BiotecVisions 2012, February

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


Contributors: Bill Mullen /bm; Danny Asling /da;Frédérique Belliard /fb; Vera Köster /vk; Joanna Cipolla /jc; Babu Varghese /bv; Gillian van Beest /gvb; Meghana Hemphill /mh; Susan Vice /sv; Mary Farrell /mf; Frances Harding /fh; Sarah Brett /sb; Materials Views /mv; Barbara Janssens /bj

EMBO Installation Grants

The 2011 EMBO Installation Grants were awarded to seven talented young scientists to assist relocation and setting up laboratories in the Czech Republic, Poland, Estonia and Turkey.

“The EMBO Installation Grants directly support young scientists in countries actively developing fundamental research capacity”, said Gerlind Wallon, Installation Grants Programme Manager and EMBO Deputy Director. “The grants benefit not only the talented scientists who receive support but also the countries where they establish laboratories.”

A committee of EMBO Members selects the successful candidates for the high standard of their research. “By helping these scientists set up their research laboratories in the participating countries, EMBO hopes to improve the competitiveness of these countries in European science”, said Wallon.

The scientists receive 50,000 euros annually for three to five years from their host countries. This helps them to establish their research groups and themselves in the European scientific community.

Grantees are also integrated into the prestigious EMBO Young Investigator Program, which provides networking opportunities with some of Europe's best young group leaders and a range of career development program.

With these newly elected grantees, the number of researchers funded by EMBO Installation Grants since the inception of the program in 2006 increases to 48. Three of the new grantees will move from the USA to establish research groups in Turkey, one moves from Germany to Poland, one from the UK to the Czech Republic, one from the USA to Estonia and one from the USA to Poland. Three of the seven scientists are women.

The recipients of the awards are Tolga Emre (Turkey), Ebru Erbay (Turkey), Nurhan Özlü (Turkey), Kvido Stříšovský (Czech Republic), Tambet Teesalu (Estonia), Bartosz Wilczyński (Poland) and Dorota Wloga (Poland).

The next application deadline for EMBO Installation Grants is 15 April 2012.

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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

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Cooking cancer with lasers and gold

A nanostructure of silicon and gold can kill cancer cells in trials four times more effectively than gold nanoshells alone.

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Trojan horse causes nanoparticle allergy

Exosomes have been implicated in the increased sensitivity to nanoparticles observed in those working with them on an industrial scale, according to Chinese researchers.

The Making of “transparent glass sponges”

Transparent glass sponges are a new class of materials ideally suited for use as a light source in photobioreactors – now a German research group want to bring them to the market.

Getting published

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To appeal or not to appeal

For seasoned authors of scientific journals, the question “to appeal or not to appeal” arises often when the paper has been “not recommended for further consideration” aka. REJECTED.

How should one go about an appeal? In my experience as an editor there is much confusion as to how and when an author should appeal an editorial decision. It is not sufficient to say the reviewer got it all wrong, regardless of how frustrating the reviewers' comments may be. It is also not appropriate to provide a list of similar papers that have been published in the same journal in recent years, as the sole basis for the appeal. After all, high-impact journals publish novel studies.

First, the authors need to discuss the reviewer reports and consider which comments can be immediately addressed, and then decide how to tackle the criticisms that they feel are not justified. The appeal should be based on scientific arguments, supported by relevant references when possible. After preparing a detailed point-by-point response, it is best to “sleep on it” and send it the next day. An author may also include comments in the letter directed towards the editor if they feel that a reviewer missed the main point of the paper or if they think that for some reason a reviewer was incapable of providing a balanced opinion on the importance of the work. As an author, one should also keep in mind that the manuscript may have been misinterpreted by a reviewer due to inadequate presentation of the work, so the authors have an opportunity to improve on this aspect when preparing a revised version.

The simple guidelines above should lead to a logical, rational appeal letter that would be dealt with professionally by the editor. /mf

Mary Farrell is Deputy Editor of Small. With a 2010 ISI Impact Factor of 7.333, Small continues to be among the top multidisciplinary journals covering a broad spectrum of topics at the nano- and microscale.

