Archive for the ‘Cover articles’ Category

Themed issue: Integrative Computational Biology

This month’s Integrative Biology issue is a themed issue, focusing on integrative computational biology. The guest editor, Dr Jan Baumbach, shares his thoughts on the issue in the editorial, available here.

Two HOT articles feature in the issue; the first of these is a paper by Jennifer Hallinan and colleagues at the University of Newcastle, in which they analyse the changes in four online databases and evaluate how these changes affect the protein function prediction performance of probabilistic functional integrated networks in Saccharomyces cerevisiae. They found that whilst the predictions improved over time, the newer datasets on their own were not necessarily always better – selecting the correct combination of datasets was important.

Is newer better?—evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae
Katherine James, Anil Wipat and Jennifer Hallinan
DOI: 10.1039/C2IB00123C

The other HOT paper is an article from Josch Pauling, Richard Röttger and co-workers, in which they introduce a new integrated online database and analysis platform, EhecRegNet. Motivated by the epidemic outbreak of a multi-resistant Enterohemorrhagic Escherichia coli (EHEC) strain in Western Europe, the group used transcriptional regulatory interactions from E. coli K-12 (a harmless strain) to predict unknown gene regulatory interactions in 16 human pathogens, to potentially aid new treatments.

On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach
DOI: 10.1039/C2IB00132B

Other papers in the issue include a laboratory information management system for DNA barcoding workflows, a novel method for annotating protein function and drug repositioning through incomplete bi-cliques.

Read the rest of the issue here

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Organs-in-chips and the role of metabolism in heat stress responses on the cover of Issue 5

Organs-on-chipsThe articles featured on the cover of this month’s issue are from Andries D. van der Meer and Albert van den Berg and Jenny Gu et al.

Andries D. van der Meer and Albert van den Berg have reviewed the current progress in realistic in vitro tissue models: organs-on-chips.  The review covers recent developments and looks to the future at how organs-on-chips can make an impact on biological research.

Organs-on-chips: breaking the in vitro impasse
Andries D. van der Meer and Albert van den Berg
DOI: 10.1039/C2IB00176D

On a completely different subject, Jenny Gu and colleagues have looked at the mechanism of metabolism response to chronic heat stress in seagrass.  Their study suggests that adaptive mechanisms are involved through metabolic pathways to dampen the impacts of heat stress.

Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness
Jenny Gu, Katrin Weber, Elisabeth Klemp, Gidon Winters, Susanne U. Franssen, Isabell Wienpahl, Ann-Kathrin Huylmans, Karsten Zecher, Thorsten B. H. Reusch, Erich Bornberg-Bauer and Andreas P. M. Weber
DOI: 10.1039/C2IB00109H

Also in this issue are several hot articles on laser ablation for studying the mechanical properties of cytoskeletons, modelling of in vitro cell-free translation and the antioxidant benefits of red wine.

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Issue 4 now available online – ‘From single cells to biology’ themed issue

The latest issue of Integrative Biology is now online, and is a themed issue guest edited by Mina J. Bissell, Cyrus M. Ghajar and Luke P. Lee, entitled ‘From single cells to biology‘.

The inside front cover features an article by Derek C. Radisky and colleagues at the Mayo Clinic, USA, which demonstrates the use of three-dimensional microenvironments to reveal key features of tumor malignancy in lung cancer cells.

Growth of lung cancer cells in three-dimensional microenvironments reveals key features of tumor malignancy
Magdalena A. Cichon, Vladimir G. Gainullin, Ying Zhang and Derek C. Radisky
DOI: 10.1039/C1IB00090J

The issue also features two other HOT articles – a perspective article from Helen M. Blau and co-workers discussing single cell studies of adult stem cell self-renewal, and a research article from Luke P. Lee, Matthias Peter and colleagues featuring an assay platform for quantitative analysis of single cell chemotaxis.

A single cell bioengineering approach to elucidate mechanisms of adult stem cell self-renewal
Penney M. Gilbert, Stephane Corbel, Regis Doyonnas, Karen Havenstrite, Klas E. G. Magnusson and Helen M. Blau
DOI: 10.1039/C2IB00148A

Quantitative and dynamic assay of single cell chemotaxis
Sung Sik Lee, Peter Horvath, Serge Pelet, Björn Hegemann, Luke P. Lee and Matthias Peter
DOI: 10.1039/C2IB00144F

Read the rest of the issue online now!

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Integrative Biology Issue 3 just published

Issue 3 coverOn the cover of Issue 3 is an article from Daniel Irimia and colleagues at Massachusetts General Hospital, on their discovery that the migration of cancer epithelial cells is possible in vitro in the absence of pre-existent chemical gradients, and their creation of a novel strategy to guide this migration within microscale mazes.

