Cosmetics got Chemistry

December 17th, 2009 by George Fitzgerald, PhD

Things have come a long way since the ancient Egyptians used galena (lead sulphite) as eye makeup. I spent most of last week in New York City at the annual meeting of the Society of Cosmetic Chemists. There is an amazing amount of very sophisticated chemistry going on in cosmetics.

One of the most enjoyable presentations was by Ricardo Diez of Chanel, Inc. Dr. Diez summarized developments in ‘cleansing products’ over the last 50 years. I put the term in quotation marks because what we call ’soap’ today is quite different from soap of 50 years ago. An excerpt from the New York Times of that era advised women to wash their hair no more often than about every 2 weeks. This stuff was really just your basic soap, i.e., fatty acid salts.

Dr. Diez reported that in the 1920’s German chemists created the first ’soap alternatives’ or detergents to support the textiles industry. These were the people who filed the patents “behind widely used anionic surfactants” still around today. Surfactants transformed soaps into milder, more effective cleaning agents. Over time, manufacturers made the products gentler (think Johnson’s ® ”No More Tears” ®). Then added silicones to combine shampoo and conditioner (e.g., Procter & Gamble’s “Pert Plus” ®). Finally, manufacturers combined moisturizers with the cleaners.

How did all this come about? Remember the DuPont slogan: Better living through chemistry? Some might find it frivolous to apply this expression to cosmetics. But the advances in ’soap’ have made a real improvements to peoples’ lives, making it easier and cheaper to practice good hygene – not just to keep up appearances. As a professional chemist, I’m proud to be associated with the scientists who’ve accomplished that.

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Materials Studio 5.0: A particle-ular challenge

December 11th, 2009 by Stephen Todd, PhD

In the last of the series of my blogs on Materials Studio 5.0 functionality, I will be writing about new functionality in the mesoscale area. Back in Materials Studio 4.4, we developed a new module called Mesocite. Mesocite is a module for doing coarse-grained molecular dynamics where the elementary particle is a bead. In coarse-grained molecular dynamics, a bead typically represents several heavy atoms. This has advantages over classical molecular dynamics such as Forcite Plus as you can access longer time and length scales.

In Materials Studio 5.0, we added the capability to do Dissipative Particle Dynamics (DPD) to Mesocite. DPD is a very coarse-grained dynamics approach where the bead can represent many atoms or even molecules. We already have a module which can do DPD in Materials Studio but this has limited ability to be extended. By developing the new DPD in Mesocite, we could take advantage of the underlying MatServer environment to easily extend DPD to run in parallel and work with MaterialsScript amongst other things.

One issue we faced is that the legacy DPD tool works in reduced units whereas MatServer requires physical units. The use of reduced units is fairly standard in DPD however it makes it more difficult to relate the results back to experimentalists. Therefore, we thought that switching to physical units would be a good idea. However, there were still questions as to how customers would work with a DPD in physical units. We asked a small focus group of customers very early in the release as to how they would like to parameterize DPD calculations. All agreed that getting the results in physical units was preferable but they still wanted to set up the calculations in reduced units as they have lots of historical data they want to re-use. So, we have a new user interface which allows setup in either reduced or physical units but then converts to physical units for the calculation!

When a new piece of functionality is added to Materials Studio, I like to add a tutorial on how to apply the software, what sort of values customers should use, and how to get the most out of the software. For the new DPD functionality, I looked at several papers before settling on an application by Groot and Rabone looking at the effect of non-ionic surfactants on membrane properties. This interested me as it demonstrates the strength of mesoscale in looking at varying concentrations of different components and seeing the effect on morphology. I also realized that I could use some of the Mesocite analysis to really analyze the system for properties such as concentration profiles and examining the diffusivity of the beads across the membrane. This mapped really well to the original results and produced what I hope is an interesting tutorial.

