BiotecVisions 2012, January

original image

Editors: Judy Peng /jp; Uta Göbel /ug; Lucie Kalvodova /lk


Contributors: Bill Mullen /bm; Danny Asling /da;Frédérique Belliard /fb; Fay Wolter /fw; Gillian van Beest /gvb; Kerstin Brachhold /kb; Karen Chu /ky; Lotte Nielsen /ln; Luaine Bandounas /lb; Meghana Hemphill /mh; Sarah Brett /sb; Simone Bayram /sba; Sarah Mellor /sm; Susan Vice /sv; Tiffany McKerahan /tf; Tiffany McKerahan /tm; Tina Wang /tw; Materials Views /mv; Prisca Henheik /pmh


Biophysicists gather in Beijing

original image

The 17th International Biophysics Congress (IUPAB) was successfully held at the China National Convention Center, Beijing, China, Oct 30–Nov 3, 2011. Sponsored by the International Union for Pure and Applied Biophysics (IUPAB), and jointly organized by the Biophysical Society of China (BSC) and the Institute of Biophysics, Chinese Academy of Sciences (IBP), the congress was hosted by China for the first time since it was first launched in 1961.

As an interdisciplinary science that covers almost every area in the life sciences, biophysics is becoming one of the most active and most innovative disciplines in the field. The congress was attended by more than 2500 delegates from 41 countries. More than 300 world renowned scientists, including three Nobel Laureates, were invited to present the latest developments in their research fields.

Aiming at the promotion of human health by applying biophysics research, the congress featured 31 sessions, 3 satellite meetings and 8 plenary lectures, with the topics covering numerous research areas such as nanobiotechnology, brain imaging and cognitive science, biophysics of the immune response, translational medicine, etc. The congress also established a Young Scientist Travel Award and a Best Poster Award to encourage active participation of young researchers and graduate students from developing countries. Overall, the 17th International Biophysics Congress provided an excellent platform for the exchange of new ideas and advances. The 18th Biophysics congress will be held at the Brisbane Convention & Exhibition Centre, Brisbane, Queensland, Australia, August 3–7, 2014. /tw

Dr. Tina Wang is Author Services Manager in the Beijing Office of Wiley-Blackwell and is the local editorial liaison for life science journals such as Journal of Separation Sciences and Proteomics.

Materials Views provides news and analysis on the most interesting and relevant breakthroughs in materials science, written by the editors of some of the top journals in the field, and covering hot subject areas such as nanotechnology, polymers, energy, electronics and more. /mv

original image

Yeast cells wrapped in graphene oxide

Interfacing living yeast cells with graphene nanosheaths is achieved via versatile layer-by-layer assembly.

original image

Highly active enzymes on graphene oxide surface

Chemically reduced graphene oxide is a good substrate for high enzyme loads, and activities comparable with those found in solution can be achieved on this surface, as shown by Chinese scientists.

Dendrimer-based drug delivery vehicles

Coupling of a novel multitargeted sunitinib analogue to a generation-3 dendrimer yields a conjugate with retained pharmacological activity.

Getting published

original image

Dashes and hyphens: Lions and lambs?

Dashes and hyphens have been long confused for one another. If you know how to use them correctly however, they bear no more resemblance to each other than a lion and a lamb. While this makes little difference to the spoken word, in technical writing they play a significant role in indicating the relationship between words and numbers.

The dashes

The most commonly used being the en dash (“–”). Long and lean like a lion, they prowl through technical writing, clarifying the relationship between facts and figures.

It is used to denote ranges, e.g. 20–40°C. When there is a chance of being misconstrued as “subtraction”, use the preposition “to”, e.g. “voltage of 50 V to 100 V” rather than “a voltage of 50–100 V”.

This type of dash is also used in relationships and connections, e.g. Poisson-Boltzmann equation.

The hyphen

A lamb? It may be short and sweet, but without it the reader might get lost.

