Archive for the ‘News’ Category

The name of the game is…game theory!

In a review by Bohl and colleagues, which appeared in the August issue of Molecular Biosystems, the principles of game theory are applied to subcellular macromolecules such as RNA, DNA and proteins. The authors recast molecules as “players” who use various strategies to achieve the goals of their host cell/organism, or selfishly, their own goals. We can “consider the result of some mutations or epigenetic modifications as changes in strategy”.

From an evolutionary standpoint the overall goal of an organism is to reproduce. Therefore, any macromolecules that affect reproduction can be considered players. This is especially true of DNA, which can be considered successful if it is able to replicate. Typically we think of genes which persist in a population as beneficial to the host organism, i.e. if a gene were detrimental, that organism would be less likely to reproduce and the gene would disappear from the population. These genes would be said to cooperate in order to promote the success of the carrier organism. However, genes can also act in their own self interest, and be detrimental to the host.

The authors describe three ways for genes to be “selfish”, interference, overreplication and gonotaxis. Interference is the gene preventing the transmission of other genes to the daughter cells, thus increasing its own chances of transmission. The gene can also replicate more than once in a cycle, using overreplication to achieve the same goal. Gonotaxis is more complicated, in that the genes have to avoid being sequestered into non-functional polar bodies during meiosis (see Figs. 1-3 below for diagrams).

InterferenceOverreplication

Gonotaxis

Interestingly, genes that are typically selfish can actually be beneficial in some circumstances. Some bacteria have toxin genes that may have been useful to avoid predators in some circumstances. In the absence of a need for toxin, the cells express “anti-toxin” as a control. Also, jumping genes are sometimes viewed as parasitic because they are usually not crucial to the survival of an organism. However, in the case of arabidopsis, a lack of the “DAYSLEEPER” jumping gene causes growth defects.

Some of the same reason that DNA can be considered players also apply to proteins. For protein complexes in particular the authors consider a game with two players, where the goal is to form a bond. Each protein can be either flexible or rigid. If both are rigid, binding is difficult, and depends on an exact matching of shapes. If both are flexible then binding is easy, but the resulting complex will lack a defined shape. Therefore, the best outcome requires one protein to be rigid, and one to be flexible. This model fits well with recent findings (cited in this paper) of unstructured/disordered regions of proteins which form secondary structure when binding to another protein (induced fit model, see Fig. 4 below).

Induced Fit Binding Model

The ideas of game theory as presented by Bohl et al. are best applied to information encoding macromolecules, such as RNA, DNA and proteins. These principles can be applied to common genetics questions such as “jumping genes”, as well as understanding the activity of disordered proteins.

Evolutionary game theory: molecules as players

Katrin Bohl, Sabine Hummert, Sarah Werner, David Basanta, Andreas Deutsch, Stefan Schuster, Gunter Theißen and Anja Schroeter

Anja Schroeter webpage at Friedrich-Schiller-University Jena (page not in English!)

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Take 1…minute for chemistry in health

Can you explain the importance of chemistry to human health in just 1 minute? If you’re an early-career researcher who is up to the challenge, making a 1 minute video could win you £500.

The chemical sciences will be fundamental in helping us meet the healthcare challenges of the future, and we are committed to ensuring that they contribute to their full potential. As part of our work in this area, we are inviting undergraduate and PhD students, post-docs and those starting out their career in industry to produce an original video that demonstrates the importance of chemistry in health.

We are looking for imaginative ways of showcasing how chemistry helps us address healthcare challenges. Your video should be no longer than 1 minute, and you can use any approach you like.

The winner will receive a £500 cash prize, with a £250 prize for second place and £150 prize for third place up for grabs too.

Stuck for inspiration? Last year’s winning video is a good place to start. John Gleeson’s video was selected based on the effective use of language, dynamic style, creativity and its accurate content.

The closing date for entries to be submitted is 30 January 2015. Our judging panel will select the top five videos. We will then publish the shortlisted videos online and open the judging to the public to determine the winner and the runners up.

For more details on how to enter the competition and who is eligible, join us at the Take 1… page.

Good luck!

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Call for Papers: Themed Issue on Proteomics

Molecular BioSystems will be publishing a themed issue on proteomics in 2015.

