BiotecVisions 2012, November

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


Contributors: Andrea Gregor /ag; Andrew Moore /am; Adrian Miller /ami; Andrea Modica /amo; Barbara Janssens /bj; Bill Mullen /bm; Babu Varghese /bva; Frédérique Belliard /fb; Fran Harding /fh; Gregor Chichetti /gc; Gillian van Beest /gvb; Jing Zhu /jz; Karen Chu /kc; Meghana Hemphill /mh; Mia Ricci /mr; Susan Vice /sv; Tiffany McKerahan /tmk; Vera Köster /vk; Vivian Killet /vki

November 2012

Are microbes the future of bioenergy?

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The recent Leopoldina report Bioenergy – Chances and Limits, provides an expert in-depth analysis on the use of bioenergy. The report is critical of the current alternative fuels policies of the EU and national governments and has generated a great deal of interest amongst members of the press. Professor Gerhard Gottschalk of Germany, a leader in the field of microbiology, talks to ChemViews magazine about the report and his views on bacteria's role in the future of bioenergy.

Prof. Gottschalk's view, also covered in his recent book Discover the World of Microbes: Bacteria, Archaea, and Viruses, is much in agreement with the report, in that “Ethanol, butanol, and biogas will be the major products of the fermentation industry in the future, but it still will be difficult to meet more than 10 % of global fuel needs with this type of bioenergy.”

Prof. Gottschalk also thinks that the microbial community will have surprises for us. New pathogenic bacteria will emerge and we will have to fight known and new bacteria. New microbial production processes in biotechnology will be used not only for production of pharmaceuticals, but also for bulk chemicals. His concern is the unpredictability of the activity of the huge microbial biomass as a consequence of the increase in the world population, the exploitation of resources for food and energy production, and the constantly increasing pollution.

Find out more about Prof. Gottschalk's views on biofuel from algae, the role of bacteria in bioenergy and more about his books on microbiology in the ChemViews magazine. [1]

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Getting published

What's in a slide show?

Especially true at conferences where only non-published material may be presented, the audience in the room may well be the very people who will be reviewing your soon-to-be submitted manuscript. Making a good first impression is therefore of critical importance.

Here's a (non-animated) bullet-point list of tips.

• People remember proportionally more from the start and the end of a presentation than the middle. So, start and end with something you want the audience to remember, even if they forget everything else! And bear in mind that the more slides you have, the more in the middle will be forgotten!

• Accordingly, keep the number of slides to an average of not more than one per minute in order to take advantage of the synergy between the spoken and the visual information: slides that “fly by” leave very little impression.

• Give your slides explicit, statement-like headings, e.g. “Lis1 is required for dynein to function in yeast and man”, not “The role of Lis1 in yeast and man.”

• Keep the quantity of primary data to the results necessary to demonstrate your conclusion(s): this will maximise the chance that your audience follows the “plot” without being distracted by details.

• If you show an animation or a movie, don't let it loop continuously whilst talking: the audience will find it hard to concentrate on your message(s). Stop the looping after 3 or 4 rounds. Never have several little “cinemas” looping simultaneously on one slide.

• Construct complicated models in stages, using animation functions.

• Make simple slide-transitions: peeling screens, rotating 3-d transitions, and the like, really distract the viewer. The most simple transition – the plain appearance of the next slide – is the best!

• When summarising, animate the appearance of bullet points, and keep each one short: a summary is just that. Emphasise the most important points briefly. And most important: leave the summary slide showing long enough for your audience to take their final notes!

Good luck with your next presentation! /am

Andrew Moore is Editor-in-Chief of BioEssays.

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Further reading: [2]

Aviation biofuels: Leaping the toxicity hurdle

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In 2012, aviation fuel was integrated into the EU Emission Trading Scheme underlining the environmental and economic importance of finding realistic routes to alternative fuels. In June this year, a terpene-derived jet fuel, AMJ 700, made by the biotech company Amyris, powered an Embraer jet in a demonstration flight. This terpene mix is a promising candidate fuel for commercial production. It contains monoterpene-derived cycloparaffins, which are critical for meeting the strict performance specifications. However, monoterpenes display a high level of toxicity to producing organisms presenting a major challenge for microbial production. Achieving higher product titres through decreased toxicity coupled with streamlined purification is imperative for the commercial viability of these terpene-derived fuels. In this article in Biotechnology and Bioengineering, Brennan and coworkers show that the use of a biphasic yeast fermentation system can not only relieve product toxicity in situ but also consolidate recovery and downstream purification steps to produce terpene fuel blends that match Jet A fuel properties. /sv [3]

