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Consurf activity- LHCII- Dmitriy, Keats, Jason

LHCII- Light Harvesting Complex II is part of photosynthesis in higher plants, algae and some bacteria. It is the primary chlorophyll binding protein, andis associated with both of the Photosystems. LHCII also controls the lamellar structure of the thylakoid membrane. It exists as a trimer its natural state composed of a varying combination of three […]

Alcohol Dehydrogenase

Dylan, Ellen, Stephen, and Jerreme

Alcohol Dehydrogenase

Alcohol dehydrogenase (ADH) is an enzyme that catalyzes the conversion of alcohols to aldehydes or ketones and a reduction of NAD+ to NADH. ADH is advantageous to humans because it prevents alcohol toxicity by breaking down alcohol. ADH oxidizes only secondary and tertiary alcohols to aldehydes and ketones […]

Jennifer and Ayla: GFP

Green Fluorescent Protein (GFP)

It’s a protein that glows green when exposed to blue light. It comes from the jellyfish Aequorea victoria. It is often used in experiments as a reporter gene. We chose it because it GLOWS!!!

PBD ID: 2g6e

Sources: http://www.pdb.org/pdb/explore.do?structureId=2G6E# http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb42_1.html

Looked at chain A in jmol

Species source Aequoria victoria (jellyfish), […]

NCBI Activity: Male Pattern Baldness

Group: Ben Ernest, Joel Bucci, Letitia Olson

Goal: to find more information on male pattern baldness, how chemical imbalances and genetic variations cause hair loss, and potential treatments for this disorder

Introduction: Male pattern baldness has several potential causes including endocrine disorders and genetic mutations, among others. The hair loss is initiated by dysfunction in […]

NCBI : Activity Personal BLAST Database Development ; Dylan Storey

Introduction/Background:

In order to compare previously sequenced RFLP clones and EST clones used in marker development for genetic mapping in pepper to a chip developed by industry a BLAST database of proprietary sequences needs to be compiled. Using the toolkit developed by NCBI I’m in currently in the process of compiling a database of these […]

Promoter Prediction in Genetics

Group: Jianzhuang, Xuejuan and Xiaomin.

Topic: Promoter Prediction in genetics

Introduction: A promoter is a region of DNA that facilitates the transcription of a particular gene. I am interested in this problem because this is one of the most important, difficult and popular topics in the genomics.

References:

Prediction and integration of regulatory and protein-protein […]

NCBI Activity:

Group: Brittany and Randy

Topic: Cyclic AMP

Introduction: Cyclic AMP, a secondary messenger, is invovled in numerous biological processes. We are interested in the research involving brain function and the role cAMP plays. Research is being done on cAMP and its involvement in mood disorders associated in the brain.

References:

Adenylyl cyclase-cyclicAMP signaling in mood […]

NCBI Activity:Canine Parvovirus

Group: Yijia, Xiaoxin, Zhou

Topic: Canine Parvovirus

Intro: Canine parvovirus is a pathogen of dogs that emerged in 1970s. It’s a highly contagious disease that inflicts adult dogs, but mostly concentrates on puppies. The most common syndroms of this disease are depression, loss of appetite, severe diarrhea, and vomiting. Vaccines can prevent this infection, but […]

NCBI Activity 2009: Exploring the stability of Taq Polymerase by Keats Shwab and Jason Harris

Topic:

We are invstigating a very well used enzyme, Taq polymerase. We wish to understand the structural characteristics which make it ideal for high temperature activity. We we also would like to see how related its peptide sequence is to non thermophillic polymerases.

Content:

All DNA polymerases have a similar structure that is related to […]

NCBI Activity: Elizabeth & Dmitriy; Hsp 70

Group: Elizabeth & Dmitriy

Topic: Gene Conversion and GC content in Hsp 70 (Heat Shock Protein)

Introduction:

HSP70 is a highly conserved family of ubiquitous chaperon proteins. This study used several HSP70 proteins with very high similarity in the amino acid sequence but in contrast, great variance in the codons which code for the amino […]