There was another reason I chose this paper too – Groot and Rabone also looked at the effect of strain on the membrane. This wasn’t possible with the old DPD module but, using some MaterialsScript, I could strain the system and then calculate the surface tension. As I like to dabble with MaterialsScript, the lure of this was irresistible and the script I made is available from the Accelrys Community website.

One minor issue was that the system sizes and relative amounts were not clear from the paper. Luckily there are several ex-Unilever people at Accelrys, so one of my colleagues, Dr Neil Spenley, contacted one of the authors, Dr Robert D. Groot. I was also lucky that Dr Groot obviously hordes his old research work and, a day later, I had the original DPD input file in my hands!

The results from the strain calculations also show the same trends as those reported by Groot and Rabone so I was pretty happy with this work.

So that wraps up my blogs on Materials Studio 5.0. I hope to have given you an insight into some of the processes that go into making a new version of Materials Studio.

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miRNA and Your Microarray

December 10th, 2009 by Nancy Miller Latimer, M.S.

As a product manager, I help map out where we move next to support omics-based research within our Pipeline Pilot™ collections.  An area of great research interest is the role of microRNA (miRNA) in understanding disease pathways, diagnosis of diseases, and possible treatments.  miRNA and small interfering RNA (siRNA) are gene products that collectively comprise a group of small nucleotides called RNA interference (RNAi).  These gene products bind to other cellular RNA products that up or down regulate gene activity which, in turn, impact the proteins that our bodies manufacture.  Proteins carry out the functions of life.  A specific miRNA, although only 20 or so nucleotides long, can impact the hundreds of genes and hence their protein products.

Our knowledge about these miRNAs is growing rapidly.  The number of miRNAs was less than 500 in May 2007; 9,539 in May 2009; and 10, 883 in Sep 2009.  The rate at which miRBase is growing at and the rate at which miRNA publications are proliferating, demonstrates the exponential growth in interest.

Nancys

We do know that miRNAs impact the immune system and cellular growth/development.  miRNAs appear to mostly turn down gene activity and are being studied for their role in cancer, cardiac, and mental illnesses.  [As an aside, I would say that the link to mental illness is sensible given the connections being proposed between infections and onset of schizophrenia or PANDAS with tics, to name a few.]

This week’s Science (Science 27 November 2009: 1284-1287) magazine contained a product summary for various technologies that are currently used for commercial miRNA microarrays:  microfluidics, electronics, and Tailored DNA.   This product summary conveniently lists several major players along with their websites, which you may find interesting.

Our omics R&D team creates component “readers” for various technology platforms to facilitate ease of analysis.  I would be very interested in knowing which technology you feel is the most reliable now, and which you see as most promising 3 years from now.  It appears that each technology has its own strength and weaknesses and the utility is also strongly based on the use case.  I welcome your comments.

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Pipeline Pilot 8.0 Beta Testing Nomination

December 8th, 2009 by Accelrys Team

Accelrys is looking for beta testers for its upcoming release of Pipeline Pilot. The beta is tentatively scheduled for the week of December 7. We’d like feedback on a number of capabilities; of particular interest will be to find out if these capabilities behave as expected in a true customer setting and if behavior for existing protocol is unchanged after an upgrade. If you are interested in becoming a beta tester, and you can commit at least 4 hours of your time before the end of the year, please send an email to Ton van Daelen (tvandaelen@accelrys.com) with the following information:
• Company
• User name
• Capabilities interested in testing (see link below)

http://forums.accelrys.org/eve/forums/a/tpc/f/7421036442/m/325109862

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Science, Fens and (No) Mountains

December 8th, 2009 by Gerhard Engel, PhD

I love the Alps: French, German, Swiss, Italian, Austrian, Slovenian, whatever. I take my family there every summer. They’ve got what Cambridge, England lacks.  You know: rocks, glaciers, waterfalls, lakes, meadows, cows, Strudel, Schnitzel, the lot.