Microbial flatulence? Gas bubbles in yeast

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Yeasts produce gas bubbles that fill a significant part of the cell. The before missing link between intracellular CO2 production by glycolysis and eventual CO2 release from cells has been resolved in this article in FEMS Yeast Research. Thus, yeasts may serve as model to study CO2 behavior under pressurized conditions that may impact on fermentation biotechnology. /fb [4]

Biomass pretreatment research

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Yield, concentration, and rate: In their commentary in Biotechnology Progress, Bruce Dale and Rebecca Ong detail which data should be collected for each category to enable comparison of various pretreatment technologies. They provide a visual summary of 20 existing pretreatments to aid the renewable resource energy community in the assessment of existing gaps in information. /sv [5]

DNA gel electrophoresis using household materials

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Gel electrophoresis for the separation of DNA is a central technique in molecular biology, yet the costs associated with performing this activity in the classroom are often prohibitive. This article in Biochemistry and Molecular Biology Education offers an alternative protocol that is less expensive because it relies on household materials. Gel boxes become plastic containers fitted with aluminum foil electrodes and 9-volt batteries. Using food-grade agar-agar and an aquarium pH buffer, DNA fragments and dyes can be separated electrophoretically and visualized by staining in gentian violet. The activity was tested in high school classrooms and meets several Life Sciences Content Standard C criteria. /amo [6]

Artificial cells with microfluidics

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Microfluidics has emerged as a powerful technology for the synthesis of artificial cells from giant unilamellar vesicles by dramatically improving control over size, lamellarity, internal contents, and membrane composition and addressing sophisticated cellular functions such as protein synthesis. This review in Bioessays presents the state-of-the-art of microfluidic technology, as a robust platform for recapitulating complex cellular structure and function in synthetic models of biological cells. /am [7]

In vitro drug permeability model

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In vitro drug permeability models predicting human oral drug absorption play a critical role in early stage drug candidate screening. Conventional in vitro models utilize a differentiated intestinal epithelial cell monolayer growing on permeable filters where perhaps the most important 3D features, the small intestinal villi, are missing. Yu and coworkers have reconstructed artificial human small intestinal villi with physiologically relevant cellular density and physical dimensions. This is the first time this environment has been recreated to almost exact physical specifications in vitro. In their article in Biotechnology and Bioengineering the March group, from Cornell University, demonstrates that accurate 3D cellular layout can make an in vitro model perform much in the same way as mammalian intestines for paracellularly-absorbed drugs. The authors expect future work will demonstrate the utility of including an accurate 3D environment in in vitro models for absorption of several types of drugs. /sv [8]

Old drug with new trick: Fighting resistant tuberculosis

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Tuberculosis represents the second leading cause of death due to infection after HIV/AIDS, accounting for up to two million deaths annually. Increasingly widespread drug resistance to frontline drugs constitutes a global public health threat. Reinvestigation of a natural antibiotic, pyridomycin, reveals it to be effective in treating drug resistant tuberculosis. Pyridomycin works in a similar way to the commonly used synthetic treatment isoniazid: by attacking the production of mycolic acid, a component of the Mycobacterium tuberculosis cell wall. However, pyridomycin uses a different mechanism to inhibit mycolic acid production, so it can overcome isoniazid-resistant bacteria. This work highlights how previously abandoned molecules can be rediscovered as leads for new therapeutic agents. /fh [9]

A one dose experimental cholera vaccine

The number of cholera vaccine doses required for immunity is a constraint during epidemic cholera. Of especial concern is the large-scale cholera epidemics that occur in fragile populations comprised of Vc-antigen na�ve individuals as highlighted during the recent cholera outbreak in Haiti. This article in FEMS Immunology and Medical Microbiology examines protective immunity following one dose of multiple Vibrio cholerae (Vc) colonization factors. This has not been directly tested although it is known that individual Vc colonization factors are protective antigens. Further testing is required, however the authors envision partial anti-LPS antibody response combined with other partial responses to protective Vc immunogens such as TcpA and TcpF will provide one dose protection for the cohort that is still the most at risk for cholera. /gvb [10]

