Progress towards the ‘Golden Age’ of biotechnology

Progress towards the ‘Golden Age’ of biotechnology

Available online at www.sciencedirect.com Progress towards the ‘Golden Age’ of biotechnology KMA Gartland1, F Bruschi2, M Dundar3, PB Gahan4, MP Viol...

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Available online at www.sciencedirect.com

Progress towards the ‘Golden Age’ of biotechnology KMA Gartland1, F Bruschi2, M Dundar3, PB Gahan4, MP Viola Magni5 and Y Akbarova3

Biotechnology uses substances, materials or extracts derived from living cells, employing 22 million Europeans in a s1.5Tn endeavour, being the premier global economic growth opportunity this century. Significant advances have been made in red biotechnology using pharmaceutically and medically relevant applications, green biotechnology developing agricultural and environmental tools and white biotechnology serving industrial scale uses, frequently as process feedstocks. Red biotechnology has delivered dramatic improvements in controlling human disease, from antibiotics to overcome bacterial infections to anti-HIV/AIDS pharmaceuticals such as azidothymidine (AZT), anti-malarial compounds and novel vaccines saving millions of lives. Green biotechnology has dramatically increased food production through Agrobacterium and biolistic genetic modifications for the development of ‘Golden Rice’, pathogen resistant crops expressing crystal toxin genes, drought resistance and cold tolerance to extend growth range. The burgeoning area of white biotechnology has delivered bio-plastics, low temperature enzyme detergents and a host of feedstock materials for industrial processes such as modified starches, without which our everyday lives would be much more complex. Biotechnological applications can bridge these categories, by modifying energy crops properties, or analysing circulating nucleic acid elements, bringing benefits for all, through increased food production, supporting climate change adaptation and the low carbon economy, or novel diagnostics impacting on personalized medicine and genetic disease. Cross-cutting technologies such as PCR, novel sequencing tools, bioinformatics, transcriptomics and epigenetics are in the vanguard of biotechnological progress leading to an ever-increasing breadth of applications. Biotechnology will deliver solutions to unimagined problems, providing food security, health and well-being to mankind for centuries to come. Addresses 1 Life Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA, Scotland, UK 2 Dipartmento di Ricerca Traslazionale, N.T.M.S., Medical School, Universita` di Pisa, Via Roma, 55 56126 Pisa, Italy 3 Department of Medical Genetics, Faculty of Medicine, 38039 Kayseri, Turkey 4 Anatomy & Human Sciences, King’s College London, Henriette Raphael Building, London Bridge, London SE1 1UL, UK 5 Fondazione Enrico Puccinelli, Research Center, via Cestellini 3, Perugia, Italy Corresponding author: Gartland, KMA ([email protected])

Current Opinion in Biotechnology 2013, 24S:S6–S13

Current Opinion in Biotechnology 2013, 24S:S6–S13 Available online 21st June 2013 0958-1669/$ – see front matter, # 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2013.05.011

Introduction: the biotechnological rainbow Biotechnology is, along with information technology, the biggest growth industry in the 21st century, with 22 million citizens employed in Europe alone, in a s1.5Tn industry, the scale of which may never have existed before. With burgeoning numbers of new techniques, applications and potential treatments, all of the disciplines contributing to biotechnology combine to give a rainbow-like effect of many colours. From the red biotechnology of pharmaceutically and medically relevant applications, through the green biotechnology of agricultural and environmental applications, to the white biotechnology of producing process feedstocks more efficiently, all types of biotechnology are contributing to this rapidly growing marketplace. Increasingly, rainbow biotechnology applications, such as human vaccines produced in plants, which span or are not easily categorised as red, green or white biotechnology, are also contributing to the plethora of applications and technologies available. In this short paper, a range of new product developments and applications of biotechnology are explored and placed in the context of our progress towards the ‘Golden Age’ of biotechnology, in which economic, environmental or health and well-being benefits are realized.

