BiotecVisions 2012, July

original image

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


Contributors: Anja Gaugel /ag; Adrian Miller /ami; Andrew Moore /amo; Bill Mullen /bm; Danny Asling /da; Fran Harding /fh; Frédérique Belliard /fb; Joanna Cipolla /jc; Jing Zhu /jz; Karen Chu /kc; Kevin Jeannette /kj; Lotte Nielsen /ln; Meghana Hemphill /mh; Mia Ricci /mr; Sarah Brett /sb; Simon Lightfoot /sl; Vera Köster /vek; Vivian Killet /vik

Sign-up for the Newsletter:

Author workshop in China

Journal of Integrative Plant Biology (JIPB) successfully held a workshop on scientific publishing at Shanghai Jiao Tong University on April 23–24, 2012. This workshop provided comprehensible guidelines on preparing a manuscript and attendees were able to find out more on how to successfully publish a paper in an international journal.

original image

Prof. Hong Ma from Fudan University chaired the opening ceremony. Prof. William Lucas from University of California (Davis), USA, covered the process of scientific writing, criteria in scientific publishing, the management of international top journals, and ethics in scientific research. Prof. Dabing Zhang from Shanghai Jiao Tong University gave a talk on how to prepare an English manuscript from the perspective of a Chinese researcher. Dr. Carol Bacchus from Wiley-Blackwell presented more information on publishing from a publisher's perspective. In addition, Dr. Ping He (Editorial Office Director, Journal of Integrative Plant Biology) gave an update of what Journal of Integrative Plant Biology has achieved in the past years and introduced more about the manuscript submission process.

There were more than 150 attendees during the workshop, including researchers, undergraduates, graduates, and editorial staff of scientific journals. The workshop was well acknowledged by the audience and they are all looking forward to the up-coming one in the near future. /jz

Getting published

Insights from the editor: John Barrett, Cytotherapy

original image

For the past decade I have served as Senior Editor of Cytotherapy, the official journal of the International Society of Cell Therapy (ISCT). My challenge as editor has been to adapt our journal to accommodate contributions from the increasing diversity of medical specialties that use cell therapy with an ever-extending spectrum of cell types.

Publication criteria: In a field that encompasses, basic cell research, gene therapy, immunotherapy, hematopoietic stem cells and non-hematopoietic cells including mesenchymal stromal embryonic stem cells, and cellular scaffolding, we have tried to maintain a focus on the translational aspects: taking lab-based observations and preclinical studies in animals through to scaled up GMP-grade cells, compliant with regulations, to treat inherited and acquired, degenerative, malignant and non-malignant disorders. Thus we highlight practical, scientifically rigorous, and ethically correct cell therapy to alleviate human disease.

Do's and don'ts for publishing in Cytotherapy: We welcome submissions within the scope outlined above. Novel and clinically relevant approaches to cell therapy will be enthusiastically handled. Most papers are rejected because they are not novel or represent only incremental advances or they fall outside the journal's scope. Do read the instructions to authors: keep to required page length and format – and don't forget the abstract! Presentation is critical! We find that attention to detail (grammar, spelling, use of proper scientific journal convention) is a good indicator of the overall quality of the paper. We love it when you are concise – length of a paper often corresponds inversely with its quality and importance. The quality of the title and abstract are critical. When responding to reviewers, please deal with each criticism point by point. Reviewers are representative of the readership of the journal – if they don't understand, it is likely many readers won't understand either. Most criticisms and suggestions will thus need a change to the manuscript, not simply a reply to the reviewer. Finally, remember editors are more benign that you might think – they really want to publish the best work in their journal and will work hard with you to finalize a good manuscript. We wish you best of luck with your papers!

Chemical production without fuel

Systems metabolic engineering combines the concepts and techniques of systems and synthetic biology, as well as evolutionary engineering from a systematic point of view. It provides a conceptual and technological framework to modify existing metabolic pathways, create new pathways and even new enzymes to produce any desired product in microorganisms. In a recent review in Nature Chemical Biology, Sang Yup Lee et al. (KAIST, Daejeon, Korea) present general strategies and the toolbox of systems metabolic engineering to produce chemicals. They are grouped into four categories, each requiring different strategies to produce them, based on whether they have been found in nature (natural vs. non-natural) and whether they can be produced by inherent pathways of microorganisms (inherent, non-inherent, or created). The concepts presented here will drive innovation for more cost effective biorefineries to relieve our dependence on fossil fuels. /ug [1]

original image

Read also this recent review by Sang Yup Lee in Biotechnology Journal on Butanol production from renewable biomass

Transition toward a bio-based economy

The transition from a fossil-input-based economy toward a bio-based economy is not an easy process. Although policy-makers in the European Union (EU) advocate this transition, still most companies and economies in the EU rely on fossil fuels for the production of materials and goods. However, the transition will not only depend on policy but will also involve all stakeholders: consumers, firms, and supporting policy with industry playing a major role. Industry expectations regarding the transition toward a bio-based economy focuses on the perceptions and expectations of industry regarding a possible transition toward a bio-based economy. /sb [2]

original image

Telomerase gene therapy slows ageing

In their recent study published in EMBO Molecular Medicine, Maria Blasco and her team show for the first time that mice that received a single treatment with telomerase show drastic improvements in health, fitness and longevity. Telomerase is an enzyme that helps to maintain the physical integrity of the ends of chromosomes. The results show that telomerase gene therapy is not only a viable anti-ageing intervention but that it also has remarkably beneficial effects without increasing the incidence of cancer. /vik [3]

original image

Combatting designer drugs head on

Illegal drugs and drug combinations are designed to be difficult to detect or characterize, and often to skirt existing drug laws. Labs generally rely on standards and libraries to identify compounds, but with designer drugs, standards may not be available. ChemViews magazine looks at one of the tools available to help law enforcement keep up with the dizzying array of new designer drugs. /vek [4]

original image

The twisted tale of saturated fat

The belief that dietary saturated fat is harmful is widespread, but recent evidence shows no link between dietary saturated fat and heart disease. It seems that it is the overconsumption of carbohydrate which drives up circulating levels of saturated fat associated with a higher risk of diabetes and cardiovascular disease. /lk [5]

original image

Chocolate under the microscope

We all know what chocolate tastes like. Would you like to know what does white chocolate look like under the electron microscope and when imaged by advanced techniques such as confocal Raman microscopy? European Journal of Lipid Science and Technology has stunning images showing the detail of the chocolate surface. Everybody has already seen the “white stuff” which appears on the surface of chocolate products – this article explains that topological imperfections are co-responsible for the so-called fat bloom. /lk [6]

original image

Zooming-in on floral nectar

Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant–pollinator–yeast systems remains unclear. The results reported in FEMS Microbiology Ecology have shown that bacteria are common inhabitants of floral nectar of South African plants, and their communities are characterized by low species richness and moderate phylogenetic diversity. The authors have identified osmotolerance, catalase activity and the ability to grow under microaerobiosis as traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar. /ln [7]

original image

Temperature regulation of yeast glycolysis

Qualitative phenotypic changes are the integrated result of quantitative changes at multiple regulatory levels. To explain the temperature-induced increase of glycolytic flux in fermenting cultures of Saccharomyces cerevisiae, the authors of this article in FEMS Yeast Research have quantified the contributions of changes in activity at many regulatory levels. A changed isoenzyme expression affects not only the interaction with the metabolic environment, but also the temperature dependence of the catalytic rate. They show how the cell regulates its responses to environmental temperature change and that it depends to a very large extent using the evolved, complex properties of enzymes and their interaction with the other components of the cell. /fb [8]

Environmental impact of biogas substrates

The Renewable Energies Source Act (EEG) 2009 has the aim to promote renewable energies in Germany and to reduce the global warming potential during energy production. A financial incentive is provided for the utilization of at least 30% of manure as feedstock in biogas plants. In the biogas Special issue of Engineering in Life Sciences, Jens Lansche and Joachim Müller investigate the potential environmental impact of anaerobic digestion processes using the life cycle assessment (LCA) method. They show that liquid manure is more advantageous compared to energy crops when digested in biogas plants as a single input substrate; however, the influence of liquid manure on the global warming potential is small for biogas plants with shares of 0–35% and does not necessarily lead to an additional reduction of greenhouse gas emissions. /ug [9]

original image

An intellectual property sharing initiative in agricultural biotechnology

The Public Intellectual Property Resource for Agriculture (PIPRA) was founded in 2004 by the Rockefeller Foundation in response to concerns that public investments in agricultural biotechnology benefiting developing countries were facing delays, high transaction costs and lack of access to important technologies due to intellectual property right (IPR) issues. From its inception, PIPRA has worked broadly to support a wide range of research in the public sector, in specialty and minor acreage crops as well as crops important to food security in developing countries. In this article in Plant Biotechnology Journal the authors review PIPRA's work, discussing the failures, successes, and lessons learned during its years of operation. To address public sector's limited freedom-to-operate, or legal access to third-party rights, in the area of plant transformation, the PIPRA's patent ‘pool’ approach is described to develop open-access technologies for plant transformation which consolidate patent and tangible property rights in marker-free vector systems. The plant transformation system has been licensed and deployed for both commercial and humanitarian applications in the United States (US) and Africa, respectively. /jc [10]

original image

Methods for iPS cell generation

Pluripotency can be induced by forced expression of defined factors in somatic cells. The resultant cells, i.e. induced pluripotent stem (iPS) cells, have an infinite self-renewal capacity in common with embryonic stem (ES) cells. Currently iPS cells can be established through various methods and factors, which can be categorized into four groups: (i) the combination of reprogramming factors, (ii) the induction method of reprogramming factors, (iii) the culture conditions and the type of original somatic cells, and (iv) the origin of the cells. In Biotechnology Journal Yuji Mochiduki and Keisuke Okita (Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan) review the current status of iPS cell studies, with a focus on the improved methods that can be used to generate iPS cells that are clinically relevant and discuss the remaining challenges. /ug [11]

original image

Property or sequence? Finding cell-selective peptides from ECMs

Surface functionalization of medical implants is a crucial requirement to reduce side-effects. Extracellular matrices (ECMs) provide a promising source of functional molecules to address this challenge. In this Spotlight article in Biotechnology and Bioengineering, Kanie and coworkers have proposed peptide-array based screening combined with in silico analysis to effectively explore cell-interacting peptides in the ECM, and extended their investigation to find cell-selective peptides. /mr [12]

original image

Biohybrid device controls acute inflammation

Sepsis, triggered by unregulated inflammation, generates more than $17 billion in healthcare costs each year in the US alone and causes nearly 10% of deaths. Researchers from the University of Pittsburgh have constructed a device that controls acute inflammation by breaking an inflammatory cascade driven by the cytokine tumor necrosis factor-α (TNF-α). In this article in Disruptive Science and Technology, small hollow fiber bioreactors were seeded with human HepG2 hepatocytes modified to constitutively express mouse soluble TNF receptor, thus attenuating the activity of TNF-α when connected into blood circulation. The device was shown to alleviate hypotension and reduce markers of organ damage when tested using a rat model of inflammation. This work constitutes an entirely new platform for controlling inflammation, which may be extended to other clinical situations where continuous synthesis and delivery of biological agents is required. /fh [13]

original image

Predicting breast cancer response to chemotherapy

Selecting the most effective treatment for a particular breast cancer patient is challenging: the patient response to a particular drug can be variable. The development of target indices based on the gene expression exhibited by a tumor now allows response to chemotherapy to be estimated before trialling treatment. TOP2A (topoisomerase) and β-tubulin are the targets of chemotherapy drugs anthracycline and taxane. By analysing the expression of TOP2A and β-tubulin genes in hundreds of breast tumor samples, gene expression signatures that indicated the susceptibility of tumor cells to the drugs were built. Combining the two gene expression indices together increased the accuracy with which chemotherapy responders could be predicted within the study cohort. Such gene expression based indices could form the basis of personalised chemotherapy regimes for cancer patients. /fh [14]

original image

IgA antibodies to treat cancer

IgA is commonly recognized as the dominant antibody at mucosal sites where it participates in shielding mucosal surfaces from invading pathogens. IgA can also potently activate neutrophils, which have been identified as potential effector cells for monoclonal antibody (mAb) cancer therapy. Scientists at Amgen in Seattle now demonstrate in the European Journal of Immunology that IgA leads to the rapid migration of neutrophils into, and destruction of, tumor colonies. Moreover, reciprocal communication between neutrophils and endothelial cells is shown, which is important in neutrophil extravasion from the circulation. Neither neutrophil migration nor cross-talk with endothelial cells was observed when IgG mAbs were used. The authors anticipate that IgA may be a prominent component of future mAb strategies in cancer treatment. /kc [15]

original image

Swimming in potential drug therapies

Phenotype-driven chemical genetic screens in zebrafish have become a proven approach for both dissection of developmental mechanisms and discovery of potential therapeutics. The embryo becomes a whole organism in vivo bioassay that can produce a phenotype upon treatment. The availability of many well-characterized zebrafish mutants has enabled the discovery of chemical suppressors of genetic phenotypes. Importantly, the application of chemical libraries that already contain FDA-approved drugs has allowed the rapid translation of hits from zebrafish chemical screens to clinical trials. This review in WIREs Developmental Biology summarizes progress in the field. /mh [16]

original image

First video highlight from Cytometry Part A

In this first Cytometry Part A Video Highlight, author Peter Hansen discusses his recently published paper entitled “Physics of a rapid CD4 lymphocyte count with colloidal gold”. /mr

original image

Watch the video:

RNA biology in a test tube

In vitro systems have provided a wealth of information in the field of RNA biology, as they constitute a superior and sometimes unique approach to address many important questions. New techniques, such as single-molecule studies, are continuously being established, providing new and important insights into the field. Thus, in vitro approaches have been, are, and will continue being at the forefront of RNA research.This review in WIREs RNA gives an overview of in vitro systems and assays. /mh [17]

original image

Light microscopy imaging

From advances in imaging probes, through super-resolution techniques, to computational image analysis, this special issue of BioEssays presents a unique collection of articles that summarize the status and developments, and speculate on future developments. /amo

original image


The June issue of the European Journal of Lipid Science and Technology is devoted to sterols. /lk

original image

Must-read reviews:

Cholesterol versus other sterols: How do they compare as physiological regulators of cholesterol homeostasis?

Cholesteryl esters and ACAT

Oxysterol-binding proteins-emerging roles in cell regulation


This Virtual issue includes articles published in IUBMB Life and BioFactors, journals published on behalf of the International Union of Biochemistry and Molecular Biology. /kj

original image

IUBS Meeting

The International Union of Biological Sciences (IUBS) will hold its 31st IUBS General Assembly and Conference on Biological Sciences and Bioindustry in Suzhou, China. Wiley-Blackwell journal editors have selected on the six key subjects ot the meeting: Evolution, Biology and Conservation, Climate Change Biology, Bioenergy, Nanobiology, Stem Cell and Reproductive Medicine and Systems and Synthetic Biology. /jz

original image


original image 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. /ami

Is coffee healthier for you when you're drunk?

original image

Research suggestions that antioxidants found in coffee get more effective in non-polar environments.

Single polymer chain folding – a review

C. Barner-Kowollik highlights the most recent progress in the area of single polymer chain folding, aimed at mimicking natural biomacromolecules.

Nanoparticles on their way through the body – medicine in miniature

Which pathways do nanomedicines take after they have been swallowed? Scientists find a recirculation pathway of polymeric micelles using multimodal nonlinear optical microscopy.


Yeast: Molecular and Cell Biology, 2nd Edition

Horst Feldmann

ISBN: 978-3-527-33252-6

A stand-alone, all-inclusive textbook on yeast biology. /da

original image

Industry News

original image

G.I.T. InnovationsAward 2012

Many manufacturers have submitted their innovative lab solutions for the G.I.T. InnovationsAward 2012. Our independent jury consisting of established scientists from all over Germany has narrowed down the choice from a large number of submissions. In the categories “Analytical Instrumentation and Software”, “Biotechnology and Life Science”, “Laboratory Equipment & Technology” and “Furniture & Accessories” there are up to 5 nominees that will be introduced in the following. Your vote decides the winner! /ag

Take a look at the nominated products and cast your vote:

Analytica 2012

The 23rd analytica, the international trade fair for Laboratory Technology, Analysis and Biotechnology, concluded in Munich with more than 30000 visitors. More than 30000 trade visitors from over 110 countries came to the fair in Munich.

1026 exhibitors from 37 countries presented their products and equipment for research and industrial laboratories. Besides Germany, the countries with the largest number of exhibitors included the United States, Great Britain, France, Switzerland and the Netherlands. /ag

Neurobiology, is a new website that offers a new way for people of all ages to learn more about how the brain works, how it drives thought and behavior, and its role in brain diseases and disorders., a public information initiative of The Kavli Foundation, the Gatsby Charitable Foundation, and the Society for Neuroscience (SfN), features nearly 1000 accessible, scientifically reviewed resources about the brain and mind. The Gatsby and Kavli Foundations generously donated a total of $1.53 million over six years to build and sustain /ag

These news are brought to you by G.I.T. Laboratory Journal Europe. Read the latest R&D and business specific news at


original image

Postdoc or not to postdoc?

These days, postdoctoral positions are almost an unavoidable part on the path to academic independence. As a PhD student, one of the first decisions that one should decide fairly early on is, “to postdoc or not to postdoc?”

For those who wish to pursue an independent academic career in the life sciences, a postdoctoral fellowship is most likely a must. For those who do not wish to continue the academic high life, the choices are perhaps somewhat more complex. A straightforward scenario is when the newly minted “doctor” has decided on a career path that does not require postdoctoral training and is able find employment in this new choice. A more common scenario – a PhD student has finished his/her PhD, but is uncertain of what to do next, or fails to find a position in his/her field of choice – in this case, a postdoc is a logical choice that ensures employment while developing further skills and looking for new opportunities. There are also advantages to this scenario, many life science-related industries, value the postdoctoral training and education of their employees.

The question is therefore, how to make the most out of the situation? Let's look at this from an employer's perspective (this is generally applicable to all industries).

Track record of success – the employer would like to see that you have been productive in whatever you do – in this case, publications are likely to be very helpful in demonstrating this.

Team player – the employer is likely looking for someone who is able to play well with others – a good reference from the PI and also any senior member of the institution, is likely to help your case.

Network of contacts – the employer would like to hire someone who already has a good network of contacts: the closer your new choice of profession to your old studies, the more likely this will be true. Think about how you could expand your network – obviously, staying in the same lab as you did your PhD, is unlikely to be very helpful in this respect.

We shall continue the postdoc discussion in the next issue of BiotecVisions, with an article how to make the right postdoc choice, stay tuned... /jp

Judy Peng is the Managing Editor of Biotechnology Journal. Judy also works on the European Journal of Immunology and prior to joining Wiley-Blackwell, Judy has worked and studied in the USA, Australia, and New Zealand.

Current Protocols

original image

Nonpathogenic gene-delivery

Adeno-associated virus is a nonpathogenic human virus that has been developed into a gene-delivery vector due to its high efficiency of infection for many different cell types and its ability to persist and lead to long-term gene expression. This virus can then be used to infect tissue culture cells or can be infused into an intact animal. Researchers from the University of North Carolina at Chapel Hill describe their efficient methods to generate high-titer, research-grade, adenovirus-free recombinant single-stranded and self-complementary adeno-associated virus in various serotypes, along with methods to quantify the viral vectors. Two detailed methods are provided for viral vector delivery into the rodent brain and spinal cord, and for histological detection of transgene expression of GFP. /bm [18]

3-Nitrotyrosine in individual proteins

Reactive nitrogen species (RNS) and reactive oxygen species (ROS) are derived as a result of inflammation and oxidative stress, and can result in protein modifications. As such, these protein modifications are used as biomarkers for inflammation and oxidative stress. In addition, modifications in single-tissue-associated proteins released into blood can provide insight into the tissue localization of the inflammation or oxidative stress. Researchers from the Pacific Northwest National Laboratory have developed an enzyme-linked immunosorbent assay antibody microarray platform to analyze the levels of 3-nitrotyrosine in specific proteins in a variety of biological samples. Selective-capture antibodies are used to immunoprecipitate individual proteins onto isolated spots on the microarray chips, then a monoclonal antibody is used to detect the amount of 3-nitrotyrosine on each spot. Their studies suggest that this approach can be used to detect trace amounts of 3-nitrotyrosine in human plasma and sputum. /bm [19]

Interview Series on Biofuels

In the first of a series of interviews for the website, editor for, Simon Lightfoot speaks to Jonathan Wolfson, the Chief Executive Officer of Solazyme Inc.

Read about Solazyme's first biofuels flight with United Airlines, their continued work with the US Department of Defence, and how Solazyme see the future of biofuels and the necessity of a progression to a bio-based economy.

Interviews coming soon include talking with Sarah Teter, of Novozymes, about the processes involved in improving enzymatic performance for biomass feedstocks – from sourcing the enzymes from fungi, and engineering the optimum performance possible, to taking the product to market.

Also appearing soon, Peter Williams, Chief Executive Officer for INEOS Bio, tells us of their unique bioenergy technology platform. With this technology and their wide ranging feed flexibility, they are championing a localised approach that both provides locally sourced biofuels as well as reduces the amount of waste going to landfill. /sl

original image


Call for Nominations: 2012 B&B Daniel I. C. Wang Award

original image

The call for nominations for the 2013 B&B D.I.C. Wang Award closes August 31, 2012. The B&B Daniel I.C. Wang Award was initiated in 2008 to honor a younger member of our dynamic community and is presented annually at the National ACS Meeting at a session of the BIOT. Information is available on the Biotechnology and Bioengineering journal homepage. /mr