Archive for March, 2012

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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Top ten most accessed articles in February

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

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
Integr. Biol., 2012, 4, 360-367
DOI: 10.1039/C2IB00148A

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

Quantitative and dynamic assay of single cell chemotaxis
Sung Sik Lee,  Peter Horvath,  Serge Pelet,  Björn Hegemann,  Luke P. Lee and Matthias Peter
Integr. Biol., 2012, 4, 381-390
DOI: 10.1039/C2IB00144F

High-throughput clonal analysis of neural stem cells in microarrayed artificial niches
Marta Roccio, Samy Gobaa and Matthias P. Lutolf
Integr. Biol., 2012, 4, 391-400
DOI: 10.1039/C2IB00070A

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
Integr. Biol., 2012, 4, 259-269
DOI: 10.1039/C2IB00106C

Quantification of local matrix deformations and mechanical properties during capillary morphogenesis in 3D
Ekaterina Kniazeva, John W. Weidling, Rahul Singh, Elliot L. Botvinick, Michelle A. Digman, Enrico Gratton and Andrew J. Putnam
Integr. Biol., 2012, Advance Article
DOI: 10.1039/C2IB00120A

Bio-inspired materials for parsing matrix physicochemical control of cell migration: A Review
Hyung-Do Kim and Shelly R. Peyton
Integr. Biol., 2012, 4, 228-236
DOI: 10.1039/C1IB00069A

Microfluidic sample preparation: cell lysis and nucleic acid purification
Jungkyu Kim, Michael Johnson, Parker Hill and Bruce K. Gale
Integr. Biol., 2009, 1, 574-586
DOI: 10.1039/B905844C

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

Hyaluronic acid matrices show matrix stiffness in 2D and 3D dictates cytoskeletal order and myosin-II phosphorylation within stem cells
Florian Rehfeldt, André E. X. Brown, Matthew Raab, Shenshen Cai, Allison L. Zajac, Assaf Zemel and Dennis E. Discher
Integr. Biol., 2012, 4, 422-430
DOI: 10.1039/C2IB00150K

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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Perspective: Single-cell analysis platforms to study stem cell self-renewal

Stem cells are defined by their ability to self-renew or to differentiate into a range of somatic cell types. Adult stem cells, such as haematopoietic stem cells are found in specialised niches within the body and have been studied for decades. Much of our knowledge about these cells is based on in vitro experiments but the effects of moving them from their in vivo niche to culture conditions are unclear.

This Perspective from Penney Gilbert and colleagues from the USA and Sweden focuses on adult stem cells found in skeletal muscle, also known as satellite cells. They address the problem that, once extracted from muscle and placed into culture, satellite cells quickly lose their ability to self-renew, complicating studies into their biology. The development of new bioengineering approaches, such as hydrogel microwell arrays, could solve this problem. These approaches can accurately monitor the behaviour of satellite cells and provide robust data sets, thanks to the number of different tests that can be carried out in parallel.

To illustrate the usefulness of such tools, the authors show how stem cell division and self-renewal can be tracked in clonal assays using time-lapse microscopy. By increasing the stiffness of the hydrogel microwells in the assays, satellite cells can be maintained in culture for up to one week and successfully engraft back into mouse muscle.

Stem cells hold the potential to become part of powerful medical treatments and therapies, but only if we understand how we are changing them by removing them from their niche. This Perspective pushes this issue to the fore and offers some suggestions as to how we can further improve stem cell culture. Read this HOT review for free for the next four weeks (following a simple registration for individual users)

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

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Diabetes reduces antioxidant benefits

Scientists in China have discovered that the blood plasma proteins of type II diabetes patients reduce the beneficial effects of dietary polyphenols.

Blood

Raised glucose levels in the blood of diabetics affects the structure of their blood plasma proteins, which prevents the proteins carrying healthy antioxidants to cells and tissues

Polyphenols are antioxidants and are found in chocolate and red wine, for example. In the body, they scavenge cell damaging free radicals. They bind to proteins in blood plasma, constantly switching between the bound and unbound forms. This may be how polyphenols are delivered to cells and tissues, but this is unproven.

Diabetics have raised levels of glucose in their blood. Glucose can also bind to plasma proteins, says Jianbo Xiao of Shanghai Normal University, who led the research. ‘Exposing plasma proteins to glucose influences their structures and functions,’ he says. So, to investigate this influence, Xiao’s team studied the polyphenol-binding abilities of healthy plasma proteins and compared them to the binding abilities of type II diabetes plasma proteins using fluorescence spectroscopy.

The team found that type II diabetes plasma proteins have an affinity 1 to 10 times lower for polyphenols than healthy proteins. ‘The non-covalent interactions between polyphenols and plasma proteins are usually caused by four major forces: hydrogen bonding, van der Waals forces, hydrophobic interactions and electrostatic interactions,’ says Xiao. The difference between the affinities was larger when more hydrophobic polyphenols were tested. There was only a slight difference in the affinity when the polyphenol’s ability to form hydrogen bonds was changed. So, the main force in the interaction between polyphenols and blood proteins is the hydrophobic force and not hydrogen bonds. It could be that as glucose alters a protein’s structure, it is this hydrophobic interaction that is altered, decreasing the binding affinity.