Nanotech weapons could reduce deaths from bacterial infections

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When the body is attacked by a dangerous microbe, the immune system releases cytokines to seek and destroy the invader. But some infections like E. coli and salmonella unleash such an excessive cytokine storm that the patient's blood pressure crashes catastrophically, multiple organ failure develops and death is often the result. The reaction is triggered by features on the outside of bacterial cells called LPS that are recognized by receptors on immune cells. In a study published by EMBO Molecular Medicine scientists created a molecular mimic that binds to the same receptors as LPS, but doesn't trigger a response. By attaching small sugar molecules to the ends of the dendrimers' branches, they made a molecule that could interact with the immune system's main detection system for bacteria. When they tested it in rabbits, they found that it protected the gut wall from the damage caused by shigella infection, and it minimised invasion by bacteria even when antibiotics were not used. /vki [11]

Secrets of Marburg virus revealed

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Marburg virus, and its cousin Ebola, are notorious as the agents of fatal hemorrhagic fever. Research published in PloS Pathogens hints at why these viruses infect and proliferate with deadly efficiency. By examining the crystal structure of the Marburg virus, the double stranded RNA genetic code of the virus was revealed to be coated entirely with a key protein, VP35. As doubled stranded RNA alerts the immune system to respond to infection, this protein envelope allows the virus to evade detection. Currently, there is no cure available for Marburg hemmorhagic fever. Understanding the strategy by which filoviruses silence immune system alarms will aid in developing a therapeutic response. /fh [12]

Goodbye wrinkles, hello collagen! A boost to skin rejuvenation technology

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Current laser based skin rejuvenation methods can say hello to the novel technology using laser-induced optical breakdown. A group of Scientists at Philips Research Eindhoven has successfully demonstrated the efficacy of a minimally invasive breakthrough skin rejuvenation technology for wrinkle reduction, without any pain and unpleasant sensations, and social down-time. A grid of intradermal lesions created by tightly focused near-infrared laser pulses stimulates selective dermal collagen production and remodeling without disrupting the epidermal surface. The present light- and laser-based skin treatment modalities rely on selective photothermolysis; a technique that is based on differences in linear absorption of optical energy by the skin's constituents and therefore balances between efficacy and side effects. The results are introducing a safe treatment procedure without damaging the epidermis, with no or little social downtime and with an efficacy that might be comparable to ablative techniques. /bv [13]

GM-CSF: A feisty new direction for an old cytokine

Granulocyte-macrophage colony-stimulating factor (GM-CSF) and Flt3 ligand are the two most prominent cytokines used to stimulate the development of dendritic cells (DCs) in vitro. Little is known about how these two cytokines coordinate DC production. In the European Journal of Immunology, Zhan et al. reveal that despite being relatively redundant for DC development in the steady state, elevated GM-CSF changes the nature of DCs generated in vitro and in vivo. The authors found that GM-CSF overrides the influence of Flt3 ligand to divert the differentiation of DCs from the conventional pathway into a new type of DC that can rapidly respond to inflammatory stimuli. This previously undefined effect of GM-CSF is presumably tailored for inflammatory emergencies but could also lead to immunopathology. Thus, restoration of the balance of the DC network in inflammatory states by targeting GM-CSF could be a useful strategy of immune intervention. /kc [14]

Turning cell growth into a gold standard

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In the emerging field of systems biology, huge datasets are generated at all omics levels and used for modeling of an organism's metabolism. Since many different research groups around the globe are working on this, an important issue is to generate consistent and comparable data originating from different culture systems. In Engineering in Life Sciences, a consortium of researchers lead by An-Ping Zeng and Ralf Pörtner (Hamburg, Germany) reports on systematically analyzed cell growth in five bioreactor systems in three different laboratories. They have found a high dependency of cell growth on certain hydrodynamic parameters of the bioreactors. The data obtained can now be used for process standardization and pave the way for possible gold standard bioreactor systems to be used for systems biology approaches and scale-up with mammalian cells. /ug [15]

Aptamers – tailorable ligands for affinity separations

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Aptamers are synthetic oligonucleotides which are able to capture their corresponding target molecule with high affinity and specificity. Therefore, they can be thought of as nucleic acid-based alternatives to antibodies and can be used as ligands in affinity separations. One major advantage of aptamers is the possibility to customize them for a specific application. For example, it is possible to generate aptamers with a 3D folding dependent on divalent cations. Since the folding of the aptamer is a the basis for the binding of the target, the addition of chelating agents (e.g. EDTA) can be used to trigger the elution of the target under mild conditions. In Engineering in Life Sciences Johanna Walter et al. (Hannover, Germany) review the state-of-the art in aptamer-based affinity separation with focus on the purification of proteins from a user's perspective. /ug [16]