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Paradigm shift in the laser based skin rejuvenation

Laser- and light-based skin rejuvenation techniques have rapidly evolved over the last few decades from ablative to non-ablative and more recently towards fractional laser resurfacing. However, all these techniques typically balance efficacy, social down-time, and side effects. To overcome this limitation, scientists from Philips research in Eindhoven developed a novel minimally invasive skin rejuvenation technology based on the principle of laser-induced optical breakdown. The physical principle of the method is based on non-linear optical absorption, which is fundamentally different from the laser based methods and devices that are commonly used for skin rejuvenation. The scientists carried out ex vivo and in vivo measurements on human skin. Using an in-house built prototype device, they focused near-infrared ultra-short laser pulses to create optical breakdown in the dermis while leaving the epidermis intact, resulting in lesions due to cavitation and plasma explosion. They successfully demonstrated a healing response and consequently skin remodelling, resulting in skin rejuvenation effects. The method proposed by the Dutch researchers is expected to bring a paradigm shift in the present laser- and light-based skin rejuvenation methods by introducing a safe treatment procedure without damaging the epidermis, with no or little social down time and with an efficacy that might be comparable to ablative techniques. /bv [1]

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Visualizing cancer therapy targets

Cancer cells are able to maintain their proliferative potential through various mechanisms, one of which is known as the alternative lengthening of telomeres (ALT) pathway. Using this pathway, cancer cells are able to retain the length of their telomeres and thus divide continuously. One of the distinct characteristics of the ALT pathway is the colocalization of promyelocytic leukemia (PML) nuclear bodies with telomeres to form ALT-associated PML nuclear bodies (APBs). Rippe and colleagues report a cell-based assay with a fully automated high-resolution confocal screening platform for 3D colocalization studies to elucidate the genes involved in the pathway, by observing changes in APB formation. Not only does the study offer the opportunity to identify candidate targets for cancer therapy, it also additional tools for high-throughput screening of cellular colocalizations. /jp [2]

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Nano-cobblestone disguise reduces implant rejection

Coating the surface of an implantable device, such as a hip replacement, with nanoparticles reduces the risk of rejection. By immobilising gold particles of around 50nm diameter on a smooth background, researchers created a surface pattern like a cobblestone street in miniature. This cobbled surface reduced the activation of the innate immune system. The curvature of the nanoparticles prevents the close packing of proteins involved in the complement cascade on the surface, and thus disrupts the signalling cascade. “It may be that the body is designed to react to smooth surfaces, because these are not found naturally in body”, says senior author Hans Elwing. “Some bacteria, on the other hand, do have a completely smooth surface.”/fh [3]

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Towards healthier, innovative fats

Due to health concerns regarding trans-fats, there is a growing interest in the production of trans-free margarines and shortenings. One way to formulate such food fats is through the use of enzymatic interesterification technology. The process is explained in a Feature article by Véronique Gibon from the Desmet Ballestra R&D Center, Belgium. /lk [4]

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Process analytical sensors for single-use bioreactors

Online measurement of process parameters within bioreactors is still a challenge. Most analytical sensor systems used in conventional stirred-tank reactors cannot be transferred to single-use bioreactors. This is because

most conventional sensor systems are invasive and must be sterilized, calibrated, and validated before use. In addition, regulations of the US Food and Drug Administration concerning process documentation, imposed by the Process and Analytical Technology (PAT) Initiative, have increased the demand for sensors that are able to very accurately monitor and document the production process. Sascha Beutel and colleagues (Hanover, Germany) compare sensor systems that are currently on the market for single-use bioreactors and discuss the potential of image-based biosensors. /ug [5]

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A screening tool for therapeutic antibodies

The development of bio-therapeutics is a long and winding road that is dependent on many variables along the way. One of these factors is the stabilitiy of a protein and its propensity for forming aggregates. Aggregrates, however little the amount present, is highly undesirable due to decreased biological activity of the protein, and also its potential to trigger unintended immune responses. A current standard method of analyzing protein stability and aggregate formation is size-exclusion chromatography (SEC). SEC however, has several drawbacks such as its inability to detect conformational differences, etc. Trout and colleagues report a novel screening tool based on dye (i.e., thioflavin T (ThT))-binding properties. ThT binds nonspecifically to the β-sheet-rich amyloid-type protein aggregates. The major advantage of ThT binding is the short duration of testing compared to SEC – results can be obtained within days as opposed to months. /jp [6]

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p53 guardian of the genome

Human p53 induces cell death in the yeast Pichia pastoris. This study shows a growth inhibition effect, which increased with the p53 protein expression level in recombinant Muts (methanol utilization slow) strain of Pichia. However, no effect of p53 was observed in recombinant strain of Mut+ (methanol utilization plus) phenotype. Interestingly, human p53 induces cell death in recombinant strains Muts with characteristic markers of apoptosis such as DNA fragmentation, exposure of phosphatidylserine, and reactive oxygen species generation. Results strongly suggest that human p53 is biologically active in this heterologous context. Thus P. pastoris could be a useful tool to better understand the biological function of human p53. /fb [7]

