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NCBI Activity: CYP12d1

Cytochrome P450s (CYPs) are found in all organisms and metabolize many xenobiotic chemicals organisms come into contact with everyday. CYP12d1 is found in Drosophila and is known to metabolize DDT. Insecticide resistant strains of Drosophila over-express CYP12d1 along with many other CYP genes.

Genome-wide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila.

J H F Pedra et al.

Proceedings of the National Academy of Sciences of the United States of America 101 (18), 7034-9 (04 May 2004)

Evaluating the insecticide resistance potential of eight Drosophila melanogaster cytochrome P450 genes by transgenic over-expression.

Phillip J Daborn et al.

Insect biochemistry and molecular biology 37 (5), 512-9 (May 2007)

Expression of Cyp6g1 and Cyp12d1 in DDT resistant and susceptible strains of Drosophila melanogaster.

R A Festucci-Buselli et al.

Insect molecular biology 14 (1), 69-77 (Jan 2005)

For background info see the book:

Cytochrome P450, Michael R. Waterman Elsevier, 1991

Saved Search Parameters:

Limited to full-text articles from the Journals Insect biochemistry and molecular biology & Insect molecular biology from 2005 on with cytochrome p450 as a search term. Alert set up to notify me of new articles being published in these journals on Cytochrome P450s.


GoogleBooks is better than NCBI if you want to find books for background info.

NCBI Activity: SIZ1

Person: Ayla

Topic: SIZ1 E3 SUMO Ligase

Introduction: The topic of my undergraduate research was overexpressing the E3 SUMO ligase, SIZ1 in turfgrass and rice to improve drought tolerance. The first article by Catala’s lab is the one that was majorly cited in my research project.  Many procedures came from it.  The article about flowering time cited this article, so I included it out of curiosity.


The Arabidopsis E3 SUMO Ligase SIZ1 Regulates Plant Growth and Drought Responses

Rafael Catala, Jian Ouyang,1 Isabel A. Abreu, Yuxin Hu,2 Haksoo Seo,3 Xiuren Zhang, and Nam-Hai Chua4

Plant Cell. 2007 September; 19(9): 2952–2966.

doi: 10.1105/tpc.106.049981.

PMCID: PMC2048692

Flowering time regulation by the SUMO E3 ligase SIZ1
Jing Bo Jin1,2 and Paul M Hasegawacorresponding author1
Plant Signal Behav. 2008 October; 3(10): 891–892.
PMCID: PMC2634407

Background:  If you wanted to learn more about the sumolyation pathway SIZ1 is involved in, I still feel it would be easier just to conduct a Google or Wikipedia search.

Search: I saved the search for “SIZ1 Catala” and have it set up to email me once per mont with updates.

Tips/Tricks: Click many related article/cited by links, even if they don’t look particularly useful.  They could lead you to more interesting things.

If you accidently search for something in PubMed instead of PubMedCentral, you will get the abstract but not a link to the full text, even if you know that the full text version is available on PMC.  It’s annoying.

Pubmed automatically links to the abstracts of  articles cited in the document, again I wish it was easier to quickly access the full-text version with one-click.

I can’t figure out how to make my font smaller for the first citation in this blog.

NCBI Activity: ICAM-1 (Intercellular Adhesion Molecule)

Group: Ellen, Jerreme, Stephen

ICAM-1 is a human gene that encodes for a protein, inter-cellular adhesion molecule-1.  The ICAM-1 is an immunoglobulin protein expressed on endothelial and antigen presenting cells.  The expression of ICAM on endothelial cells can be induced by inflammatory cytokines, which promotes firm adhesion of the leukocytes to the site of inflammation.
LFA-1 is a beta-2 integrin located on several leukocytes which subsequently binds to ICAM-1 when the inflammatory cascade is activated.  This process mediates leukocytes immigrating to sites of inflammation in the blood stream along the vascular wall.

ICAM-1 expression determines malignant potential of cancer.
Christina L Roland et al.
Surgery 141 (6), 705-7 (Jun 2007)

Cell adhesion molecules: potential therapeutic & diagnostic implications.
Shaker A Mousa
Molecular biotechnology 38 (1), 33-40 (Jan 2008)

There are many references available about ICAM-1 and its functions specifically relating to cell signaling and cancer.  The link for an immunobiology textbook []   gives a large amount of information on ICAM-1 functions with an immune and inflammation response.

Our search strategy tracks articles containing “ICAM-1.”  An email will automatically be sent to us when new articles become available.

Search alternative names for the item or subject you are looking for (e.g. ICAM-1 is also known as CD54) when using an NCBI database.

Often Pubmed and other databases can be confusing to navigate.  Use a single article to begin your research and then search an author’s name or specific journal to find other relevant articles on your topic of interest.

Are there any suggestions for organizing saved tags in Connotea?
Help using Pubmed to find articles relating to experimental techniques for circular permutation.

NCBI Activity: Neanderthal DNA

Group: Sam and Ethel

Topic: Neanderthal DNA

Introduction: I’ve been interested in human evolution for a while now and I think it is amazing that they are able to pull DNA from Neanderthal remains. Some of the sequence has been used to estimate a divergence time between humans and neanderthals of about 700,000 years ago. But neanderthals were around for another 350,000 years so there was a lot of overlapping co-existence.


No evidence of a Neanderthal contribution to modern human diversity.
Jason A Hodgson and Todd R Disotell
Genome biology
9 (2), 206 (2008)

Sequencing and analysis of Neanderthal genomic DNA.
314 (5802), 1113-8 (17 Nov 2006)

Background: There is lots of information about human evolution and neanderthals in the Book DB of NCBI. This link [] if from a biochemistry text that has a figure of the evolutionary relatinships. This section of text from the same book shows how quickly our understanding is changing based on the newly available DNA sequence data [].

Search: I built a search to track articles that have “neanderthal” in the title or have “Paabo” as an author.  I will automatically get an e-mail when new articles are available.


The NCBI News [] is a great resource for keeping up with the changes at NCBI. You can sign up to have it delivered as an e-mail.

There are automatic connections between PubMed and the Books DB which are described here, []. You can also see all the books included in the db by looking here [].


I would really like to know how to build an alert that would let me know when someone cites an article. I do something with google alerts but it is not quite what I want.

I still struggle sometimes when searching the NCBI Taxonomy DB because names change and common names are often not recognized. I’m not sure how to be efficient when searching here.

Can games contribute?

folditWho doesn’t like to play games … especially games in which you contribue to science!  If you haven’t visited Foldit you have been missing something special.  In addition to reminding us about the properties of proteins and their amino acids, we can begin to connect shape (structure) with function.  Check out their blog to get the lastest on current competitions and information already obtained from this project.


model_2005_chemlinks_bqsw1This first week of conference presentations and workshop “work time” are a great way to meet other UTK graduate students, professors, and projects.  You will have an opportunity to engage in contemporary biological problem solving using online resources and tools that should prove helpful in graduate school. 

Our goals for this week are to introduce:

  • collaborative problem solving;
  • new tools (bioinformatics and visualization);
  • online data;
  • community resources; and,
  • sharing group projects.

We look forward to working with you this week!

What’s happening in every cell…

Inner Life of the Cell

Inner Life of the Cell

The “Inner Life of a Cell” is an ~8 min movie put together using structures from PDB and tools from NewTek LightWave 3D and Adobe After Effects. Click here to view it and see how many proteins you can identify!