So why exactly do I live and work in one of the flattest areas of the UK, a city just south of an area  of former swampland that the natives lovingly call “The Fens?”

It’s a long story really, a story of science  and adventure initially, but I suppose I ended up here because Cambridge is both the seat of a world-famous university and a European innovation hub that benefits from the ready availability of smart people and a prestigious address. That, and the absence of valleys, turned a wet piece of English countryside into Europe’s “Silicon Fen.”

No wonder then that at some point, around  1990, a Cambridge University spinoff called Cambridge Molecular Design became one of the precursors of Accelrys and evolved into what is now our European Headquarters.

I had an opportunity to reminisce about Accelrys’ roots and connections with Cambridge on the occasion of a recent meeting with the CEO of Cambridge Network, Matt Schofield. Cambridge Network provides many invaluable services to the Silicon Fen community. It helps employers find the right employees, it organizes and helps companies host outstanding events , runs special interest groups, and it offers a range of member benefits and business development opportunities for its members. In short, it offers tools and information that bring the Cambridge community together.

Accelrys has deep roots within this community.  Some of our flagship Materials Science products such as CASTEP and ONETEP originated here and are being continuously enhanced by teams of researchers at Cambridge University and their collaborators, and we benefit from many other fruitful  partnerships such as the one with Cambridge Crystallographic Data Centre. Several Accelrys scientists, myself included, learned their trade as part of thriving university departments such as the Cavendish Laboratory. Many of our customers benefit from the close geographical proximity that the Silicon Fen provides; and several of our partners have a presence in Cambridge and surrounding areas.

But at the same time, the Cambridge Network meeting reminded me that even more could be done to join efforts with Cambridge companies and university departments. Globalization is wonderful, but nothing beats partners next door. So we’ll continue to look to for Silicon Fen collaborations. Which is easy thanks to Cambridge Network, and because there’s not a single mountain obstructing our view …

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Warren.

December 4th, 2009 by Accelrys Team

Like hundreds of scientists around the world, I too was shocked to hear the news about Warren DeLano’s sudden passing away on Nov 3rd. He was young, extremely bright, and had a contagious enthusiasm about his passion: PyMOL, the open source and most widely used molecular visualization tool around.

Axel Brunger and Jim Wells contributed a brief article to this week’s issue of Nature (Structural and Molecular Biology).  I encourage all scientists around the world to read this article: http://www.nature.com/nsmb/journal/v16/n12/pdf/nsmb1209-1202.pdf. I had met Warren personally several times and after reading this article, I know I was privileged to have known him.

Warren DeLano speaking at the Open Source Bioinformatics conference 2005 part of the Annual Meeting of the International Society for Computational Biology (http://open-bio.org/bosc2005/finalProgram/images/ WarrenDelano.JPG).

Warren DeLano speaking at the Open Source Bioinformatics conference 2005 part of the Annual Meeting of the International Society for Computational Biology (http://open-bio.org/bosc2005/finalProgram/images/ WarrenDelano.JPG).

An excerpt from the article (volume 16 number 12 december 2009 nature structural & molecular biology, p1202):

“For Warren, programming was not just a job or a means to another goal—it was like playing a musical instrument. The programs he designed were symphonies in computational space: integrated, complex and elegant at the same time. What’s more, these masterpieces can be played by everyone…
For Warren’s superb thesis, published as a first-author paper in Science entitled “Convergent solutions to binding at a protein-protein interface”
(W.L. DeLano, M.H. Ultsch, A.M. de Vos and J.A. Wells, Science 287, 1279–1283, 2000), he was awarded the annual Julius Krevans Award for the best PhD thesis at UCSF. Not bad for a computational geek.”

Unlike our other blogs, this blog isn’t scientific but is a celebration of a scientist whose contribution to the community is immeasurable.

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If a picture paints a thousand words, can I learn from an Image?

December 3rd, 2009 by Tim Moran

Machine learning continued as a growing theme at this years HCA conference.

