What are your colleagues reading in Molecular BioSystems?

The articles below are the most read Molecular BioSystems articles in July, August and September 2014.

Isothermal amplified detection of DNA and RNA
Lei Yan, Jie Zhou, Yue Zheng, Adam S. Gamson, Benjamin T. Roembke, Shizuka Nakayama and Herman O. Sintim 
DOI: 10.1039/C3MB70304E

Logical modelling of Drosophila signalling pathways
Abibatou Mbodj, Guillaume Junion, Christine Brun, Eileen E. M. Furlong and Denis Thieffry
DOI: 10.1039/C3MB70187E

Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms
Anagha Joshi and Berthold Gottgens  
DOI: 10.1039/C4MB00354C

A metabolomics approach for predicting the response to neoadjuvant chemotherapy in cervical cancer patients
Yan Hou, Mingzhu Yin, Fengyu Sun, Tao Zhang, Xiaohua Zhou, Huiyan Li, Jian Zheng, Xiuwei Chen, Cong Li, Xiaoming Ning, Ge Lou and Kang Li  
DOI: 10.1039/C4MB00054D

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez 
DOI: 10.1039/C3MB25489E

Structure-based virtual screening of novel, high-affinity BRD4 inhibitors
Charuvaka Muvva, E. R. Azhagiya Singam, S. Sundar Raman and V. Subramanian
DOI: 10.1039/C4MB00243A

Trials and tribulations of ‘omics data analysis: assessing quality of SIMCA-based multivariate models using examples from pulmonary medicine
Åsa M. Wheelock and Craig E. Wheelock 
DOI: 10.1039/C3MB70194H

Differential protein profile in sexed bovine semen: shotgun proteomics investigation
Michele De Canio, Alessio Soggiu, Cristian Piras, Luigi Bonizzi, Andrea Galli, Andrea Urbani and Paola Roncada  
DOI: 10.1039/C3MB70306A

Crosstalk between kinases and Nedd4 family ubiquitin ligases
Heeseon An, David T. Krist and Alexander V. Statsyuk 
DOI: 10.1039/C3MB70572B

Mechanism of action-based classification of antibiotics using high-content bacterial image analysis
Kelly C. Peach, Walter M. Bray, Dustin Winslow, Peter F. Linington and Roger G. Linington  
DOI: 10.1039/C3MB70027E

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The name of the game is…game theory!

Published on behalf of Kelly E. Theisen, web-writer for Molecular BioSystems

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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Recent HOT Molecular BioSystems articles

The following HOT articles have been highlighted by the reviewers of the articles as being particularly interesting or significant pieces of research. These are all free to access until 31st December 2014. The order they appear in the list has no meaning or ranking.

 Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering
Joris Beld, D. John Lee and Michael D. Burkart  
DOI: 10.1039/C4MB00443D, Review Article

C4MB00443D GA


Studies of N9-arenthenyl purines as novel DFG-in and DFG-out dual Src/Abl inhibitors using 3D-QSAR, docking and molecular dynamics simulations
Shaojie Ma, Guohua Zeng, Danqing Fang, Juping Wang, Wenjuan Wu, Wenguo Xie, Shepei Tan and Kangcheng Zheng  
DOI: 10.1039/C4MB00350K, Paper
C4MB00350K GA

C4MB00457D GA

Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features
Tingting Zhao, Jinyuan Xu, Ling Liu, Jing Bai, Chaohan Xu, Yun Xiao, Xia Li and Liming Zhang  
DOI: 10.1039/C4MB00478G, Paper
C4MB00478G GA

UHPLC-LTQ-Orbitrap MS combined with spike-in method for plasma metabonomics analysis of acute myocardial ischemia rats and pretreatment effect of Danqi Tongmai tablet
Bingpeng Yan, Yanping Deng, Jinjun Hou, Qirui Bi, Min Yang, Baohong Jiang, Xuan Liu, Wanying Wu and Dean Guo  
DOI: 10.1039/C4MB00529E, Paper
C4MB00529E GA

