Archive for the ‘Third Year’ Category

Week 2-3 lectures (Part I- Chapters 2-3) now online

Saturday 6 October, 2007

Dr. Aymen Yassin has released the online version of his lectures as online PowerPoint presentations. You can browse these lectures and review all the slides that were presented in the lecture room. Obviously, the purpose of putting these slides online is to provide you with the color figures and to let you take notes if you have missed a slide or two. However, they are not handouts or summaries and are NOT lecture notes (Don’t print them as your study tool!) Always resort to the book, or–better–to your own notes taken during the lecture and matched with info in the book.

How to access the lectures?

Well, the lectures will permanently be a part of the online course that will be coming out very soon next week on There is one trick: you will need a password! Temporarily, you may access them following the links below. You will be asked to enter a username and password (these may be changed every week or two).

The username is:
The password is the answer to the following question (one word- small letters):
What is the third domain of life discovered by Carl Woese? (pay attention to the spelling)

Chapter2: Classification and Identification of Microbes

Chapter 3: Structure of the Prokaryotic Cell.

If you have any problems with reading the text, or if some characters are scrambled, make sure you set your broswer’s encoding to Unicode (UTF-8) (how?)

Good luck!

When bacteria were called viruses!

Saturday 29 September, 2007

The word “virus” was used in the past to refer to any poison (Latin: virus = poison), such as snake venom, and was later used to describe the causative agent of any infectious disease.

Pasteur often referred to pathogenic bacteria as viruses, but by the end of the nineteenth century, things have changed and infectious agents smaller than bacteria kept the name “filterable viruses” or viruses.

Source: Brock’s Biology of Microorganisms, Eighth Edition (P. 250)

Try to find more info and post it in the comments area…

Sep 25 microbiology lecture: Learning objectives and review questions

Tuesday 25 September, 2007

This week, lectures 3 and 4 of your course are about:
Classification and Identification of Microbes.
(Part1/Chapter 2 in your book)

The following are the learning objectives for this lecture. Use them as review questions to guide you through your study. They tell you what is more important in this chapter… Feel free to suggest more questions and to ask for details in the comments section. Please include your name and student# if you wish follow-up on your questions.

Note: The learning objectives are mainly taken from Bauman’s Microbiology which is one of the textbooks I use to prepare your lectures.

Learning Objectives/ Review Questions:

* Define binomial nomenclature.
* Discuss the purposes of classification and identification of organisms.
* Discuss the difficulties in defining species of microorganisms.
* Describe the historical attempts to classify living organisms.
* List and describe the three domains proposed by Carl Woese.
* Compare and contrast fungi, algae, and plants
* Compare and contrast bacteria and archaea.
* Mention the main differences between rickettsiae, chlamidiae, and mycoplasma.
* Mention the different bacterial shapes.
* Mention the differences between spirochaetes and spirilla.
* Discuss whether viruses are living organisms.
* Describe how viruses and prions propagate.

If you can answer the above questions, you know it all!

Third-year students: welcome to the world of microbes.

Tuesday 25 September, 2007

This is a special message to the third-year students of the Faculty of Pharmacy, Cairo University.

In the next few lines, I hope to introduce you to this weblog (created in February 2007) that aims to be a learning tool of microbiology and immunology, but also a place where you can express your thoughts about this exciting science and your opinions about the course as well.

Don’t hesitate to comment on every post in this weblog. Don’t hesitate to add information, correct errors, critique the course outline and lectures, etc…

The third year’s first semester is focused on general microbiology, microbial genetics, and immunology (teaching team), while the second semester is a medical microbiology course.

Textbooks I suggest you read are:

You will find at least the first four textbooks in the library.
Otherwise, you can find plenty of good resources online (find links in the blogroll on the right side bar, in this same page). I specially recommend:
Todar’s Online Textbook of Bacteriology
University of South Carolina Microbiology and Immunology Courses

Wait for more details about the course, the lectures, the quizzes, and the labs…
Best of luck this year!

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…

%d bloggers like this: