BiotecVisions 2013, March

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Editors: Judy Peng /jp; Adriana Kantcheva /ak; Lucie Kalvodova /lk


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Contributors: Danny Asling /da; Bill Mullen /bm; Fran Harding /fh; Frédérique Belliard /fb; Joanna Cipolla /jc; Meghana Hemphill /mh; Vera Köster /vek; Gillian van Beest /gvb; Loes van de Pasch /lp; Erwin Ripmeester /er; Adrian Miller /am; Anja Gaugel /ag; Mia Ricci /mr

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March 2013

Cover Story

Cardiac pacemaker cells created through cell reprogramming

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Each heartbeat begins with an electrical impulse that arises in a tiny population of specialised cardiac pacemaker cells. When this mechanism fails, current treatment requires the implantation of an artificial pacemaker. In work recently published in Nature Biotechnology, researchers from the Cedars-Sinai Heart Institute in Los Angeles offer an alternative. By using adenoviral vectors to deliver a single gene, Tbx18, cardiomyocytes within guinea pig hearts could be directly converted into pacemaker cells. Within two to four days, these reprogrammed cardiomyocytes functioned identically to pacemaker cells, independently initiating heart contraction. Transient expression of Tbx18 transcription factor was sufficient for pacemaker programming, indicating it may be possible to induce the creation of replacement pacemaker cells using a single targeted treatment./fh [1]

Biotechnology Journal

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Biotechnology Journal is a broad scope, peer-reviewed scientific journal covering all aspects of biotechnology. The Journal is edited by Prof. Sang Yup Lee (KAIST, Korea) and Prof. Alois Jungbauer (BOKU, Austria).

Each year, the Journal publishes a “Methods and Advances” Special Issue. In addition to publishing your research alongside some of the best-known names in the field (previous authors in the Journal include: Jay Keasling, Doug Clark, Jens Nielsen, Lars Nielsen, Leroy Hood, and many more), publishing in this special issue ensures that your research receives the highest exposure possible – the “Methods and Advances” special issue is our annual sample issue, which means that all articles are freely available throughout the year.

Title: Methods and Advances

Edited by: Alois Jungbauer and Sang Yup Lee

Scope: Latest methods and breakthrough advances in biotechnology.

Submission: April 15, 2013 (research papers) May 13, 2013 (reviews)

Reviews: Send your review proposal (200 words) and CV to the editorial office at

More about Biotechnology Journal

High visibility: indexed in all major databases, including Pubmed/Medline, ISI Web of Knowledge, Scopus, etc.

Impact Factor™: first IF will be released in June 2013, current predictions put the Journal on par with leading journals in biotechnology

Rapid peer-review: submission to first decision within 1 month, out-of-scope papers are notified within 1 week

Rapid publication: primary research articles online within 1 week of acceptance

Personal service: dedicated in-house editorial staff to facilitate timely peer-review and answer your queries asap

Getting published

Artful discussions

Many authors, especially younger ones, find writing the discussion the most difficult part of writing their paper. While writing a good discussion is an art i.e. “the expression or application of human creative skill and imagination” (as per Google), like many things in life, some sound training coupled with years of practice, usually leads to something presentable.

The basic structure of a discussion is as follows:

Statement of principal findings

The reader has just finished reading the results section – it is therefore time to bring the message home with a summary of the key findings of the paper.

Appraisal of methods

It is unlikely that the methods used in the study were perfect – and you are even less likely to pull the wool over any educated reader's eyes – so might as well be upfront about it and discuss both its strength as well as weaknesses.

Comparison with previous work

This is not a listing of ALL previous work, but a selection of the most relevant work in the field. Again, here is a chance for you to prove that you are indeed a knowledgeable researcher in this area.

Clinical and scientific implications

The value of scientific research lies in its implications – does your study have clinical implications? Contribute to further research in the basic sciences? Build a better picture of how we understand the world around us? Tell us about it!

Further work

Now that we have the implications of the study, what might be further work in the area? This is a speculative part that may be of interest to many – although, be careful not to have your ideas scooped by sharing them prematurely.

While writing the discussion, it is important to keep in mind that here is the chance for you to rationalize your study with the reviewer and convince the reader that you know what you are doing – your study may not be perfect, but you are aware of its caveats and in spite of any shortcomings, your research makes real contributions to scientific knowledge.

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Derived from “How to Write a Paper – 5th Edition”. Edited by George M. Hall. Wiley, ISBN: 978-0-470-67220-4

Breath test can identify lung infection

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The development of a method to analyse the molecular “fingerprints” of bacteria present in the lung from breath samples paves the way for simple, rapid testing to diagnose lung infection. Real time analysis of volatile compounds given off by common lung pathogens Pseudomonas aeruginosa and Staphylococcus aureus was demonstrated using secondary electrospray ionization mass spectrometry (SESI-MS). SESI-MS could differentiate between breath samples taken from infected and uninfected mice. In addition the technique could discriminate infection by specific pathogen species and between specific strains of P. aeruginosa. Conventional diagnosis of bacterial lung infection requires culture of infected samples, a process that may take days or weeks. In contrast, a SEIS-MS based analysis could reduce the time to diagnosis to just minutes. /fh [2]

Tracking cellulase behaviors

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Cellulases have been extensively studied due to their ability to depolymerize cellulosic materials into mono- and oligosaccharides. Renewable sources of inexpensive fermentable sugars hold promise for industrial applications, notably biofuel production. A key to understanding how cellulases break down cellulose is the surface interaction of these enzymes with their substrate. Although cellulase/cellulose interactions have been studied extensively through bulk measurements, high-resolution fluorescence microscopy and nanoscopy methods offer an unprecedented view into this system. In this work, Moran-Mirabal, Bolewski, and Walker study the surface diffusion dynamics of three different thermophilic bacterial cellulases at two different microscopic length scales. Micron scale surface diffusion is reported through fluorescence recovery after photobleaching microscopy, while single molecule tracking experiments uncover complex, non-steady surface motions of cellulases at the nanometer level. The reported results offer new insight into cellulase surface diffusion and show the potential of nanoscopy methods in studying cellulase/cellulose interaction dynamics. /mr [3]

Review of reactive kinetic models describing reductive dechlorination of chlorinated ethenes in soil and groundwater

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Reductive dechlorination is a major degradation pathway of chlorinated ethenes in anaerobic subsurface environments, and reactive kinetic models describing the degradation process are needed in fate and transport models of these contaminants. In this study by Julie C. Chambon and coworkers, the modeling approaches used to simulate reductive dechlorination and interactions with fermentation and redox processes, and the experimental data needed to calibrate them are reviewed, classified and discussed. /mr [4]

Special Issue on Cytometry in Stem Cell Research – Highlights

Guest editors Vera S. Donnenberg and Henning Ulrich have worked closely with Cytometry Part A's Editor-in-Chief Attila Tárnok to create a compelling collection of reviews and original research articles that describe the current state of flow cytometry applications in stem cell research. As they state in their Editorial “The major strength of flow cytometry is its ability to rapidly perform highly multiplexed quantitative measurements on single cells within a heterogeneous cell population.” Please go to the link below to see several highlights from the issue or enjoy the entire Special Issue freely available online. /mr

Enzyme clustering – smaller or closer?

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Enzyme immobilization to particles has become important in biotechnology, as it brings about substantial improvement in enzyme catalytic efficiency. But how important a factor is particle size when it comes to enzyme performance? While it is generally believed that the smaller the particle size, the higher the enhancement, Tsai et al. (University of Delaware, USA) present a different story. These researchers employ a simple method based on metal affinity coordination to directly conjugate two different enzymes onto quantum dots (QDs) of different sizes, which they use to systematically study the influence of particle size and QD/enzyme ratio on overall enzyme enhancement. Surprisingly, the authors show that enzyme proximity is the most important factor for activity enhancement, while the influence of particle size is relatively modest. These results are important in designing improved nanobiocatalysts for biofuel production, bioremediation, and drug design. [5] 10.1002/biot.201100503

Polypeptide bionanotechnology – engineered to be cost-effective and scalable

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Scaling up manufacturing of bionanotechnological products beyond pharmaceutical and diagnostic applications remains a major challenge in large part due to issues of feasibility and cost. Rouvière et al. (Dupont) solve this problem by designing a polypeptide capable of self-assembly into higher-order structures that binds two distinct surfaces, namely pigments and hair. At the same time, the controlled solubility properties of this polypeptide permit its scalable production in Escherichia coli via inclusion bodies and a cost effective purification. This approach of combining multi-functionality with cost-effective production will find applications in materials science, biocatalysis, personal care and agriculture. [6]

Synthesizing viral building blocks with controlled dimensions

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Often scientists view viruses as nanomaterials of fixed sizes that are used merely as templates to synthesize other useful materials such as metal or metal oxide nanoparticles. Contrary to this view, Rego et al. from Tufts University (MA, USA).employ the elegant self-assembly mechanism of the tobacco mosaic virus (TMV) to create nanoscale building blocks with controlled dimensions, or what they affectionately call “baby” TMVs. They show that one can reproducibly create such viral particles by simply mixing purified coat proteins with RNA molecules of pre-designed lengths that contain the sequence thus triggering coat protein self-assembly. The outcome is well-controlled nanoarchitectures and hybrid nanomaterials for a wide variety of applications including nanoelectronics and nanocatalysis. [7]

Antioxidants from yerba mate

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Yerba mate (IIlex paraguariensis) is a tree well known as the source of the mate beverage. With their antioxidant and therapeutic properties, polyphenolic extracts from yerba mate leaves can improve the sensorial quality and shelf life of fatty foods and vegetable oils and at the same time provide many benefits for human health. The present study published in European Journal of Lipid Science and Technology is concerned with obtaining natural antioxidants such as caffeic acid and rutin from yerba mate and formulating blends with improved effectiveness. /lk [8]

Traceability of the palm oil supply chain

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Palm oil is mainly produced in Malaysia and Indonesia while the main users are India, China, Indonesia and the EU. For most of these users, the supply chain is long and complex, including overseas shipping. Procedures in this supply chain guarantee stepwise traceability as required by food safety regulations. Continuous traceability is usually not achievable. Also the RSPO trace and traceability systems do not improve this. Exception is the Identity Preserved system, however, the high costs and low volume of this system makes it only applicable for niche market products. [9]

Yeast-based isobutanol production

This is the first demonstration in the open literature of direct fermentation of D-xylose to isobutanol, which can be used as a biofuel, by recombinant yeast cells. /fb [10]

Elderly mice on a diet

Intestinal microorganisms are well-known to be highly important for a healthy digestive system in elderly people. The composition of intestinal bacteria can be influenced through changes in diet. The authors of this paper have investigated the composition of intestinal bacterial communities in aged mice by high-throughput sequencing. They demonstrate that a diet of resistant starch directly affects specific bacterial species and that this is correlated to an improved health of aging mice. This shows the possibilities of dietary interventions in the prevention of age-related declines in health by targeting specific intestinal bacteria. /lp [11]

Iron piracy

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Iron is in many environments the limiting nutrient for microbial life. Two novel members of the colicin M bacteriocin family (pectocin M1 and M2) were discovered in Pectobacterium, which may represent the first example of iron piracy directly from a host protein by a phytopathogen. /er [12]

Chromatin meshwork defence against invaders

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This well-illustrated study investigates the in vitro response of human peripheral blood mononuclear cells (PBMCs) from healthy blood donors to cord-forming Mycobacterium abscessus strains from cystic fibrosis patients with clinical lung infection. Microscopic examination revealed that the PBMCs produced a coarse fibrous meshwork containing DNA and histones, which surrounded the mycobacterial cords. Thus, the bacterial cord formations were entrapped by monocytes and lymphocytes aggregated onto the DNA-rich meshwork fibers. Mycobacterium abscessus strains with smooth colony morphology, which do not form cords and are readily phagocytosed, did not induce any meshwork formation in PBMCs. The chromatin meshwork may represent a defense mechanism against nondigestible invaders. /gvb [13]

Understanding seaweed

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Seaweeds (macroalgae) play an essential role in aquatic ecosystems. There is substantial laboratory-based evidence that macroalgal health, performance and resilience are functionally regulated and assisted in part by epiphytic bacteria. This functional assistance implies that macroalgae and all their associated microbiota form a singular entity or holobiont, analogous to the previous suggested relationship in corals. Given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal–bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept. /gvb [14]

PHA bioplastics, biochemicals, and energy from crops

Large scale production of polyhydroxyalkanoates (PHAs) in plants can provide a sustainable supply of bioplastics, biochemicals, and energy from sunlight and atmospheric CO2. PHAs are a class of polymers with various chain lengths that are naturally produced by some microorganisms as storage materials. The properties of these polyesters make them functionally equivalent to many of the petroleum-based plastics that are currently in the market place. However, unlike most petroleum-derived plastics, PHAs can be produced from renewable feedstocks and easily degrade in most biologically active environments. This review highlights research efforts over the last 20 years to engineer the production of PHAs in plants with a focus on polyhydroxybutryrate (PHB) production in bioenergy crops with C4 photosynthesis. PHB has the potential to be a high volume commercial product with uses not only in the plastics and materials markets, but also in renewable chemicals and feed. /jc [15]

The incentive gap: LULUCF and the Kyoto mechanism before and after Durban

To-date, forest resource-based carbon accounting in land use, land use change and forestry (LULUCF) under the United Nations Framework Convention on Climate Change (UNFCCC), Kyoto Protocol (KP), European Union (EU) and national level emission reduction schemes considers only a fraction of its potential and fails to adequately mobilize the LULUCF sector for the successful stabilization of atmospheric greenhouse gas (GHG) concentrations. Recent modifications at the 2011 COP17 meetings in Durban have partially addressed this basic problem, but leave room for improvement. The presence of an Incentive Gap (IG) continues to justify reform of the LULUCF carbon accounting framework. Frequently neglected in the climate change mitigation and adaptation literature, carbon accounting practices ultimately define the nuts and bolts of what counts and which resources (forest, forest-based or other) are favored and utilized. For Annex I countries in the Kyoto Mechanism, the Incentive Gap under forest management (FM) is significantly large: some 75% or more of potential forestry-based carbon sequestration is not effectively incentivized or mobilized for climate change mitigation and adaptation. /jc [16]

IUBMB Events

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Future congresses, conferences and special meetings

14th IUBMB Conference: “Host-Microbe Interactions”

Marrakesh, Morocco, 17–20 November 2013

Contact: Prof. HMYENE Abdelaziz, President of SMBBM, E-mail: hmyeneaziz2002[at]

Upcoming symposia

Cancer Genomics and Personalized Medicine

Zhandong, CHINA, 5–9 May 2013

Contact: Hongbing Zhang, E-mail: hbzhang[at]

XIV International Symposium on Cholinergic Mechanisms

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Hangzhou, China, 5–9 May 2013

Contact: Prof. Karl Tsim, E-mail: iscm[at]

8th International Conference for Plant Mitochondrial Biology ICPMB 2013

Rosario, Argentina, 12–16 May 2013

Contact: Dr. Daniel H. Gonzalez, E-mail: dhgonza[at]

7th International Conference on Protein Kinase CK2

Lublin, Poland, 10–13 September 2013

Contact: Prof. Ryszard Szyska, E-mail: szyskar [at]

Society for Free Radical Research Europe 2013 Conference

Athens, Greece, 23–25 September 2013

Contact: Dr. Efstathios S. Gonos, E-mail: sgonos [at]

Biotech-related portals

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Biofpr Webinar: Measure Biofuel Parameters – When and Where you need to

Tuesday, March 5th, 2013 – 16:00 UTC

08.00am PST / EST / 16.00 GMT / 17.00 CET

Learn more about the “Ready-to-go” mobile systems that allow you to analyse biodiesel concentration and biogas composition on location without compromising performance.

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Tissue engineering scaffolds from natural polymers

Researchers have fabricated controllable scaffolds from functionalised Kappa carrageenan, a naturally occurring polymer. /am

Micro- and nanoengineering of biomaterials for healthcare applications

The future of nano and micromaterials for healthcare, described by Ali Khademhosseini and Nicholas Peppas as part of an Advanced Healthcare Materials issue. /am

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Exciting Asprin®

Aspirin® is the most widely used medicine in the world. Originating in the laboratories of Bayer AG, Aspirin® is one of the very few drugs of the 19th century still used today. Professor Dodziuk, Warsaw, looks at the history and synthesis of this molecule and discusses how Aspirin is experiencing a second youth thanks to its applications in cancer treatment and stroke prevention. /vek [17]


Extremophiles: Sustainable Resources and Biotechnological Implications

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Om V. Singh

ISBN: 978-1-1181-0300-5

This new fascinating book explores the utility and potential of extremophiles in sustainability and biotechnology. It features outstanding articles by expert scientists who shed light on broad-ranging areas of progress in the development of smart therapeutics for multiple disease types and products for industrial use. /da

Perinatal Stem Cells, 2nd Edition

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Editors: Kyle Cetrulo, Curtis L. Cetrulo, Jr., Rouzbeh R. Taghizadeh

ISBN: 978-1-1182-0944-8

Building on the first edition, this book provides an updated tutorial on perinatal stem cells, including stem cells harvested from the amniotic fluid, placenta, maternal blood supply, umbilical cord and Wharton's Jelly. With contributions from some of the top academic stem cell laboratories in the United States as well as new chapters from international stem cell scientists, Perinatal Stem Cells presents and update on the cutting-edge research in the field while maintaining its signature clinical focus. /da

Derived from the renowned Encyclopedia of Industrial Biotechnology

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Upstream Industrial Biotechnology

2 Volume Set

Edited by Michael C. Flickinger

ISBN: 978-1-1181-3123-7

Hardcover | 1854 pages | March 2013

Introductory Price, valid until 30th April 2013: $395.00 | £265.00 | €342.00

Thereafter: $495.00 | £330.00 | €430.00

BiotecCareers: Industry postdoc

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After her PhD, Maria Nyblom decided to pursue her postdoctoral training in industry, here is her experience:

Q: Please tell us about what you do:

A: I investigate membrane protein structure through X-ray crystallography. The 3D image of proteins offers insights to protein function and how the protein relates to disease and associated drugs.

Q: What do you enjoy most about the job?

A: My project is very exciting and working in industry is different from academia. Prior to Novo Nordisk I was not sure of the amount of freedom in industry research; however, the way Novo Nordisk works appeals to my curious side. Also, in a company you have more of a “team” feeling and you are not alone in a project, which is a better fit for my personality.

Q: Are there any aspects that could be different?

A: Personally, I would not like to have it differently; I have been very fortunate with my work environment and my boss - he really has the ability to create a collegial and positive working atmosphere so that we feel our work is important. If you feel that your work is important you will be more creative and ambitious in your tasks.

Q: Why/how did you decide to move from academia to industry?

A: I had been in academia for 8 years, and I wanted to get insight into how research is conducted in a company. This opportunity came up; it was a good way to learn the thinking process of a company.

Q: What aspects of your academic experience have been most useful in getting the job, and doing the job?

A: The company wanted to learn more about membrane proteins, so my experience within the field fitted well. Taking in collaborators or postdocs is a common and good way for companies to gain more know-how within a field.

Q: What is your one tip for PhD students or postdocs who might be considering a move to this sector?

A: It is important to first and foremost have a genuine interest in your research area – in academia as well as in a company. You may also consider making contact with companies within the field already during your PhD!

Interview by Adriana Kantcheva, Assistant Editor, Biotechnology Journal.


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Changes in cardiopulmonary function induced by nanoparticles

The biological impact of nanoparticle exposure are dependent on size, chemical composition, and route of exposure (oral, dermal, intravenous, inhalation). Cardiac consequences include disruption of heart rate and electrical activity via catecholamine release, increased susceptibility to ischemia/reperfusion injury, and modified baroreceptor control of cardiac function. These likely contribute to adverse health effects promoting myocardial infarction, hypertension, cardiac arrhythmias, and thrombosis. /mh [18]

Mechanisms of memory enhancement

The ongoing quest for memory enhancement magnifies as the global population continues to age. Targeting many of the same mechanisms used to form long-term memories, including CREB activation, AMPA/NMDA receptor trafficking, neuromodulation, and metabolic processes, may all lead to enhancement of memory. These approaches have been tested via genetic or pharmacological methods in animal models as well as humans. /mh [19]

The curious case of miRNAs in circulation: Potential diagnostic biomarkers?

The pervasive occurrence of cell-free miRNAs in circulation suggests that they play an emerging role as regulatory molecules in the secretory environment. This review discusses the diversity of acellular miRNAs from a functional perspective and explores their utility in a clinical setting as blood-based biomarkers for diseases. /mh [20]

Industry news

Rotation announced

Following the Second Annual SLAS Annual Conference and Exhibition (SLAS2013), Jan. 12-16, 2013, in Orlando, FL, USA, SLAS will consistently rotate its annual conference between the east and west coasts of the US. Starting 2014 in San Diego, CA, while Washington, DC will serve as home to SLAS2015. /ag


Morphosys announced that the sale of its research and diagnostic antibody segment AbD Serotec to Bio-Rad Laboratories has been completed. All assets and liabilities of the AbD Serotec segment of Morphosys as well as all shares of the subsidiaries MorphoSys UK, Morphosys AbD and Morphosys US. have been transferred to Bio-Rad. Read more on this topic at

Restoring human tissue

Scientists at the Texas Biomedical Research Institute have for the first time demonstrated that baboon embryonic stem cells can be programmed to completely restore a severely damaged artery. These early results show promise for eventually developing stem cell therapies to restore human tissues or organs damaged by age or disease. /ag

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