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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Q1 Top Ten most accessed Molecular BioSystems articles

During January, February and March this year, the following articles were the Top Ten most accessed:

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  
Mol. BioSyst., 2013,9, 1576-1583
DOI: 10.1039/c3mb25489e

The powerful law of the power law and other myths in network biology
Gipsi Lima-Mendez and Jacques van Helden  
Mol. BioSyst., 2009,5, 1482-1493
DOI: 10.1039/b908681a

Crosstalk between kinases and Nedd4 family ubiquitin ligases
Heeseon An, David T. Krist and Alexander V. Statsyuk  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/c3mb70572b

A novel paradigm for potential drug-targets discovery: quantifying relationships of enzymes and cascade interactions of neighboring biological processes to identify drug-targets
Lina Chen, Qian Wang, Liangcai Zhang, Jingxie Tai, Hong Wang, Wan Li, Xu Li, Weiming He and Xia Li  
Mol. BioSyst., 2011,7, 1033-1041
DOI: 10.1039/c0mb00249f

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  
Mol. BioSyst., 2014,10, 970-1003
DOI: 10.1039/c3mb70304e

Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations
Sónia Carneiro, Silas G. Villas-Bôas, Eugénio C. Ferreira and Isabel Rocha  
Mol. BioSyst., 2011,7, 899-910
DOI: 10.1039/c0MB00143k

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange
Ralf Beer, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Lorenz Adlung, Hannah Meyer, Dominik Niopek, Tania Christiansen, Fanny Georgi, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Katharina Niopek, Tim Heinemann, Roland Eils and Barbara Di Ventura
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/c3mb70594c

Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model
Alexandra Pokhilko, Anna Flis, Ronan Sulpice, Mark Stitt and Oliver Ebenhöh
Mol. BioSyst., 2014,10, 613-627
DOI: 10.1039/c3mb70459a

Engineering reduced evolutionary potential for synthetic biology
Brian A. Renda, Michael J. Hammerling and Jeffrey E. Barrick
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/c3mb70606k

Combining radiation, immunotherapy, and antiangiogenesis agents in the management of cancer: the Three Musketeers or just another quixotic combination?
Mitchell Kamrava, Michael B. Bernstein, Kevin Camphausen and James W. Hodge  
Mol. BioSyst., 2009,5, 1262-1270
DOI: 10.1039/b911313b

If you have any thoughts or comments on any of these articles, please leave these in the box below.

If you have an article you would like to submit to us, please visit our submission site today!

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Recent HOT Molecular BioSystems articles

Understanding and applying tyrosine biochemical diversity
Lyn H. Jones, Arjun Narayanan and Erik C. Hett  
Mol. BioSyst., 2014,10, 952-969
DOI: 10.1039/C4MB00018H

Understanding and applying tyrosine biochemical diversity

Free to access until 7th May 2014


Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures
Yingdan Zhang, Chun Kiat Ng, Yehuda Cohen and Bin Cao
Mol. BioSyst., 2014,10, 1035-1042
DOI: 10.1039/C3MB70520J

Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures

Free to access until 7th May 2014


Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins
Xiaoyan Qin, Chaoya Zheng, John R. Yates III and Lujian Liao  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70565J

Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins

Free to access until 7th May 2014


Regulation of cell survival by the HIP-55 signaling network
Chengzhi Yang, Zenggang Li, Zhi Shi, Kangmin He, Aiju Tian, Jimin Wu, Youyi Zhang and Zijian Li  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70552H

Regulation of cell survival by the HIP-55 signaling network

Free to access until 7th May 2014


Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression
Shao-Wu Zhang, Dong-Dong Shao, Song-Yao Zhang and Yi-Bin Wang
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70588A

Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression

 

Free to access until 7th May 2014

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Free access to HOT articles

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

A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study
Xujun Liang, Huiying Li and Shao Li  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70507B, Paper

Graphical abstract: A novel network pharmacology approach to analyse traditional herbal formulae: the Liu-Wei-Di-Huang pill as a case study

A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network
Kristoffer Sjöholm, Christofer Karlsson, Adam Linder and Johan Malmström  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70555B, Paper

Graphical abstract: A comprehensive analysis of the Streptococcus pyogenes and human plasma protein interaction network

Engineering reduced evolutionary potential for synthetic biology
Brian A. Renda, Michael J. Hammerling and Jeffrey E. Barrick  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70606K, Review Article

Graphical abstract: Engineering reduced evolutionary potential for synthetic biology

Structure-based engineering and comparison of novel split inteins for protein ligation
A. Sesilja Aranko, Jesper S. Oeemig, Dongwen Zhou, Tommi Kajander, Alexander Wlodawer and Hideo Iwaï  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C4MB00021H, Paper

Graphical abstract: Structure-based engineering and comparison of novel split inteins for protein ligation
*Free access to individuals is provided through an RSC Publishing personal account. It’s quick, easy and more importantly – free – to register!

