Author Archive

Shuichi Takayama’s highlights

Shuichi Takayama

We are delighted to draw your attention to Associate Editor Shuichi Takayama‘s top picks on the topic of immuno-engineering.

The immune system is indispensable for health and central to many diseases. Its importance and complexity make the immune system fertile grounds for innovation and integration of biological models with the latest tools to provide biological insights otherwise difficult to obtain. Below are several articles from 2016 issues of Integrative Biology that highlight such efforts where the tools used range from microfluidics and biomaterials to computational.

Neutrophils are the most abundant white blood cells in humans and the 1st responders at sites of injury or insult. The first two articles highlighted below describe new tools to study neutrophil extracellular traps (NETs) which are DNA-protein fibres that these cells produce to physically catch bacteria and protect our body but can also damage tissues as well.


Please follow the links below for free access* to the full papers.

1) Capillary plexuses are vulnerable to neutrophil extracellular traps
L. Boneschansker, Y. Inoue, R. Oklu and D. Irimia

This article describes the use of blood vessel-like branching microfluidic channels to study how NETs can alter blood flow and negatively impact health. An interesting finding is that NETs produced from a small number of neutrophils can have a surprisingly large impact on which downstream channels red blood cells can flow to. This finding provides unique insights into how inflammation, which lead to NET production, may lead to tissue hypoxia and organ injury.

2) Microfluidic device for simultaneous analysis of neutrophil extracellular traps and production of reactive oxygen species
S. F. Moussavi-Harami, K. M. Mladinich, E. K. Sackmann, M. A. Shelef, T. W. Starnes, D. J. Guckenberger, A. Huttenlocher and D. J. Beebe

Neutrophil function can be an indicator of health and disease. Profiling such cellular level functions in patient blood, however, is tricky because of the rapid deterioration of such function with time and the inherent cell-to-cell variability. This paper describes a microfluidic device that can quickly isolate neutrophils from blood and measure their ability to recognize bacteria, produce NETs, and generate reactive oxygen species with single cell resolution.

3) Stiff substrates enhance monocytic cell capture through E-selectin but not P-selectin
J. L. MacKay and D.A. Hammer

Many diseases such as atherosclerosis, diabetes, and obesity cause chronic inflammation.  Interestingly, these types of disease are also associated with blood vessel stiffening.  This paper provides a mechanistic link between these two observations by clever use of biomaterials to show that E-selectin, but not P-selectin, mediate monocyte adhesion in a substrate stiffness-dependent manner.

4) 3-D individual cell based computational modeling of tumor cell–macrophage paracrine signaling mediated by EGF and CSF-1 gradients
H. Knutsdottir, J. S. Condeelis and E. Palsson

Macrophages and tumor cells mutually influence directed migration to metastasize. The details of such behavior, however, is difficult to grasp intuitively or with simple equations especially in 3D environments. This article uses computational models to reveal how chemical communications through EGF and CSF-1 explains complex cellular behaviors observed both in vitro and in vivo such as what macrophage numbers maximize tumor cell migration.

Integrative Biology publishes novel insights into biological questions, which have been achieved through the use of new technologies, techniques and methods. If your research scope fits that of the articles above, please get in touch; we would be very interested to hear more.

We hope you enjoy reading these articles.



*Access is free until 06/05/2016 through a registered RSC account.

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MMB Lab selects their top cancer-related articles

Microtechnology, Medicine and Biology Lab

The Microtechnology, Medicine and Biology Lab (MMB Lab, University of Wisconsin-Madison, USA) is interested in applying the lab’s technologies to cancer.

Led by David J. Beebe, Editorial Board member for Integrative Biology, the team works across disciplines and disease boundaries to create solutions that can be translated into widespread use.

The lab has selected their top cancer-related articles published recently in Integrative Biology. Please see below what they say about each article – all free to access for the next 4 weeks!*


1) Human breast cancer invasion and aggression correlates with ECM stiffening and immune cell infiltration
I. Acerbi, L. Cassereau, I. Dean, Q. Shi, A. Au, C. Park, Y. Y. Chen, J. Liphardt, E. S. Hwang and V. M. Weaver

Mary Regier- This paper supports other articles pointing out the importance of microenvironmental factors including cell-cell interactions, cell-matrix interactions, and matrix mechanics and architecture and their intratumoral heterogeneity in breast cancer behavior and patient prognosis. Our selection highlights the variety of microenvironmental factors that influence cancer progression and spread.


