My Ph.D. life

Today, I was trying to wrap up a manuscript done in the last year of my graduate study. I opened the fold containing all my Ph.D. research data. I started to look my lab presentations from the first year I jointed my Kentucky lab. I found that I really did tons of works. As always, particularly during my graduate study, I am trying to ask myself why many projects didn't complete and published even I worked so hard. I only published one paper from the work of my first three years. Some project stopped in the middle due to unable to connect a gene to its function (only cloning and expression data), while others are stuck at solving the technique problems...

In a word, 80% of projects are failure, only 20% are kind of completed..... I don't know if my case is special. But I do think I have learned a lot from those failure and matured from those lessons. I have learned that I should always pick up a manageable project regardless how ambitious I am. Like baby step, a small step at a time, I should accomplish one small experiment at a time and slowly accumulate each piece of data together to form a publication. Of cause, this requires the confidence and constant interest in the project and unsolved problems, and hard work.

I remember that there was a quote saying: "Vision without action is a daydream, but action without vision is a nightmare." I am probably the second one and now I am trying very hard to have both vision and action....

I metamorphosed....

Last two years was my transition from a graduate student to a postdoctoral researcher. So it was kind of busy. You know, wrapping up experiments, writing dissertation, looking for jobs, job interview, Ph.D. degree defense.....

Now I've been working as a postdoctoral researcher at Brown University for one year. I am studying the molecular mechanism of aging foe. Although it is kind of different from insect development and metamorphosis, I still use insect as my model. This time the model is fruit flies, Drosophila melanogaster.

The whole scientific career just likes the life cycle of an holometabolous insect (complete metamorphosis). Undergrad and graduate study are the embryonic and larval stages. Postdoctoral training is the pupal stage. Faculty is the adult stage where next generation young scientists were 'produced'. The graduate study are the tough time. Some take longer time, others take shorter time. Eventually we make through the graduation, 'the metamorphosis', it is a bit of success. Just like the former lab mate, Alan said after he graduated from Brown,''Pupa here I come". ....

Roger Tsien won 2008 Nobel prize in chemistry!

The Nobel Prize in Chemistry 2008

Osamu Shimomura, Martin Chalfie and Roger Y. Tsien
"for the discovery and development of the green fluorescent protein, GFP"

Interestingly, the father of Roger Tsien (Chinese name 钱永健) is a cousin of Tsien Hsue-shen (钱学森). And many his family members are also famous scientists.

By reading his interview in JBC, Vol. 179 2007, I start thinking that maybe I can do some similar experiments to image small signal molecules (ep. Calcium) during JH action in particular JH target tissues and confirm JH action really through some membrane factors.

Allatotropin receptor found!

Yamanaka N, Yamamoto S, Zitnan D, Watanabe K, Kawada T, Satake H, Kaneko Y, Hiruma K, Tanaka Y, Shinoda T, Kataoka H.

Neuropeptide receptor transcriptome reveals unidentified neuroendocrine pathways.

PLoS ONE. 2008 Aug 25;3(8):e3048.

PMID: 18725956 [PubMed - in process]

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Dr. Tetsuro Shinoda (National institute of Agrobiological Sciences, Japan) and Dr. Hiroshi Kataoka (University of Tokyo, Japan) reported an exiting finding last month in PLOS one, in which they show an identification of the first allatotropin receptor from silkworm, Bombyx mori. Allatotropin and allatostatin are two neuropeptides that up- and down-regulate juvenile hormone bisynthesis in corpora allata. The receptors for these neuropeptides belong to G protein-coupled receptor superfamily, the largest gene family.

What impressing me is their straightforward strategy. First of all, they got all homologues neuropeptide GPCRs using bioinformatics tools. Then comprehensive cloining for all neuropeptide GPCR genes was performed. Afterward, they used tissue specific expression analysis to narrow down candidate genes that are only expressed in certain tissues, such as corpora allata-corpora cardiaca complex. I think this is a critical step. Then functional analysis using cell-based assay to test the interaction between ligand and each receptors. With lucky or wisdom, they got a receptor for allatotropin,a receptor for allatostatin,a receptor for ecdysis triggering hormone. Wow, that is perfect. Hope I also can do the same thing and find one JH receptor~~~

Larval RNAi won't work in Drosophila?

Miller SC, Brown SJ, Tomoyasu Y.

Larval RNAi in Drosophila?

Dev Genes Evol. 2008 Sep;218(9):505-10. Epub 2008 Jul 29.

PMID: 18663472 [PubMed - in process]

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Research from Kansas State University showed some interesting finding last month. They reported that in Drosophila larvae most of tissues (except for hemocyte) were not able to uptake dsRNA, which is the reason why direct injection of dsRNA into Drosophila larvae won't trigger RNA interference (RNAi), but not due to lack of RNAi machinery.

Wow, what a surprise to me? I have been work for larval RNAi in Aedes mosquito for years by injection or feeding. Based on this article, what I did before was a waste of time. If I can read this paper long time ago, I may be able to do a lot of useful experiments and publish more paper~~ Sigh!!!

Fortunately, I am doing Tribolium now~~

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? ~~