Archive for March, 2011

Top ten most accessed articles in February

This month sees the following articles in Integrative Biology that are in the top ten most accessed:-

Sequencing transcriptomes in toto 
Karin S. Kassahn, Nic Waddell and Sean M. Grimmond 
Integr. Biol., 2011, Advance Article, DOI: 10.1039/C0IB00062K, Review 

DNA assembly for synthetic biology: from parts to pathways and beyond 
Tom Ellis, Tom Adie and Geoff S. Baldwin 
Integr. Biol., 2011, 3, 109-118, DOI: 10.1039/C0IB00070A, Frontier 

Multi-scale modelling and simulation in systems biology 
Joseph O. Dada and Pedro Mendes 
Integr. Biol., 2011, 3, 86-96, DOI: 10.1039/C0IB00075B, Review 

Computational design approaches and tools for synthetic biology 
James T. MacDonald, Chris Barnes, Richard I. Kitney, Paul S. Freemont and Guy-Bart V. Stan 
Integr. Biol., 2011, 3, 97-108, DOI: 10.1039/C0IB00077A, Perspective 

Subcellular spatial segregation of integrin subtypes by patterned multicomponent surfaces 
Ravi A. Desai, Mohammed K. Khan, Smitha B. Gopal and Christopher S. Chen 
Integr. Biol., 2011, Advance Article, DOI: 10.1039/C0IB00129E, Paper 

Homing peptides as targeted delivery vehicles 
Pirjo Laakkonen and Kirsi Vuorinen 
Integr. Biol., 2010, 2, 326-337, DOI: 10.1039/C0IB00013B, Critical Review 

Biological applications of microfluidic gradient devices 
Sudong Kim, Hyung Joon Kim and Noo Li Jeon 
Integr. Biol., 2010, 2, 584-603, DOI: 10.1039/C0IB00055H, Critical Review 

Advancing stem cell research with microtechnologies: opportunities and challenges 
Yi-Chin Toh, Katarina Blagović and Joel Voldman 
Integr. Biol., 2010, 2, 305-325, DOI: 10.1039/C0IB00004C, Critical Review 

L-5F, an apolipoprotein A-I mimetic, inhibits tumor angiogenesis by suppressing VEGF/basic FGF signaling pathways 
Feng Gao, Sergio X. Vasquez, Feng Su, Svetlana Roberts, Neha Shah, Victor Grijalva, Satoshi Imaizumi, Arnab Chattopadhyay, Ekambaram Ganapathy, David Meriwether, Brad Johnston, G. M. Anantharamaiah, Mohamad Navab, Alan M. Fogelman, Srinivasa T. Reddy and Robin Farias-Eisner 
Integr. Biol., 2011, Advance Article, DOI: 10.1039/C0IB00147C, Paper 

Determinants of leader cells in collective cell migration 
Antoine A. Khalil and Peter Friedl 
Integr. Biol., 2010, 2, 568-574, DOI: 10.1039/C0IB00052C, Review 

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

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

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Off to Anaheim? Meet Deputy Editor Michael Smith there

We are excited to be off to the ACS Spring 2011 meeting in Anaheim next week – especially as Molecular BioSystems Editorial Board member Dr Madan Babu will be giving the Molecular BioSystems Award Lecture on Wednesday morning, at 8.30 am in the Marquis Northeast Ballroom of the Anaheim Marriott .

Michael Smith

Deputy Editor Michael Smith will be at the meeting on behalf of Molecular BioSystems, Journal of Environmental Monitoring and Integrative Biology and would be delighted to meet you, so do come and say hello!

RSC Publishing will also be at Booth 903, find out more about what we’ll be doing here.

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HOT article: picking out the protease – simultaneous determination of multiple protease activities

The enzymes Matrix metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) are two related protease families which play key roles in physiological processes. MMPs are involved in processes such as development, angiogenesis and tissue remodeling, whilst ADAMs mediate various cellular behaviour. Many useful methodologies currently exist to study metalloproteinases but none simultaneously allow for direct, non-invasive, multiplex, real-time measurements of specific protease activity.

Proteolytic Activity Matrix Analysis (PrAMA) is an integrated experimental measurement and mathematical analysis framework, developed by Douglas A. Lauffenburger et al., Massachusetts Institute of Technology, in an attempt to address this issue.

This method uses panels of FRET-substrates to infer a dynamic, quantitative and specific profile of MMP and ADAM proteolytic activities and by utilising predetermined signatures, from purified enzymes, it is possible to deconvolute signals from complex protease mixtures to ascertain specific protease activity. PrAMA appears to be able to distinguish closely related enzymes with a high accuracy and can do so even when there is  unknown background proteolytic activity present.