Do hyphenate

– prefixes that are words in their own right, e.g. half-life

– compound terms and adjectives, e.g. salt-leached water

Do not hyphenate

– prefixes that cannot stand as words in their own right, e.g. non, anti, bi, co, etc.; exception: when two vowels or the same consonants follow each other, e.g. pre-operative, anti-inflammatory

The hyphen can be used generally for all kinds of wordbreaks in printed texts, but make sure you get them right, e.g. the-rapist is misleading.

If a lion comes across a lamb, he'll more than likely devour it, but the dashes and the hyphen can live together in a sentence in harmony, and they can become an ally to the technical writer if used correctly. /fw

This is an excerpt of an article by Fay Wolter in the December 2011 issue of ImmunoVisions.

Full article at:

ErbB network model for personalized medicine

Determining which patients will benefit from a given treatment remains one of the most challenging problems in oncology. With the increase in molecular-targeted therapies, many drugs fail in clinical trials because they are applied broadly rather than to just the subset of cancer patients most likely to respond. In this study, Prasasya, Vang, and Kreeger tackle the question of how to use molecular information to identify the sensitive group. Through quantitative experiments and mathematical modeling, they identify a multivariate function linking protein-level expression of ErbB receptors and ligands to sensitivity to an ErbB kinase inhibitor in ovarian cancer cells. Examination of the successful models demonstrated that ErbB ligands were more informative than ErbB receptors in predicting cell response. Through model analysis they identify a minimal signature of only three proteins needed to predict sensitivity, suggesting this approach could be implemented clinically. /sv [1]

original image

Breast implants: Can nanotechnology improve them?

original image

This review discusses the history of implants used in breast reconstruction and augmentation, the most frequently performed plastic surgery today. Currently, only silicone rubber-based silica nanocomposite implants are available in the US. The most prevalent issues involving breast implants include capsular contracture, gel bleed, implant rupture, and infection. In the past, studies have been reported which linked breast implants to increased incidence of systemic diseases such as autoimmune disease, various forms of cancer, and psychological disease. Additionally, it is largely unnoticed that nanotechnology is involved: the silicone rubber shell is reinforced with nanosilica so implants appear to be homogeneous and crystal clear. The authors hope that this review will contribute to a better understanding of the controversial issues and motivate material scientists and medical doctors to work together to develop alternatives based on new nanotechnology. /mh [2]

original image

Olive oil protects the kidneys

Researchers from Tunisia show that extra virgin olive oil can protect the kidneys from damage caused by some nephrotoxic compounds. They used whole and fractionated extra virgin olive oil to treat rats which had been exposed to the effect of the pesticide 2,4-dichlorophenoxyacetic acid. This pesticide is toxic and chronic exposure leads to kidney damage. The renal condition was evalutaed by monitoring the oxidative stress markers and lipid peroxidation in the kidneys. Whole olive oil protected the kidneys against the harmful effects of the pesticide better than the oil's lipophilic and hydrophilic fractions. /lk [3]

original image

Will biodiesel derived from algal oils live up to its promise?

Algae are attracting considerable attention as a potential source of biodiesel. Gerhard Knothe from the US Department of Agriculture discusses the properties, performance problems, and production of biodiesel from algal oils in a recent Feature article in Lipid Technology. /lk [4]

original image

Automated microtissue production for drug testing

Although it is widely recognized that 2D cell cultures do not reflect the physiological environment of cells in native tissues, 3D culture systems are not commonly used in pre-clinical drug testing. This is mostly due to a lack of automated high-throughput systems for 3D cultivation. Researchers at InSphero AG, Z�rich, Switzerland, show the robustness of spherical microtissues (multicellular spheroids) production and drug testing in a 96-well hanging-drop multiwell plate format, on a standard 96-well channel robotic platform. Microtissue models derived from six different cell lines were produced and characterized according to their growth profile and morphology. The presented technology will aid the implementation of more organotypic model systems at early stages of the drug discovery process. /ug [5]