Please e-mail the Editorial Office if you are interested in contributing an article. The Guest Editor for this issue is Professor Massimo Castagnola of The Italian Proteomics Association.

We invite scientists in the field of proteomics and integrative biology to contribute to this themed issue dedicated to these rapidly developing topics. It will be a comprehensive collection of papers that showcases the rapid advances in the proteomics field.

Both research Papers, and Communication are welcome to this issue – these must be within the scope of issue and be of the highest quality.

Please note that the deadline for submissions is 19 December 2014

Manuscripts can be submitted using the our online article submission service. Please clearly state that the manuscript is submitted in response to the call for papers for the themed issue on Proteomics.

All submissions will be subject to the normal peer review procedures of Molecular BioSystems.

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Seasons Greetings from Molecular BioSystems!

The holidays are nearly here!!

We know everyone’s been working hard to finish off semesters and write up those papers. Here in Cambridge we’ve been working hard too, planning for the New Year and wrapping up 2013. To spread the holiday cheer, we’ve chosen three highly accessed papers and made them *FREE TO ACCESS* for the next four weeks. Enjoy!

Merry Christmas from the MBS team!



Paper: Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30, by Aaron T. Wright, Pacific Northwest National Laboratory

Paper: The structural properties of DNA regulate gene expression, by Sattar Soltani, Shahid Beheshti University

Paper: Integrated gene co-expression network analysis in the growth phase of Mycobacterium tuberculosis reveals new potential drug targets, by Srinivasan Ramachandran, Institute of Genomics and Integrative Biology, Delhi


Access is free through a registered RSC account – click here to register

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Free to access HOT articles!

These HOT articles have been recommended by our referees and are free to access for 4 weeks*

An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors
Yan Li, Weimin Gao, Feng Li, Jinghui Wang, Jingxiao Zhang, Yinfeng Yang, Shuwei Zhang and Ling Yang  
DOI: 10.1039/C3MB70186G 

GA 

Theoretical study on the interaction of pyrrolopyrimidine derivatives as LIMK2 inhibitors: insight into structure-based inhibitor design
Mingyun Shen, Shunye Zhou, Youyong Li, Dan Li and Tingjun Hou
DOI: 10.1039/C3MB70168A

GA

Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification
Susana M. Tomasio, Heather P. Harding, David Ron, Benedict C. S. Cross and Peter J. Bond 
DOI: 10.1039/C3MB70234K

GA

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores
Valeri Metelev, Surong Zhang, David Tabatadze, Anand T. N. Kumar and Alexei Bogdanov
DOI: 10.1039/C3MB70108E

GA 

BH3 helix-derived biophotonic nanoswitches regulate cytochrome c release in permeabilised cells
Robert J. Mart, Rachel J. Errington, Catherine L. Watkins, Sally C. Chappell, Marie Wiltshire, Arwyn T. Jones, Paul J. Smith and Rudolf K. Allemann  
DOI: 10.1039/C3MB70246D

GA

Metabolomic identification of diagnostic plasma biomarkers in humans with chronic heart failure

Juan Wang, Zhongfeng Li, Jianxin Chen, Huihui Zhao, Liangtao Luo, Chan Chen, Xuegong Xu, Wenting Zhang, Kuo Gao, Bin Li, Junpeng Zhang and Wei Wang
DOI: 10.1039/C3MB70227H

GA

*Free access to individuals is provided through an RSC Publishing personal account. It’s quick, simple and more importantly – free – to register!

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Final chance to register for ISACS11 – don’t miss Shokat, Trauner, Yonath and many more!

Registration Deadline – Friday 21 June 2013

 

You have just a few days left to secure your place at the 11th conference in the International Symposia on Advancing the Chemical Sciences (ISACS) series as registration for Challenges in Chemical Biology (ISACS11) closes on Friday 21 June 2013.

Don’t miss your opportunity to join outstanding researchers from across the globe to explore the themes of immunology, microbiology, chromatin biology, epigenetics, cancer biology, systems biology and neuroscience.

Registration is quick and simple via the online booking system and spaces are filling up fast so be sure to guarantee yours now.

Programme Live

We are pleased to announce that the ISACS11 programme is now available to view online. Take a look at the schedule to discover the full speaker line up and stimulating lecture titles over the entire four days.