Red biotechnology: enhancing medical and pharmaceutical science for the good of mankind As our knowledge of the molecular and cellular mechanisms influencing gene expression, cellular processes, growth and development has increased, the range of potential applications of biotechnology to medical and pharmaceutical challenges has risen dramatically. Detailed understanding of how the 23 pairs of chromosomes in the human genome, encompassing 20–25,000 genes interact with proteins, transcription factors and

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other elements in the cell, tissue and organ environments is being amassed at an unprecedented rate. Epigenetic studies, analysing the effects of the methylation, acetylation and other forms of DNA and histone modification from the ENCODE project and the development of epigenetic factor atlases are revealing startling new insights into the complex nature of controlling gene expression and how, where regulation is defective, biochemical disorders can rapidly occur [1,2]. Understanding of localised, small scale mutations leading to single gene (or monogenic) disorders [3] as well as more complex, polygenic disease susceptibilities and pathologies [4,5] is benefitting from dramatic reductions in the cost of genomic sequencing through new generation technologies, meaning that truly personalised medicine is just advancing over the horizon [6,7]. Overcoming the genetic basis of disease will also require an in-depth knowledge not just of the genetics of human disease, but also of genetic counselling strategies and their application to improving patient healthcare and the development and application of predictive diagnostic tests and therapeutic agents derived from molecular biotechnology. Increasing longevity means that the commercial opportunities for therapeutic advances from cancer studies, neurological disorders such as Alzheimer’s or Parkinson’s disease and the enhanced long-term effectiveness of human immunodeficiency virus inhibitors such as azidothymidine, a nucleoside analogue reverse-transcriptase inhibitor (AZT) [8] to treat chronic conditions will undoubtedly increase in the years ahead, taking the marketplace for cell therapeutics alone from an estimated $1bn in 2011 to $5bn by 2014. Progress in the science of stem cell therapy and regenerative medicine will prove vital to extending this market further. Experimental models, immunotherapeutics and novel vaccines

Biotechnologies have provided new tools for the study of several human and animal diseases, including recent findings of growth differentiation factor GDF11 reversing age-related cardiac hypertrophy from murine studies [9]. Use of transgenic or knock-out mice [10], for example, has led to a better comprehension of host immune response against infectious and parasitic agents, an example is represented by experimental infections in animals where genes coding for either cytokines or transcription factors have been disrupted or overexpressed, as in the case of experimental infection with nematodes where the role of eosinophils has been completely re-evaluated [11,12]. Understanding of the in vivo functions of human cells and tissues as well as of the human immune system has received significant advances from the development of the so-called ‘humanized’ mouse strains. These are on the basis of severely immunodeficient mice in which the interleukin-2 receptor common g-chain locus is mutated, www.sciencedirect.com

with the effect to tolerate the engraftment of a functional human immune system [13]. Recombinant immunotherapeutics [14] are promising biological tools for the treatment and prevention of various diseases. Immunotherapy can be passive or active. In the first case, the success of treatment with antibody and cytokine therapeutics represent a promising future and opportunity for improvements. Efforts, such as cell engineering, antibody engineering, human-like glycosylation in yeast, and Fab fragment development, have opened the way to improve antibody efficacy while decreasing its high manufacturing costs. Both new cytokines and currently used cytokines have demonstrated therapeutic effects for different indications. As regards active immunotherapy, recently approved HPV vaccines have encouraged the development of preventive vaccines for other infectious diseases. Immunogenic antigens of pathogenic bacteria can now be identified by genomic means (reverse vaccinology) [15]. Due to the recent outbreaks of pandemic H1N1 influenza virus and related genotypes, recombinant influenza vaccines using virus-like particles and other antigens have also been engineered in several different recombinant systems [14]. Mucosal vaccination represents a valid perspective to control infectious diseases, it induces in fact both humoral and cell-mediated responses. In addition, the delivery of vaccines to mucosal surfaces makes immunization practice safe and acceptable [16]. In the past 100 years, vaccination has contributed immensely to public health by preventing a number of infectious diseases. Attenuated, killed or part of the microorganism is employed to stimulate the immune system against them. Progress in biotechnology has provided protective immunity also through DNA vaccines [17]. Another frontier is represented by genetically modified plants which can be used as bioreactors for the production of mucosally delivered protective antigens. This technology shows great promise to simplify and decrease the cost of vaccine delivery. In particular, there are advantages and disadvantages of using plants for the production of mucosal vaccines against widespread infectious diseases such as HIV, hepatitis B and tuberculosis [18]. In comparison with traditional vaccines they have advantages of low cost, greater effectiveness, and in certain circumstances, greater safety [19]. An increasing number of vaccines have been successfully expressed in various transgenic plants [18]. The number of articles published every year on transgenic plant vaccines has increased dramatically in recent years, to approximately 800 by 2011 [19]. In recent years, nanovaccination is a novel approach to the methodology of vaccination. Nanomaterials are delivered in the form of microspheres, nano-beads or micro-nano-projections. Current Opinion in Biotechnology 2013, 24S:S6–S13