A metabolomic and pharmacokinetic study on the mechanism underlying the lipid-lowering effect of orally administered berberine
Shenghua Gu, Bei Cao, Runbin Sun, Yueqing Tang, Janice L. Paletta, Xiao-Lei Wu, Linsheng Liu, Weibin Zha, Chunyan Zhao, Yan Li, Jason M. Radlon, Phillip B. Hylemon, Huiping Zhou, Jiye Aa and Guangji Wang  
DOI: 10.1039/C4MB00500G, Paper

C4MB00500G GA


Modeling the mitotic regulatory network identifies highly efficient anti-cancer drug combinations
Yiran Wu, Xiaolong Zhuo, Ziwei Dai, Xiao Guo, Yao Wang, Chuanmao Zhang and Luhua Lai  
DOI: 10.1039/C4MB00610K, Paper

C4MB00610K GA


Prediction of advanced ovarian cancer recurrence by plasma metabolic profiling
Haiyu Zhang, Tingting Ge, Xiaoming Cui, Yan Hou, Chaofu Ke, Meng Yang, Kai Yang, Jingtao Wang, Bing Guo, Fan Zhang, Ge Lou and Kang Li  
DOI: 10.1039/C4MB00407H, Paper

C4MB00407H GA


A pre-structured helix in the intrinsically disordered 4EBP1
Do-Hyoung Kim, Chewook Lee, Ye-Jin Cho, Si-Hyung Lee, Eun-Ji Cha, Ji-Eun Lim, T. Michael Sabo, Christian Griesinger, Donghan Lee and Kyou-Hoon Han  
DOI: 10.1039/C4MB00532E, Communication

C4MB00532E GA

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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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Recent HOT Molecular BioSystems articles

The following HOT articles have been highlighted by the reviewers of the articles as being particularly interesting or significant pieces of research. These are all free to access until 30th November. The order they appear in the list has no meaning or ranking.

Systems biosynthesis of secondary metabolic pathways within the oral human microbiome member Streptococcus mutans
Rostyslav Zvanych, Nikola Lukenda, Xiang Li, Janice J. Kim, Satheeisha Tharmarajah and Nathan A. Magarvey
DOI: 10.1039/C4MB00406J, Paper

Systems biosynthesis of secondary metabolic pathways


Structural mass spectrometry of tissue extracts to distinguish cancerous and non-cancerous breast diseases
Kelly M. Hines, Billy R. Ballard, Dana R. Marshall and John A. McLean
DOI: 10.1039/C4MB00250D, Paper

Structural mass spectrometry of tissue extracts


Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus–host coevolution
Eugene V. Koonin and Yuri I. Wolf
DOI: 10.1039/C4MB00438H, Review Article

Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes


Clearance of the intracellular high level of the Tau protein directed by an artificial synthetic hydrolase
Ting-Ting Chu, Qian-Qian Li, Tian Qiu, Zhan-Yi Sun, Zhi-Wen Hu, Yong-Xiang Chen, Yu-Fen Zhao and Yan-Mei Li
DOI: 10.1039/C4MB00508B, Communication

Clearance of the intracellular high level of the Tau protein directed by an artificial synthetic hydrolase


CIP2A regulates cancer metabolism and CREB phosphorylation in non-small cell lung cancer
Bo Peng, Ningjing Lei, Yurong Chai, Edward K. L. Chan and Jian-Ying Zhang
DOI: 10.1039/C4MB00513A, Paper

CIP2A regulates cancer metabolism and CREB phosphorylation in non-small cell lung cancer


Molecular dynamics-based discovery of novel phosphodiesterase-9A inhibitors with non-pyrazolopyrimidinone scaffolds
Zhe Li, Xiao Lu, Ling-Jun Feng, Ying Gu, Xingshu Li, Yinuo Wu and Hai-Bin Luo
DOI: 10.1039/C4MB00389F, Paper

phosphodiesterase-9A inhibitors with non-pyrazolopyrimidinone scaffolds

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Q2 Top Ten most accessed articles

The 10 most accessed Molecular BioSystems articles between April and June 2014. Free to access until the end of the month.