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Fibrils, oligomers or just precursors? New probe characterises beta-amyloid aggregates

Published on behalf of Kelly Theisen, web writer for Molecular BioSystems and Integrative Biology

Beta-amyloid (Aβ) aggregates are infamous for forming the toxic plaques in the brain of Alzheimer’s disease patients. The detrimental effects are fairly well studied, but the mechanism of formation remains largely a mystery.

Now, thanks to Ifor D. W. Samuel, J. Carlos Penedo and colleagues at University of St. Andrews and Glasgow University, researchers have a new fluorescent probe to study the process of Aβ aggregation. This paper was featured on the cover of the January 2014 issue of Molecular Biosystems.


The most common probe of Aβ currently in use is Thioflavin T (ThT), which has been very successful at detecting the presence of aggregates. However, this probe has a limited pH range where it can be used. Aggregate structures can form at low concentrations of Aβ, and in the slightly acidic (pH = 6) endosome, but both of these are beyond the detection limits of ThT. For maximum utility, a probe would be able to track Aβ formation under any biological conditions.

Fig 1: Representative aggregation time course and relative fluorescence quenching during the HFIP-induced aggregation of Ab1–42

To address this disadvantage, Samuel & Penedo et al. have used a HiLyte Fluorescent probe attached to the N-terminal position of Aβ monomers. When monomers associate with each other, the probe undergoes fluorescence self-quenching (FSQ), a well-documented process where the presence of two probes proximal to each other will cause a decrease in the observed fluorescent signal. This decrease in signal can be monitored and correlated with the aggregation rate and type of Aβ structure formed.

First the researchers determined that the probe did not affect the final Aβstructures obtained by a TEM image comparison to ThT Aβ under various conditions (see Figure 1 below). They also showed that the rate of Aβ formation stayed the same. Because the HiLyte probe does not affect the normal Aβ function, they could then use the probe under biological conditions not accessible to ThT.

They found that they were able to detect fibrils under biological conditions (Figure 2a below), oligomers under endosomal conditions (Figure 2bbelow) and ADDLs (early precursor structures that occur at low Aβ concentrations). Each of these Aβ structures produced a different fluorescent signature, allowing them to be distinguished from each other. This ability to detect the different Aβ assembly rates will allow researchers to better characterize biological samples, hopefully leading to new treatment options for Alzheimer’s disease.

Fig 2: (a,b) Transmission electron micrographs of negatively stained Ab555


Read Samuel & Penedo et al’s HOT paper by following the link below!

DOI: 10.1039/C3MB70272C

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Free access to HOT articles!

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

A metabolomics investigation into the effects of HIV protease inhibitors on HPV16 E6 expressing cervical carcinoma cells
Dong-Hyun Kim, J. William Allwood, Rowan E. Moore, Emma Marsden-Edwards, Warwick B. Dunn, Yun Xu, Lynne Hampson, Ian N. Hampson and Royston Goodacre  
Mol. BioSyst., 2014,10, 398-411
DOI: 10.1039/C3MB70423H, Paper

E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs
Yiling Luo, Bin Chen, Jie Zhou, Herman O. Sintim and T. Kwaku Dayie  
Mol. BioSyst., 2014,10, 384-390
DOI: 10.1039/C3MB70467J, Paper

An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis
Min Zhao, Eric D. Austin, Anna R. Hemnes, James E. Loyd and Zhongming Zhao  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70496C, Paper

Hyperdiploid tumor cells increase phenotypic heterogeneity within Glioblastoma tumors
Prudence Donovan, Kathleen Cato, Roxane Legaie, Rumal Jayalath, Gemma Olsson, Bruce Hall, Sarah Olson, Samuel Boros, Brent A. Reynolds and Angus Harding  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70484J, Paper

Paxillin suppresses the proliferation of HPS rat serum treated PASMCs by up-regulating the expression of cytoskeletal proteins
Yang Chen, Bin Yi, Zhi Wang, Jianteng Gu, Yongshuai Li, Jian Cui and Kaizhi Lu  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70391F, Paper

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange
Ralf Beer, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Lorenz Adlung, Hannah Meyer, Dominik Niopek, Tania Christiansen, Fanny Georgi, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Katharina Niopek, Tim Heinemann, Roland Eils and Barbara Di Ventura  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70594C, Paper

A systematic study of chemogenomics of carbohydrates
Jiangyong Gu, Fang Luo, Lirong Chen, Gu Yuan and Xiaojie Xu  
Mol. BioSyst., 2014,10, 391-397
DOI: 10.1039/C3MB70534J, Paper 

The ubiquitin system: an essential component to unlocking the secrets of malaria parasite biology
Michael J. Hamilton, Michael Lee and Karine G. Le Roch  
Mol. BioSyst., 2014, Advance Article
DOI: 10.1039/C3MB70506D, Review Article

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

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