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Painless, effective and safe needle-free routes such as the intranasal or the oral route, or patches of microprojections to the skin are some of the approaches which are in the experimental stage at present but may have a great future ahead in nanovaccination [20]. Epigenomics

Understanding the many ways by which packaging of genomes is influenced by histones and histone-related proteins is a key target for epigenomics investigations aimed at novel therapeutics for a wide range of diseases from immunoinflammation to cancer studies [21]. Textmining and comparative analysis studies have identified the role of histone methyltransferases, demethylases, acetylases and deacetylases, particularly of lysine and arginine residues in acting as binding sites for transcription factors and other proteins associated with upregulating or downregulating gene expression in a dynamic and reversible process [22]. Understanding the effectiveness of epigenetic signal molecules will reveal major insights into how growth, development and gene expression are controlled in both normal and abnormal physiological states. Such understandings will doubtless provide fertile ground for discovering new pharmaco-therapeutics for preventing and ameliorating disease states. One recent example of the success of this approach is the inhibition of the lysine specific demethylase (LSD1) to reprogramme drug-resistant leukaemia cells to once more become drugsensitive [23]. Epigenetic findings are just one form of the ‘genome dividend’ whereby every dollar spent on the human genome project is estimated to have realised more than $140 in economic returns [24]. The dramatic effects of new sequencing technologies, including ‘454’ and next generation approaches, resulting in huge reductions in the price of sequencing individual genomes, can only realise further such gains, especially in the areas of biomarkers, personalised, predictive and preventative medicine [25]. One example of this is the declining cost of clinical exome sequencing, concentrating on the 1% of the human genome encoding proteins or associated with splicing junctions [26]. 85% of the more than 2000 disease causing variants identified to date occur in the exomic 1%. Clinical exomic sequencing and comparisons with the ‘1000 Genomes Project’ can be used to help identify previously unspecified disorders, such as the 3-M syndrome growth disorder, at costs of less than $8000, being less than the cost of testing for just six individual genetic disorders [27]. Whilst sequencing costs will undoubtedly continue to fall towards the $1000 genome scan, as yet we do not have adequately effective databases or tools for interpreting population polymorphisms to allow many of the predicted benefits of clinical exome or whole genome sequencing to be realised, for example, in cancer research studies [28]. Achieving the potential benefits that personalised Current Opinion in Biotechnology 2013, 24S:S6–S13

medicine can bring will require much greater coordination and standardisation of the information collected from patients and the well-public, integration of the use of this information in order to increase the numbers of healthcare applications benefitting from biomarker and population based studies [29]. Pharmacogenetics has a vital role to play in personalised medicine, through helping to identify patients at risk of adverse effects [30], for example, in tuberculosis patients where glutathione-S-transferase polymorphisms may be associated with metabolic deactivation and adverse drug reactions in the liver [31]. Epigenetics advances will play a part in reducing adverse drug reactions, not least due to the paucity of our current knowledge of gene activation/ inactivation mechanisms and even diet, in a wide range of conditions, including psychotherapeutic applications [32,33]. Our fragmentary understanding of the effects of the microbiome [34], the microbial flora making up 90% of the cells in our bodies on responses to therapeutics and the potential consequences of disturbing the gut microflora on drug toxicity will provide significant opportunities for pharmacogenomics and epigenomics to impact on truly personalised medicine [30]. Small interfering (also known as micro-) RNAs can silence gene expression, through mechanisms such as DICER. Fragile X syndrome studies of FMR1 protein binding suggest that there may be thousands of RNA binding sites with unknown characteristics in the human genome [35]. Increasing understanding of how circular noncoding RNAs are involved in signalling and the regulation of gene expression will generate novel diagnostics and ultimately therapeutics [36]. Circulating nucleic acids as diagnostic tools

The application of circulating nucleic acids has opened up a large field in the search for early markers of disease by non-invasive methods for use in predictive and preventive medicine as well as in monitoring treatment. Advances in foetal and maternal plasma studies have allowed the identification of specific markers for foetal gender, foetal rhesus status, aneuploid chromosome disorders, for example, trisomy 13, 18, 21, a-thalassemia and b-thalassemia, haemophilia and sickle cell anaemia [37,38]. In addition, the development of pre-eclampsia can be predicted from the first trimester. Although an invasive procedure, analysis of DNA and RNA from amniotic fluid has revealed disorders that may permit the start of remedial treatment in utero. Furthermore, high-throughput sequencing of foetal DNA has allowed the construction of the complete foetal genome while salivary nucleic acids can be used to monitor development of premature infants [39]. Although less dramatic, steady progress is being made in identifying early markers for especially cancers and diabetic related disorders, whilst markers for monitoring treatment are also emerging, for example, identifying www.sciencedirect.com

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Kras mutations for determining whether or not to use antiEFGR therapy with colorectal cancer. Searching for novel antibiotics

The success of antibiotics in controlling many types of bacterial infection over the last 70 years is undisputable. Overuse, failure to complete prescribed treatment courses and an ability to rapidly mutate has led to the evolution of multi-drug resistant (MDR) bacteria across the world. Bacterial induced sepsis leads to the death of 350,000 citizens in Europe and the US each year [40] and an increasing healthcare costs burden for those who recover from MDR infections, with European survivors of hospital acquired infections requiring ongoing treatment costing up to s70,000. The extra membrane surrounding Gram-negative bacteria can result in antibiotics being ineffective through not entering the cell, being detoxified, or actively pumped out. MDR bacteria have themselves evolved to become extremely drug resistant (XDR) genotypes, which are susceptible to only two remaining types of antibiotics, polymyxins and tigecyclines. These antibiotic classes themselves are only used in extremis, since they have adverse effects on kidney functions. Biomedical scientists face increasing difficulty in finding continuing effective antibiotic treatment regimes, since only two new classes of antibiotics have entered the marketplace in the last 30 years [41]. Increasingly, novel approaches to antibiotic discovery from natural products, or design from chemical synthesis, are required. The pipeline of potential new antibiotics is however, strictly limited and may not be keeping up with the adaptive threat from XDR Gramnegatives harbouring the plasmid-borne New Delhi metallo-B-lactamase 1 (NDM1) [42] and other carbapenem resistant Klebsiella, Escherichia and Enterobacter, capable of rapidly spreading and recently found in 30% of Belgian hospitals [43]. Big Pharma is however, finding new ways to fight back, despite global financial uncertainty, with both GSK and Astra Zeneca having novel antibiotic classes under development, potentially effective against MDRs and able to reverse physiological resistance processes. Pharmacologists have identified 11 compounds, each representing a new antibiotic class, eight may prove effective against pseudomonads, mycobacteria and staphylococci, with a further three, under development by GSK, having a broader spectrum [44]. Metagenomic techniques, including in silico analysis of non-culturable microorganisms, use of extremophiles and the tracking of resistance gene spread in microbial communities through resistome studies are also likely to play an increasingly important part in the continuing battle against antibiotic resistance [45]. The BRAIN project

