Sigma BioBlogs

We’re excited to announce our sponsorship of Pubget’s new app designed to deliver the ease of finding full text PDFs for any journal, straight to your iPad®. Together with Pubget, we’re bringing life science research to the iPad in a simple and convenient app.

As a research tool, Pubget.com is the search engine for life science PDFs providing content from over 450 institutional libraries. Its 28 million article index includes all of PubMed and more. The article level tools on Pubget.com provide a seamless workflow tailored for scientists’ needs, plus it’s free!

The app provides search and one-click access to any journal available from your school or work’s library. What’s great is the results are full-text PDF’s, not just abstracts.

You’ll log in only once and then have convenient access to any journal. You can easily search all of PubMed and more. Once you’ve found your article of interest, save the full text PDF to take with you and read offline anywhere. Another great feature is you can add notes to any PDF while you’re reading it. You also have the option to share your viewed and saved papers with friends and colleagues by email.

Looking for the perfect Sigma product or gene-related content? Keep an eye out for the DNA helix icon as an indicator that there’s a Sigma product or information source that can assist in your research around the article you’re viewing.

Download the app today and save time with fast search and easy access to the latest papers from your favorite journals. You can now search and take full text PDFs with you wherever you go!

Ricardo Reis of the Faculdade de Medicina da Universidade do Porto

The last two winters, our Your Favorite Gene team has held a Holiday Gene contest. Our 2010 winner is Ricardo Reis, from Portugal.

Where did your bio begin?

My bio began in my first year of Medical School at Faculdade de Medicina da Universidade do Porto. It is located in the city of Oporto, in the northern part of Portugal.  The Molecular and Cell Biology lab opened one-year vacancies for an extra-credit internship at their lab.   I was keen on research, so I applied and got one of the vacancies. After the year and the extra-credit,  I was invited to stay.  So, to my great pleasure, I became a member of that team.  It is thanks to them that I still do research in biological sciences.

What inspired you to become a biologist?

I am training to be a physician, and I think that research in biosciences should be a compulsory part of every medical doctor’s curriculum.

I love the complexity of biological systems and their unpredictability.   I think it is this challenge that keeps me going, searching for answers.  Indeed, for me, research is always about the passion for knowledge.

Tell us about your research.

I am currently studying the post-translational modifications – (PTMs) of a homeodomain transcription factor which is crucial for the development of nociceptive afferents and their 2nd order relay neurons in the Central Nervous System (CNS).
It is subject to a number of PTMs which may impact its ability to bind to other proteins and activate its transcriptional program. Although my focus is mainly on the PTMs, we are also trying to unravel its partners and devise efficient assays to measure its transcriptional activity.

Do you plan to tend to patients as a physician and continue your research?

That is certainly a future goal and that’s where I like to picture myself in 5-years time.  However, I am well aware of the demands of being both, and I am afraid that one of them will be preponderant.  I don’t know which one I’ll be:  either a PHYSICIAN-researcher or a physician-RESEARCHER.

What genes won the contest?

For Christmas- SNTA 1 – syntrophin alpha 1…or Santa

ADAM7 – protease, or the inital seven members of the Addam’s family (halloween themed)

Each year our Your Favorite Gene Manager, Kyle Brueggeman, challenges scientists to bend their minds and find gene symbols or genes that are holiday related.

The mission:

Look at gene symbols, squint your eyes, imagine, and show us the new meaning you see in the genes.

All winter holiday celebrations are fair game.  Bring on Hanukkah, Kwanzaa, Winter Solstice,  New Year’s Eve, or even Festivus “related” genes!

Enter before Dec 31, 2010, and you will be entered to win an iPad!

Here are some great entries that we’ve had so far:

Lectin from Viscum album (European mistletoe)

Who needs a sprig of green when you can substitute the purified stuff!

Five favorite genes of  Santa Claus are: ELF1 (E74-like factor 1 (ets domain transcription factor), ELF2, ELF3, ELF4, ELF5.

ACHE-what you get after eating a big Holiday Dinner!!