original image

The ancient beast within: Cancer as an alternative organism

In a recent issue of BioEssays, Mark Vincent argues that cancer represents a re-emergent, ancient program (“atavism”) inherent to all eukaryotic cells. Cancer cells thus result from the adoption of an ancient default program which consists of three programmatic elements: taxonomic phylogenation, atavistic re-primitivisation and adaptive resilience. The author indicates that cancer is a “species” entirely different from the host (e.g. it shows gross aneuploidy) and therefore occupies a different place in the Tree of Life from the original host (phylogenation). Furthermore, he proposes that the path from unicellularity to multicellularity is bi-directional and that cancer is a result of the return journey (re-primitivisation). Cancer cells thus display traits that have re-emerged from a distant past, such as fermentation (Warburg Effect) and immortality. Finally, cancer cells forsake their membership in the multicellular host, leading to deconstruction of the metazoan phenotype (adaptive resilience). /kb [6]

original image

Tissue engineering – to scaffold or not to scaffold

Tissue engineering refers to the in vitro culture of tissues and organs, and offers the promise of replacing worn/damaged body parts that are vital to our survival and wellbeing. There are three basic components to tissue engineering: cells, bioactive agents to induce cells to function, and scaffolds that house the cells and act as the substitute for the damaged tissue. The question “to scaffold or not to scaffold” is however, dependent on various parameters, as each has its relative advantages and disadvantages. Using various applications as examples (such as cartilage, bone and nerve regeneration), Hasirci and colleagues provide a comprehensive review on cell-based therapies with or without scaffolds. This review serves as an excellent entry point and literature reference to those wishing to understand the role of scaffolds in tissue engineering. /jp [7]

original image

Cell-based biosensors

Cell-based biosensors can be applied in environmental monitoring, drug screening as well as for clinical diagnostics. Compared to molecular-based biosensors, cell-based biosensors mimic physiological situations more closely, show enhanced specificity and sensitivity, and can detect unknown compounds and toxins. Current limitations include weak cell-substrate attachment, the 2D cell microenvironment, and limited shelf life. To address these limitations, one can encapsulate cells in hydrogels to provide a 3D environment, which can be combined with novel biomaterials and microtechnologies. TianJian Lu, Feng Xu (Xi'an Jiaotong University, China) and collaborators present the state of the art in hydrogel-based cell-based biosensor development and review remaining challenges as well as potential solutions to these problems. /ug [8]

original image

Protein-based optical device with reset function

Analytical single-use test strips evaluated by a color change have been used in industry/academia for almost half a century. Ulla Wollenberger and co-workers (Golm and Gie�en, Germany) present the development of a reusable sensing system coupled to optical detection. In their model, cytochrome c was immobilized in a mesoporous indium tin oxide film. The cytochrome c-catalyzed oxidation of a redox-sensitive dye is then measured spectroscopically. When the dye is co-immobilized with the protein, its redox state can be easily controlled by application of an electrical potential at the supporting material. This electrochemical reset function enables repetitive signal generation and direct calibration of small test devices. The described principle can be extended to other color-forming redox reactions and enzyme systems. /ug [9]

original image

Why is hypertrophy not discussed in papers on aging?

Yeasts are attractive models for cellular aging. There is only on eproblem: The hypothesis of accumulation of the senescence factor, which was the basis for introducing yeast to the group of model organisms of gerontology, finds no experimental support. Only one phenomenon, hypertrophy, the increase in size of the cells, always accompanies symptoms of aging, not only in Saccharomyces cerevisiae, but also in Schizosaccharomyces pombe. The idea that an increase in size of yeast cells is the cause of replicative aging of Saccharomyces cerevisiae is not new. This observation accompanies all studies, and the fact of reaching exceptionally big volume by cells approaching reproductive limit is accepted by all experimenters. The question arises why the role of hypertrophy, the only phenomenon always accompanying replicative aging, is never discussed in scientific papers? The authors of one experimental paper rejected this explanation and concluded that “an increase in cell size does not necessarily lead to a shortening in life span”. The results of the current study lead to quite different results, fully supporting the hypertrophy hypothesis. The hypertrophy hypothesis seems to explain the phenomenon of replicative aging of yeast much better than the hypothesis of the senescence factor accumulation. /fb [10]