Find Out More

For the latest information on Challenges in Chemical Biology (ISACS11) or any of the conferences in the series, please sign up for the exclusive newsletter, follow ISACS on twitter or visit the dedicated webpage.

I look forward to welcoming you to Boston.

Best regards

Professor Ben Davis
Chairman of the Conference Committee
isacs@rsc.org

The International Symposia on Advancing the Chemical Sciences (ISACS) partner the RSC’s flagship journal Chemical Science – Winner of the ALPSP Award for Best New Journal 2011.

                    

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Medicinal Chemistry Residential School – early bird deadline approaching!

17- 21 June 2013, Loughborough University, UK

Don’t miss your chance to be part of the RSC Medicinal Chemistry Residential School, an intensive course which has trained some of the world’s leading medicinal chemists working in the pharmaceutical industry.

The early bird registration deadline of Monday 22 April 2013 is almost upon us. If you are a graduate or post-doctoral chemist with 1-5 years’ experience in the field of drug research or a final year PhD student in pharmacy and organic chemistry contemplating a career in medicinal chemistry, be sure to secure your space before this date to benefit from a great saving on the standard fee.

Please visit the dedicated webpage for full details about the RSC Medicinal Chemistry Residential School including the course programme, bursary applications and poster presentation opportunities.

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Top ten most accessed MBS articles in January 2013

This month sees the following articles in Molecular BioSystems that are in the top ten most accessed:-

Analysis of omics data with genome-scale models of metabolism 
Daniel R. Hyduke, Nathan E. Lewis and Bernhard Ø. Palsson 
Mol. BioSyst., 2013, 9, 167-174 
DOI: 10.1039/C2MB25453K  
 
Predicting cancer drug mechanisms of action using molecular network signatures 
Justin R. Pritchard, Peter M. Bruno, Michael T. Hemann and Douglas A. Lauffenburger 
Mol. BioSyst., 2013, Advance Article 
DOI: 10.1039/C2MB25459J  
 
Learning the molecular mechanisms of the reprogramming factors: let’s start from microRNAs 
Chao-Shun Yang and Tariq M. Rana  
Mol. BioSyst., 2013, 9, 10-17 
DOI: 10.1039/C2MB25088H  

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies 
Yolanda Schaerli and Mark Isalan  
Mol. BioSyst., 2013, Advance Article 
DOI: 10.1039/C2MB25483B  
 
Network motifs provide signatures that characterize metabolism 
Erin R. Shellman, Charles F. Burant and Santiago Schnell  
Mol. BioSyst., 2013, 9, 352-360 
DOI: 10.1039/C2MB25346A  
 
Split-superpositive GFP reassembly is a fast, efficient, and robust method for detecting protein – protein interactions in vivo 
Brett D. Blakeley, Alex M. Chapman and Brian R. McNaughton  
Mol. BioSyst., 2012, 8, 2036-2040 
DOI: 10.1039/C2MB25130B  
 
Analysis of temporal patterns of GPCR–ß-arrestin interactions using split luciferase-fragment complementation 
Mitsuru Hattori, Miho Tanaka, Hideo Takakura, Kiyono Aoki, Kenji Miura, Tomohiro Anzai and Takeaki Ozawa  
Mol. BioSyst., 2013, Advance Article 
DOI: 10.1039/C2MB25443C  

Non-traditional roles of G-protein-coupled receptors in basic cell biology 
Xin Zhang and Ulrike S. Eggert  
Mol. BioSyst., 2013, 9, 586-595 
DOI: 10.1039/C2MB25429H  

Engineering Ecosystems and Synthetic Ecologies 
Michael T. Mee and Harris H. Wang  
Mol. BioSyst., 2012, 8, 2470-2483 
DOI: 10.1039/C2MB25133G  
 
Systematic analysis of histone modification readout 
Miroslav Nikolov and Wolfgang Fischle 
Mol. BioSyst., 2013, 9, 182-194 
DOI: 10.1039/C2MB25328C  

Why not take a look at the articles today and blog your thoughts and comments below.

Fancy submitting an article to Molecular BioSystems? Then why not submit to us today or alternatively email us your suggestions.

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Madan Babu awarded 2014 Colworth Medal!

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 50th 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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Challenges in Chemical Biology (ISACS11) – Oral Abstract Deadline 15 March 2013

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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