Bioinformatics, local blast and BioEdit

Bioinformatics for me is a wonderful tool that make my research life easier~~ Just like you cannot live in today's world without internet.

Since Drosophila (fruit fly) whole genome sequence was done in 2000, more and more insect genomes have been sequenced and will be sequenced. Mass genome data sometimes make you feel lost.

I always wonder where I can find a great tool to help me dig useful information out of genome database. And local BLAST(Basic Local Alignment Search Tool) is what I need from time to time. Unlike blast using NCBI and other online interface, local blast allows you to perform blast in your local computer with your local database without the connection to internet. That is neat! So I can do blast when I am actually flying~~ I've been tried using NCBI blastall, but I was confused with many scripts. Recently, I happened to find BioEdit program can all do local blast. This program is free, easy to use, and faster than online blast. I fall in love with it immediately when I first tried it. It is really great. Now I downloaded latest Tribolium beetle's genome sequence from beetlebase and setup in BioEdit for local blast. I hope everyone should take a look at it and find out more neat functions.

Thank you Dr. Tan! Without you I will not know the exist of BioEdit and still have a miserable life.

For more detail about BioEdit program, please go to http://www.mbio.ncsu.edu/BioEdit/BioEdit.html

Riddiford's 2008 JH review

This year Dr. Riddiford published a JH review in Journal of Insect Physiology (JIP). Take a look at it and you may get some ideas about future JH research. Looks like she think Met is at the top of JH signal transduction cascade, although more evidences needed to prove that Met is a JH receptor.

What is interesting to me is her comments on Dr. Yiping Li's JBC paper. She said, "This model (Dr. Li's model) is greatly oversimplified and ignores the fact that 20E directs and coordinates
nearly the same TF cascade during a molt, irrespective of whether or not JH is present, with only a few metamorphic-specific genes such as broad being induced at the time of metamorphosis in the absence of JH...... The indication from all these studies of JH-regulated
genes with different putative JHREs suggests that in addition to a ''JH receptor'', there is likely a myriad of interacting factors that can modulate the final outcome."

Maybe JH action IS really a complicate biological process......

Dr. Jindra's PNAS

Last year, Konopova B and Jindra M. published a paper titled as "Juvenile hormone resistance gene Methoprene-tolerant controls entry into metamorphosis in the beetle Tribolium castaneum" in Proc Natl Acad Sci U S A. 2007 May 30. This paper was considered as a breakthrough of JH action research.

In the abstract , they wrote, "Here we show that impaired function of the Met ortholog TcMet renders Tribolium resistant to the effects of ectopic JH and, in a striking contrast to Drosophila, causes early-stage beetle larvae to undergo precocious metamorphosis".

So their data seems to support that Met protein is a stong putative JH receptor. Are we close to dig JH receptor out in the near 5~10 years?

Automatic journal searching using Pubmed

Recently, I register My NCBI at
http://www.ncbi.nlm.nih.gov/entrez/login.fcgi?call=0NTQw95KEIM-1pLA3k...

So I can received updated email of the recent publications of
interested authors and topics. For example,
Pubmed search for recent papers from the Palli lab
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=palli+sr[au]

Many of you may already know it. If not, register one today!

Finding Juvenile hormone receptor(s)

Juvenile hormone (JH) was discovered as a as a humoral factor that could prevent metamorphosis of many insects. It is also involved in many other aspects of insect life, such as reproduction, diapause, polyphenisms and behavior. As an insect physiologist, understanding how JH is able to control metamorphosis and reproduction will be the great accomplishment, especially identification of JH receptor protein (s).

However, scientists have been searching for JH receptor(s) for more than 50 years and none of them got satisfied answers. Why is it so difficult? ~~

Advantages of metamorphosis

I have to say insects get lots of advantages from the metamorphosis, especially the complete metamorphosis insects, so call holometabolous insects like butterflies and mosquitoes. Almost 80% of insect species (total number around 925,000) are holometabolour insects, which are more than all other animal groups combined together.

In holometabolous insects, larvae enjoy in only eating and growing, while adults are responsible for producing offspring and they don't eat much in some species. Pupal stage is the intermediate stage when all the transformation safely occur. Therefore, larvae and adults don't share food source, in another word, no food competition. And there is a division of labor, growing and reproduction separately. Living in different habitat is another amazing thing that only insect can do through metamorphosis. For instant, mosquito larvae live in the water, while adult can fly around and find blood meal. Imagine that, if human beings have the same ability as insects, then we will be able to swim like a fish and fly like a bird in our life. Isn't that great?

What is metamorphosis?

Metamorphosis in biology is physical development of the individual after birth or hatching involving significant change in form as well as growth and differentiation (From wikipedia). Especially in insects, such as butterfly and moth, you will find there are three different forms in its life cycle: larva, pupa and adult.

About me

I am an old student, still working hard in graduate school. I am studying the metamorphosis of insects now, and trying to find out how those beautiful bugs can change their body form during their life. It is metamorphosis that make insects the most successful animal in our world!!!

Blog open today

Communication and Interaction are everywhere, from telephone to internet, from the magnetic interaction between stars to proteins binding to their receptors. Now we have our own Blogs. What is a magic thing! So I hurry up and try to catch up with you guys.

In this small space, I would like to share with you the ideas and thoughts that come from my daily bug research and scientific readings. Hope you will enjoy reading and find something useful for you.

AND please let me know what you think. THANKS!!!