Posts Tagged Project

Lucky: Canine Parvovirus type 2

Our names are Joanna and Anna, and we have a puppy named Lucky.  Two weeks ago Lucky started vomiting and having diarrhea, so we took him to the vet.  He was diagnosed with having canine parvovirus type 2.  Because we are inquisitive scientists, we took it upon ourselves to research this disease and document our findings.  Here they are!

Don’t worry guys, Lucky is on the mend 😀


Comparison Between SIV and HIV: Shalanda and Raphael

We want to show differences between HIV and SIV as demonstrated by data we present. Using ImageJ we counted the number of spikes from tomograms of HIV-1 and SIVmac239 published in PNAS (Zhu, P. et al, PNAS, 100(26): 15812, 2003). We then looked at available PDB data for viral spikes and present PyMOL and Consurf images of SIV gp41, HIV gp41 and HIV gp120 protein components. Both SIV and HIV have gp120 and gp41 which is cleaved from gp160. Our concept map created with Cmap uses current data on SIV and HIV in Proteopedia.

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Drug Delivery Project (Stefan and Mauricio)

micelle measure


Project (Pawel and Tara)

Phylogenetic Tools presentation


Jennifer, Kate R, Anastasia A. Project



Walk the Line (Ben/Kyle/Thomas)

Walk the Line

Kinesin (3Kin)



-Kinesin is a type of motor protein found in eukaryotic cells

-Its structure is a dimer, it includes two heavy chains (which are called the motor domains) and two light chains (α-helical stalks)

-The image seen here is from PyMOL, and it was used to separate the individual chains/proteins from larger complexes

-PyMOL can be used to learn about molecular structures including molecular size, bond lengths/angles, and specific sites of inter/intramolecular forces (important for binding of ligands)


-The motor domains contain highly conserved regions, which is expected because these are the sites of microtubule and ATP (discussed later) binding.

-These regions cannot change much or binding would not commence.


-Kinesin proteins move across microtubules and its main functions include transport and motility

-The motor domains contain 2 binding sites, 1 for ATP and 1 for microtubules

-Movement along the microtubules is powered by hydrolysis of ATP to ADP

-Hydrolysis of ATP causes a conformational change which leads to “power strokes”

-Kinesintransport a wide range of structures including vesicles and organelles, and are also important in chromosome movement during cell division


– Spactic Paraplegia

– Polycystic Kidney Disease

– Alzheimer’s Disease

– Salmonella

Link to Powerpoint


kate R. Jennifer O. and Anastasia A.

We used many of the resources taught to us in this seminar such as: google reader, diigo, mendeley, c map and pymol to create an interactive concept map that could be used to teach young college and high school students. This map could be used in class as a teaching tool as well as if posted to a blog site like blackboard, used as a tool for students to study or learn more about a specific topic. In this project we looked at luciferase which is a protein that catalyzes the production of light in fireflies.


Project (Thomas, Steven, Rachel)

Project aimed at integrating tools.  We want to develop a system in which a conscious stream of thought would produce keywords and tags.  These key words and tags would then be utilized in networking sites and search systems to find information of interest to the researcher.  The current set up would take input as a blog entry interpreting to tags and keywords.  Those tags and keywords would link up to similar blog entries and find links to associated information, including tools.

Would be a great tool to link colleagues, mentors and advisees up with one another.

link to presentation: Automated Research Assistant

link to example blog: