Archive for the ‘Board News’ Category

Dr Lyn Jones joins the MBS Editorial Board

Lyn Jones Editorial Board Member of Molecular BiosystemsEveryone at Molecular BioSystems would like to warmly welcome Dr Lyn Jones to his new role on the journal’s Editorial Board.

Lyn received his undergraduate education at the University of Bath and then completed PhD studies with Prof. Alan Armstrong at the University of Nottingham in synthetic organic chemistry. He then started his post doctorate research with Prof. Kim Janda at The Scripps Research Institute, California in the area of chemical biology. In 2001, he joined Pfizer in Sandwich, UK as a medicinal chemistry team leader and his contributions to the early clinical portfolio were recognised with the inaugural Royal Society of Chemistry Young Industrialist of the Year Award in 2009.

He recently transferred to Cambridge, Massachusetts to lead the Chemical Biology and Rare Diseases Chemistry groups in Pfizer. His research interests include the development of novel chemoproteomic technologies that report on target engagement in intact cells, and the use of medicinal chemistry to advance biotherapeutic modalities. He is a Fellow of the Royal Society of Chemistry (FRSC) and the Society of Biology (FSB), and is an elected member of the Chemistry-Biology Interface Division of the RSC. Recently, he was also a Guest Editor for a themed issue on Chemical Biology for Target Identification and Validation in our sister MedChemComm.

“It’s an honour to join the board of this prestigious journal, which has become essential reading for those working at the interface of chemistry and biology. In particular, I’m very keen to see the inevitable growth in the application of chemical biology research within the drug discovery setting, and MBS is ideally poised to share these advances with a wide audience.” – Lyn Jones

Some of Lyn’s recent publications include:

Aryloxymaleimides for cysteine modification, disulfide bridging and the dual functionalization of disulfide bonds
Chem. Commun., DOI: 10.1039/C4CC02107J, Communication

Understanding and applying tyrosine biochemical diversity
Mol. BioSyst.,  DOI: 10.1039/C4MB00018H, Review Article

Target validation using in-cell small molecule clickable imaging probes
Med. Chem. Commun., DOI: 10.1039/C3MD00277B, Review Article

Chemical motifs that redox cycle and their associated toxicity
Med. Chem. Commun., DOI: 10.1039/C3MD00149K, Concise Article

Biotherapeutics
Recent Developments using Chemical and Molecular Biology
Lyn H Jones (Editor), Andrew J McKnight (Editor)
ISBN (print): 978-1-84973-601-5

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Introducing Editorial Board member Michael Washburn

We’re extremely pleased to welcome Michael Washburn as the most recent addition to the Molecular BioSystems Editorial Board and in this blog we like to introduce him and his research vision:

Michael Washburn

Michael Washburn received his B.A. in chemistry from Grinnell College (Iowa, USA).  He then started his graduate studies at Michigan State University and received a Ph.D. in 1998 under the supervision of Prof. William W. Wells.  He then conducted post-doctoral training in proteomics in the Department of Molecular Biotechnology at the University of Washington with Dr. John R. Yates, III.   In 2000, he moved to San Diego with Dr. Yates and worked at the Torrey Mesa Research Institute as a staff scientist and a senior staff scientist.  In 2003, he started his independent career as the Director of Proteomics at the Stowers Institute for Medical Research in Kansas City, MO, USA.   His research interests are in quantitative proteomics and systems biology with a particular focus on the analysis of transcriptional regulatory complexes and chromatin remodeling complexes and their protein interaction networks.  He has published more than 140 scientific papers to date.

Below, Dr. Washburn shares his view on quantitative proteomics, systems biology, and the research areas he is working in currently:

RESEARCH VISION: Remarkable advances in mass spectrometry and computational analysis over the last decade have resulted in the emergence of powerful proteomics technologies.  Furthermore, protein mass spectrometry and proteomics have become more and more of a quantitative science.  This has resulted in proteomics analysis having a growing impact on biological and biochemical research.  In particular, state of the art and innovative approaches are enabling fascinating studies into protein complexes and protein interaction networks providing information and insights that were not previously possible.  We are now in a period where protein interaction networks can be defined, and the technology exists to discern the dynamics of protein interaction networks and protein complexes when stimulated or disrupted.  My research group at the Stowers Institute for Medical Research uses innovative and state of the art computational and quantitative proteomics approaches to study protein complexes and protein interaction networks.  We also continually develop novel proteomic methods that we then apply to this research.  Currently we couple these studies to advanced imaging and genomic techniques to gain deeper insights into the function of novel proteins in complexes and the dynamics of protein interaction networks after stimulation or disruption. 

