Molecular BioSystems Blog

MBS Issue 5 online! Focus on Chemical Biology in Asia

10 Apr 2013

Coinciding with the 70^th anniversary of the discovery of streptomycin, Issue 5 puts the focus on chemical biology research in Asia, beginning with an editorial from guest editors Minoru Yoshida, Seung Bum Park and Charles Boone. This issue contains 24 top articles from chemical biologists working in Asia.

Focus on chemical biology in Asia
Minoru Yoshida, Seung Bum Park and Charles Boone
DOI: 10.1039/C3MB90008H

The outside front cover highlights work from Pohang University of Science and Technology on overcoming the difficulties in delivering oligonucleotides to specific tissues using estrone-conjugated siRNAs.

Tissue specific delivery of estrone-conjugated siRNAs
Eun-Kyoung Bang, Eun Mi Jeon, Wanil Kim, Kyung-Ha Lee, Kyong-Tai Kim and Byeang Hyean Kim
DOI: 10.1039/C2MB25258A

A communication from Junko Ohkanda et al. at Osaka University is featured on the inside front cover. The researchers improve the efficiency of protein-protein interaction inhibitors by 200% using 14-3-3 peptides. This article was the subject of a blog post in January, read it here for further explanation.

Chemical ligation of epoxide-containing fusicoccins and peptide fragments guided by 14-3-3 protein
Toshio Maki, Akie Kawamura, Nobuo Kato and Junko Ohkanda
DOI: 10.1039/C2MB25388G

There are several intriguing review articles in Issue 5, including three HOT reviews:

Chemical biology-based approaches on fluorescent labeling of proteins in live cells
Deokho Jung, Kyoungmi Min, Juyeon Jung, Wonhee Jang and Youngeun Kwon
DOI: 10.1039/C2MB25422K

Small-molecular modulators of cancer-associated epigenetic mechanisms
Yukihiro Itoh, Takayoshi Suzuki and Naoki Miyata
DOI:10.1039/C3MB25410K

Synthetic cysteine surrogates used in native chemical ligation
Clarence T. T. Wong, Chun Ling Tung and Xuechen Li
DOI: 10.1039/C2MB25437A

Plus plenty more HOT primary research articles:

Dual-labeled glycoclusters: synthesis and their application in monitoring lectin-mediated endocytosis
Xizhe Tian, Kyung-Hwa Baek and Injae Shin
DOI: 10.1039/C3MB25491G

Innate immunomodulation by lipophilic termini of lipopolysaccharide; synthesis of lipid As from Porphyromonas gingivalis and other bacteria and their immunomodulative responses
Yukari Fujimoto, Atsushi Shimoyama, Akinori Saeki, Naohiro Kitayama, Chika Kasamatsu, Hiroko Tsutsui and Koichi Fukase
DOI: 10.1039/C3MB25477A

Read the issue in full

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HOT review: The paradigm shift in target protein identification methods

02 Apr 2013

By Helen Bache, Development Editor.

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:

Limitations of affinity-based methods
The shift to using chemoreactive groups
Use of photoreactive groups for wider applications
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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HOT article: Modernising Traditional Chinese Medicine

22 Mar 2013

By Helen Bache, Development Editor.

Understanding the active components in traditional Chinese medicines is crucial to standardising and modernising them. In this HOT article, researchers in Beijing use pathway pattern-based prediction to identify active components, gene targets and target interactions in the action of a formula that was used to fight H1N1 during the swine-flu epidemic. Read more »

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Madan Babu awarded 2014 Colworth Medal!

19 Mar 2013

By Helen Bache, Development Editor.

The 2014 Colworth Medal has been awarded to Molecular BioSystems Associate Editor Madan Babu for his exceptional expertise in bioinformatics analysis of protein structure and gene networks.