original image

Profiling a killer: The development of Cryptococcus neoformans

The ability of fungi to switch between unicellular and multicellular hyphal growth has a profound impact on our health and the economy. Many fungal pathogens of humans, animals, and plants are dimorphic, and the ability to switch between morphological states has been associated with their virulence. This review describes and discusses the most interesting aspects of Cryptococcus neoformans development and addresses their impact on pathogenicity. C. neoformans is a human fungal pathogen that causes life-threatening meningoencephalitis mostly in immunocompromised hosts. C. neoformans grows vegetatively as a budding yeast and can be frequently found in tree hollows and pigeon guano. During the sexual cycle, Cryptococcus switches from yeast growth to hyphal growth. Spores resulting from sexual development are infectious propagules and can colonize the lungs of a host. Recent studies have raised intriguing questions and hypotheses that may lead to better treatments against this emerging pathogen. /gvb [11]

original image

Quantitative analysis of glycerol fermentation by E. coli

Glycerol has become a highly attractive and exploited carbon source for the production of fuels and reduced chemicals due to its availability, low price, and high degree of reduction. While the recent discovery that Escherichia coli is able to utilize glycerol under anaerobic conditions has provided a new platform for metabolic engineering strategies aimed at fuel and chemical production, none of the recent reports using glycerol as a carbon source have focused on a quantitative analysis of fermentative glycerol metabolism in E. coli. In the work reported here, the Gonzalez group at Rice University extends their work on glycerol fermentation by E. coli through the use of kinetic modeling and metabolic control analysis. In addition to gaining a more quantitative understanding of glycerol fermentation by E. coli, this analysis identified key genetic manipulations that enabled the efficient production of ethanol from crude glycerol under anaerobic conditions, demonstrating the potential for the industrial scale conversion of glycerol waste streams to higher value products. /sv [12]

original image

Microbial diversity in sea

Cobalt-rich crusts are important metallic mineral resources with great economic potential, usually distributed on seamounts located in the Pacific Ocean. Microorganisms are believed to play a role in the formation of crusts as well as in metal cycling. To explore the microbial diversity related to cobalt-rich crusts, 16S ribosomal RNA gene clone libraries were constructed from three consecutive sediment layers. In total, 417 bacterial clones were obtained from three bacterial clone libraries, representing 17 distinct phylogenetic groups. Proteobacteria dominated in the bacterial communities, followed by Acidobacteria and Planctomycetes. Compared with high bacterial diversity, archaea showed a remarkably low diversity, with all 137 clones belonging to marine archaeal group I except one novel euryarchaeotal clone. The microbial communities were potentially involved in sulfur, nitrogen and metal cycling in the area of cobalt-rich crusts. Sulfur oxidation and metal oxidation were potentially major sources of energy for this ecosystem. This is the first report on microbial diversity in sediments associated with cobalt-rich crusts, and it casts fresh light on the microbial ecology of these important ecosystems. /ln [13]

original image

Directed evolution improves the activity of potential thrombolytic agent

Compared with widely used thrombolytic agents, such as tissue plasminogen activator and urokinase, several cheaper and safer resources have been extensively investigated over the years to combat thrombotic diseases. Among them, nattokinase, which was extracted from a traditional Japanese fermented natto, has attracted significant interest. Whether nattokinase may become a widely used thrombolytic agent mainly depends on the enhancement of its properties, e.g. prolonging the half-life with oral administration and improving the stability and catalytic efficiency. In this study, researchers used directed evolution to improve the fibrinolytic activity of nattokinase to broaden its medical or commercial applications. They demonstrate that it is feasible to generate a mutant library of nattokinase to obtain a mutant with enhanced catalytic efficiency. /lb [14]

original image

Why HIV structure alone would not pave the way for an HIV vaccine

In spite of 25 years of intensive research, no effective human immunodeficiency virus type 1 (HIV-1) vaccine has yet been developed. One reason for this is that investigators have concentrated mainly on the structural analysis of HIV-1 antigens – based on the assumption that it would be possible to identify elements of the antigen that would be relevant for vaccine design by examining the structure of viral antigens bound to the antibodies. In this comprehensive review, Marc Van Regenmortel (CNRS/ UDS, Strasbourg, France) sets the story straight and explains in detail why focusing on HIV antigen structure alone will not provide the solution we need when it comes to developing an effective HIV vaccine. /sb [15]