Another example of the power of biotechnology is the brain research through innovative neurotechnologies (BRAIN) project, to which the US government has www.sciencedirect.com

committed $100 million [24]. The development of new technologies will be accelerated, to image and map dynamic pictures of how individual brain cells process and store information from intact tissue and organ studies, as well as how complex neural circuits are formed and reformed at lightning speeds [46]. The insights gained from applying new nanoscience and nanotechnology techniques will aid investigation of a wide range of neuroscience disorders and conditions, from Alzheimer’s disease to epilepsy and from traumatic brain injury to psycopathy [47]. Gene editing

Amongst the emergent technologies likely to prove particularly important for the future of biotechnology, gene editing stands out. Two approaches to the highly precise modification of genomes through gene editing are the use of transcription activator like effector nucleases (TALENs) and zinc finger nucleases (ZFNs) [48]. TALENs have been developed from TALE proteins injected by the bacterial pathogen, Xanthomonas spp., with differing DNA binding specificities, causing disease in more than 200 plant species, but based upon a common 16 base pair sequence. By combining specific DNA recognition and binding TALE elements with the DNA cleaving domain of FokI, TALENS have been used in pairs to precisely modify human stem cells [49], and edit rat, zebrafish and worm genomes [48,50,51]. TALENs can be designed to target almost any DNA sequence and will have major impacts for the design and testing of therapeutic agents for specific genetic diseases [52,53]. ZFNs offer another method to edit genomes precisely, being available commercially from Sangamo and have been used with HIV positive patients having extremely low immune cell counts, by removing CD4+ T cells, typically affected by HIV, and editing out the CCR5 gene, encoding a protein used by the HIV to enter the CD4+ cells, before adding the modified CD4+ cells back into six patients. Five out of six patients receiving the treatment had increased immune cell numbers [54,55]. This approach may reduce viral spread and limit the need for lifetime antiviral drug treatment. The gene editing approach specifically replaced a gene associated with susceptibility to African swine fever, able to kill European pigs within 24 hours of infection, in ‘Pig 26’ with a resistance gene from an incompatible wild African pig species, to make ‘Pig 26’ disease resistant. This advance has been likened to the cloning of ‘Dolly the Sheep’ and has a 15fold increased success rate over conventional gene insertion methods [56], with applicability to all major livestock species for specific, targeted disease resistance. TALENS and zinc finger nuclease mediated editing are likely to represent major advances in the design and application of specific regulatory elements to turn up, turn down or provide simple visual indicators of gene expression in almost any eukaryote. As such, the Current Opinion in Biotechnology 2013, 24S:S6–S13

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potential biotechnological applications of gene editing are unbounded.