2) Marker-free detection of progenitor cell differentiation by analysis of Brownian motion in micro-wells
F. Sekhavati, M. Endele, S. Rappl, A.-K. Marel, T. Schroeder and J. O. Rädler

Patrick Ingram- In this paper, the authors present a marker-free, high throughput, and single cell compatible method to monitor granulocyte-macrophage progenitor differentiation via the changes in Brownian motion as the cells differentiate into adherent macrophages. Though not investigated directly, these same methods can be further applied to monitor molecular binding events in living cells, allowing the high throughput study of membranes and surface receptors in heterogeneous cancer cell populations. Sekhavati et al. provide a compelling proof-of-concept that uses ubiquitous and accessible physics to readout underlying biological processes.


3) A cell-ECM screening method to predict breast cancer metastasis
L. E. Barnery, E. C. Dandley, L. E. Jansen, N. G. Reich, A. M. Mercurio and S. R. Peyton

José A. Jiménez-Torres- In this paper, the authors presented an in vitro biomaterial system to investigate the role of cancer-cell integrin binding to different ECM matrices inspired by in vivo secondary tissue targets of breast cancer metastasis. Their experiments highlight the heterogeneity of breast cancer and how this is an obstacle in the clinical success of integrin-targeted therapeutics.


4) Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories
D. E. White, J. B. Sylvester, T. J. Levario, H. Lu, J. T. Streelman, T. C. McDevitt and M. L. Kemp

Brian Johnson- An interesting paper tackling a challenge problem; White et al. explore multi-cellular interactions in morphological development using a network analysis approach that enables the quantitative comparison of experimental data to computational modelling simulations. While the technique was applied to characterize emergent spatial phenotypic patterns found in developing tissues, these same principles could be used to tease apart and model the extensive spatial heterogeneity found in the tumour microenvironment of patient derived samples.



We hope you enjoy reading these articles as much as we did.

Integrative Biology publishes novel insights into biological questions, which have been achieved through the use of new technologies, techniques and methods. If your research scope fits that of the articles above, we would be very interested to hear more.

Please email us today, read more about our scope, or submit your article via our online submission portal.


*Access is free until 20/03/2016 through a registered RSC account
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Regulating with RNA in Bacteria and Archaea Conference

Many congratulations to Bridget Watson, Maya Shamir and Adrien Chauvier on their poster prize success at the Regulating with RNA in Bacteria and Archaea Conference, which took place from 5th-8th December 2015 in Cancun, Mexico.

This conference was the fourth in a series of extremely successful meetings exploring the latest findings regarding this important class of regulators.

The event was a premier forum for the presentation of cutting-edge advances and the latest perspectives in the areas of discovery, mechanism, structure and evolution of bacterial riboregulators. Sessions covered prominent and emerging roles of small RNAs in regulatory networks as well as their diverse mechanisms of action.

Integrative Biology was the proud sponsor of the poster prizes at this conference. The recipients received a books voucher and a Royal Society of Chemistry certificate.

The winner and runners-up were:

Winner: Bridget Watson (University of Otago, New Zealand)
Runners-up: Maya Shamir (Weizmann Institute, Isreal) & Adrien Chauvier (Université de Sherbrooke, Canada)

The picture shows Professor Gerhart Wagner (Uppsala University) handing the certificates and vouchers to the winners

The judges of the prizes thought the quality of the presentations and posters were really high and, from the Integrative Biology team, we would like to thank everyone that attended or presented at the meeting.

For more details on this event, please visit the conference website.

Many congratulations on this achievement from the Integrative Biology team

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Global Engage to host 3 exciting Congresses in October 2015

Global Engage are pleased to announce a set of 3 co-located events,  attracting over 400 attendees and more than 50 poster presentations in 2014.


October 20 – 21 2015, London UK

Radisson Blu Edwardian Heathrow
140 Bath Road
Hayes
UB3 5AW
United Kingdom


Microfluidic Congress

Attracting experts working in microfluidic development and application, including point-of-care diagnostics, single cell analysis, lab-on-a-chip applications, droplet microfluidics and next generation microfluidics, the conference will examine the latest developments in the technologies and techniques being used for progressing medical research in areas such as disease monitoring, diagnostics, organ-on-a-chip and synthetic biology. The challenges and possibilities of microfluidics will also be examined.

Confirmed Speakers

Agenda

More information


Synthetic Biology Congress

Designed for experts working in genome engineering, technological developments, protein design, cell building, bio-manufacturing and gene editing, the Synthetic Biology Congress will examine the latest developments in these fields in both the healthcare and plant biology sectors. New to the conference will be the addition of a third stream, focusing on Investment, Start-Ups, Strategy and Bioethics, for those looking for investment opportunities and seeking to further exploit their research.