This first HCA conference east held in Boston, September of this year, showed promise of the increasing use of machine vision tools. These tools are making their way in to the hands of the biologist for everything from subcellular classification and pattern recognition to predictive mechanism of action based on a multivariate image output. The theme continues to grow and will be a major focus at the upcoming HCA 2010 conference in January, as is evidenced by numerous talks around the subject. Mark-Anthony Bray, Ph.D., Computational Biologist, Imaging Platform, Broad Institute, will talk on quantifying  image-based phenotypes with machine learning algorithms. Peter Horvath, Ph.D., Image Processing Scientist, Light Microscopy Centre, ETH Zurich, will also discuss  machine intelligence both for classification as well as for quality control. Pattern Recognition will be applied to Image-Based Small Molecule Screening Data by John McLaughlin, Ph.D., Scientist & Manager, Biology, Rigel Pharmaceuticals, Inc. Numerous other talks by Acclerys, Novartis and Carnegie Melon, to name a few, will also have repeating themes of learning.  I can’t help but wonder if the growth in this area is due primarily to the need or if the adoption has been increased by the growing  number of informaticians working alongside the High Content Screening biologist.

For some good background on machine learning by sure to follow Dana Honeycutt’s blog postings, here’s a link to get you started. Good Models Require Good Data October 1st, 2009 by Dana Honeycutt, Ph.D.

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Great success at the Chemical & Biological Science & Tech Conference

December 1st, 2009 by Robert Walker

I started the Thanksgiving Week thankful that it was a short week. It needed to be short to recover from the action packed agenda at the 2009 Chemical and Biological Science and Technology Conference in Dallas the week prior. The conference was a huge success on many different levels. Although, the conference has been ongoing for the last few years, this was a first time combination of physical science and medicinal disciplines and to the credit of the conference organizers, it was well done! There were over 1400 people in attendance with over 600 poster presentations and countless oral presentations; however, even with the number of people and logistical challenges that existed, this was one of the best events I have attended (and I have attended a few).

I enjoyed the conference from the perspective that I was able to connect with former colleagues and make new friends (accomplices).  However, the most important aspect for me was hearing about some of the great work that is going into making our country safer. The science and technology is cutting edge and driving innovation in so many different disciplines.

As mentioned in a previous post we were honored to present two posters;

Nancy Miller Latimer presented a poster on “Using Data Pipelining to Analyze Biological Threats: A Biomarker Case Study”.

And

Dr. Nick Reynolds presented a poster on “Applications of nanoscale simulations methods for understanding the structure and mechanisms of chemical sensors”.

Both posters were well received and very applicable to the technology challenges that we face; Dr Reynolds and Ms. Miller Latimer directed and managed the traffic expertly (and there were a lot of people at the presentation).

Over the past few conferences that I have been to, data management and integration is becoming an increasing concern to all the Federal Agencies as more and more data intensive programs come into existence. From new drug and vaccine discovery to biometrics, the data produced for use and reuse is overwhelming legacy systems and there is increasing focus on how to address this challenge.

Addressing this challenge and back to Ms. Miller Latimer’s discussion on Data Pipelining;

She demonstrated “data pipelining”, using Pipeline Pilot™, in a biomarker case study for ALI (Acute Lung Injury). As part of this analysis, Pipeline Pilot was used to analyze and integrate mass spec proteomics data with gene expression data and sequences using data pipelining. Additionally, this study also showed how to automatically mine the literature analysis results for differentially expressed genes/proteins and then publish enterprise-wide interactive solutions via web portals.

To underscore the interest in this integrative and flexible capability, Ms. Miller Latimer’s work was recognized as the best poster overall (over 600 poster were presented). I was proud to be there as she received the award from Colonel Michael O’Keefe, Deputy Director, Chemical/Biological Technologies, Defense Threat Reduction Agency.  Accelrys is proud of Ms. Miller Latimer’s contribution. Well Done!!

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