Ann Hagerman, an expert in the interactions of proteins and polyphenols and their bioactivity at Miami University, US, says that as research has been focused for many years on unmodified proteins, seeing how such modifications affect the interaction is quite interesting. She would like to see the work extended to other small molecules, using methods in addition to fluorescence spectroscopy to study the interactions.

Xiao’s team will now investigate why hydrophobic polyphenols cause a larger difference between the binding affinities of healthy and type II diabetes plasma proteins. The findings may affect the use of polyphenols in diabetes therapies, they say.

Glycation of plasma proteins in type II diabetes lowers the non-covalent interaction affinities for dietary polyphenols
Yixie Xie, Jianbo Xiao, Guoyin Kai and Xiaoqing Chen
DOI: 10.1039/C2IB00185C

Read the original article at Chemistry World

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Top ten most accessed articles in January

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

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

Quantitative and dynamic assay of single cell chemotaxis
Sung Sik Lee,  Peter Horvath,  Serge Pelet,  Björn Hegemann,  Luke P. Lee and Matthias Peter
Integr. Biol., 2012, Advance Article
DOI: 10.1039/C2IB00144F

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

Bio-inspired materials for parsing matrix physicochemical control of cell migration: A Review
Hyung-Do Kim and Shelly R. Peyton
Integr. Biol., 2012, 4, 228-236
DOI: 10.1039/C1IB00069A

Hedgehog signaling in myofibroblasts directly promotes prostate tumor cell growth
Maribella Domenech, Robert Bjerregaard, Wade Bushman and David J. Beebe
Integr. Biol., 2012, 4, 142-152
DOI: 10.1039/C1IB00104C

Migration dynamics of breast cancer cells in a tunable 3D interstitial flow chamber
Ulrike Haessler, Jeremy C. M. Teo, Didier Foretay, Philippe Renaud and Melody A. Swartz
Integr. Biol., 2012, Advance Article
DOI: 10.1039/C1IB00128K

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

Quantification of local matrix deformations and mechanical properties during capillary morphogenesis in 3D
Ekaterina Kniazeva, John W. Weidling, Rahul Singh, Elliot L. Botvinick, Michelle A. Digman, Enrico Gratton and Andrew J. Putnam
Integr. Biol., 2012, Advance Article
DOI: 10.1039/C2IB00120A

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

Biophysical regulation of tumor cell invasion: moving beyond matrix stiffness
Amit Pathak and Sanjay Kumar
Integr. Biol., 2011, 3, 267-278
DOI: 10.1039/C0IB00095G

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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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

View the rest of the issue here

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Proteomics offers insight into how bacteria infect and colonise the lungs of cystic fibrosis patients

Proteomics has given scientists new insights into how bacteria infect and colonise the lungs of cystic fibrosis (CF) patients.

The paper from Gabriella Bergamini and colleagues from Verona, Milan and Tuebingen, uses MudPIT analysis of polypeptides produced by strains of the bacterium Pseudomonas aerunginosa, which is commonly found in the lungs of CF patients, to discover molecules which allow the bacterium to evade the host immune system and cause inflammation in the lung. The authors found that strains isolated at different stages of infection expressed different sets of proteins to either help establish a culture or maintain growth in the lung.

In strains taken from the early stages of infection, bacteria secrete pro-inflammatory molecules, such as metalloproteases (MMPs). MMPs also prevent host neutrophils from destroying bacteria by cleaving the chemokine receptor CXCR1. This prevents signalling which would stimulate the neutrophil to phagocytose the bacterium.

Pseudomonas aerunginosa infection is the main cause of death in CF patients and this study has given us some clues as to how infections in the future could be treated. To find out more, download this HOT article here – it’s free for the next four weeks.

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
Integr. Biol., 2012, 4, 270-279
DOI: 10.1039/C2IB00127F

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Deciphering the regulatory networks of pathogenic EHEC

Almost a year has passed since the devastating Enterohemorrhagic E. coli (EHEC) epidemic in Western Europe and the numbers still make sombre reading. Farmers lost millions of Euros in an outbreak where nearly 4,500 people became infected and more than 50 people lost their lives. Scientists are still learning lessons from the bacterium at the centre of  last year’s events, in the hope that, should a similar pathogen threaten human lives again, we will be better equipped to fight it.

This paper from Josch Pauling, Richard Roettger and colleagues from Germany, Mexico and Brazil presents the resource EhecRegNet, an online database and analysis platform to investigate the transcriptional regulatory networks which control traits such as pathogenicity, reproduction and survival of cells. Using the lab-based E. coli K12 strain as a model, the authors were able to identify interactions which had been conserved between K12 and any one of 16 human pathogenic strains. An interaction was designated as conserved if both the target gene and binding site were preserved between strains. The authors hope that this resource will be used to show suitable targets for further investigation and lab work.

This article forms part of our upcoming themed issue on Computational Integrative Biology and will be available online for free for the next four weeks. Download the article here and see what else EhecRegNet has to offer.

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

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