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Aptasensor platform based on surface plasmon resonance

Aptamers are synthetic single-stranded oligonucleotides exhibiting several advantages for their use as biosensors compared to antibodies: target molecules include toxic or pathological substances, production is quicker and cheaper, they are easy to modify without loss of activity and show high stability under a width range of conditions. Researchers from the Technical University and Fraunhofer Institutes in Dresden, Germany present a novel aptasensor platform based on a surface plasmon resonance (SPR)-system using a thrombin-aptamer interaction as a model system. The platform is intended to be used as a low-cost biosensor, which is robust, easy to transport, and demonstrates sensitive and label-free detection of target molecules, such as peptides, proteins, nucleotides and whole virus particles. /ug [8]

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Physiological model of glucose and lipid metabolism

One of the challenges in understanding human physiology is a lack of relevant model systems. Many studies have clearly demonstrated that while animal models provide some insight, it nevertheless is a poor substitute for the real thing. The static and two-dimensional nature of most in vitro cultures is also widely acknowledged to be highly artificial. Ahluwalia and colleagues come a step closer to mimicking the human system with a multicompartmental modular bioreactor (MCmB) that reproduces the salient aspects of glucose and lipid metabolism in vitro. The MCmB consists of different bioreactor chambers connected together by the flow of media – it is the first example of an in-vitro model of glucose and lipid metabolism and paves the way for further and detailed studies. /jp [9]

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Forwards and backwards: De-differentiation improves cell graft survival

Poor survival of transplanted cells is a barrier to clinical uptake of cell based therapies. Work recently published presents a possible way to improve cell survival rates after transplant. Bone marrow mesenchymal stem cells were first differentiated towards a neuronal fate, then removed from the differentiation conditions, allowing the cells to revert back to state closer to the original stem cell population. Following this process, researchers noted the de-differentiated cells were resilient to hostile environments. After transplant, de-differentiated cells had higher survival rates than unmanipulated stem cells. The de-differentiated cell population also retained a predisposition towards forming neurons. In an animal model, they were effective in improving cognitive function and in aiding recovery from stroke. /fh [10]

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Accounting of CO2 emissions from biomass combustion

Carbon dioxide (CO2) emissions from biomass combustion are traditionally assumed climate neutral if the bioenergy system is carbon (C) flux neutral, i.e. the CO2 released from biofuel combustion approximately equals the amount of CO2 sequestered in biomass. This convention, widely adopted in life cycle assessment (LCA) studies of bioenergy systems, underestimates the climate impact of bioenergy. Besides CO2 emissions from permanent C losses, CO2 emissions from C flux neutral systems (that is from temporary C losses) also contribute to climate change: before being captured by biomass regrowth, CO2 molecules spend time in the atmosphere and contribute to global warming. In this paper, a method to estimate the climate impact of CO2 emissions from biomass combustion is proposed. Our method uses CO2 impulse response functions (IRF) from C cycle models in the elaboration of atmospheric decay functions for biomass-derived CO2 emissions. Their contributions to global warming are then quantified with a unit-based index, the GWPbio. Since this index is expressed as a function of the rotation period of the biomass, our results can be applied to CO2 emissions from combustion of all the different biomass species, from annual row crops to slower growing boreal forest. /jc [11]

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Understanding algae flocculation

In the production of algal biofuels, efficient harvesting of algae cells from the growth medium using current technologies continues to be a significant technical and economic barrier. Wyatt and coworkers seek to provide the means for enhancing both reliability and efficiency through a better understanding of the flocculation process using a combination of experimental measurements and modeling. In this issue of B&B, the authors link measurements of cell surface functional groups, interpreted through models for surface complex formation, to identify pH limits on effective flocculation. Limits associated with the required concentration of flocculant as a function of algae concentration are also identified and linked to models for floc growth which is explained in terms of a stoichiometric regime and a differential-settling driven floc growth regime. The overall result is a map for effective flocculation as a function of pH, flocculant concentration and algae concentration. /sv [12]

Enzymatic biofuel cells

Enzymatic biofuel cells have a great potential to be a next-generation small power source that can provide orders of magnitude higher energy density in a much smaller size than batteries. As an example, implantable enzymatic biofuel cells – using blood glucose as fuel and generating the power for implanted bio-devices such as pacemakers – can prevent multiple surgeries to replace batteries. However, the practical applications of biofuel cells are being hampered by their short lifetime and low power density. This article describes the direct immobilization of glucose oxidase onto the carbon paper in the form of highly stable and active enzyme precipitation coatings (EPCs), which were fabricated via a three-step process: covalent attachment, enzyme precipitation, and chemical crosslinking. The EPC-based enzyme electrode improved both operational stability and power density of biofuel cells, which can make their applications more feasible. /sv [13]

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How sustainable are biorefineries?

