Volume 7 Issue 1 June 2008

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https://doi.org/10.33697/ajur.2008.006

Alternative Energies and Undergraduate Research

https://doi.org/10.33697/ajur.2008.007

Author(s):

C. C. Chancey

Affiliation:

American Journal of Undergraduate Research, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA


A Graph Theoretical Approach to DNA Fragment Assembly

https://doi.org/10.33697/ajur.2008.008

Author(s):

Jonathan Kaptcianos

Affiliation:

Saint Michael’s College, Colchester, Vermont 05439 USA

ABSTRACT:

Built on prior work on sequencing by hybridization, fragment assembly is a newly explored method of determining whether or not a reassembled strand of DNA matches the original strand. One particular way to analyze this method is by using concepts from graph theory. By constructing data models based on these ideas, it is possible to come to various conclusions about the original problem regarding reassembled strands of DNA. In this paper we will detail this approach to DNA fragment assembly and present some related graph theoretical proofs in the process, including the BEST theorem. Further, we will explore the Eulerian superpath problem and its role in aiding fragment assembly, in addition to other recent applications of graph theory in the field of bioinformatics.


Acetylation-Dependent Binding Analysis of the Yeast Gcn5 Bromodomain Protein

https://doi.org/10.33697/ajur.2008.009

Author(s):

Jesús Francisco Glaus Garzón, Christopher Kupitz, Joshua Bailey, and Martin Thompson

Affiliation:

Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 USA

ABSTRACT:

The 439 amino acid yeast Gcn5 protein contains a C-terminal bromodomain, which is required for SAGA (Spt-Ada-Gcn5-Acetyltransferase) mediated nucleosomal acetylation and transcriptional coactivation. Bromodomains are acetyl-lysine binding modules found in many chromatin binding proteins and histone acetyltransferases. Recently, both in vivo and in vitro studies indicate that bromodomains are able to discriminate the acetylation state of lysine side-chains within histone proteins. Here, the cloning, expression and bioactivity of a recombinant bromodomain from the yeast Gcn5 protein is described. The bromodomain from Gcn5 was cloned from yeast genomic DNA enabling effective one-step purification by affinity chromatography. Steady-state fluorescence anisotropy was used to quantify the interaction of Gcn5 with acetylated histone H3. The present cloning, expression, and purification procedure enabled the preparation of large quantity and high yields of biologically active recombinant Gcn5 bromodomain for in vitro structure and function studies.


Band Gap Energy in Silicon

https://doi.org/10.33697/ajur.2008.010

Author(s):

Jeremy J. Low, Michael L. Kreider, Drew P. Pulsifer, Andrew S. Jones and Tariq H. Gilani

Affiliation:

Department of Physics, Millersville University, P. O. Box 1002, Millersville, Pennsylvania 17551 USA

ABSTRACT:

The band gap energy Eg in silicon was found by exploiting the linear relationship between the temperature and voltage for the constant current in the temperature range of 275 K to 333 K. Within the precision of our experiment, the results obtained are in good agreement with the known value energy gap in silicon. The temperature dependence of Eg for silicon has also been studied.


Advice for Student Authors How to Organize Your Research Article

https://doi.org/10.33697/ajur.2008.011

Author(s):

Editorial Staff

Affiliation:

American Journal of Undergraduate Research, University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

ABSTRACT:

General information about article organization is presented. Questions about equation placement, chart or graph usage, figure placement, and bibliographic style are answered. Information about how a paper is reviewed is discussed, and steps for submitting a research paper are outlined.