The Colworth Medal is an annual award from the Biochemical Society, presented to researchers under the age of 35 for their outstanding contribution to biochemical research. This prestigious award has been presented since 1963 with many extraordinary researchers being past recipients, and we are delighted that Madan is the recipient in its 50^th year. This follows on from his Early Career Research Award from the Biochemical Society in 2010.

Madan continues to carry out such outstanding research and lead the Regulatory Genomics and Systems Biology group at the MRC Laboratory of Molecular Biology, Cambridge, UK. He will present his award lecture at the 2014 Biochemical Society conference.

Submit your work to Madan Babu’s editorial office today via our simple online submissions system: http://mc.manuscriptcentral.com/mb.

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In-depth study of inhibitors of Schizophrenia-implicated enzyme PDE10A

15 Mar 2013

By Helen Bache, Development Editor.

Phosphodiesterase PDE10A is an enzyme is highly expressed in certain neurons of the brain and has been identified as a potential target for schizophrenia treatment. In this HOT article, researchers in Dalian and Weifang, China, explore the mechanism of quinolone derivatives that inhibit PDE10A via an in silico analysis.

PDE10A is able to inactivate the messaging of nucleotides cAMP and cGMP, which are implicated in the activation of dopamine receptors on neurons in the brain. Therefore, inhibiting PDE10A could be a route to preventing the disruption of these dopamine receptors in Schizophrenic patients.

In this article, Yan Li et al. undertake 3D-QSAR statistical modelling, molecular docking and molecular dynamics simulations to carry out the most in-depth study so far of the inhibition mechanism of 116 quinoline derivatives on PDE10A. They make several conclusions to aid in the future design of more effective inhibitors and reduce time to drug development. The study included a look at hydrogen bonding, concluding that H-bonds are vital for determining binding affinity to PDE10A.

This HOT article recommended by the referees is free to access for the next 4 weeks*. Read the full detail to discover the insights from this thorough study:

Inhibition mechanism exploration of quinoline derivatives as PDE10A inhibitors by in silico analysis
Qian Wu, Qingping Gao, Huanmei Guo, Dan Li, Jinghui Wang, Weimin Gao, Chunxiao Han, Yan Li and Ling Yang
DOI: 10.1039/C2MB25501D

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

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HOT review article: Redefining the essential gene set of model organism Bacillus subtilis

11 Mar 2013

By Helen Bache, Development Editor.

In this high quality review article, Jörg Stülke and colleagues at Georg-August-Universität Gottingen, Germany, take a fresh look at the important genes and proteins of Bacillus subtilis, a commonly used Gram-positive model organism that was one of the first to have its essential gene set to be studied. This review uses B. subtilis to highlight the integral problems with defining the essential gene set of an organism.

The original study was carried out 10 years ago and more detailed analysis has altered the view of which genes are essential; in January 2013 261 essential genes were identified as oppose to 271 in 2003. 31 thought to be essential in 2003 are now not regarded as such and 20 new essential genes were identified this year. 99 of the 261 are involved in protein synthesis, secretion and quality control. Just 6 have unknown functions.

This review covers:

The definition of an essential gene
Obligatory versus facultative essential genes
Are the glycolytic enzymes essential?
Dispensable ribosomal proteins
Unknown and unusual essential functions

This review highlights some surprising differences between what was thought back in 2003, what was expected and what we know now from more detailed analysis. It’s been made free to access for the next 4 weeks* and more information can be gleamed from viewing the essential genes at subtiwiki.com by scanning the QR code.

Essential genes in Bacillus subtilis: a re-evaluation after ten years
Fabian M. Commichau, Nico Pietack and Jörg Stülke
DOI: 10.1039/C3MB25595F

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

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Themed Issue 4 online now! Reviews from the Editorial and Advisory Board members

05 Mar 2013

By Helen Bache, Development Editor.