Green biotechnology: contributing to food security for all The Aqua-Advantage salmon, produced by inserting a fast growth gene from a wild Chinook salmon under the control of an Ocean pout promoter, into farmed infertile, triploid female Atlantic salmon, seems likely to be the first commercially available (or deregulated) genetically modified animal for food purposes in the USA [57]. A preliminary finding of ‘no significant environmental impact’ has been declared by the US Food and Drug Administration, with formal approval likely to occur during 2013. Polymerase chain reaction (PCR) is a well established tool for detecting DNA or RNA sequences of interest and has been widely used in European studies on horsemeat contamination of ‘beef products’ [58] and in the detection of genetically modified materials in a wide range of foodstuffs, which, depending upon national regulations, may require specific food labelling [59]. Internationally standardised methods for using PCR in detecting genetically modified materials now form part of industry actions to establish confidence amongst European citizens in food traceability [60]. Despite increasing areas of Bacillus thuringiensis (‘Bt’) maize being grown in Spain and Portugal in co-existence with conventional and ‘organic’-labelled maize, European consumer confidence still lags far behind that in the 29 countries where genetically modified crops are routinely grown. 66% of these countries are now developing, rather than industrial nations, across six continents. One hundred and seventy megahectares of GM crops were grown in 2012, including 81% of soya bean and cotton, 35% of maize and 30% of oil seed rape (canola) [61]. The most widely deployed traits are herbicide resistance, insect resistance of a gene stacked combination of both traits. In a global GM seed market worth $15bn. By not embracing GM crops, the European Union risks falling even further behind in growing enough crops for food security. Use of genetically modified crops to overcome food crop pathogens, is for example, fully established in the United States of America, where 95% of papaya grown in Hawaii is resistant to the endemic papaya ringspot virus, by overexpression of viral coat protein genes [62], and plum pox virus resistant plums are currently deregulated allowing commercial use, amongst many others. Deregulation petitions currently anticipating American federal approval during 2013 include a browning resistant apple with significantly restricted levels of polyphenol oxidase expression. A wide range of crop plants have been genetically modified for resistance to insect pests through ‘Bt’ crystal toxin gene expression, including the majority of cotton grown in India, for example, although Indian ‘Bt’ food crops have stalled in the regulatory process. Strategies for using ‘Bt’ Current Opinion in Biotechnology 2013, 24S:S6–S13

genes have become more sophisticated, to reduce the possibility of insect resistance arising, through the use of two or more different crystal toxin gene elements, to which insect pests such as the corn borer, would not normally be exposed. A further extension of this approach is to combine multiple ‘Bt’ and biopesticide genetic elements in chimaeric proteins encoded by synthetic genes. Expression of a synthetic protein combining domains from an insect calcium channel antagonist (Hvt) fused with the ‘Bt’ cry1Ac domains in prokaryotic systems is toxic to larvae from Helicoverpa armigera and Spodotera littoralis, two lepdiopteran pests found in the Indian Sub Continent [63]. Gene silencing using RNA interference (RNAi) is also being used to successfully combat a wide range of plant pathogens [64,65]. Drought resistance is another desirable trait which would improve plant productivity and enhance the economic potential of green biotechnology. Various physiological and molecular biological strategies are being investigated to achieve this goal, including osmotic adjustment, hormone application, epigenetic modification and genetic modification, for example, of proline-rich proteins [66]. Extending the growth range of economically valuable plants has also been achieved in the fast-growing Eucalyptus hybrids, for bioenergy and pulp fibre needs using freeze-tolerant genes [67]. The potential economic significance of extending the growing range of eucalypt hybrids to the Southern US States is shown by the US Department of Agriculture authorising, for the first time, large scale flowering field trials with 260,000 trees [68], whilst petitions for deregulation of these cold tolerant eucalypt hybrids are under active deliberations for potential deployment across 250,000 hectares. Genetically manipulating lignin structure and composition is an interesting application of biotechnology for energy production, which spans green and white biotechnology [69].

White biotechnology: feedstocks and industrial process chemicals Bioenergy production

Increased use of existing plant resources can make a major contribution to energy production, especially as new combustion technologies are making biomass fired power stations economically viable throughout the Northern Hemisphere. Using fast growing tree species such as willow and poplar, or grasses such as Miscanthus, bred for productivity and pest resistance, can along with use of waste wood processing and forest residues, significantly reduce energy import needs. Another valuable source of bioenergy comes from biodiesels prepared from oil seed rape (canola, Brassica napus), soya bean, or safflower (Carthamus tinctorius). Safflower is a particularly interesting source of biodiesel, since it grows well on semi-arid, arid, or indeed degraded landscapes, having a significant potential as a fuel from much of South-Eastern Europe [70]. www.sciencedirect.com

