Posts Tagged “PCR”

Is it a luxury to “think like a microbe” and to publish blogs such as “Adopt a Microbe and books like “The Other End of the Microscope: the Bacteria Tell Their Own Story (find it on Google Books)? Is it just about understanding or “getting to know” bacteria, or is it a necessity to be “microbe-oriented” for better understanding of pathogenesis and for developing the appropriate eradication and prevention strategies (I can’t think of better examples other than Reverse Vaccinology and H. pylori)?

When I first read this commentary “The Case for Biocentric Microbiology”* by Dr. Ramy Aziz, published by the journal “Gut Pathogens, I was shocked! The article was presenting a very different perspective, at least different from what I always dreamed of as a pharmacy student, to kill the bad bugs by designing an effective, highly selective chemotherapeutic! Plus it was my first time to read an opinion article, and I used to take the microbiology courses for granted; “this is a bad microorganism, causing this bad infectious disease with serious manifestations including these, diagnosed by the following and the antibiotic of choice is this.” And then Dr. Aziz came with this article with the cool, simple and exciting writing style that keeps one alerted the entire article, gathering all those thoughts and examples of our human-centered/self-centered view of microbiology.

Four parts I enjoyed the most in the commentary:

  • The tabular form of “differences between the anthropocentric and biocentric views of microbes.”
  • The final balancing paragraph -the conclusion.
  • The “competing interests” part, which is funny.
  • The questions part, which is an excellent idea to open up discussions, especially for those who are not-natural-born brain stormers like me!

Even though microbiology is a new science, it suffers from anthropocentric view that Galileo suffered from; starting with the field’s name itself, “microbiology” -liked what Dr. Elio Schaechter mentioned: “Small,” says who? Not the microbes… till the funding agencies that give priority to studying bad microbes (i.e., pathogens), and good microbes (i.e., fuel-producing and yogurt-making bacteria) nothing else!

Bacteria conversation - http://www.towardslife.com/

Bacteria convention - http://www.towardslife.com/

We, in our human-centered view; automatically classify any newly-discovered bacterium to fall into one of three categories: the good, the bad and the ugly… no, not that one! They are: the useful guys, the harmful guys and the just-existing guys. Now, let’s take a look at the biocentric view of microbes: Humans and microbes share many ecosystems. To microbes, humans are just an ecosystem that is a “relatively safe” habitat with a source of nutrition.

As victims, we think about pathogenesis/infection as it’s shedding from the immune system, invasion and toxin production; but microbe-oriented microbiologists/bacteria whisperers know that, to bacteria, pathogenesis is  just defense, seeking nutrition, and excretion of metabolic byproducts. Being pathogenic or opportunistic is not their reason of existence, it’s just a form of adaptation to survive in this hostile environment (aka the human body).

You do not believe me!? OK, bacteria lived –happily- thousands of millennia before mammals and humans, so their reason of existence can’t be to harm humans, like what Dr. Aziz is mentioning: “Who attacks whom”, are the bacteria the “one” that start the fight, or is it the human immune system that starts the war against them?  A very interesting example to understand adaptation is Legionella pathogenesis, and how they adapted to human macrophages because they used to survive in amebas, which are similar to our macrophages.

Back to the basic question, is it a luxury or a necessity?

Studying “all” bacteria from their perspective will help us in understanding pathogenesis and subsequently developing strategies to combat infectious diseases (immunization and design highly selective chemotherapeutics), will give us a better idea of the tree of life and the metabolic map, and studying environmental microbiology will allow us to meet new “useful” microbes like what happened with the PCR Taq-polymerase, we knew how to make use of this bacterial polymerase that can work at those very high temperatures required for the PCR steps.

Here are two interviews about the commentary covering two segments of readers, the first one is with Dr. Betsey Dyer, Professor of Biology at Wheaton College, and the second one is made with Radwa Raed, a micro-writer and a final-year FOPCU student:

1- What is your opinion about (the commentary)? To what extent do you find it compatible with your bacteriocentric view of bacteriology? How strong are the arguments?

Dr. Betsey D. Dyer, Professor of Biology at Wheaton College.

“I thoroughly enjoyed Ramy Karam Aziz’s article “The Case for Biocentric Microbiology.” I think he is absolutely right that some old fashion thinking about the divisions of microbiology and anthropocentrism in general have hindered a more complete understanding of the microbial world. I also think Dr Aziz is quite bold and daring. I’m not sure I could have gotten such forceful statements accepted for publication! Good for “Gut Pathogens” to print it! I hope Dr Aziz gets lots of readers and citations.”

2- How did (the commentary) change your point of view? Are you with or against the biocentric view for microbiology? Do you think about it as a view against, or at least far from, your beliefs as a pharmacy student dreaming of fighting diseases? What are your opinions regarding studying environmental microbiology in pharmacy school?

Radwa Raed, Pharmacy student, Faculty of Pharmacy, Cairo University – Egypt.