During the months April – June 2014, the most downloaded Molecular BioSystems articles were:

Isothermal amplified detection of DNA and RNA
Lei Yan, Jie Zhou, Yue Zheng, Adam S. Gamson, Benjamin T. Roembke, Shizuka Nakayama and Herman O. Sintim
DOI: 10.1039/C3MB70304E

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez
DOI: 10.1039/C3MB25489E

TGF-β upregulates miR-182 expression to promote gallbladder cancer metastasis by targeting CADM1
Yinghe Qiu, Xiangji Luo, Tong Kan, Yongjie Zhang, Wenlong Yu, Yongpeng Wei, Ningjia Shen, Bin Yi and Xiaoqing Jiang
DOI: 10.1039/C3MB70479C

A cyclic dinucleotide containing 2-aminopurine is a general fluorescent sensor for c-di-GMP and 3′,3′-cGAMP
Benjamin T. Roembke, Jie Zhou, Yue Zheng, David Sayre, Allan Lizardo, Laurentee Bernard and Herman O. Sintim
DOI: 10.1039/C3MB70518H

Crosstalk between kinases and Nedd4 family ubiquitin ligases
Heeseon An, David T. Krist and Alexander V. Statsyuk
DOI: 10.1039/C3MB70572B

Logical modelling of Drosophila signalling pathways
Abibatou Mbodj, Guillaume Junion, Christine Brun, Eileen E. M. Furlong and Denis Thieffry
DOI: 10.1039/C3MB70187E

Trials and tribulations of ‘omics data analysis: assessing quality of SIMCA-based multivariate models using examples from pulmonary medicine
Åsa M. Wheelock and Craig E. Wheelock
DOI: 10.1039/C3MB70194H

Peroxisomes are juxtaposed to strategic sites on mitochondria
Yifat Cohen, Yoel Alexander Klug, Lazar Dimitrov, Zohar Erez, Silvia G. Chuartzman, Dalia Elinger, Ido Yofe, Kareem Soliman, Jutta Gärtner, Sven Thoms, Randy Schekman, Yael Elbaz-Alon, Einat Zalckvar and Maya Schuldiner
DOI: 10.1039/C4MB00001C

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane
Nishu Goyal, Hanifah Widiastuti, I. A. Karimi and Zhi Zhou
DOI: 10.1039/C3MB70421A

A time resolved metabolomics study: the influence of different carbon sources during growth and starvation of Bacillus subtilis
Hanna Meyer, Hendrikje Weidmann, Ulrike Mäder, Michael Hecker, Uwe Völker and Michael Lalk
DOI: 10.1039/C4MB00112E

Access to these articles is free until the end of October through a registered RSC account – click here to register for free

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Recent HOT Molecular BioSystems articles

The following are HOT articles, as recommened by the reviewers of the articles. These have all been made free to access until 24th October:

Network pharmacology study on the mechanism of traditional Chinese medicine for upper respiratory tract infection
Xinzhuang Zhang, Jiangyong Gu, Liang Cao, Na Li, Yiming Ma, Zhenzhen Su, Gang Ding, Lirong Chen, Xiaojie Xu and Wei Xiao
Mol. BioSyst., DOI: 10.1039/C4MB00164H, Paper


Vitreous proteomic analysis of idiopathic epiretinal membranes
Jing Yu, Le Feng, Yan Wu, Hao Wang, Jun Ba, Wei Zhu and Chunlei Xie
Mol. BioSyst., DOI: 10.1039/C4MB00240G, Paper


