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:

• Some sequences of certain importance, e.g. the prediction of signal peptides that can lead us to know the secretory proteins of one organism
• 2ry structure of your protein
• 3ry structure of your protein

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.

Tags: algorithms, alignment, analysis, artificial intelligence, Bioinformatics, biology, computer science, DNA, PCR, phylogenetic, phylogenetic analysis, protein, RNA, sequence, signal peptide, single nucleotide polymorphism, SNPs

This is not a prison break scheme. I was shocked to hear on BBC that researchers published a study, in the journal Genetic Vaccines and Therapy, about a new route for the delivery of specifically DNA virus vaccinations. Using the vibrating needle, normally used in tattoo parlors, they first experimented with mice & found a 16-fold increase in the humoral & cell-mediated antibody response elicited by these animals compared to the intramuscular injection. The needle implants small DNA fragments into the epidermis, which triggers a non-specific immune response believed to be the reason for the higher antibody levels found despite the lower dose of DNA used.

Flattering as it sounds, a lot of skeptics doubt that it would become a complete replacement of the conventional routes currently in use. It does not come without a cheap price either. Many tattoo lovers loathe the accompanying pain. Plus, potential users won’t be getting a tattoo in the process either because the needle won’t be loaded with ink.

Just truly amazed at whoever first comes up with such ideas and tries putting them to the test.

Image Credit: Enquirer

Tags: DNA, Gene Therapy, immune response, tattoo, vaccine

On February 28, 1953, James Watson and Francis Crick announced to their friends that they have discovered the chemical structure of the DNA. After publishing their paper in Nature on April 2, the official announcement took place on April 25.

That is what I have read in Al-Ahram newspaper today. What a discovery! Imagine if they had not done it, we would have had no clue about genes & protein synthesis, no recombinant DNA tech- & no sequencing. We would have had no molecular biology departments in universities! Abby from NCIS & Greg from CSI would have had no job!

So, what was the real story? To what extent are the “rumors” saying that Rosalind Franklin is the real discoverer of the DNA double helix right? Is she really the “Dark Lady of DNA”?

I hope we can get the story through your comments after we read this:

1- Crick papers from the National Library of Medicine.

2- Watson’s interview with a group of top North Carolina high school students in 2003.

3- BBC celebrating the 50th anniversary of DNA structure discovery in 2003. (really interesting)

4- Rosalind Franklin: Dark Lady of DNA by NPR (National Public Radio)

Image credits:
Watson – Crick DNA model: http://www.cs.princeton.edu/
Rosalind Franklin: http://www.npr.org/

Tags: 1408f278d2a6f884de58c0c44b7a6af7, DNA, Francis Crick, James Watson, Rosalind Franklin

What could the two possibly have in common? Surprisingly, deep within the human genetic code, researchers have discovered a previously un-noticed gene that encodes a DNA-binding protein which closely resembles proteins produced by archaea bacteria. The gene, named hSSB1, was cloned to obtain sufficient amounts of the protein for analysis.

Studies have shown that this protein attaches to single stranded pieces of DNA. “Red marks shown in the picture indicate areas of attachment to the DNA”. Furthermore, it activates the production of other proteins which indicate the occurence of damage in that specific area of the genetic material. Cells deficient in this gene are more liable to DNA damage & eventually die at a faster rate.

Now, researchers are faced with the challenge of understanding the exact mechanism of how it signals the damage of the DNA & determining the roles, if any do exist, in the development of cancer.

Tags: archaea, DNA, hSSB1 gene