View source for Styles Bitchly Chem430 F16

Chemistry Research 430
:Spring 2017
:Mohanad Ahmad
:Senior Chemistry Major

==Research Times==
T/W 2-6 pm
: section 02 = 0.50 credit = 8 hours per week.

==Proposed Research Project==
===Attachment of DNA to cAMP transcription factor: Atomic Force Microscopy study===

===General Information===
:Advisor: Dr. Laura Moore
:Other research student collaborators: Khdr Eskander


===Proposal===
The goal of this project is to introduce of a strand of DNA that carries a specific mutation into E.coli bacteria in order to over express the bacteria to synthesize the mutated c-AMP receptor protein (CRP), a transcription factor that regulates DNA to mRNA transcription. The intended mutation will expose a cysteine amino acid on the surface of the protein that will, as a result, bind to a gold surface through a thiol bond (R-S-H) in order to obtain images using Atomic Force Microscopy (AFM). Moreover, images of DNA-CRP complex will be taken using AFM, where the DNA will be attached to the tip of the AFM at one end and to the protein at the other end.

===Instruments to be used===
Atomic Force Microscopy

===References===
Ditzler, Lindsay R.,  Arundhuti Sen, Michael J. Gannon, Amnon Kohen, Alexei V. Tivanski. "Self-Assembled Enzymatic Monolayer Directly Bound to a Gold Surface: Activity and Molecular Recognition Force Spectroscopy Studies." ''J. Am. Chem. Soc'', 2011, 133 (34), pp 13284–13287.


===Research pledge===
I, Mohanad Ahmad, have read the Chem/Bioc 430 course syllabus and understand the general structure and expectations of the research program. The above material was prepared after consultation, and in conjunction with my research advisor.

==Written Report==

...from the course syllabus...

[https://www.acs.org/content/dam/acsorg/about/governance/committees/training/acsapproved/degreeprogram/preparing-a-research-report.pdf ACS Guide to Research Reports]

:''Research students are expected to write a report and submit it to the research coordinator by the last day of regular semester classes. These reports are intended to summarize the data collected over the course of the semester. Since this research course requires you to enroll in at least two semesters of research, two reports will be generated. The first semester report should be considered a work in progress, where as the final report should be a more comprehensive summary of your research project. These reports are necessary since several researchers may work on each project. The report will be organized so that it is clear what material is new and what material is review.  When available, research students will be provided with an electronic copy of the latest report on their project. The research student is expected to update and improve the introduction, background, and literature sections with each report. Results that challenge earlier conclusions will be justified in a discussion section. Reports will be submitted in both electronic and hard copy to the Faculty Research Advisor AND Research Coordinator.''

===1. Descriptive information===
A project title, the names of the researcher (past and current), faculty research advisor, and other relevant student researchers and/or collaborators, the name and page numbers of the lab notebook(s) where the research is described, the dates when the work was done, and the names of the document file and its immediate precursor.

Example:

'''Detection of Radical Intermediate generated from the MAO enzymatic system.'''

Styles Bitchly*, Donald Hump, Penn Mickey, and Bradley E. Sturgeon#

*lead author, #research advisor

Research work documented in lab notebooks, SB_01 pages 1-25.

===2. Introduction===
State of the motivation for the project of interest in terms of current literature. When we make reference to current literature, this is where you provide specific reference(s) to this work. This section can be largely copied from an earlier report(s), if they exist, but it is expected that this section is edited to include newly found background information. Note: if the author of previous report(s) is included as a contributor to the project, you may cut and paste text; this is not plagiarism, it is collaboration.

===3. Background from earlier reports===
This section will summarize the work reported in earlier reports.  If significant results were presented in the most recent report, these results will be summarized and in most cases can be added to that reports background section. This section is included mainly to confirm the current students overall understanding of the project.

===4. Experimental===
This section describes experiments done during the period covered by the report.  Usually, this work will be similar or identical to that described in the prior report, if they exists.  Any new experiments will be written up and added to the experimental section. Any experiments preformed under identical conditions need only reference previous reports.

:''Example:''

::'''Reagents''': ''List reagents used by product number and the source''.

::'''Enzyme Reactions''': All enzyme reactions were done using a totlal volume of 5.0 mL. Substrate concentration ranged between 1-12 mM. Reactions were initiated be the addition of enzyme.

::'''HPLC''': HPLC data was collected using the Waters Breeze HPLC with a C18 column (insert specs here). Specific HPLC conditions are given in the figure captions.

::'''UV-Vis''': UV-Vis data was collected using the HP 5832 UV-Vis spectrometer using a quartz cuvette. Sample concentrations were adjusted so as to not exceed 1.0 absorbance unit. Significant data was exported in the ".CSV" format and then worked up in Igor.

===5. Results===
This section documents the results of the experiments done during the period covered by the report.  Tabulation of data is encouraged; representative spectra presented.

===6. Discussion===
In this section, the student will discuss the results of their work in context of the literature and the results of earlier reports.  Questions that have been raised in earlier reports may be addressed here.

===7. Conclusions===
Restate the findings of this period of research. The statement “No conclusions have been reached,” is an acceptable statement.

===8. Future Directions===
In this section, the student will discuss possible experiments intended to address unanswered questions or technical problems on the project.

===9. Literature references===
Literature referenced in the report will be cited.  This will be copied from the earlier report, and the student is expected to contribute to the accumulation of relevant literature. Remember that all cited literature must be read. 

===10. Signature===
Two copies of the report will be signed and dated and turned in to the Faculty Research Advisor and archived by the Research Coordinator.