Epithelial cell guidance by self-generated EGF gradients
Cally Scherber, Alexander J. Aranyosi, Birte Kulemann, Sarah P. Thayer, Mehmet Toner, Othon Iliopoulos and Daniel Irimia
DOI: 10.1039/C2IB00106C

This issue also features HOT articles from Claudio Sorio et al. on their research on proteins released by Pseudomonas aeruginosa during lung infections of cystic fibrosis patients using a MudPIT approach; and from Xizheng Feng and colleagues at Nankai University on their work in evaluating the toxicity of nanoparticles in zebrafish.

MudPIT analysis of released proteins in Pseudomonas aeruginosa laboratory and clinical strains in relation to pro-inflammatory effects
Gabriella Bergamini, Dario Di Silvestre, Pierluigi Mauri, Cristina Cigana, Alessandra Bragonzi, Antonella De Palma, Louise Benazzi, Gerd Döring, Baroukh Maurice Assael, Paola Melotti and Claudio Sorio
DOI: 10.1039/C2IB00127F

A progressive approach on zebrafish toward sensitive evaluation of nanoparticles’ toxicity
Yang Liu, Bin Liu, Daofu Feng, Chunying Gao, Ming Wu, Ningning He, Xinlin Yang, Lei Li and Xizeng Feng
DOI: 10.1039/C2IB00130F

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Issue 2 now online – including pure human pancreatic alpha cells, a Dectin-1 probe and bacterial motility

This month we’re revelling in Technical Innovations with two on the cover of the issue.

First we have a paper from Martin Kohler and  Elisabetta Dare et al. that deals with the difficulties in identifying and purifying alpha cells from pancreatic tissue to be used in diabetes research. The paper describes a novel protocol for isolating human alpha cells by FACS using autofluorescence and scatter, without staining the cells, and improves the procedure for rat alpha cells

One-step purification of functional human and rat pancreatic alpha cells
Martin Köhler, Elisabetta Daré, Muhammed Yusuf Ali, Subu Surendran Rajasekaran, Tilo Moede, Barbara Leibiger, Ingo B. Leibiger, Annika Tibell, Lisa Juntti-Berggren and Per-Olof Berggren
DOI: 10.1039/C2IB00125J

On the inside front cover Jatin M. Vyas and colleagues at Harvard Medical School and the Whitehead Institute for Biomedical Research describe technology probe a key pathway in invasive fungal infections, which present a significant risk to immunocompromised patients.  ß-1,3-glucan, a major cell wall component of fungal pathogens has been attached to polystyrene beads to probe pathways related to Dectin-1, the major receptor for ß-1,3-glucan.

Use of fungal derived polysaccharide-conjugated particles to probe Dectin-1 responses in innate immunity
Jenny M. Tam, Michael K. Mansour, Nida S. Khan, Nicholas C. Yoder and Jatin M. Vyas
DOI: 10.1039/C2IB00089J

The issue also includes a hot article from Bhushan Toley and Neil Forbes from the University of Massachusetts on how bacterial motility is affected by the strain used and the composition of the tumour when using bacteria as drug delivery vectors

Motility is critical for effective distribution and accumulation of bacteria in tumor tissue
Bhushan J. Toley and Neil S. Forbes
DOI: 10.1039/C2IB00091A

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Issue 1 just published!

Welcome to the first 2012 issue of Integrative Biology!

With this issue we welcome our new Editorial Board Chair, Professor Douglas Lauffenburger, and thank Professor Mina Bissell for her leadership as the inaugural Chair.  Professor Lauffenburger sets out his aim for the journal’s future in his editorial, The multiple dimensions of Integrative Biology.

The exciting cover image is courtesy of Alexander Goryaynov et al., to accompany their review article on single-molecule studies of nucleocytoplasmic transport.  This article is free to access for 6 weeks, so do take a look.

The issue also contains hot review articles from Paolo Gualtieri et al., Fundamental questions and concepts about photoreception and the case of Euglena gracilis and Bio-inspired materials for parsing matrix physicochemical control of cell migration: A review by Hyung-Do Kim and Shelly R Peyton.

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Collective cell invasion of the ECM and neuron patterns on the cover of Issue 12

Welcome to the final issue of 2011!

On the front cover is an article from Integrative Biology Chair, Mina Bissell, and coworkers on how the extracellular matrix acts as a physical barrier to collective cell invasion, an important process in branching morphogenesis, tissue repair and tumour dissemination.

Collective epithelial cell invasion overcomes mechanical barriers of collagenous extracellular matrix by a narrow tube-like geometry and MMP14-dependent local softening
Jordi Alcaraz, Hidetoshi Mori, Cyrus M. Ghajar, Doug Brownfield, Roland Galgoczy and Mina J. Bissell
DOI: 10.1039/C1IB00073J


On the inside front cover is an article from Rashid Bashir and coworkers on the spatial distribution of neurons in cell culture using ink-jet printing and microarray scanners to resolve the large-scale distribution of patterned and unpatterned neuron populations.

