A recent study in Science Magazine ⁽²⁾ demonstrates, for the first time, the ability of animals (insects: the pea aphids that infect peas and other plants) to synthesize carotenoids.

Well, they didn’t exactly inherit it vertically from their ancestors, but rather got the genes as a kind gift from some fungus, long long time ago.

I will let you read the study, and uncover the new convoluted link between peas and carrots: Carrots –make–> carotenoids –also synthesized by–> fungi –horizontally transferred to–> pea aphids–infect–> peas (it’s still below six degrees of separation)!

(1) Liu, G., & Nizet, V. (2009). Color me bad: microbial pigments as virulence factors Trends in Microbiology, 17 (9), 406-413 DOI: 10.1016/j.tim.2009.06.006

(2) Moran, N., & Jarvik, T. (2010). Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids Science, 328 (5978), 624-627 DOI: 10.1126/science.1187113

Your skin is more than what you think it is. Even if you don’t leave a “visible” fingerprint on my laptop monitor, on your car windows, or anywhere else, you are leaving millions of bacteria there. What’s new? We all new that our fingers are a wonderful niche where invisible bacteria thrive?
What IS new is that these bacteria are highly diagnostic too. Tell me which bacteria you left behind; I tell you who you are. Thus claims a paper by Noah Fierer and coworkers from Colorado…

Fierer, N., Lauber, C., Zhou, N., McDonald, D., Costello, E., & Knight, R. (2010). Forensic identification using skin bacterial communities Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1000162107

It is hard with conditions such as the current eventual flu pandemic to get the facts straight. I cannot claim having any additional knowledge, but I would rather read what the World Health Organization (WHO) and the US Centers for Disease Control and prevention (CDC) have to say first:

WHO:

• 24 April 2009: Influenza-like illness in the United States and Mexico
• 26 April 2009: Swine flu illness in the United States and Mexico – update 2

CDC:

• MMWR April 24, 2009 / 58 (Dispatch);1-3 
  Update: Swine Influenza A (H1N1) Infections — California and Texas, April 2009 
• MMWR April 24, 2009 / 58(15);400-402: A case report 
  Swine Influenza A (H1N1) Infection in Two Children — Southern California, March–April 2009

In the advance online section of the journal Nature comes the news: viruses are not safe from infection! There is now a “virophage”: a virus that attacks a bigger virus. The first virophage has been named Sputnik (after a prototypic satellite).

Meet Sputnik: the first virophage (image from Nature)

(image source)

We were talking about the pathogen’s pathogen, the bacteriophage! Here comes the pathogen’s pathogen’s pathogen!

Read more here and here.

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!

Dr. Mostafa Elshahed–a graduate of Faculty of Pharmacy, Cairo University (FOPCU), Class of 1993–will give a seminar about his research to uncover the hidden soil microbiome. Dr. Elshahed was a demonstrator in the Department of Microibology and Immunology at FOPCU who got his PhD from the University of Oklahoma and is currently an assistant professor at Oklahoma State University.

Dr. Elshahed’s work is focused on the discovery of new microbial strain, especially extremophilic bacteria and archaea. It is really an interesting job to isolate microorganisms from the environment; the challenge is that most of these organisms cannot be cultured!

This work raises a lot of interesting questions: How to find new organisms when you cannot culture them? How to know that the microbial DNA you belongs to a new organism? How to analyze complex metagenomic data (with multiple living forms involved in a single habitat)? How to name the new organisms? Can you give them your name (aren’t there bacteria called Pasteurella after Louis Pasteur)? Do you have to study Latin grammar?

Dr. Elshahed has kindly accepted to answer all these questions in an article that he wrote specially to Egybio.net. Read the article here…

The movie can be viewed here.

So, away from Shakesperian plays where two twins are separated since their birth, even in similar geographical environmental conditions, there are other factors that can make identical genes behave differently: what a pregnant woman eats can not only affect her baby’s phenotype, but also his or her genotype and even the grandchildren genotype.

Enjoy the show while it lasts (I don’t know how long it will be available online)…

The site is relatively easy to use and browse; however, it is a bit different from forums and blogs, that’s why some of you may not find it familiar. Below are some tips to help you find your way between the courses:

• When you go to the site, you have to create a username and a password. These are general for the whole system and not for a particular course. There are many courses and there will be more as time progresses. Only few courses are directed to you (for now, it’s the Basic Microbiology and Immunology, and the Practical Micro courses). You can be a member of each course by enrolling to it. Even if you already have a username and password for the whole site, you might need to enroll to each course independently.
• Some courses are open for guest access but others are only for those enrolled to it. Sometimes enrollment is open to every user, and sometimes it requires an “enrollment key.” If so, request an enrollment key from the teacher. Why all this? Because some courses may be special workshops directed only to some participants and because in some courses, there is a grading system, so only enrolled students can get grades.
• Why enroll if you can access as a guest? Even when guest access is available, enrollment will offer you additional privileges:
  • you can chat online with other students or with teachers.
  • you can post discussions to forums.
  • you can submit assignments and participate in online quizzes (if any).
  • you can create groups of students and do some group activities.