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HOT review: The paradigm shift in target protein identification methods

This HOT review article from MBS Associate Editor Seung Bum Park and colleagues at Seoul National University, Korea, reviews the changing methods used for target protein identification.

This review covers:

  1. Limitations of affinity-based methods
  2. The shift to using chemoreactive groups
  3. Use of photoreactive groups for wider applications
  4. Increased specificity of Fluorescence difference in 2D Gel Electrophoresis (FITGE)

They conclude that each approach has its advantages for different applications and no one method is dominant. However, there has been an obvious move from non-covalent to covalent-based methods, with increasing specificity and general applicability leading to higher success rates.

Read the detailed review of the pros and cons of current methods and where the latest technology may take us in this HOT review, which is free to access for the next 4 weeks*:

From noncovalent to covalent bonds: a paradigm shift in target protein identification
Jongmin Park,  Minseob Koh and Seung Bum Park
DOI: 10.1039/C2MB25502B

 *Free access to individuals is provided through an RSC Publishing personal account. Registration is quick, free and simple

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Introducing our new Associate Editor – Professor Seung Bum Park

We at Molecular BioSystems are very pleased to announce our newest Associate Editor – Professor Seung Bum Park. Professor Park is an Associate Professor in the Chemistry Department at Seoul National University, and joined the team at Molecular BioSystems in May.

Seung Bum Park received his B.S. in chemistry and M.S. in organic chemistry at Yonsei University (Seoul, Korea). After one and half years of military service in the Korean Air Force, he started his graduate studies at Texas A&M University and received a Ph.D. in 2001 under the supervision of Prof. Robert F. Standaert. He was then appointed as a HHMI Postdoctoral Research Fellow in the Department of Chemistry and Chemical Biology at Harvard University (with Prof. Stuart L. Schreiber). In 2004, he started his independent career as an Assistant Professor, and was promoted to an Associate Professor with tenure in the Chemistry Department at Seoul National University in 2008. In 2009, he spent his sabbatical as a visiting Professor at the Scripps Research Institute, San Diego, USA (with Prof. Peter Schultz). His research interests range from chemical biology, diversity-oriented synthesis, combinatorial chemistry, and bioorganic/organic chemistry, to medicinal chemistry, target identification, and fluorescent bioprobes. He has published more than 120 scientific papers, 3 books and filed 25 patents so far.

Below, Professor Park shares his views on chemical biology, and the research areas he is working in currently:

In the last decades, a new terminology has emerged from the interface of chemistry and biology, known as Chemical Biology. The unique basic concept of this field is the collaborative approach to answer mysterious biological questions through the use of chemical probes. Chemical biology involves the study of living systems which aids our understanding of the molecular basis of complex phenotypes. It assumes that small organic molecules can selectively modulate the cellular network of complex interactions and cause phenotypic changes. Actually bioactive small molecules have been used in biological research to induce dramatic cellular phenotypes and provide insights into biological processes, even without knowing their protein targets. In this basic research, bioactive small molecules (or chemical probes) can serve as an enhancer/inhibitor of specific biological events. The ever-increasing demand for molecular agents possessing desirable properties places a high priority on the development platform enabling access to such bioactive small molecules. My research group at the Chemistry Department of Seoul National University, under the title of “Chemical Biology Laboratory”, has been focused on interdisciplinary research for the efficient discovery of novel bioactive small molecules using various technologies such as molecular diversity using pDOS strategy, high throughput/high content screening using fluorescent bioprobes (glucose bioprobe and Seoul-Fluor-based bioprobe), medicinal chemistry using rational design, combinatorial chemistry, chemoinformatics, and target identification (FITGE technology).

We are very pleased to welcome Professor Park to the Molecular BioSystems Editorial Board as Associate Editor and feel that this is another step forward to further meeting the needs of our authors.

If your research falls under Professor Park’s expertise, why not submit your next article to him?

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Interview: Rising research

Charles Boone talks to Laura Howes about yeast, Canada and hockey 


Charles Boone is a professor at the University of Toronto, Canada. His research focuses on developing an automated approach for genetic analysis in yeast. This work has enabled the mapping of genetic networks on a large-scale and the determination of the function of all genes in a yeast model system. The function of many yeast genes is conserved in humans and this work has the potential for discovery of therapeutic drug targets. He is the chair of the
Molecular BioSystems editorial board. 


When did you decide you wanted to be a scientist?

I really liked doing science, and when I went to university I tried to get summer jobs in science. But the reality is I just loved doing research. Basic science was the fun part – figuring out how life works. When I go to hang out with my hockey team, they all wish that they were professors. At one level or another, they all do cool things too but they realise that the world of science gives you a lot of freedom and nowadays there’s a worldly aspect to it. But I didn’t know that when I started, so the bottom line is that science was interesting and something I really liked.