Confirmed Speakers

Agenda

More information


qPCR & Digital PCR Congress

Bringing together over 300 industry & academic experts working in areas such as molecular biology/diagnostics, gene expression, genomics, biomarkers, pathogen detection, GMO, mRNA, NGS, bioinformatics and data management, the congress will examine the latest developments, opportunities and applications of both dPCR and qPCR through case studies across diverse areas such as oncology, virology, infectious diseases, vaccines, prenatal diagnosis, clinical applications, microbiology, food microbiology, plant/ecology genomics and other novel applications.

Confirmed Speakers

Agenda

More information

We look forward to seeing you in London!

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The dynamics of breast cancer mechanics

According to Cancer Research UK, Breast Cancer in the third commonest type of cancer diagnosed and accounts for 15% of all female cancer deaths. A clear understanding of the biology behind this malignancy is urgently needed. With that in mind, researchers at the University of California San Francisco have unravelled the specific invasive properties of breast cancer tumours.

Acerbi et al. investigated the link between breast cancer tissue and the stiffness of the tissue scaffold, the extracellular matrix (ECM). In non-cancerous tissues, the ECM is integral for the maintenance of tissue structure and is a regulator of the dynamic communication between cells. Characteristically, the ECM is collagen-rich yet can take many forms depending on the need of the tissue because of its responsive nature. This active role of the ECM unfortunately presents the opportunity for deleterious remodelling. The researchers found that hallmarks of the tumour transformation include deposition of excessive collagen, elevated mechanosignalling and an association with a stiffened ECM at the invasive front of the tumour.

Compared to normal breast tissue, the collagen was progressively assembled into thicker fibres and linearised, causing stiffening of the ECM. Macrophages sent by the immune system release soluble factors that assist with the remodelling. The researchers correlated the influx of immune cells with the increase in SMAD signalling, a cascade which changes the gene expression of the tissue and is likely to be part of the molecular pathway behind the extra collagen production.

The core tissue of the tumour was less stiff than the invasive edge

The researchers identified that tumours caused by different breast cancer-associated mutations can have diverse ECM compositions, and even different regions of the same tumour can be biochemically distinct. This has important implications for the testing and imaging of breast cancer tumours and provides convincing evidence that the ECM is more complex in cancer pathology than previously thought.


You can read the full paper for free* using the link below:
Human breast cancer invasion and aggression correlates with ECM stiffening and immune cell infiltration
I. Acerbi, L. Cassereau, I. Dean, Q. Shi, A. Au, C. Park, Y. Y. Chen, J. Liphardt, E. S. Hwang and V. M. Weaver
Integr. Biol., 2015, Advance Article
DOI: 10.1039/C5IB00040H, Paper

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About the webwriter

Rebecca Muir is a research assistant in the Medical Sciences Division of Oxford University. Her research interests include cell biology, gender studies, philosophy of science, and mitochondrial disease. Rebecca was shortlisted for the Chemistry World’s Science Communication Competition 2015. She tweets at @rebeccalydiam and her personal website can be found on rebeccamuir.co.uk.

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*Access is free until 16/08/2015  through a registered RSC account.

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Computational Integrative Biology Themed Issue

We are delighted to announce the publication of Issue 11, Volume 6 of Integrative Biology, which is a themed issue dedicated to Computational Integrative Biology, guest edited by Jan Baumbach from the University of Southern Denmark.

The discovery of differentiated new medicines that provide clear benefits to patients remains challenging in spite of ever increasing investments. At the same time the quantity and diversity of patient related data continues to grow exponentially (pre-clinical data, clinical data, patient data, EHR, ‘OMICs data, and information associated with medicines in general). The scientific community is starting to leverage this wealth of information in ways that have the potential to disrupt the traditional drug discovery and development process as we know it.

Within this themed issue are five HOT research papers, which received particularly high scores during peer review – click on the links to download the articles*:

1. Researchers from the Imperial College London discuss the network wiring of pleiotropic kinases yields insight into protective role of diabetes on aneurysm.

2. Binding free energy based structural dynamics analysis of HIV-1 RT RNase H–inhibitor complexes, a research paper from scientists at the University of Southern Denmark.

3. Nataša Pržulj and colleagues give their approach on the integrated disease network.

4. Interesting research on multi-omics interactome analysis applied to the elucidation of epithelial–mesenchymal transition-related pathways

5. Our last HOT article is focused on an improved interolog mapping-based computational prediction of protein–protein interactions.

Click here to view the full Computational Integrative Biology themed issue.

We hope you enjoy reading this collection as much as we did.

*Access is free until 24.11.14 through a registered RSC account – click here to register

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