Host cell clearance in antibody purification

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Protein A chromatography is typically the first capture step in the purification of monoclonal antibodies. Although exploiting an affinity interaction, the level of host cell proteins in the elution pool after purification varies significantly with different feedstocks. In Biotechnology Journal Vikram Sisodiya et al. (Genentech, San Francisco, CA, and University of Wisconsin-Madison, WI, USA) demonstrate using a high-throughput batch binding chromatography method and 21 antibodies that antibody-host cell protein interactions are primarily responsible for the variable levels of host cell proteins in the protein A elution pool. In addition, they show that the interactions may be disrupted using additives, reducing the level of host cell proteins present after protein A purification. The reduction in the level of host cell proteins differed between antibodies suggesting that the interaction varies between individual antibodies but encompasses both an electrostatic and hydrophobic component. /ug [17]

Biomaterials from soybean oil

There are many ways to utilize soybean oil – of course it can be used for food purposes, but skilled chemists can also turn this oil into advanced materials for biomedical applications. A new class of soybean oil-based biocompatible polyurethans with good mechanical properties is reported in European Journal of Lipid Science and Technology. The researchers synthesized soybean oil polyols which were further reacted to form cross-linked polyurethanes. The tensile strength of the resulting polymer can be controlled by adjusting the molar ratios of the reacting groups and the content of the chain extender. The synthesized material was shown to support the growth of mouse fibroblasts and a wide range of potential applications such as porous scaffolds for soft tissues can be envisaged. /lk [18]

Animal nutrition to decrease saturated fat in meat and milk

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Milk and meat, because of their relatively high saturated fat concentration and level of consumption, make a large contribution to human saturated fat consumption. Read about the strategies to decrease the saturated fat content in meat and milk in Lipid Technology. The present Feature article focuses on including forage in the ration of ruminants and on supplementation of the diet of ruminants and monogastrics with unsaturated fatty acid-rich oilseeds, fish oil or marine algae. /lk [19]

Special issue: Euro Fed Lipid Highlights 2012

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In this European Journal of Lipid Science and Technology Special issue, you will find four keynote lectures presented at the olive oil, biotechnology, and processing sessions of the Euro Fed Lipid Congress in Cracow this September and one paper from last year's processing session in Rotterdam. /lk

Virtual Issue: Innovations and applications from MRT

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This free Virtual Issue of Microscopy Research & Technique highlights some of MRT's latest cutting-edge research, including an innovative application in conservation science, a new illumination technique for improved visualizations of complex structured transparent specimens, and a novel system to efficiently segment brain MR images. /tmk

Advertorial: CSH Asia – Synthetic Biology

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The 2nd round of Cold Spring Harbor Asia conference on Synthetic Biology will be held at the Suzhou Dushu Lake Conference Center in Suzhou, China. The conference will begin at 7:00pm on the evening of Monday November 26, and will conclude after lunch on Friday November 30, 2012.

The conference will include eight oral sessions and one poster session. Many talks will be selected from the openly submitted abstracts on the basis of scientific merit and relevance. Social events throughout the conference provide ample opportunity for informal interactions. The major topics covered in the CSHA conference:

1. Microbial genome engineering;

2. Genome engineering of eukaryotic system;

3. Designing cellular circuits;

4. Metabolic engineering for chemicals, fuels and materials;

5. Emerging tools of synthetic biology.


Fungi and Lignocellulosic Biomass

Christian P. Kubicek (Editor)

ISBN: 978-0-470-96009-7

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Fungi and Lignocellulosic Biomass offers a comprehensive review of the use of fungi in efficient and cost-effective conversion of cellulosic biomass into fuel. Complete, up-to-date coverage ranges from the biochemical basis of cellulose degradation by fungi to the application of key fungal enzymes in the biofuel industry. /ag

Current Protocols

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Keeping mice healthy

Good science and good animal care go hand in hand. A sick or distressed animal does not produce the reliable results that a healthy and unstressed animal produces. Researchers from the National Institutes of Health in Bethesda, MD, describe the essentials of assessing mouse health, colony health surveillance, common conditions, and determination of appropriate endpoints. Tremendous effort and expense is expended maintaining Specific Pathogen Free (SPF) colonies, and it is critical that all staff entering colonies and handling animals understand disease transmission and the importance of good practices to prevent pathogens from being introduced or spread. Understanding the health and well-being of the mice used in research enables the investigator to optimize research results and animal care. /bm [20]

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RT-PCR for small-molecule screening

