Archive for the ‘Second Semester’ Category

To learn about microbes, think like a microbe!!

Monday 25 February, 2008

Adopt a Microbe! a very interesting blog that artistically represents microbes, makes you think like one of them, then you will definitely know them better.

I think each microbiology student should have his own way of representing a microbe: draw a picture of them, write a song, even a play!


Staph pigments competition: Three winners already!

Monday 2 April, 2007

We already have three winners for the Staph pigments competition.

The winners are
1) Samar Galal Ahmed Kabeel (سمر جلال أحمد قابيل) emailed the right answer at 4:28 PM, Cairo Time
2) Mohammed Shehta Mostafa (محمد شحتة عبد النبي مصطفى) posted the right answer at 9:02 PM, Cairo Time
3) Soha Khairy ElMekkawy (سهى خيري المكاوي) handed out a full answer at 3:30 PM, Cairo Time, in the laboratory.

All others, please keep sending your answers.

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.

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

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