Sustainability today is a ubiquitous word that is sometimes overused, and many times misused. Proposing good indicators to measure sustainability is a challenging task; the most common methodologies for evaluating the sustainability of processes and products do so by comparing various designs and selecting the best option, according to predefined criteria. Julio C Sacramento-Rivero, proposes a new sustainability scale that integrates the most important aspects that affect the sustainability of biorefineries. The framework consists of 5 indicator categories, and 14 metrics for sustainability-evaluations. The key to this approach is that it avoids the use of an excessive number of indicators and difficult to access data, and provides a simplified clear indication of the sustainability of the main aspects of a biorefinery. [14]

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Limitations in current nematode control strategies

Plant-parasitic nematodes are primary biotic factors limiting the crop production. Current nematode control strategies include nematicides, crop rotation and resistant cultivars, but each has serious limitations. RNA interference (RNAi) represents a major breakthrough in the application of functional genomics for plant-parasitic nematode control. RNAi-induced suppression of numerous genes essential for nematode development, reproduction or parasitism has been demonstrated, highlighting the considerable potential for using this strategy to control damaging pest populations. In an effort to find more suitable and effective gene targets for silencing, researchers are employing functional genomics methodologies, including genome sequencing and transcriptome profiling. Microarrays have been used for studying the interactions between nematodes and plant roots and to measure both plants and nematodes transcripts. Furthermore, laser capture microdissection has been applied for the precise dissection of nematode feeding sites (syncytia) to allow the study of gene expression specifically in syncytia. In the near future, small RNA sequencing techniques will provide more direct information for elucidating small RNA regulatory mechanisms in plants and specific gene silencing using artificial microRNAs should further improve the potential of targeted gene silencing as a strategy for nematode management. /jc [15]

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Special Issue

Bio-based industry

Plant and animal fats/oils can be used for the production of biofuels or be converted to valuable building blocks for bioplastics – in other words, renewable oils can be used in place of fossil oils and petrochemicals. The 4th workshop on the use of Fats and oils as renewable feedstock for the chemical industry was held in March 2011 in Karlsruhe, Germany. The January special issue of the European Journal of Lipid Science and Technology brings the proceedings of this conference to all readers interested in this exciting topic. /lk

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Special Issues

Rickettsia and other intracellular bacteria: recent outbreaks, novel pathogens, emerging diseases, new tools and outstanding discoveries

This special issue contributes to the understanding of the pathogenesis, epidemiology, diagnosis and clinical presentation of rickettsial diseases as well as human and animal infections by various other intracellular bacteria, such as Anaplasma, Bartonella, Coxiella, Ehrlichia, Waddlia and Wolbachia. In addition to cutting edge technologies and outstanding discoveries in basic research, recent outbreaks – for example the recent 2007–2010 Q fever outbreak that took place in the Netherlands – have been analyzed in depth, providing clues on transmission, attack rates and associated morbidity and highlighting the importance of coordinated efforts between clinical microbiologists and the environmental protection agencies, public health and veterinary authorities. /gvb

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Improving Crop Resistance to Abiotic Stress: -omics approaches

Narendra Tuteja, Sarvajeet Singh Gill, Antonio F. Tiburcio, Renu Tuteja

ISBN: 978-3-527-32840-6

This multivolume reference work is a long awaited must-have update on improving crop resistance against abiotic stress, and is presented by well-balanced international mix of contributors from industry and academia. /da

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Bioscience Laboratory Techniques: A Pocket Guide

Philip Bonner, Alan Hargreaves

ISBN: 978-0-470-74309-6

A portable, pocket-sized guide and reference to everything first year bioscience and biomedical science students need to know. /da

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Fungi: Biology and Applications, 2nd Edition

Kevin Kavanagh

ISBN: 978-0-470-97709-5

Comprehensive coverage of fungi, including biochemistry, genetics and the medical and economic significance of these organisms at the introductory level. /da

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ChemViews talks to Frances Arnold

Prof. Frances H. Arnold of Caltech: “Evolution is an excellent algorithm for designing biology. It's responsible for the great diversity and high functionality of biological systems that exist today. It is also an algorithm that we can use to redesign organisms to solve human problems like curing diseases or making fuels and chemicals sustainably.” /vk

See full interview in ChemViews Magazine.


“Do what you love”

“Do what you love and you'll never work a day in your life” (Confucius) – all clichés are based on some degrees of truth. What Confucius said 2500 years ago could still be valid today, although love does not bring bread to the table. And when you find something you love, how do you apply yourself in the job while also further advancing your potential to reach the next level of challenges? These are some of the questions that we would like to address with this new BiotecCareers column:

Interviews with “real” people

Graduate students tend to be familiar with the academic career ladder but are often less familiar with other options. While there is no list of “professions for scientists”, inspiration can be found in personal stories from scientists at work. With interviews from real people in the real world, we will present various scientific career options available in academia and beyond.

Getting ahead in academia

For those interested in staying in the ivory tower, just how does one go about it? Concrete advice from those who have “made it”, is likely to shed some insight to this question. More interestingly, what are the secrets of those making the transition between industry and academia and back?

Career advice from professional advisors

With career advice from professional advisors, we would like to provide a proactive approach to career development.

Technical know-how – getting the job you want

Getting a job involves searching networking, CV writing, applying, interviewing... Yet two thirds of the time employers hire a person connected to them. How do you go about efficient networking? How do you write a convincing CV and cover letter?

Whether you are a novice or a seasoned player, BiotecCareers will have something to offer to everyone. /jp and bj

Judy Peng is Managing Editor of Biotechnology Journal and thoroughly enjoys her work.

Barbara Janssens used to work in publishing and now loves being PhD Careers Manager at the German Cancer Research Center.

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Current Protocols

Detecting drug-resistant Staph

In 2009, the Clinical and Laboratory Standards Institute introduced new guidelines for staphylococcal susceptibility testing, indicating that Kirby Bauer disk diffusion is not a reliable method for detection of reduced susceptibility to vancomycin in this genus. Vancomycin has been the mainstay of antimicrobial therapy for infections with methicillin-resistant Staphylococcus aureus for decades. Accurate detection of S. aureus isolates with reduced susceptibility to vancomycin is a challenge for clinical laboratories, and the optimal method for detection of such isolates remains an area of controversy. Researchers from Washington University in St. Louis describe a method using a brain-heart infusion medium containing 3 μg/mL of vancomycin (BHI-V3) to screen for isolates of S. aureus with reduced susceptibility to vancomycin. This medium represents a sensitive and cost-effective method for detection of such isolates in the clinical or research laboratory. /bm [16]

A little help from Sleeping Beauty

Recent advances in whole genome analyses made possible by next-generation DNA sequencing, high-density array comparative genome hybridization (aCGH), and other technologies have made it apparent that cancers harbor numerous genomic changes. Nevertheless, without functional correlation or validation, it has proven difficult to determine which genetic changes are necessary or sufficient to produce cancer. Thus, it remains necessary to perform unbiased functional studies using model organisms to help interpret the results of whole genome analyses of human tumors. To this end, a Sleeping Beauty (SB) transposon–based mutagenesis technology was developed to identify genes that, when mutated, can cause cancer. Researchers from the University of Minnesota in Minneapolis have detailed their methodology to initiate and carry out an SB transposon mutagenesis screen. Although this system might be used to identify genes involved with many cellular phenotypes, it has been primarily implemented for cancer. /bm [17]

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Free Virtual Issue

Omega-3 PUFA

The health benefits of omega-3 polyunsaturated fatty acids are now widely recognized and the demand for omega-3-enhanced functional foods and dietary supplements is growing. The European Journal of Lipid Science and Technology and the Lipid Technology magazine present a joint virtual issue covering different aspects of fish oil and omega-3 PUFA research including the biology, technology, analysis and medical science. All featured articles are freely accessible through the end of February 2012. /lk

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Beyond DNA origami: The unfolding prospects of nucleic acid nanotechnology

In 2006, DNA origami transformed the field of nucleic acid nanotechnology by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA ‘staples’. This revolutionary approach has led to the creation of a multitude of two-dimensional and three-dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. /mh [18]

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