Lauffenburger et al. believe that this has the potential to be used in areas ranging from systems biology to in vitro inhibitor screening as well as other protease families.

Find out more about PrAMA by reading this HOT article, which is part of a forthcoming Integrative Biology themed issue in honour of Mina J. Bissell. Go on, it’s free for 4 weeks!

Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities
Miles A. Miller, Layla Barkal, Karen Jeng, Andreas Herrlich, Marcia Moss, Linda G. Griffith and Douglas A. Lauffenburger
Integr. Biol., 2011, Advance Article
DOI: 10.1039/C0IB00083C

This article was published as part of a themed issue in honor of Mina J. Bissell.

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3D model to study breast cancer

Slice from the normal acini model after 12 days. Green: membrane, blue: nuclei, red: dividing cells

Scientists from the US have made a computational model of the formation of breast acini, the sac-like part of the milk-producing glands, to understand complex events occurring during the progression of breast cancer.

Jonathan Tang from the University of California, Berkeley, and colleagues, made a 3D model of acini formation, for the first time, to study how three different cell activities – apoptosis (programmed cell death), proliferation (cell division) and polarisation (organisation of cell components) – work together to form the tissue. In doing so, they hoped to determine how changes to these activities cause cancer.

‘We believed that such a model would enable us to identify which perturbations cause disorganised structures that resemble tumours, giving us a deeper insight into the complex nature of cancer,’ says Tang.

To read more, check out Elinor Richards’ Chemistry World article here or read the full paper online:

Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling
Jonathan Tang, Heiko Enderling, Sabine Becker-Weimann, Christopher Pham, Aris Polyzos, Chen-Yi Chen and Sylvain V. Costes
Integr. Biol., 2011
DOI: 10.1039/c0ib00092b

This article was published as part of a themed issue in honor of Mina J. Bissell.

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Issue 3 now available online

This month’s cover article is the HOT paper from Jangwook P. Jung, José V. Moyano and Joel H. Collier on optimizing of cell growth using modular synthetic extracellular matrices.

Richard P. Sear’s article on combining modelling with FRAP to study diffusion dynamics is our other HOT article this month, and comes highly recommended by the referees.

The issue also includes reviews from Vicente Aguilella, Florin Despa and S. Dewitt:

Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
Vicente M. Aguilella, María Queralt-Martín, Marcel Aguilella-Arzo and Antonio Alcaraz
Integr. Biol., 2011, 3, 159

Biophysical alteration of the secretory track in ß-cells due to molecular overcrowding: the relevance for diabetes
Constantin Ionescu-Tirgoviste and Florin Despa
Integr. Biol., 2011, 3, 173

A trick of the light: the optical properties of living cytoplasm which can mislead
Maurice B. Hallett and S. Dewitt
Integr. Biol., 2011, 3, 18

Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
Vicente M. Aguilella, María Queralt-Martín, Marcel Aguilella-Arzo and Antonio Alcaraz
Integr. Biol., 2011, 3, 159

Biophysical alteration of the secretory track in ß-cells due to molecular overcrowding: the relevance for diabetes
Constantin Ionescu-Tirgoviste and Florin Despa
Integr. Biol., 2011, 3, 173

A trick of the light: the optical properties of living cytoplasm which can mislead
Maurice B. Hallett and S. Dewitt
Integr. Biol., 2011, 3, 18ptimization of endothelial cell growth using modular synthetic extracellular matrices

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HOT article: combining modular synthetic ECMs and multifactorial experiments

Optimising extracellular matrices (ECMs) for tissue engineering or 3D cell culture is no mean feat due to the inherent complexity of the native matrices, and reports to date have failed to accurately determine multiple ligand concentrations.

In this HOT article, Joel Collier and colleagues from the University of Chicago demonstrate a breakthrough approach using modular synthetic ECMs derived from multiple co-assembling peptides to enable straightforward factorial optimization for several different matrix-bound ligands. They used their new method  to investigate the complex interplay between multiple ECM-derived peptide ligands on HUVEC proliferation, and discovered a previously unknown interaction between RGDS and YIGSR peptide ligands.  The interaction, which only occurs in specific concentration ranges of the two peptide, may have gone unnoticed in traditional one-factor-at-a-time analyses.  The authors also discovered a multi-peptide mixture that provides optimal endothelial cell growth.

Read this fascinating piece of work – which comes highly recommended by our expert referees – the article is currently free to access:

Multifactorial optimization of endothelial cell growth using modular synthetic extracellular matrices
Jangwook P. Jung, José V. Moyano and Joel H. Collier
Integr. Biol., 2011, Advance Article
DOI: 10.1039/C0IB00112K, Paper

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