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.

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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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Top ten most accessed MBS articles in Q4 2013

Top ten most accessed articles from October – December 2013

Reverse engineering of metabolic networks, a critical assessment 
Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot    
Mol. BioSyst., 2011,7, 511-520 
DOI: 10.1039/C0MB00083C    

Identification and comparative analysis of hepatitis C virus–host cell protein interactions 
Patrick T. Dolan, Chaoying Zhang, Sudip Khadka, Vaithilingaraja Arumugaswami, Abbey D. Vangeloff, Nicholas S. Heaton, Sudhir Sahasrabudhe, Glenn Randall, Ren Sun and Douglas J. LaCount    
Mol. BioSyst., 2013,9, 3199-3209 
DOI: 10.1039/C3MB70343F     

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome 
Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto and Tiziana Bonaldi    
Mol. BioSyst., 2013,9, 2231-2247 
DOI: 10.1039/C3MB00009E     

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30 
Lindsey N. Anderson, David E. Culley, Beth A. Hofstad, Lacie M. Chauvigné-Hines, Erika M. Zink, Samuel O. Purvine, Richard D. Smith, Stephen J. Callister, Jon M. Magnuson and Aaron T. Wright    
Mol. BioSyst., 2013,9, 2992-3000 
DOI: 10.1039/C3MB70333A     

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     

Optogenetic tools for mammalian systems 
Konrad Müller and Wilfried Weber    
Mol. BioSyst., 2013,9, 596-608 
DOI: 10.1039/C3MB25590E    

Expanding the chemistry of fluorescent protein biosensors through genetic incorporation of unnatural amino acids 
Wei Niu and Jiantao Guo    
Mol. BioSyst., 2013,9, 2961-2970 
DOI: 10.1039/C3MB70204A    

Sirtuin 6: a review of biological effects and potential therapeutic properties 
Jade M. Beauharnois, Beatriz E. Bolívar and John T. Welch    
Mol. BioSyst., 2013,9, 1789-1806 
DOI: 10.1039/C3MB00001J     

Real-time probing of ß-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes 
Steven D. Quinn, Paul A. Dalgarno, Ryan T. Cameron, Gordon J. Hedley, Christian Hacker, John M. Lucocq, George S. Baillie, Ifor D. W. Samuel and J. Carlos Penedo    
Mol. BioSyst., 2014,10, 34-44 
DOI: 10.1039/C3MB70272C    

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    

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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Mathematical model takes on the gene expression pathway responsible for whooping cough infections

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

Dr. Saini and colleague at the Indian Institute of Technology, Bombay have used a mathematical model to track the gene expression pathway of a bacterium that causes whooping cough (or pertussis). The understanding of gene regulation along the growth and infection process for Bordetella could lead to new ways to block its action.

The Bordetella bacterium colonizes the respiratory tracts of several hosts, including humans, to cause the infection most commonly referred to as whooping cough. There are two stages of the infection, with the first being mild (cold like symptoms), followed by the intense coughing and difficulty breathing which creates the characteristic “whooping” sound for which the infection is named. This second stage of the infection is controlled by a specific set of genes in the bacterium DNA, and regulated by one pathway known as BvgAS.

This pathway BvgAS is a series of three phosphorylation reactions, where a phosphate group is added to specific proteins in turn, and the final protein then activates the genes responsible for virulence (infection). The addition or removal of a phosphate group is a standard way for cells to turn proteins “on” or “off” as needed. Figure 1 below shows the activation pathway of the final protein in the series (BvgA, triangle), which is the gene promoter.

Figure 1

The researchers were able to recover experimentally observed gene activation for four important classes of genes. They monitored where the pathway of interest changes from a repressed state (i.e. genes are inactive, or unexpressed), to an intermediate state, and finally to an active state (i.e. genes are expressed). The expression levels for each class of genes observed during the transitions are shown in Fig. 2 below.