(Hint: Take a little time to look at this entry before jumping to the “punchline” below!)

MR1, RYK, HRaS, TyMS, TAL2, NDsT1, AL118921, GaD1, N5, GH1, (and a “T” Thrown in for good measure…)

Can you figure out what it says?

Ignore the numbers, add necessary vowels, and you get:

MeRRY KHRiSTMaS To ALL aND To ALL a GooD NiGHT

From everyone at Sigma Life Sciences, have a Safe and Happy Holiday Season!



Do you know who your molecules are interacting with?  If you visit the Interaction Network tab in YFG, you will not only get to see every molecule it’s interacting with, but what they’re doing together.

Here is an example…

To learn the action between ALB and HIF1A, click on the line between them

I’ve pulled up the Interaction Network for HIF1A, filtered it by interactors that have an antagonist small molecule available, then zoomed in to examine the connection between ALB and HIF1A, just by clicking on the line between the two.

Interaction Network tabs, Gene Details, and Canonical Pathways are possible thanks to our collaboration with Ingenuity Systems, Inc. to integrate their manually curated Knowledge Base.

The Interaction Networks tab shows detailed biological molecular networks curated from scientific literature.

As I look at it, I think “I’d really like to have an antagonist to work with related to ALB and HIF1A” so I click on ALB to find the antagonists.

To see available antagonists, click on ALB

So go check out who YOUR molecules are interacting with on the Your Favorite Gene website.

Have you ever used a tag cloud in Web searching and browsing?

When we upgraded our Your Favorite Gene site, we added a full PubMed search, and made keyword relationships more obvious by adding a tag cloud.

The image below is a collection of key words in a PubMed search for HIF1A (Hypoxia inducible factor 1).  The size of the keyword shows how frequently it appears within the search results as related to just HIF1A.

Tag cloud results allow a user to pick and choose filters by the terms that appear.

Find a term that relates to your research within the result, and you can whittle your search before checking the listings below.  Here we chose Vascular Endothelial Growth Factor A.

You can see that the cloud has now brought in additional terms that relate to the combination of HIF1A and Vascular Endothelial Growth Factor A, like AKT1. It has also resized the terms as they relate to this combination, so Vascular Endothelial Growth Factor A is now larger, as is Tumor Cells, Cultured.

Keep going!  The filters to the left are categorizations of the keywords.  If you want to see the diseases most prevalent, choose “disease”, and you have the diseases for HIF1a with VEGFa.

Display more terms by changing the drop down for analyze size at the top right of the cloud.

The results for the terms selected appear beneath the cloud. By default they are sorted by biological relevance, but you can also view by the date of publication.

We’d love to know what you think about the updates we’ve made to YFG. Please use the comment boxes throughout to let us know what you think!

When we set out to create a leading destination for researchers and students exploring diseases, functions and gene pathways we were excited to learn an engaged group was accessing Your Favorite Gene powered by Ingenuity, a collection of scientific information including dynamic biological pathways, interaction networks and gene overviews.

We also knew we could count on scientists to provide feedback to improve this resource and those suggestions are at the heart of this new version.  The overwhelming response was a request for more literature!!!

When designing experiments researchers focus on peer-reviewed publications and data to help them explore ways to answer their scientific questions.  Until this version of YFG, those resources were scattered across the web in several different locations such as:
ChemBLdb
PubMed
Gene Expression Omnibus (GEO)
National Cancer Institute (NCI)
Online Mendelian Inheritance in Man (OMIM)
Clinical Trials.gov

Now it is all in one place!  YFG now contains expanded content with greater functionality to quickly connect you to the information that is relevant to your research.  I could go on but I don’t want to steal Kyle’s thunder.

Listen to Kyle Brueggeman give the highlights of the updated version of Your Favorite Gene Powered by Ingenuity.

It isn’t everyday that we can get a product manager to talk to the camera so take a minute to listen and then feel free to tell us what you think at yfgsuggestions@sial.com.

We are also hoping that Kyle’s willingness to speak to the camera will inspire you to do the same and enter our video contest at AACR.