for LSD, specifically diabetes. These
techniques enable us determine clearly different diseases that may affect our
DNA, and also to identify our DNA. To round up the workshop we were oriented
about graduate school, different roles that exist in a lab, and the research our
mentors were doing. From DNA to protein was a multidisciplinary workshop
that pushed us to be better scientists.
Nanotechnology and Electron Microscopy
Dr. Otaño’s workshop was about nanotechnology and electron
microscopy. During this experiment we created a polymer nanotube utilizing the
electrosipining process. To form the nanotube a polymer solution was dispensed
from a needle with a capillary tip at a high voltage. Then as the fiber formed it

3. was deposit on the fiber mat over a counter electrode. This fiber is then
processed on an air and a vacuum or gas atmosphere at 600 oC. The processed
fiber was then taken to a machine where the process of sputtering covered it
with Gold atoms. In this machine, the Gold plaque is bombarded with Argon and
the ion made the gold atoms spread through the chamber, which are collected
over the substrate. This substrate was then examined in a SEM, which provided a
3D visualization of the nanotubes. With this experiment bioactive fibers can be
developed to treat bones in different medical situations and also MEMS (Micro-
Electro-Mechanical devices) can be developed.
Column Chromatography and SDS-Page
Dr. Bansal’s workshop objective was to isolate Plasminogen Activators
(PA) from a mammalian cell culture broth using magnetic affinity
nanoabsorbents. These magnetic nanoparticles (MNPs) are mostly used because
when magnetic separation is combined with affinity binding it condenses the
pretreatment and the column chromatography stages into one single isolation.
During the pretreatment of the particles the weighed MNPs were combined with
PABA binding buffer and then were sonicated to equilibrate the particles at a
specific pH. Then the supernatant was decanted magnetically using magnets.
During the separation process the pretreated MNPs were added to the HeLa cell
culture broth and then they were separated magnetically and washed three
times. After the washes, the protein was separated from the particles to obtain
an elute. All of the samples, from each step, were taken to a machine to read their
absorbance at 280 nm (nanometers) and days (how many?) later an SDS-Page
was performed. Protein isolation is performed to obtain purer proteins that can
be use for dietary supplements, structure studies, as therapeutics or as catalysts.
Protein – Protein Interactions: an Insilico approach
Dr. Maldonado’s workshop was about Insilico drug discovery and
development. This process is based on four primary steps. During the first part, a
protein was downloaded from a 3D structure database and a grid was created to
select the part from which a benzene map was developed. From this map,

4. optimal targets were selected and during the second part, after an interaction
analysis using the “Ligand Scout” program, a pharmacophore model was
generated. During the third part, a primary screening of the pharmacophore
model was run and at the end one compound was selected. These results were
converted from .sdfto .mol2. After uploading the .mol2 file to the “Cyberduck”
program this file was again converted but now to a .pdbqt file. Now, in the fourth
part, this file is run in “AutoDockvina” where a docking/screening is performed
and then analyzed to determine how the model should be refined. This process is
helpful because it gives science a more precise alternative and also a more cost
effective way to determine the correct compounds needed to create new drugs.