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!



What would the beginning of the holiday season be without the YFG Holiday Gene Hunt Contest?**

Sure, YFG is a great place to see Interaction Networks and Gene Regulation viewers…but if you look closely at gene symbols and squint your eyes  you’ll find that they morph into words that are quite festive!

Find a holiday gene, and you’ll be entered into our drawing for a $250 Visa gift card!

Here are some hints that we have for the United States Thanksgiving!

Traditional Turkey for USA Thanksgiving dinner!

Can you find more?

**Hint: we eat a big meal with Turkey, cranberry, stuffing, gravy and give thanks…**

ATM – Where you need to go before Black Friday? or it encodes an important cell cycle checkpoint kinase that regulates tumor suppressor proteins p53 and BRCA1

CHUK – Your cousin sitting next to you at Thanksgiving dinner? OR a conserved helix-loop-helix ubiquitous kinase ?

Represent any other holidays that are common!  We want to hear all kinds of holiday genes!

Participants will also gain access to special holiday discounts on antibodies, shRNA, miRNA, and more.

How to play:

1)     Explore YFG to find holiday themed genes and molecules like HOHO and Nik related kinase

2)     Submit your genes here

3)     Gain access to discounts after you submit your entry

**One lucky participant will win a $250 Visa gift card.

**Play by December 31, 2010 to be entered into the drawing.

Dr. Nicholson's work made it possible for so many to visualized complex bioprocesses

Donald Nicholson’s bio is the starting place for many of us…

The first time I saw the metabolic pathway maps, I was enchanted.  They contained a road map for the secret inner workings of cells and biological systems.

The origin of a metabolic pathway map is quite fascinating, and a lot of work!  I was lucky enough to get to speak with Donald Nicholson in person about how he came to create the first pathway maps. Watch the video of my conversation with Donald Nicholson!

Here is a brief overview of how to illustrate metabolic pathways in the 1960′s:

1- Type or print all the names and structures.

2- Construct the pathway by cutting out each individual pathway and sticking it on a piece of paper

3- Repeat annually.

This process required Dr. Nicholson to spend 9 months out of each year creating the Metabolic pathways charts.

Dr. Nicholson is also keeping up with the times.  At the age of 80, he bought his first computer and has been working to create animated versions of his maps.

We salute this biolegend.

We have two more videos of Dr. Nicholson available covering how he first became interested in biology and his use of the Inborn errors of metabolism maps to capture the interest of his medical students, who up until that point, didn’t really like Biochemistry .

Watch the videos:

Dr. Donald Nicholson Teaching Med Students Biochemistry.

Dr. Donald Nicholson: Where his bio began

This blog post brought to you by the Your Favorite Gene search, home to interactive biological pathway maps and interaction networks.

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.

AMPK AMPK AMPK!!!!  That’s all that Larry Shapiro’s lab at Columbia University in NYC can talk about in “Naturally Obsessed: The Making of a Scientist“.   The excellent documentary was produced and directed by Richard A Rifkind  Emeritus Chairman of Memorial Sloan-Kettering.

“Maybe today I’ll have the answer…” says Robert Townley, rebel grad student.  Townley points to what drives scientists…a single perplexing question or problem.  He and 2 other grad students in Shapiro’s lab are working to crystallize the elusive AMPK structure.  As my Physiology teachers used to say “Structure points to function.”   As soon as they know the structure its regulation can start to be determined.

To honor the stars of this documentary, we spotlight AMPK in Your Favorite Gene.

AMPK, AMP-activated protein kinase, regulates the activities of a number of key metabolic enzymes through phosphorylation.  In Your Favorite Gene we have a map of 51 literature citations documenting AMPK’s interactions, 79 citations which I can filter by Enzyme Activation to narrow my search to 17 citations for AMPK and Enzyme Activation (which is why AMPK’s function intrigues Shapiro’s lab).

One of our goals with the Your Favorite Gene tool is to create one place for as much information as possible about a specific gene or protein of interest.

Here we highlight gene regulation for hypoxia inducible factor 1 or HIF1A.

To create the gene regulation viewer, the Sigma Life Science bioinformatics team pulled together data for each gene related to the conservation pattern of sequence alignment for human, mouse, and rat, the calculated CpG island, and the DNA methylation patterns where relevant.

Please take a look with your favorite gene!  And notice that there is always a spot to give feedback on every page of YFG. We would love to hear your suggestions.

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.