Project 2: Sequence Search &
Analysis
The HtrA (high temperature resistance A) protein
of the bacterium, Borrrelia burgdorferi
by Dr. Judy Sakanari
Objectives:
1. Apply collaborative problem solving strategies to a
bioinformatics problem.
- Gather necessary background through discussion with
presenter and utilize necessary resources.
- Determine presenter's desired outcome or goals and
define specific questions related to the problem.
- Break down the problem and develop approaches to
finding solutions.
2. Become more familiar with the databases and tools
introduced in Exercise 2.
- Be able to refine and adapt search strategies to the
problem at hand.
- Be able to identify useful applications and to apply
them to assist in your inquiry.
- Be able to analyze and evaluate the quality of your
results.
3. Become familiar with making a scientific presentation
and short report.
Description of expectations on reporting your analysis,
along with presentations and discussion in class is given at
the end of this section. Points = 10. Due 9/23.
Background:
Lyme disease is considered the most common tick-borne
disease in the United States. The infection is initiated
when the bacterium, Borrelia burgdorferi, is
transmitted during the blood meal by an infected tick. Early
symptoms of Lyme disease include flu-like symptoms, muscle
and joint pain, and a characteristic skin rash known as
erythema migrans. Without proper treatment, infections may
persist in individuals for years, and patients may exhibit
symptoms such as arthritis, cardiac arrhythmias, and nervous
system disorders for years after initial infection.
Although antibiotics are effective against the organism
in vitro and are in current use for treatment of Lyme
Disease, efficacy of particular antibiotic therapy remains
controversial. In addition, with the long term use of
antibiotics for therapy, antibiotic resistance is a
possibility. Thus my laboratory is interested in identifying
possible targets for the development of new drugs for the
treatment of Lyme Disease. My lab has identified a protein
called HtrA (high temperature requirement A), and we are
currently investigating its potential as a target for the
development and design of new chemotherapeutic drugs.
Questions to consider:
1. Why would we have selected this particular
protein over the thousands of other proteins in
Borrelia?
2. Are there other HtrA proteins in other bacteria
or other phylogenetic groups?
3. What information can you abstract by comparing
the HtrA with other HtrAs or similar proteins from other
organisms?
4. Do you think that it would be possible to
design drugs based on knowing just the protein sequence?
5. How do you think we first identified the HtrA
protein as a possible target?
Getting started:
Things to think about and discuss while getting
organized:
1. What kinds of biological questions do you need
to pose before you start?
2. What type of searches will you use? How can you
refine these searches to produce what you want?
3. What else can you do? [You should create a
prioritized list.] For example, you may have run a
blastn, but you'd like to compare the protein sequences. How
can you do that with the information you have?
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The next steps:
1. Analyze preliminary results; look for areas
needing improvement. Make adjustments and repeat the process
as deemed necessary.
2. Although not required, you may extend beyond
the applications found in Exercise 2. If you find something
which will help in improving your analysis, don't feel too
constrained. Part of the process of learning bioinformatics
is being able to go out and find what you need and learning
how to use them. You can share what you've learned with
others.
3. When do you stop and decide you have done
enough? Sometimes it is easy to determine that you have
answered your targeted questions. Other times, it is less
clear. Discuss within your group any areas which appear
ambiguous, keeping in mind the scope of the project and
timeframe. If some loose ends can be easily cleared up, do
so. If the problem lies in lack of available data and there
is a need for more extensive research, either in the lab or
computationally, define what the focus should be for further
work.
4. As a group, decide how to best present your
work. In scientific meetings, presentation time is
frequently 10 minutes, plus a couple of minutes for
questions. It is a good skill to learn how to fit your
presentations into this time limit. [See below.]
Designate one person as the presenter. [During the
semester, everyone will have opportunities to
present.]
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Discussion and report
summary:
1. For discussion on 9/23, prepare a presentation
[10 minutes maximum] of your findings, including a
brief summary of methods, results, and conclusions. Include
recommendations for further extensions of the research.
a. For visual aids, you may include
overheads of results or use a computer presentation, such
as PowerPoint. Let me know what you plan, so I can make
the appropriate arrangements.
b. Be prepared to field questions from other
groups and from the presenter.
2. Submit the following as a typed report. As a
guideline, a finished report on the search should be about
three pages of text [12 pt standard font] and no
more than four pages of appended graphs, tables, images,
etc. [Final page length is to be determined by what the
group identifies as appropriate*]:
a. Name of the project and names of the
members in your group.
b. A brief report in scientific format,
including abstract [100 word limit],
introduction, methods, results, discussion/conclusions,
and citations. Include figures as appropriate.
* Excessive length, either hoping to impress or due to
failure to filter and organize, will not be well
rewarded. Take the approach that you are submitting a
professional consulting report. The recipient expects
concise accurate information, which is clearly presented
and well documented.
Grading will be on content, organization, spelling,
& grammar.
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