original image

T-cell quality for HIV-vaccines

Different pathogens stimulate different innate immunity responses, which in turn lead to distinct qualities of the elicited T cells. T-cell quality plays a key role in orchestrating immune responses and delivering the ultimate effector control of invaders. At the same time, different qualities of T-cells are generated in response to different vaccine modalities employing the same antigen. Therefore, vaccines using benign viruses and bacteria as vectors can prime T cells that control some pathogens better than others. Hopkins et al. map the unique signatures of intercellular signaling molecules released by T cells elicited by six different HIV-1 vaccine candidates used singularly and in combination in mice. The findings encourage studies on rational vaccine regimen design, but also await a more complete understanding of the workings of the immune system and its interactions with HIV-1. /ky [16]

original image

Seeing is believing: Improved imaging technique

Multiphoton fluorescence microscopy (MPFM) has many advantages over fluorescence microscopy techniques that use one photon excitation. In this study, Combs et al. (NIH, USA) describe their newly developed add-on system for in vivo imaging, which uses a parabolic mirror external light collection system. The authors demonstrate significant improvements with various tissue samples, including the mouse brain and skeletal muscle as well as the rat kidney, with a variety of fluorophores and without compromising spatial resolution. Their design has the advantage of not touching the sample and enables the use of highly corrected commercially built objectives. /sb [17]

original image

Journal of Basic Microbiology: Special Issue: Biotechnology

This special issue gives the reader the possibility to learn about general microbiology by investigating bacteria, archaea, fungi or other eukaryotic microorganisms from the application side, e.g. with regulatory mechanisms, with specifically adapted enzymatic features or with response to contaminated environments. Reviews highlight the versatility of microorganisms and antifungal proteins produced by fungi. Research papers reflect e.g. the discovery of new enzymes which might be of interest for industrial application or discuss the use of organisms generally regarded as safe. /pmh

Current Protocols

original image

Flow cytometry protease assays

The protease family of proteins is considered to be one of the major targets for small molecule drug discovery. Adaptation of a flow cytometry assay to high-throughput screening applications makes a cost effective and robust platform for drug screening against target proteases. One such microsphere-based protease assays is used to measure a loss of fluorescence from the surface of a microsphere due to the cleavage of an attached fluorescent protease substrate by a suitable protease enzyme. The assay format can be adapted to any site or protein-specific protease of interest and results can be measured in both real time and as endpoint fluorescence assays on a flow cytometer. Endpoint assays are easily adapted to microplate format for flow cytometry high-throughput analysis and inhibitor screening. /bm [18]

Alphaviruses for gene transfer into neurons

Alphaviral vectors based on Semliki Forest virus and Sindbis virus infect many host cell types, causing rapid and high-level transgene expression. In the CNS, Semliki Forest virus and Sindbis virus exhibit an outstanding preference for neurons rather than glial cells, compared to other viruses. Conventional SFV and SIN vectors are cytotoxic because they block host gene expression and can cause apoptosis, but are still extensively used. However, to reduce or even circumvent potentially limiting effects with regard to host cell survival, less cytotoxic and even noncytopathic replicons have been developed for the commonly used SFV4 and SIN vector systems. Alphavirus vectors have been successfully used not only in neuroscience, but also for other applications including drug discovery, structural biology, vaccine development, and cancer therapy. /bm [19]


original image

New in 2012: WIRES Membrane Transport and Signaling

An important new forum to promote cross-disciplinary discussion on transport and signaling aspects in membrane biology for researchers in science and medicine.

An authoritative, encyclopedic resource addressing key topics from perspectives of biophysics, cell biology, neuroscience, physiology and medicine.

Content is fully citable, qualifying for abstracting, indexing, and ISI ranking.