Effect of a Ru(II) polypyridyl complex [Ru(bpy)2(mdpz)]2+ on the stabilization of the RNA triplex poly(U)·poly(A)*poly(U)
Xiaojun He, Jia Li, Hong Zhang and Lifeng Tan
Mol. BioSyst., DOI: 10.1039/C4MB00304G, Paper


Informative Bayesian Model Selection: a method for identifying interactions in genome-wide data
Mehran Aflakparast, Ali Masoudi-Nejad, Joseph H . Bozorgmehr and Shyam Visweswaran
Mol. BioSyst., DOI: 10.1039/C4MB00123K, Paper


Prioritizing candidate disease miRNAs by integrating phenotype associations of multiple diseases with matched miRNA and mRNA expression profiles
Chaohan Xu, Yanyan Ping, Xiang Li, Hongying Zhao, Li Wang, Huihui Fan, Yun Xiao and Xia Li
Mol. BioSyst., DOI: 10.1039/C4MB00353E, Method


Molecular docking and molecular dynamics studies on the structure–activity relationship of fluoroquinolone for the HERG channel
Fang Luo, Jiangyong Gu, Lirong Chen and Xiaojie Xu
Mol. BioSyst., DOI: 10.1039/C4MB00396A, Paper


Dynamic changes in metabolic profiles of rats subchronically exposed to mequindox
Limiao Jiang, Xiuju Zhao, Chongyang Huang, Hehua Lei, Huiru Tang and Yulan Wang
Mol. BioSyst., DOI: 10.1039/C4MB00218K, Paper


Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms
Anagha Joshi and Berthold Gottgens
Mol. BioSyst., DOI: 10.1039/C4MB00354C, Paper


A multi-omics strategy resolves the elusive nature of alkaloids in Podophyllum species
Joaquim V. Marques, Doralyn S. Dalisay, Hong Yang, Choonseok Lee, Laurence B. Davin and Norman G. Lewis
Mol. BioSyst., DOI: 10.1039/C4MB00403E, Paper

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Call for Papers: Themed Issue on Proteomics

Submission Deadline 19 December 2014

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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Recent HOT Molecular BioSystems articles

FMRP regulates miR196a-mediated repression of HOXB8 via interaction with the AGO2 MID domain
Ying Li, Wei Tang, Li-rong Zhang and Chun-yang Zhang  
Mol. BioSyst., 2014,10, 1757-1764
DOI: 10.1039/C4MB00066H

Graphical abstract

Free to access until 4th July 2014


Discovery of protein–RNA networks
Davide Cirillo, Carmen Maria Livi, Federico Agostini and Gian Gaetano Tartaglia  
Mol. BioSyst., 2014,10, 1632-1642
DOI: 10.1039/C4MB00099D

Graphical abstract

Free to access until 4th July 2014


Systems pharmacology strategies for anticancer drug discovery based on natural products
Fang Luo, Jiangyong Gu, Lirong Chen and Xiaojie Xu  
Mol. BioSyst., 2014,10, 1912-1917
DOI: 10.1039/C4MB00105B

Graphical abstract

Free to access until 4th July 2014

 


 

The metabolic impact of methamphetamine on the systemic metabolism of rats and potential markers of methamphetamine abuse
Tian Zheng, Linsheng Liu, Jian Shi, Xiaoyi Yu, Wenjing Xiao, Runbing Sun, Yahong Zhou, Jiye Aa and Guangji Wang  
Mol. BioSyst., 2014,10, 1968-1977
DOI: 10.1039/C4MB00158C

Graphical abstract

Free to access until 4th July 2014


Experimental design, validation and computational modeling uncover DNA damage sensing by DNA-PK and ATM
R. J. Flassig, G. Maubach, C. Täger, K. Sundmacher and M. Naumann  
Mol. BioSyst., 2014,10, 1978-1986
DOI: 10.1039/C4MB00093E

Graphical abstract

Free to access until 4th July 2014 

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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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