Ask Dr. Science!

Are there scientific terms or concepts that you'd like to know more about? Looking for a bit more of an explanation? Confused about the difference between DNA and RNA?

Some of my fellow SciBlings, Tara, Chad, John, Janet, and Bora; have proposed that we consider going back to basics. Others have pointed out that we ScienceBloggers might be a little clueless ourselves about which basics that you'd like us to define.

Here's my proposal:
You can ask me a question in the comments here - or via e-mail (digitalbio at gmail.com) and I will pick one every week or so and try to answer it. Or, if I can't answer it, I probably tell you where to find the info.

I'll put a link to this post in the side menu so you find it later on.

What kinds of questions can I answer?

I can do best with subjects that I've either studied or taught.

As a graduate student, I studied bacteria that transfer DNA to plants. So, I know something about bacteria, plants, and DNA that moves around in the wild.

As a post-doc, I worked on the molecular genetics of Trypanosomes (protozoan parasites that cause sleeping sickness).

As a college instructor, I taught and developed courses in:

  • Bioinformatics
  • Biotechnology
  • Genetics
  • Immunology
  • Microbiology
  • Media and Solution preparation
  • DNA Technology: restriction mapping, cloning, sequencing, blots, PCR
  • Protein Purification: enzyme assays, columns, etc.
  • Immunochemistry: antibodies, ELISAs, blots
  • Tissue Culture: growing cells in the lab

And lately, I've been working on developing teaching activities with bioinformatics and doing research with bioinformatics on DNA sequencing, genetics, and genetic testing.

Now's your chance, ask away!

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This might entail a series of posts rather than just one, but I'd find it enlightening to see a piece, written for the educated layman, on the steps, techniques and procedures entailed in elucidating the complete genome of an organism.

Sandra, your blog is one of the easier reads out there, especially for those who might be new to molecular biology/bioinformatics. If I had a suggestion, it might be one on the whole concept of protein homology and how it can be applied.

One thing I would like is a commented list of biological databases because it is sometimes hard to judge if a database is reliable and if it is applicable for certain questions or if it is biased due to the way the data were collected. E.g., alternaive splicing databases, transcription factor databases, expression databases

Ok, so I'm reading up on bioinformatics and have come across a question.
Since I like to learn while I'm actually DOING something productive, what kind of productive research can be done solely using information available online and bioinformatics tools?
In other words, is a wet lab generating data always necessary to get to an end result? Or can one person (such as myself) do some sort of research and obtain decent or almost conclusive results?

Thanks,
Dr Science! ;)

I don't think a wet lab is completely necessary, although, it can be extremely helpful.

People do all kinds of productive research with bioinformatics/computational biology. If you want to see some examples, check out the recent papers from David Haussler's lab. Also, I would take a look at Plos computational biology, they have some great examples of things that can be done.

can i develope technique to screen the pathogens instead of detecting by culturing it and doing biological tests?

By baskaran.s (not verified) on 16 Feb 2007 #permalink

Baskaran,

This topic deserves a longer answer, but until I get to it, the quick answer is "yes." People do use combinations of PCR and DNA sequencing assays to detect pathogens. You're right - this is quicker than culturing microbes and you don't have to worry about having the correct media.

If you're interested in that subject, here are the names of some commonly used methods. Just enter them in wikipedia or a search engine of your choice to learn more about them:

random amplified polymorphic dna: rapd
(terminal) restrction fragment length polymorphism: trflp
temperature/denaturating gradient gel electrophoresis: t/dgge
amplified ribosomal dna restriction analysis: ardra
ribosomal intergenic spacer analysis: risa
single strand conformation polymorphism: sscp

The general premise is that you have 2 sequences that are conserved (so you can make primers for PCR to amplify them) that encompass a sequence that is (highly) variable (so that there are differences one can detect). Usually rRNA genes are used, because they fit those criteria pretty well.
For human pathogens, trflp and dgge seem to be the most used methods, while the rest is used in ecology studies. At least that was my impression from the classes I had.

I think right now there are at least 24 versions of PCR assays. You might wonder why there so many, but I think it's because everyone wants to avoid using an assay whose patent is owned by someone else.