Additionally, the same simulations were carried out on mutant bacteria containing one phosphorylation event in the pathway. This was done to understand the role of having three phosphorylation reactions for BvgAS, while typical pathways in bacteria have one or two events. This extra complexity was found to provide the bacterium with sensitivity and flexibility to respond to environmental factors, by changing the gene expression profile.

Understanding how the bacterium can respond to changing environmental factors by regulating gene expression could lead to new treatments for the infection in humans.

Figure 2






Read the full HOT paper by Mahendra Kumar Prajapa and Supreet Saini here:

Role of feedback and network architecture in controlling virulence gene expression in Bordetella, DOI: 10.1039/C3MB70213H

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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*

Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Steven D. Quinn, Paul A. Dalgarno, Ryan T. Cameron, Gordon J. Hedley, Christian Hacker, John M. Lucocq, George S. Baillie, Ifor D. W. Samuel and J. Carlos Penedo  
Mol. BioSyst., 2014,10, 34-44
DOI: 10.1039/C3MB70272C, Paper

Graphical abstract: Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
J. Song, Z. Wang and R. M. Ewing  
Mol. BioSyst., 2014,10, 45-53
DOI: 10.1039/C3MB70417C, Paper

Graphical abstract: Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks
On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+
Carolina R. Córdula, Marcelo A. Lima, Samuel K. Shinjo, Tarsis F. Gesteira, Laércio Pol-Fachin, Vivien J. Coulson-Thomas, Hugo Verli, Edwin A. Yates, Timothy R. Rudd, Maria A. S. Pinhal, Leny Toma, Carl P. Dietrich, Helena B. Nader and Ivarne L. S. Tersariol  
Mol. BioSyst., 2014,10, 54-64
DOI: 10.1039/C3MB70370C, Paper

Graphical abstract: On the catalytic mechanism of polysaccharide lyases: evidence of His and Tyr involvement in heparin lysis by heparinase I and the role of Ca2+

*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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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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Top ten most accessed MBS articles in Q3 2013

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

Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome
Michael Bremang, Alessandro Cuomo, Anna Maria Agresta, Magdalena Stugiewicz, Valeria Spadotto and Tiziana Bonaldi
Mol. BioSyst., 2013,9, 2231-2247
DOI: 10.1039/C3LC90080K

Secretome profiling with antibody microarrays
Shakhawan Abdulrahman Mustafa, Jörg D. Hoheisel and Mohamed Saiel Saeed Alhamdani
Mol. BioSyst., 2011,7, 1795-1801
DOI: 10.1039/C3LC90080K

Network representations and methods for the analysis of chemical and biochemical pathways
Conner I. Sandefur, Maya Mincheva and Santiago Schnell
Mol. BioSyst., 2013,9, 2189-2200
DOI: 10.1039/C3MB70052F

Sirtuin 6: a review of biological effects and potential therapeutic properties
Jade M. Beauharnois, Beatriz E. Bolívar and John T. Welch
Mol. BioSyst., 2013,9, 1789-1806
DOI: 10.1039/C3MB00001J

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

Optogenetic tools for mammalian systems
Konrad Müller and Wilfried Weber
Mol. BioSyst., 2013,9, 596-608
DOI: 10.1039/C3MB25590E

Chemical biology-based approaches on fluorescent labeling of proteins in live cells
Deokho Jung, Kyoungmi Min, Juyeon Jung, Wonhee Jang and Youngeun Kwon
Mol. BioSyst., 2013,9, 862-872
DOI: 10.1039/C2MB25422K

Global signatures of protein and mRNA expression levels
Raquel de Sousa Abreu, Luiz O. Penalva, Edward M. Marcotte and Christine Vogel
Mol. BioSyst., 2009,5, 1512-1526
DOI: 10.1039/B908315D

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
Mol. BioSyst., 2013,9, 2408-2416
DOI: 10.1039/C3MB70234K

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

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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