Quantitative measurement of the levels of mRNA expression via real-time reverse transcription polymerase chain reaction (RT-PCR) has long been used for analyzing expression differences in tissue or cell lines of interest. This method has been used somewhat less frequently to measure the changes in gene expression due to “perturbagens” such as small molecules or siRNA. The availability of new instrumentation for liquid handling and real-time PCR analysis, as well as the commercial availability of start-to-finish kits for RT-PCR, has enabled the use of this method for high-throughput small-molecule screening on a scale comparable to traditional high-throughput screening (HTS) assays. This protocol focuses on the special considerations necessary for using quantitative RT-PCR as a primary small-molecule screening assay, including the different methods available for mRNA isolation and analysis. /bm [21]


Top tips for your application

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At The EMBO Meeting 2012 a pre-conference Career Day offered young scientists the possibility to gain soft skills and contacts for their careers in academia and beyond. Workshops offered ranged from presentation skills (“Capture your audience”) to Science Communication (“Make science make sense”) and Job Application (“Understand the do's and don'ts”). The latter also provided a preparation for the Career Options lunch where participants could meet, eat and discuss with three scientists who ended up in various professional areas.

For each of the workshops a video summary with five “top tips” can be found on YouTube. For job applications the top tips are:

1. Imagine YOU are the recruiter

2. Learn to present yourself in an “elevator pitch”

3. Actively network

4. Most important FIRST

5. Tell stories as examples for your skills

If you imagine that you are the recruiter you can really understand what the employer is looking for and why the position becomes available. This of course implies that you can present yourself in what is called an “elevator pitch”. If you meet an interesting or important person in the elevator or while waiting for your coffee at a meeting, it's good to be able to say something really interesting about yourself in maximum 30 seconds. This really requires some practice and will make you be remembered – which connects to the third point.

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Actively networking is indeed more efficient than applying for advertised positions. Also “small talk” can be done in a very structured way – the main point being that you always focus on informing yourself, never ask for a job at first, and always inquire about who else you could talk to.

When talking or interviewing, but also in your cover letter and CV, it is crucial to mention the most important things first – you only have half a minute to convince! Finally telling stories means that you can give examples of what you did in the past – these are the real proofs of what you will bring your future employer! /bj

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Natural and synthetic immune synapses

Microfabricated platforms to modulate and monitor T cell synapse assembly

Microfabricated platforms have made great contributions to our understanding of the assembly dynamics and functional roles of the T-cell synapses over the past decade. In this recent article in WIRES Nanomedicine and Nanobiotechnology, H. R. Jung and colleagues from South Korea and the USA, describe three such microfabricated platforms, including multi-protein micropatterned surfaces, micropatterned supported bilayers, and T-cell/antigen presenting cell pair arrays. /mh [22]

In addition to providing new insight into biophysical principles, investigations into immune synapse function may allow control over ex vivo T-cell expansion. Bioreactors based on these concepts may find immediate application in enhancing cell-based immunotherapies. /mh [23]

Stem cell bioengineering at the interface of systems-based models and high-throughput platforms

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This recent article in WIREs System Biology and Medicine by G. H. Hill from University of Illinois at Urbana-Champaign, provides an excellent overview of various tools, including high-throughput and systems-based approaches to understand stem cell biology. /mh [24]


Biotechnology Progress Award

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Wilfred Chen, Gore Professor of Chemical Engineering in the Department of Chemical and Biomolecular Engineering, University of Delaware, is the 2012 winner of the Biotechnology Progress Award for Excellence in Biological Engineering Publication. The award will be presented at the 2012 American Institute of Chemical Engineers Annual Meeting in Pittsburgh, PA. /sv

Tribute to Elmer Gaden

Twelve individuals have provided their reflections on Elmer L. Gaden, Jr., founding editor of Biotechnology and Bioengineering, who died earlier this year. Their insights and experiences regarding how Elmer Gaden influenced them are captured in very personal anecdotes. Biotechnology and Bioengineering's current Editor-in-Chief, Douglas S. Clark caps these twelve short pieces with his own personal recollections. /sv [25]

Materials Views

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DNA for future electronics

German researchers develop conducting nanostructures based on metallized DNA.

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Biomimetic fibrous scaffolds

Researchers from Imperial College, London, report a series of modified g-PGA polyester scaffolds for tissue engineering applications.

Nanocarriers for therapeutic delivery

Nanocarriers for encapsulation, delivery, release, and accumulation of drugs are reported in a special issue of Advanced Materials.

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