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J Chem Biol. 2009 November; 2(4): 203–208.
Published online 2009 October 14. doi:  10.1007/s12154-009-0030-x
PMCID: PMC2763146

Welcome to this latest edition of the JoCB Bulletin containing items of information for the Chemical Biology Community

We are pleased to announce that the Journal of Chemical Biology has, in just its second year of publication, been included in PubMed.

We hope that this will encourage readers to submit articles at the interface of the physical and life sciences and would welcome any contributions that workers in this area might want to share in this section concerning studentships, courses or conferences, book reviews or news about recent publications that are of interest for our co-workers corner.

Please send to

Dr C A Rosser

Rye St Antony

Pullens Lane

Oxford, OX3 0BY

email: crosser@ryestantony.co.uk

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GRADUATE STUDIES IN BILBAO, SPAIN

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The University of the Basque Country offers Master and PhD degrees in Molecular Biology and Biomedicine. The one-year Master degree (60 ECTS) consists of lecture courses (30 ECTS) and a research project (30 ECTS).

No knowledge of Spanish required.

MSc in Chemical Biology

Subject to approval by Cardiff University, this course is expected to be available from September 2009.

Duration

1 year full-time, 3 years part-time.

Entry Requirements:

Suitable for graduates in chemistry or a related discipline, e.g. chemistry, biology, microbiology, chemical engineering, physics, pharmacy, pharmacology and biochemistry, with a First or Second class UK Honours degree or equivalent.

Applicants whose first language is not English will be required to demonstrate competency in English language (at least 6.5 in IELTS or a TOEFL score of 580 or 232 CBT).

This programme is currently Subject to Validation. Applications can be submitted at this point using our paper-based application form, which you can download from www.cardiff.ac.uk/postgraduate/pgapply.

Once the programme has been made available for online applications, you can access the Apply Online link from the above webpage.

For further enquiries, please contact:

Dr Thomas Tatchell

Tel: +44 (0)29 2087 0759

Email: TatchellT@cardiff.ac.uk

http://ecm25.ecanews.org/

The scientific programme will be prepared jointly by the European Crystallographic Association and the leading persons of the Special Interest Group network. The congress will cover all topics of crystallography, including Biological and Macromolecular Crystallography, Materials and Minerals, Chemical Crystallography, Experimental and Computational Techniques and Fundamental Crystallography. Internationally renowned speakers will be invited to present these topics, in order to create an enjoyable scientific atmosphere for interactive discussions.

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http://sebbm.bq.ub.es/XXXIICongreso/

ISABC 10

10th International Symposium on Applied Bioinorganic Chemistry

25–28 September, 2009 Debrecen, Hungary

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http://www.isabc10.unideb.hu

The symposium is organized by the University of Debrecen.

e-mail:isabc10@dragon.unideb.hu

NANO2009

Perspectives in nanoscience and nanotechnology

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San Sebastian, Spain, 28–30 September 2009.

Info at: http://atombyatom.nanogune.eu

51st International Conference on the Biosciences of Lipids

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Bilbao, Spain

7–11 September 2010

Lipids and Biomembranes

Preliminary Scientific Programme:

  • Physical chemistry of lipids
  • Lipids and biomembranes
  • Bioactive lipids and lipidomics
  • Lipids in health and disease
  • Lipid-protein interactions and lipid trafficking
  • Plant lipids
  • Microbial lipids

The next ICBL will be held in Regensburg, Germany, 1–5 September 2009 (see picture below)

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The World of ICBL

ICBL is a conference format designed for scientists with common interest in lipid research. It was founded more than 50 years ago and is a prominent forum for the exchange of ideas, communication of novel developments and discussion of a broad variety of aspects related to lipid bioscience. ICBL is proud of attracting colleagues from all continents to the frontiers of lipid research presented and discussed during the conferences. Another major aim of ICBL is supporting research of young scientists, giving them the opportunity to meet renowned scientists, and thus providing the scientific inspiration for future careers in lipid research.

The Conferences

Each year ICBL offers the lipid community to meet at venues organized by groups representing a center of lipid research. Most conferences are held in Europe, but in its long-standing history ICBL has also visited Israel, Japan and the United States. During these conferences, experts in the field present and discuss most recent developments in lipid bioscience. Traditionally, the warm and friendly atmosphere of ICBL has always been a melting pot for fruitful collaborations between laboratories and close personal relationships. Attendants also enjoy an appealing social program and the culture of the host cities which includes sightseeing tours for accompanying persons, and the traditional half day excursion and congress dinner for all.

More information about ICBL 2009 and the upcoming events can be found on this web site. www.icbl.unibe.ch

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September 19–20, 2009, The Royal Sonesta Hotel, Cambridge, MA, USA.