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Bioplastics

Biotechnology is developing new types of biodegradable plastics (bioplastics) and improving the efficiency of existing bioplastics processes. Bioplastics can make a positive contribution to reducing solid wastes and carbon dioxide emissions associated with packaging, surgical sutures and medical device materials, as they degrade without leaving polluting residues. Amongst bioplastics, the production of polyhydroxyalkanoates (PHA) has received considerable attention, with the Gram-negative bacteria Cupriavidus necator and Alcaligenes latus being used industrially to achieve up to 80% polyhydroxybutyrate (PHB) of bacterial dry cell weight. Although entirely suitable for packaging, production of PHB from such Gram-negative bacteria requires an additional purification step, to remove outer membrane lipopolysaccharide endotoxins, for use in biomedical applications. Using Grampositive bacteria, such as Bacillus species, which lack this lipopolysaccharide facet, may prove to be more appropriate for biomedicine. Novel Bacillus megaterium strains have recently been shown to be able to produce 59% and 60% dry weight PHB using glucose or glycerol as carbon sources in bioreactors [71]. This approach is both economically and environmentally attractive, since low costs waste materials such as glycerol from biodiesel refining can be used under conditions that prevent sporulation. The Gram negative Burkholderia cepacia has also been shown to produce up to 51.4% PHAs in batch systems fed with hemicellulosic wood hydrolysates [72]. Using renewable materials or industrial byproducts with such species in bioprocessing to produce PHAs should, when allied to improved bioreactor design, prove valuable to produce existing and new types of biopolymers since carbon sources can contribute up to 50% of PHA production costs [71]. Looking further into the future, tissue specific expression of introduced pathways has led to PHB production in soybean seed coats [73]. Although production levels were low and highly variable, these findings demonstrate that metabolic engineering using the phb A, B, C genes from Ralstonia eutropha and a seed coat peroxidase promoter can be effective in producing PHAs from heterologous systems. This also demonstrates the potential of such phytofactories, since 80% of the >255 million tonnes of soya beans harvested annually, are genetically modified. Biofiltering

Biofiltration of industrial wastes including volatile organic compounds offers a means to reduce the environmental impact of semiconductor manufacturing. Kinetic analysis of the effectiveness of novel strains of Pseudomonas, Paracoccus and Burkholderia species in batch-fed biodegradation systems holds great promise for a biotechnological solution to this problem [74]. Use of adaptive microbiomes, microbial communities acting in concert, has high potential to bioremediate industrial process wastes. Model systems for enhanced biotechnological www.sciencedirect.com

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phosphorus removal (EBPR) have been developed, on the basis of a core microbiome including previously uncultured polyphosphate accumulators, known as ‘Accumilobacter’ [75]. Some core microbiome constituents can also produce PHAs under suitable conditions. Optimisation of such EBPR microbiomes integrates knowledge from several biotechnological disciplines operating at vastly different scales, from genomic sequencing to single cell studies, to large-scale bioreactor design [76] in what has been christened a ‘systems microbiology’ approach [77]. TALENS biotechnologies may also prove highly valuable in biofiltration settings, through the use of sentinel plants, which will change colour or emit an easily assayed signal molecule in the presence of trigger concentrations of pollutants. Proteins and carbohydrates as process agents

White biotechnology has developed series of detergents with advantageous properties. Typically these have included detergents able to remain effective at lower temperatures in laundry processes, reducing water heating costs, or able to function over a broad pH range. One example of this is an extracellular low temperature active and alkaline stable peptidase from Acinetobacter species MN12 [78], which is effective in removing hard to shift blood stains from cottons from 15 to 358C and retained more than 75% of optimum activity between pH 7.0–11.0. Biotechnology has also provided a range of plant derived starches with diverse release properties including fast or slow release and pH sensitivity, to make digestants for tablet formulation. Examples include starches from maize, potato and rice modified by mild acid treatment have been shown to suitable for encapsulation of ascorbic acid (vitamin C) as a dietary supplement [79]. A wide range of derivative starch properties including moisture content, hydration capacity, swelling ability and flow characteristics can be modified, depending upon the intended function, typically site and rate of disintegration. Phosphate treatment or pregelatinisation of sweet potato and maize starch could alter disintegration rates by up to 240% and doubled hydration and swelling capacities [80]. The range of industrial processes benefitting from biotechnological interventions is huge, from aspartame production to brewing and from paper making to artificial soil production. In the coming years, the range of activities and processes using extracts or derivatives from living cells seems certain to increase, as we enter the ‘Golden Age’ of biotechnology, from which the economy, wider society and the environment can all realise substantial, ongoing benefits.

