Archive for March, 2007

Staph pigments: Three weeks-no answer? Now there is a prize!

Friday 30 March, 2007

Three weeks ago, exactly on March 7th 2007, I have posed a question related to the pigements of Staphylococcus aureus.
Until now, I have not received a single comment–not even a question–about that post. This surprises me because many people visit the weblog everyday and comment on other posts. In addition, a simple Google search will reveal the answer; so…?!

OK. I will not post the answer yet. I will give you another week. This time, there is an incentive: a prize!
The first three who email me the correct answer will be eligible to win. Alternatively, you can write the answer on a piece of paper and bring it to me in person in the laboratory on Monday April 2nd at 3 pm or Wednesday April 4th at 4 pm.

Condition: I will discuss with you how you got the answer. If you fail to explain how you exactly found it, or I realize that you received it from someone else: no prize!!


Want to learn more about PCR and electrophoresis?

Sunday 25 March, 2007

I have no doubt that many of you did not understand the principle of PCR in the lecture; it is really hard to get it in 20 minutes. I hope that the printed material helped you a little bit better.
Moreover, many of those who understand the principle still cannot imagine how things are performed in practice.
It is very hard to get enough PCR thermocyclers to let you all perform the reaction, but you may enjoy the following links that present illustrations and animations on the principle and methodology of PCR and gel electrophoresis.

A PCR thermocycler looks like this one below:

A typical electrophoresis apparatus is shown here:

Now, more resources:

Principle of electrophoresis (includes a simple animated cartoon)
Principles of gel electrophoresis

PCR (The University of Alabama in Huntsville Laboratory for Structural Biology)
Principle of the PCR
PCR animation (The page takes a while to launch but it’s really worth waiting. BEST ANIMATION TO DELIVER THE AMPLIFICATION CONCEPT)
Another good animation

Please suggest more links and I will put them one by one for you…

The Florida Dentist: HIV Molecular Forensics

Tuesday 20 March, 2007

–The “Florida Dentist” exercise, that is being solved in the Micro labs this week, is a simplified version of an exercise about in the book “Microbes Count!“–

As I told you in the lecture, the exercise is an accurate–but simplified–version of a real story that was in the news in the early 1990s. As a matter of fact, the case was published in one of the most prestigious journals, Science, in 1992. (Check the article’s abstract here).

The real story, in full details, can be found in the following Centers for Disease Control (CDC) reports:

Initial report (27 July 1990)
Report showing three more cases (18 January 1991)
The story of patients E, F, G (14 June 1991) – This is the story on which the lab exercise was based.
One year later (15 May 1992)
A later report summarizing results of screening most people who were treated by this dentist (7 May 1993)

Although the reports support the hypothesis that the dentist was the source of HIV infection, there were always doubts concerning the mode of viral transmission. For example, a journalist debates the case in the following article The 1990 Florida Dental Investigation: Is the Case Really Closed?

More interestingly, a book was written about the whole story…
(Click the book title for information)

WOW! It seems that you can buy the book for less than a dollar, if you’re in USA.

This case may make the Florida dentist as famous as Typhoid Mary. [Do you know her story?]

p.s. You may want to read more details about DNA forensics.

Diagnostic Virology Prelab: Lecture Notes (March 19)

Monday 19 March, 2007

It’s never too late.
Here are the Diagnostic Virology lecture notes, released few hours before the first lab section of this week.

The notes are available for all. You need no password. I put the lecture notes in two sizes:
1) A “regular” size: 4 pages (PDF file)
2) A “smaller” size: 2 pages (PDF file- same everything, but the font is smaller and the lines are less spaced)

Because PCR is a very important technique and because some of you want to understand it better, I put some more information about PCR in an appendix (PDF file). Obviously, information in this appendix is not for memorization and will not be a part in the exam (to calm down exam-oriented students) but only for those who want to read and learn.

– Please, give me feedback on these lecture notes. Are they clear? long? short? too brief? too detailed? Also please let me know if you find any spelling (or scientific) mistake!

Hepatitis C Epidemiology

Sunday 18 March, 2007

Egypt is definitely one of the countries with highest incidence (definition) and prevalence (definition) of Hepatitis C.

Check this map, click it, and read more…


The World Health Organization (WHO) fact sheet on hepatitis C
Hepatitis C: The silent Killer
Study examines the incidence and risk factors associated with Hepatitis C infection in rural Egypt
– Study: Intrafamilial transmission of hepatitis C in Egypt

Want to know more about bird flu?

Saturday 17 March, 2007

In the prelab lecture, I gave you a very brief idea about the efforts to contain the avian flu epidemic. Below is a list of resources that may help you discover more about this very serious viral threat.

* Check out:
Transmission of avian flu
Why/How avian flu infects humans?
The NAMRU-3 laboratory in Egypt


The Center for Disease Control (CDC) report
The World Health Organization (WHO) report
Wikipedia page
Infleunza Virus Resource: Information, Search and Analysis
The bird flu blog
Bird flu monitor

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