“From my humble point of view, I would have to agree (with the biocentric view of microbiology). It goes without saying that studying more about certain bacteria “the ones some would consider to be of the least priority” will definitely expand our knowledge about the overall, and in many cases analogous or even similar, methods of survival, adaptation to existing conditions, etc.., which all pretty much ultimately serve medical microbiology. Plus, leaving a whole chunk, simply unexplored, can only raise several “what if” questions; one of which, that comes to mind, is what if the simplicity and less dramatic forms of life could help researchers better grasp the machinery behind these fascinating little creatures :)

As for studying environmental microbiology in pharmacy schools, I would have to oppose the idea, because the field of pharmaceutical science is taught so the future students can come to understand, and hopefully later suggest, treatment methods against pathogenic microorganisms, prophylaxis, and so forth..so studying the harmless ones would not point in this direction. It can only lead them to drift away from the pharmaceutical science branch of study into a more microbiology-oriented career.”

You can read the paper, share your comments and debate the arguments here, and you can also vote for it on BioWizard.

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*Full Citation:

Aziz, R. (2009). The case for biocentric microbiology Gut Pathogens, 1 (1) DOI: 10.1186/1757-4749-1-16

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What is bioinformatics?

It can simply be defined as a link between biology and computer science, in which the biological data is processed and computed through software, to yield an output, that is later interpreted in different ways.

Biological data indicates the nucleic acid or protein sequences, their simple or complicated forms, whereas the software is the computer program, specially designed for processing these data in a certain way, done using a certain algorithm (it is a recipe to solve a program problem). The data output is usually numerical or visual (often graphical), but mostly it needs to be well understood. The last one is the key point in the bioinformatics.

What is the need of bioinformatics?

In the research field, we need to be led to certain road, to choose one way or another, or to try many options until we define our research plan. Bioinformatics simply brings the solutions into your hands by a few mouse clicks.

One simple example to make it all clear is the PCR (Polymerase Chain Reaction). We always need to design a primer to trigger our reaction. If we did this through the ordinary ways, we would have to practically try out so many primers and this would surely take a tremendous amount of time. Now, what if you are computer- and internet-literate? You can simply use software to get many primer options for the DNA piece under investigation; doesn’t this save time, efforts and money?

Can bioinformatics be useful in different ways, other than the PCR example?

Some people may think that using bioinformatics is limited to some fields of biological research, and some others might think it is only a matter of prediction, which always needs to be evaluated for its accuracy, specificity and efficiency. But indeed, bioinformatics can be used in the analysis of nucleic acids and proteins.

Analysis?!! That is a vague word, how can you analyze a protein using bioinformatics?

Now you’ll see what bioinformatics can do for protein analysis:

  1. Retrieving protein sequences from different databases, either specialized or general databases and it is not an easy job if you would think so.
  2. Computing a protein or amino acid sequence to obtain:
  • So much of the physicochemical properties of you sequence like the molecular weight, and isoelectric point…etc
  • Hydrophilicity / hydrophobicity ratio

Both of the above can provide us with the probabilities of one protein acting as a receptor on the cell surface or it might be antigenic or even secreted outside the cell.

3. On the prediction aspect, we can predict:

The last two points are applications of what is called structural bioinformatics, through which computer is capable of predicting the 2ry and 3ry (3-D) configuration of your protein, using special programs with advanced algorithms and artificial intelligence. Amazingly, this may be useful in understanding the receptor-substrate interactions.

4. Comparing sequences to obtain the best alignment (it means compare 2 or more sequences to find their relation to each other, i.e. finding similarities and differences), it will help in:

  • Classifying your protein and relate it to its protein family
  • Making your evolutional expectations about your protein to define whether it descends from another protein or not. This is called phylogenetic analysis, at which the proteins under investigation are studied to know which protein is considered a mother to the others, which are the daughter, the grand daughter, and so on
  • Detection of the common domains, this will help us understanding the functions of unknown protein when it is compared to sequences of other proteins of known functions

Then, what will we gain if we compute DNA? Or you can say, what can bioinformatics do for DNA research?

On the same level as with protein, though different applications, we can use it in:

  • Retrieving DNA sequences from different databases
  • Computing a sequence to obtain information about its properties (like proteins) e.g. GC% which could be used with other properties to identify a gene
  • Assembling sequence fragments (usually DNA is sequenced in the form of fragments which are needed to be assembled in the best way, bioinfo. does this in a faster and more accurate way rather than the ordinary assembly)
  • Designing a PCR primer
  • Prediction of DNA and RNA secondary structures (e.g. prediction the stems and loops of the t-RNA)
  • Performing alignments between 2 or more sequences that can lead to many applications (as those mentioned above in protein alignments)
  • Finding of repeats, restriction sites, Single Nucleotide Polymorphism (SNPs), and/or open reading frames, all of which have so huge applications in the medical and paramedical fields and typically in the research activities.

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