You started as a chemist, how did that come about and how did you then move to biology?
When I went to university I decided to study things I’m not very good at to learn more, so I studied Maths and Chemistry. I’m not a mathematician but by the end of my math course I was in classes with the geniuses. They’d be reading a book in class and I’d be trying to figure out what fuzzy logic was. I really liked chemistry but I’m like those guys that were looking for the chemical basis of life. Once I’d seen what you can do with microbiology, I thought it was really exciting so even though we didn’t have much of that at our university at the time, once I read about it I had no problem switching over straight away.

I know several people who’ve done the move from chemistry to biology, I think the biology to chemistry switch is probably more difficult?
There’s probably some problems making the shift either way. I don’t have the best grounding in some bits of biology and in some of the breadth of biology I’d like. But I’d agree that generally biologists don’t shift to being mathematicians or chemists. Chemistry is a major foundation of almost all sciences so that may make it easier.

Your work is in yeast genomics, why did you choose to research this topic?
Yeast is a major model system. I went into it by chance, because going from chemistry to biology I had to find someone to take me into their lab as most of them were sceptical that this chemist could do biology. But I have to admit that when I started working on yeast I realised that it’s an almost perfect organism for a transition from chemistry to biology because you can do almost anything with yeast. And it’s so simple – it’s a single cell so you don’t have to worry about development, at least in a major way (there are developmental programs) and you don’t have to worry about different tissues.

Can you tell us more about what you do in your lab?
There is a fairly large community working in yeast molecular genetics and genomics – about a thousand labs around the world. And there’s an incredible database called the sacaromyes genome database that houses all the information. The idea is to understand how yeast works at the level of almost every nucleotide in the genome and one of the ways we do that is to delete each gene individually. This has defined 1000 of the 6000 genes to be essential in yeast – so if you delete an essential gene the yeast dies. This indicates that most genes in eukaryotic organisms are non essential and we think one of the reasons for this is that pathways in the cell are wired with many back up pathways for any individual essential process in the cell. So there are many ways to solve a particular problem that the cell may encounter and we try to decipher which pathways are working together to solve essential functions and come up with a wiring diagram for the cell.

To do this we have identified all possible double mutants of yeast – which comes to the order of 18 million. We’ve developed a system that we call synthetic genetic array analysis that allows you to take a gene and either delete it if it is non essential or make a partially functional version if it is essential. Then make all possible double mutants with that gene and score if the mutant dies or has a fitness phenotype than is worse than we’d expect by combining the two single mutations, so it’s quantitative.

We call that a genetic interaction – so we’re scoring genetic interactions and have come up with our genetic interaction map. We hope to link each gene to those of related function and sort all the genes in a cell into clusters that work together and thereby provide a global view of how the cell is wired functionally.

Million dollar question – why do we care about yeast genetics?
Because it is a fundamental eukaryotic cell and if we can understand how it works we’ll have a much better understanding of how human cells or higher order cells in a eukaryotic organism work and then the genetic network problem is important because it is a model for the genotype to phenotype problem where if you sequence an individual and you know their variations, which combinations of mutations or alleles of genes control pathways and lead to inherited phenotypes. And no-one knows how to solve that problem beyond just the single gene.

What would you be if you weren’t a scientist?
There are two things I think I would like to be. One is an explorer, but it’s such a drag that the world’s been figured out by all those great British explorers because that would have been fun. And being a hockey player would have been way up on the list but maybe not as realistic as being a scientist. But I think the science path I took is related to exploring because it’s a great avenue for coming up with dreams and going out and trying to find them.

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Award for Molecular BioSystems Board Member

Congratulations to Molecular BioSystems Editorial Board member, Dr Madan Babu, who has been awarded the 2011 Balfour Lectureship by the Genetics Society. This honour, awarded to a young scientist with less than 10 years’ postdoctoral experience, adds to several other recent awards received by this Cambridge scientist.

In November last year Madan was selected as an EMBO young investigator. EMBO’s Young Investigator programme identifies some of Europe’s most promising and creative young life scientists and out of the 17 winners in 2009 Madan was one of the youngest at 29 years of age.

When appointed to the Cambridge MRC Laboratory of Molecular Biology in 2006 Madan was one of the youngest independent group leaders and he now leads the Computational Systems Biology Group at the LMB. He also holds a fellowship at Darwin College, Cambridge. His research focuses on the structural, functional and evolutionary constraints that shape biological systems.

Further Congratulations will be in order early next year when Madan delivers the Molecular BioSystems Award lecture during the American Chemical Society’s Spring meeting in Anaheim, California.

Madan Babu has been a member of the Molecular BioSystems Editorial Board since 2008. He recently edited a special issue of the journal on the theme of Computational and Systems Biology .

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