Scientists in both industry and academics seek new approaches for finding the next generation of therapeutics. The 2009 symposium will explore how chemical biology is opening up new avenues for identifying therapeutic targets and discovering small molecule drugs. This two-day meeting will address the following topics, across a range of diseases:

  • Cell-based screening and target deconvolution
  • Targeting pathways and systems
  • Expanding druggable chemical space
  • Expanding druggable targets

If you want us to send you further information about the meeting, send an email to: nchembioconf@nature.com

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The Golgi Apparatus

State of the art 110 years after Camillo Golgi’s discovery

Mironov, Alexander A.; Pavelka, Margit (Eds.)

Springer, Wien

ISBN: 978-3-211-76309-4

Hardcover, 716 pages, 2008

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Last year marked the 110th anniversary of the discovery of the Golgi apparatus by Camillo Golgi. This book reviews the history and recent achievements in understanding this organelle and describes the cell physiology with a strong emphasis on the role of the Golgi apparatus in intracellular transport and molecular mechanisms of morpho-functional organisation with a focus on mammalian organisms. It is intended for a wide audience, including students, cell biologists, histologists and scientists working in many other fields. The editors’ main idea of the book is to give a broad and detailed overview of the Golgi apparatus from different points of view, especially considering the problem of mechanisms of traffic. For this reason each chapter is written by a different author and thus each one is independent of the other.

The book has four main chapters, the first of which is a relatively short introduction to the history of the discovery of the Golgi apparatus and its morphological and functional basics. In view of the target audience, this section is rather short and lacks comprehensible pictures as a means of illustrating and visualising the structural and functional basics of the Golgi apparatus. A lot of specific technical terms are used without explanation, although these are explained in later chapters.

Then follow the core chapters introducing the main machineries involved in the secretory pathways, including SNAREs, Rabs, COP I and II, ARFs, ARFGEFs, ARLs, COG, TRAPP, dynamin and cortactin, Golgi enzymes and sugar transporters. Subsequently the respective transport steps are presented in detail. Mechanisms of regulated secretion and especially of mucin granule formation are explained later. These two core parts of the book are very comprehensive and detailed and can be perceived as review articles.

The book finishes with the description of some peculiarities of intracellular transport in different organisms and the endomembrane ultra structure and dynamics in yeast and models of Golgi evolution are discussed. For people interested in the plant or yeast Golgi apparatus other books might be more appropriate as this section is rather short.

In general this is a very good and comprehensive book with the latest findings in Golgi apparatus and trafficking research. This book will be appreciated by young postgraduate researchers in the field of cell biology, histology and membrane trafficking processes. Even experts in the field will profit from this summary of new and up-to-date information, however for scientists with less expertise a few more illustrations would be helpful. Furthermore, researchers expecting to learn about methods and techniques will be disappointed and undergraduate students will not profit so much from this book due to its lack in basics and its focus on detail. Also the index is rather cumbersome. Most of the indexed words are referenced to such a large number of different pages (more than 30 in many cases, more than 80 in some), so that looking them up, if you are in search of specific information, will be a long winded process.

Marie Lis Kirsten, PhD student

Chemical Biology Centre, Imperial College London, SW7 2AZ, United Kingdom

email: marie.kirsten06@ic.ac.uk

Chemistry for Pharmacy Students—a book review from a student’s perspective

Chemistry for Pharmacy Students

Satyajit D Sarker, Luftun Nahar

John Wiley and Sons Ltd, West Sussex, England

ISBN: 978-0-470-01781-4

Paperback, 396 pages, 2007, £29.95

Hardback, 396 pages, 2007, £80.00

“Chemistry for Pharmacy Students” is a general, organic and natural product chemistry textbook tailored for the pharmacy and pharmaceutical science student. The book opens with an overview of chemistry’s role in modern life, with particular emphasis on medicinal applications. Chapter 2 introduces the fundamental concepts of atomic structure and chemical bonding, highlighting the significance of each in drug-receptor interactions. The text then moves on (Chapters 3–4) to discuss the topics of stereochemistry and organic functional groups, emphasizing the importance of each in determining drug action and toxicity. The final chapters (5–6) introduce various organic reactions focusing on their significance in drug discovery and natural product chemistry.

Each chapter commences with bullet point learning objectives, allowing the reader to see what they will encounter as the chapter progresses. Information is provided in a clear manner, and good use is made of diagrams and tables, helping to explain the key concepts and aid understanding. In particular, the use of flow diagrams in chapter 4 is very useful, guiding the reader through functional group inter-conversion. The main text provides an informative introductory section, which leads the reader through the basics and concludes by emphasizing the medicinal applications. Chapters close with a recommended reading section, which is highly useful for any reader keen to learn more on the subject presented.