Pattern analysis and spatial distribution of neurons in culture
Larry J. Millet, Mitchell B. Collens, George L. W. Perry and Rashid Bashir
DOI: 10.1039/C1IB00054C

As with all our cover articles these are free to access for 6 weeks.

View the rest of the issue here

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On the cover: Vascular smooth muscle contractility depends on cell shape

The hot article on the cover of Issue 11 from Kevin Kit Parker and coworkers shows that smooth muscle cell structure plays a significant role in both functional and dysfunctional vascular regulation.

They engineered in vitro vascular tissues with strictly defined geometries using microcontact printing and muscular thin film technology to test their contractile function, finding that changing cellular shape did not correlate with the more traditional phenotype markers for measuring contraction in vascular tissues.

Vascular smooth muscle contractility depends on cell shape
Patrick W. Alford, Alexander P. Nesmith, Johannes N. Seywerd, Anna Grosberg and Kevin Kit Parker
Integr. Biol., 2011, 3, 1063-1070
DOI: 10.1039/C1IB00061F

As with all our cover article, you can download the article for free for 6 weeks.

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Effects of covalently bound VEGF on cell signalling on the cover of Issue 9

Vascular endothelial growth factor (VEGF) is a highly important growth factor in promoting angiogenesis and is used in tissue engineering to induce the development of blood vessels in the growing tissue. To regulate and maintain VEGF levels during tissue engineering, the factor is usually bound to a tissue scaffold. Interestingly, recent studies have found that mutations in VEGF which change the affinity between VEGF and the scaffold can change the signals that cells receive from VEGF. These changes ultimately cause the production of vessels with different morphologies. However, the effects of different binding affinities on VEGF signaling pathways have not yet been studied in vitro.

Sean Anderson and colleagues from the University of California and Emory University have developed a method to study signalling pathways in vitro by growing a confluent cell monolayer on a flexible base, then exposing the cells to a growth factor (in this case VEGF) and studying the resulting signalling pathways. The main advantage of this method is that the exposure of the cells to the growth factor can be tightly controlled and analysis can begin minutes after exposure, rather than hours or days.

Using this system and mathematical models, the authors show that VEGF covalently bound to a matrix causes a longer response in its receptor VEGF2R and that the interaction between ligand and receptor in stronger. Covalently bound VEGF also has a longer half-life than soluble VEGF.

This knowledge of how a molecule’s signaling properties are affected by its being bound to a matrix will allow tissues to be engineered in greater detail and with increasing complexity. There’s still a lot of work to do in this fascinating area of research. Find out more by downloading the article here – it’s free for the next 6 weeks:

VEGF internalization is not required for VEGFR-2 phosphorylation in bioengineered surfaces with covalently linked VEGF
Sean M. Anderson, Bhupinder Shergill, Zachary T. Barry, Eleana Manousiouthakis, Tom T. Chen, Elliot Botvinick, Manu O. Platt, M. Luisa Iruela-Arispe and Tatiana Segura
Integr. Biol., 2011, 3, 887-896
DOI: 10.1039/C1IB00037C

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The great migration: analysing the behaviour of NK cells

Natural killer (NK) cells form a vital component of the immune system. Regulation of their function is based on interactions with potential target cells in the body, which determine whether the cell becomes activated or not. NK cells have to be capable of migrating towards these target cells for these interactions to occur.

NK cell migration has already been studied in a range of different systems, from viral infection to tumours. However, these studies were only able to analyse the migration of the NK cell population as a whole and could not analyse the behaviour of an individual cell.

This Technical Innovation article from Mohammad Ali Khorshidi and colleagues from The Royal Institute of Technology and the Karolinska Institute in Stockholm, as well as the University of California combines a new in vitro imaging technique with mathematical modelling to quantitatively assess the migration of fluorescently labelled NK cells. Not only does this method allow the movements of a single cell to be tracked, it can also distinguish between both directed and random movement and moments where the cells pause. The results from this work show that cells were more likely to pause in the presence of target cells, but that only a fraction of these pauses were linked to the destruction of  target cells. The reasons for this will only be found with further research.

This article is on the cover of Issue 7 and is free to access for the next six weeks, so download the paper here to find out more about the technique:

Analysis of transient migration behavior of natural killer cells imaged in situ and in vitro
Mohammad Ali Khorshidi, Bruno Vanherberghen, Jacob M. Kowalewski, Kym R. Garrod, Sara Lindström, Helene Andersson-Svahn, Hjalmar Brismar, Michael D. Cahalan and Björn Önfelt
Integr. Biol., 2011, 3, 770-778
DOI: 10.1039/C1IB00007A

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