The fun outside front cover features the contribution of Seung Bum Park, MBS Associate Editor based at Seoul National University, Korea, to this month’s special issue featuring work from many of our Editorial and Advisory Board members. Seung Bum Park and colleagues review methods for identifying the targets of bioactive small molecules, the difficulties faces and the new shift towards covalent bonds via use of chemoreactive groups changing the nature of target protein identification.

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

Editorial Board member Ulrike Eggert and colleague Xin Zhang review the more unusual, overlooked functions of G protein-coupled receptors in cells, such as in membrane trafficking and cell division in addition to their more widely known roles in cell signalling.

Non-traditional roles of G protein-coupled receptors in basic cell biology
Xin Zhang and Ulrike S. Eggert
DOI: 10.1039/C2MB25429H

Wilfred Weber, also a member of the Editorial Board, and Jonrad Muller at University of Freiburg, Germany, provide a fascinating look at how we can control biological processes in mammalian cells by the manipulation of light using optogenetic tools in their review article:

Optogenetic tools for mammalian systems
Konrad Müller and Wilfried Weber
DOI: 10.1039/C3MB25590E

These are just a couple of examples of the high quality review articles produced by board members past and present for this themed issue. Have a look at the whole issue here to see the ones that are of interest to you.

This issue also still contains plenty of high quality primary research articles in chemical biology, -omics and systems biology, including several HOT communications and articles such as:

Identifying subcellular localizations of mammalian protein complexes based on graph theory with a random forest algorithm
Zhan-Chao Li, Yan-Hua Lai, Li-Li Chen, Chao Chen, Yun Xie, Zong Dai and Xiao-Yong Zou
DOI: 10.1039/C3MB25451H

Protein intrinsic disorder in the acetylome of intracellular and extracellular Toxoplasma gondii
Bin Xue, Victoria Jeffers, William J. Sullivan and Vladimir N. Uversky
DOI: 10.1039/C3MB25517D

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Challenges in Chemical Biology (ISACS11) – Oral Abstract Deadline 15 March 2013

05 Mar 2013

By Helen Bache, Development Editor.

This is your last chance to submit an oral abstract for Challenges in Chemical Biology (ISACS11) which will be held on 23-26 July in Boston, USA.

Act before the deadline of Friday 15 March 2013 to take advantage of this exceptional opportunity to showcase your work alongside researchers from across the globe.

For details of speakers and conferences themes, please visit the dedicated website.

The second ISACS event of 2013 is building on the successes of ISACS5: Challenges in Chemical Biology.

The themes of ISACS11 include topics that are extremely relevant to readers and authors of Molecular BioSystems, such as chromatin biology & epigenetics, cancer biology, systems biology. The aim is to discuss the latest applications of chemical tools and techniques for probing biological problems.

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Hot Review: Directed evolution for synthetic genetic circuits

27 Feb 2013

By Helen Bache, Development Editor.

Directed evolution is a method normally used for protein engineering, but in this HOT review, Yolanda Schaerli and Mark Isalan at Universitat Pompeu Fabra, Barcelona, Spain, highlight the ways in which it can be used to design novel gene networks.

The challenges of synthetic biology mainly revolve around the fact that our knowledge of complex natural biological systems is incomplete. Therefore, creating biological networks is often a tedious trial-and-error process. Using the principles of directed evolution can be a tool to bridge the gaps. In protein engineering, this means from a large library of diverse individuals only those with the desired properties survive the rounds of screening and selection; the same principle is now being applied to biological circuits.

This review includes:

- Choice of library size and where to introduce diversity in the network in regulatory components such as promoters and ribosomal binding sites, or protein components

- Screening for desired variants using fluorescence and flow cytometry

- Selection methods, including tailoring the selection to the application and careful analysis of the results.

Concluding remarks are centred around the emerging technologies which will enable more practical options for screening of genetic circuit libraries and cellular networks where each cell carries out a simple task contributing to the complex function of the group.

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies
Yolanda Schaerli and Mark Isalan
DOI: 10.1039/C2MB25483B

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

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