Articles will be available on the WIREs site from mid-December, including:

Overview: Functions of proton channels in phagocytes

Nicolas Demaurex, University of Geneva, Switzerland

Focus article: Evolution and diversity of opsins

Akihisa Terakita, Emi Kawano-Yamashita and Mitsumasa Koyanagi, Osaka City University, Japan

Advanced Review: Structure of P2X receptors

Liam E. Browne, University of Manchester, UK

/sm /sba

original image

Recommend to your librarian now


Aquaculture Biotechnology

Garth L. Fletcher and Matthew L. Rise

ISBN: 978-0-8138-1028-7

original image

This important new book looks at a broad spectrum of biotech research efforts and their applications to the aquaculture industry. /da

Handbook of Macroalgae – Biotechnology and Applied Phycology

Se-Kwon Kim

ISBN: 978-0-470-97918-1

original image

Anniversary Celebration

BTJ celebrates with a prize draw

At the beginning of 2011, Biotechnology Journal celebrated its 5th anniversary. To mark this milestone, we set-up a prize draw with three complimentary subscriptions of the Journal. We are pleased to announce the following winners and would like to take this opportunity to highlight their work at their respective institutions. /jp

Stéphane Bach

Stéphane Bach is working at the Station Biologique in Roscoff, France. Since 2001, he has developed and used various strategies to characterize small chemical inhibitors of disease-relevant protein kinases. He recently used BRET (bioluminescence resonance energy transfer) in budding yeast for the identification of protein-protein interaction inhibitors (BTJ, July 2011). He is now head of the open screening platform of the USR3151 laboratory.

Reshetilov Anatoly

Reshetilov Anatoly is the head of the Laboratory of Biosensors at G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (Pushchino). The area of his interests is the use of electrochemical transducers in combination with enzymes, antibodies/antigens, microbial cells in order to develop biosensors for detection of bioactive substances. Currently he is carrying out investigations on the development of nano-sized planar structures with the aim of creating the next generation of biosensors.

Seppe Vander Beken

Seppe Vander Beken workes at the Lab of Molecular Immunology, Dept. for Biomedical Molecular Biology, Ghent University, Belgium under the tutelage of Prof. Johan Grooten. The research interest of the group lies in macrophages and its multi-faceted functions. Gene expression profiling of macrophages from inflamed airways (models of asthma, pneumonia and COPD) with in-house made macrophage focus arrays is combined with functional analysis of in vivo airway macrophage-targeting strategies. Special emphasis is placed on the regulatory role of macrophages at the innate-adaptive immune interface.

original image

Free Virtual issue

original image


The actin cytoskeleton has a fundamental role in numerous cellular processes from cell migration and morphogenesis to vesicle trafficking and cell division. Consequently, the actin cytoskeleton is also a key player in many developmental and physiological processes in multicellular organisms, and abnormalities in the regulation of actin dynamics are typical for many pathological states such as in cancer and during infection processes of several pathogenic bacteria and viruses.

During the past two years, many important articles concerning biochemistry and biology of actin and actin-associated proteins have been published in Cytoskeleton. A selection of these papers is gathered in “Actin and Regulatory Proteins,” a new Virtual Issue from Cytoskeleton, now freely available online. /tm

Special issues

NMR in Biomedicine

NMR is unique among imaging modalities in its ability to measure metabolic pathways in real time; however, the use of 13C MRI in vivo has been limited because of the low signal-to-noise ratios of metabolites. Recent strides in polarization technology and in the use of external nuclear polarization to realize a many-fold increase in the signal from biologically useful compounds have the potential to expand dramatically the applications of 13C for real-time metabolic imaging. Read about this landmark development in MRI in this special issue of NMR in BioMedicine, edited by Rahim R. Rizi (University of Pennsylvania, USA). /sb

original image

Focus: Biosensors

The Engineering in Life Sciences focus on Biosensors, edited by Dieter Beckmann, (Institut f�r Bioprozess- und Analysenmesstechnik e.V., Heilbad Heiligenstadt, Germany) addresses several current challenges in life science engineering for biosensor development and applications, the opportunities of microfluidic systems as well as solutions for analytical systems in fermentation processes. /ug