Below are the steps to register to the e-learning site (copied from the site’s welcome page) and to start enjoying it:

1. Fill out the New Account form with your details.
2. An email will be immediately sent to your email address.
3. Read your email, and click on the web link it contains.
4. Your account will be confirmed and you will be logged in.
5. Now, select the course you want to participate in.
6. If you are prompted for an “enrollment key” – use the one that your teacher has given you. This will “enroll” you in the course.
7. You can now access the full course. From now on you will only need to enter your personal username and password to log in and access any course you have enrolled in.

خطوات التسجيل في موقع التعلّم الإلكتروني واستخدام المقررات:

١) املأ نموذج حساب جديد.
٢) على الفور تصلك رسالة على عنوانك البريدي.
٣) قم بقراءة البريد واضغط على الرابطة الموجودة به.
٤) سيتم تأكيد اشتراكك ويسمح لك بالدخول.
٥) والآن قم باختيار المقرر الدراسي الذي ترغب المشاركة فيه.
٦) من الآن فصاعدا يمكنك الدخول عن طريق إدخال اسم المستخدم وكلمة المرور ، وتستطيع الاتصال الكامل المقرر الدراسي ، وتصل إلى أي مقرر دراسي تريد التسجيل به.
٧) إذا طلب منك ”مفتاح التسجيل” – استخدم المفتاح الذي أعطاه لك المدرس. هذا سيجعلك ”تشارك” في المقرر الدراسي. لا حظ أن كل مقرر دراسي قد يكون له أيضا “مفتاح تسجيل” ستحتاج إليه لاحقا.

Group A:

The winners are those (top FIVE) who found the largest number of bacteria where quorum sensing and biofilm formation have been discovered. Any spelling mistake negatively affected the score. Those who listed the references got extra points.

1. Radwa Raed Sharaf رضوى رائد شرف (second fastest, more than 40 strains + 5 references)
2. Sarah Atef Amin سارة عاطف أمين (fastest, got 20 strains, but mentioned no references)
3. Eman Adel إيمان عادل (got 18 strains but 2 spelling mistakes, listed 8 references)
4. Aya Ali Elhusseiny آية علي الحسيني (got 20 strains, with 7 capitalization errors, listed 9 references
5. Ahmed Said أحمد سعيد (got 16 strains, no references)
6. Gehad Mahmoud جهاد محمود علي الصوفاني (got 7 strains)
7. Mariam Medhat مريم مدحت تكلا (got 8 strains but all the genus names were not capitalized – corrected them in a second email)

Group B:

Question: If the generation time of M. tuberculosis is 15 hours, approximately how long it takes 100 actively dividing cells of this bacterium to form a 3 km-long line? (length of 1 cell is 3 microns)

Answer: 346.5 h (approximately 345 h or

The winners are those the first four who solved the problem:

1. Mohammed Hassan Ahmed محمد حسن أحمد (Wed 17 Oct, 11:10 AM)
2. Nada Essam El Din Mohammed Radwan ندا عصام الدين محمد رضوان (Wed 17 Oct, 11:15 AM)
3. Yasmeen Saad ياسمين سعد (Wed 17 Oct, 2:00 PM)
4. Nehal Adel Mohamed Fahmy نهال عادل محمد فهمي (Thur 18 Oct, 5:00 PM)
5. Noha El Shamy نهى الشامي (Fri 19 Oct, 4:00 PM)

This time I overlooked تغاضيت عن spelling mistakes in writing the organism names; but next time, please follow the rules in writing any binomial name. Also, any answer should be supported by the references used.

Below is a list of all who sent the correct answers from both groups. Initially, only the first three winners per group were supposed to get the awards, but because many of you reported the answers on the same day, small prizes will be given to the first seven in each group. Thanks to all participants. Wait for competitions to come!

Group A:

1. Hossam Khaled Mohammed (answered at 12:35 PM on 9 Oct 2007, only 90 minutes after the lecture!)

2. Hossam Allam (9 Oct, 5:07 PM)

3. Abdel Rahman Medhat Mahmoud (9 Oct, 6:04 PM)

4. Rania Abou Zeid (9 Oct, 8:41 PM)

5. Radwa Raed (9 Oct, 10 PM)

6. Soha Gamal (9 Oct, 10:18 PM)

7. Ahmed Said (10 Oct, 1:18 AM)

8. Reem Belal Saber (10 Oct, 12:00 PM)

9. Gehad Essam Mohammed (11 Oct, 2:05 PM)

10. AbdulRahman Ibrahim (12 Oct, 7:03 PM)

11. Bishoy Saad (15 Oct, 1:43 AM)

12. Eman Adel (15 Oct, 8:43 PM- answered both questions!)

and…

• Ola Amr (12 Oct, 1:43 AM): provided answer but source is missing

• Aya ElSayed Mounib (9 Oct, 10:55 PM): provided sources but no answer yet

Group B:

1. Noha El Shami (10 Oct, 2:11 PM)

2. Mariam Reyad (10 Oct, 4:14 PM- Very well written answer!)

3. Yasmin Mostafa (10 Oct, 6:18 PM)

4. Motaz Taher (10 Oct, 7:53 PM)

5. Marco Azmy (10 Oct, 10:19 PM)

6. Marwa Mohamed Hamam (10 Oct, 11:26 PM)

7. Christina George (10 Oct, 11:34 PM)

8. Mohammed Saber (11 Oct, 12:38 AM)

9. Mariam Medhat Aziz (11 Oct, 1:30 AM)

10. Linah Hatem (11 Oct, 11:40 AM)

11. Somayya Hussein Hassan #1423 (11 Oct, 2:05 PM)

12. Nehal Abaza (11 Oct, 8:27 PM)

13. Nada Taha (12 Oct, 3:22 AM)

Find the name of a halophilic microorganism (a bacterium or preferably an archaeon) that has been isolated from the Dead Sea (البحر الميّت)…

Send the answer (name + source of information) by email or bring it in person. The fastest three will have prizes (of course, if the answer is correct!)

Send the answer (name + source of information) by email or bring it in person. The fastest three will have prizes (only if the answer is correct!)

This week’s lectures (Tue 9 October, Wed 10 October) are about microbial nutrition and growth conditions. This topic is straightforward but really interesting. I hope you can attend and follow the lecture as if you’re watching a documentary about microbes rather than a part of the curriculum.

If you have half an hour to get prepared, I suggest the following:

1. Read the main points in Part I, Chapters 4 and 5 in your book. Use speed reading and don’t get scared by the tables in these chapters. Most tables are just for additional knowledge, but the amount to be memorized is really minimal.
2. Read about bacterial nutrition and growth in Todar’s Online Textbook of Bacteriology; it is the main reference for these chapters in your book. You can always look in the USC School of Medicine site: Bacteriology, Chapter Three (and like last time, you may even download the whole lecture from this page, or see the presentation and listen to the lecture here!).
3. If you really have time and want to enjoy some deep reading, go to the library and read Chapters 4 and 5 in Brock’s Biology of Microorganisms. Dr. Thomas Brock has discovered plenty of thermophilic bacteria and you can expect his textbook to carry his legacy.

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 courses.egybio.net. 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:
thirddomain
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!

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…

1. Read the main points in Part I, Chapter 3 in your book. You don’t need to read the whole chapter. Alternatively, get used to “skimming” though the text: read the main titles/ find the keywords by reading rapidly through the chapter/ look at the figures and get an idea about what they represent (More tips on speed reading can be found here and here)
2. Read about bacterial structure in Todar’s Online Textbook of Bacteriology or USC School of Medicine Bacteriology, Chapter One (you may even download the whole lecture from this page, or see the presentation and listen to the lecture here!). Isn’t all this amazing?
3. Check the “Explore the bacterial cell” interactive animation (by clicking on the image below). Try to find out the function of each part of the cell.
   

I found this story on the BBC web site

“Wherever humans go, microbes go; you can’t sterilise humans. Wherever we go, under the oceans or orbiting the Earth, the microbes go with us, and it’s important that we understand… how they’re going to change,” Cheryl Nickerson, from the Center for Infectious Diseases and Vaccinology at Arizona State University, US, told the Associated Press.

• Read the full story here
• Read an older scientific article explaining this finding in the Proceedings of the National Academy of Science (for advanced readers only!)
• An older story about “bacteria on the moon”

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!

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:

• Brock’s Biology of Microorganisms (Eighth edition- free online summary and outline available)
• Alcamo’s Fundamentals of Microbiology
• Hugo and Russel’s Pharmaceutical Microbiology
• Roitt’s Essential Immunology (Book not free, but the site includes questions, figures, glossary, etc…)
• Janeway’s Immunobiology
• Bauman’s Microbiology

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!

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.

Congratulations.
All others, please keep sending your answers.

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 2^nd at 3 pm or Wednesday April 4^th 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!!

A PCR thermocycler looks like this one below:

A typical electrophoresis apparatus is shown here:

Now, more resources:

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

PCR:
- 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…

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.

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.

IMPORTANT:
- 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!

Check this map, click it, and read more…

Read:

- 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

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

Resources:

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

Golden pigment-producing staphylococci (left) cause mouse skin lesion unlike non-golden colonies (right).

Try to find out how this golden pigment can help staphylococci overcome the human defenses- Make a guess before you find the answer in literature. The answer is not in textbooks yet! You have to find it by searching scientific literature: check, for example, PUBMED, or… how about Google Scholar?

The answer will be posted in this weblog next week month. You can always click on the “comments” link below these lines and post whatever you found. All you need is to put your email address, which will be kept private. I prefer that you put your name and serial number as well- but it is not a condition.

Hints:

• What do you know about pigments in general from your pharmacognosy classes?
• What do you know about golden pigments in general? In food products?