The authors adopt a writing style which is clear and to the point, avoiding jargon when possible, and topics are logically presented with a minimum of fuss. Nothing is dwelt on at length, but nevertheless the key points are covered. This approach has delivered a textbook written at a level suitable for non-chemistry students.

This textbook in my opinion would have benefited from incorporating a chapter covering basic spectroscopic techniques used in chemical identification. Topics such as nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) would have been a welcome accompaniment. Such techniques are fundamental in the natural product drug discovery processes, providing key information on chemical structure. However, this omission does not detract from the book, which remains a concise, well written general chemistry text.

This book has succeeded in covering the basic chemistry essentials required by the pharmaceutical science student. With a price tag of £29.95 the undergraduate reader, be they chemist, biologist or pharmacist will find this an interesting and valuable read.

Neil Wilson, PhD student, Department of Chemistry, Imperial College London, SW7 2 AZ, United Kingdom.

Email: neil.wilson06@imperial.ac.uk

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A synthetic protein selected for ligand binding affinity mediates ATP hydrolysis

Chad R. Simmons et al.

ACS Chemical Biology 2009, Vol. 4. No. 8, 649–658

Researchers from Arizona have carried out experiments to begin to understand how the first primordial enzymes evolved in the primordial soup, which existed billions of years ago. Being able to create simple enzymes from de novo protein sequences, a situation akin to that which occurred in the primordial soup, will be fundamental for the field of synthetic biology.

6 × 1012 random 80 amino acid sequences were synthesised and assayed for their ability to bind to ATP. A number of these proteins bound tightly to ATP and were noted to be dissimilar in sequence to any proteins in the NCBI protein sequence database. The protein sequences were optimised for their affinity to ATP and this resulted in a lead protein, termed Protein DX, which bound to ATP with a Kd of 250 nM.

An X-ray crystal structure of Protein DX and ATP was determined to 1.9 Angstrom resolution. However the researchers were surprised to see that the structure revealed Protein DX bound to ADP, not ATP, in an unusual bent conformation, unlike any other ATP binding proteins. It was deduced that Protein DX was acting as an enzyme to catalyse the hydrolysis of ATP to ADP. Bridging of a water molecule to Tyr 43 of Protein DX facilitated this reaction. Mutating Tyr 43 to Phe, to abrogate the interaction with the water molecule, resulted in an inactive Protein DX enzyme, which was crystallised with ATP, instead of ADP.

This research has shown a design free method, which has created a novel short protein sequence with accidental enzymatic activity. It is suggested that it may not be that much harder for a protein to catalyse an enzymatic reaction, than to simply bind to its ligand, which may explain how the first enzymes came to be.

Kate Bowman

Imperial College

London SW7 2AZ

UK

Identification and characterisation of posttranslational modification-specific binding proteins in vivo by mammalian tethered catalysis

Tanya M. Spektir and Judd C. Rice

PNAS 2009, Vol. 106, No. 35, 14808–14813

Researchers from the University of Southern California Keck School of Medicine have created an important biological tool to discover novel proteins, which bind to posttranslationally modified proteins. Posttranslational modifications (PTMs) provide high affinity and specificity binding sites for the binding of PTM-specific binding proteins (PTMBPs). Since many proteins can contain PTMs and indeed require them for important biological processes such as downstream signalling cascades, it is important that these are researched.

The researchers have developed an in vivo tool termed mammalian tethered catalysis (MTeC). The protein of interest is cloned into an MTeC bait plasmid, along with a tag for purification and an enzyme, which will catalyse the PTM on the protein. The plasmid is then transfected into mammalian cell lines or potentially primary cell cultures and the protein is expressed and modified by the enzyme. PTMBPs, which bind to the PTM protein, can then be determined by affinity purification of the tagged protein and mass spectrometry. The researchers hope that this direct method will allow the discovery of novel protein binding partners and the role of PTM in the binding of interacting proteins.

As a proof of principle, experiments were carried out using the histone H3 lysine 9 (H3K9) protein, which can be methylated by a methyl transferase enzyme. Both enzyme and substrate were cloned into the MTeC Bait plasmid and transfected into HEK-293 cells to allow expression and methylation of H3K9. Panning for PTMBPs was achieved and the complex was purified. It was determined that endogenously expressed heterochromatin protein HP1β bound selectively to H3K9, when methylated.

The authors have developed an exciting in vivo tool, which can be used in a cellular context to mimic the physiological conditions and interactions, which may occur. It is plausible that the effect of other PTMs such as ubiquitination can also be studied by this method.

Kate Bowman

Imperial College

London SW7 2AZ

UK


Articles from Journal of Chemical Biology are provided here courtesy of Springer-Verlag