References 1.

Ecker JR, Bickmore WA, Barroso I, Pritchard JK, Gilad Y, Segai E: Genomics: ENCODE explained. Nature 2012, 489:52-55.

2.

Sanyal A, Lajoie BR, Jain G, Dekker J: The long-range interaction landscape of gene promoters. Nature 2012, 489:109-113. Current Opinion in Biotechnology 2013, 24S:S6–S13

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3.

Ordonez MP, Goldstein LSB: Using human-induced pluripotent stem cells to model monogenic metabolic disorders of the liver. Semin Liver Dis 2012, 32:298-306.

4.

Akbarian S, Halene T: The neuroepigenetics of suicide. Am J Psychiatry 2013, 170:462-465.

5.

Jabrocka-Hybel A, Skalniak, Piatkowski J, Pach D, HubalewskaDydejczyk: How far are we from understanding the genetic basis of Hashimoto’s thyroiditis? Int Rev Immunol 2013 http:// dx.doi.org/10.3109/08830185.2012.755175.

6.

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M: Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012, 22:1790-1797.

7.

Zanker KS, Mihich E, Huber H-P, Li A: Personalized cancer care conference. J Personal Med 2013, 2:70-81.

8.

Werayingyong P, Tosanguan K, Butchon R, Phanuphak N, Chokephaibulkit K, Kullert N, Teerawattananon Y, Tantivess S: The feasibility study on introducing three-antiretroviral combinations as standard regimens for prevention of mother to child HIV transmission in Thailand. J Health Sci 2013, 22:99-112.

9.

Loffredo FS, Steinhauser ML, Jay SM, Gannon J, Pancoast JR, Yalamanchi P, Sinha M, Dall’Osso C, Khong D, Shadrach JL, Miller CM, Singer BS, Stewart A, Psychogios N, Gerszten RE, Hartigan AJ, Kim M-J, Serwold T, Wagers AJ, Lee RT: Growth differentiation factor 11 is a circulating factor that reverses age-related cardiac hypertrophy. Cell 2013, 153:828-839.

10. Capecchi MR: Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century. Nat Rev Genet 2005, 6:507-512. 11. Hokibara S, Takamoto M, Tominaga A, Takatsu K, Sugane K: Marked eosinophilia in interleukin-5 transgenic mice fails to prevent Trichinella spiralis infection. J Parasitol 1997, 83:1186-1189. 12. Fabre V, Beiting DP, Bliss SK, Gebreselassie NG, Gagliardo LF, Lee NA, Lee JJ, Appleton JA: Eosinophil deficiency compromises parasite survival in chronic nematode infection. J Immunol 2009, 182:1577-1583. 13. Shultz LD, Brehm MA, Garcia-Martinez JV, Greiner DL: Humanized mice for immune system investigation: progress, promise and challenges. Nat Rev Immunol 2012, 12:786-798. 14. Huang C-j, Lowe AJ, Batt CA: Recombinant immunotherapeutics: current state and perspectives regarding the feasibility and market. Appl Microbiol Biotechnol 2010, 87:401-410. 15. Rappuoli R, Black S, Lambert PH: Vaccine discovery and translation of new vaccine technology. Lancet 2011, 378:360-368. 16. Długon´ska H, Grzybowski M: Mucosal vaccination: an old but still vital strategy. Ann Parasitol 2012, 58:1-8. 17. Ulmer JB, Wahren B, Liu MA: Gene-based vaccines: recent technical and clinical advances. Trends Mol Med 2006, 12:216-222. 18. Lo¨ssl AG, Waheed MT: Chloroplast-derived vaccines against human diseases: achievements, challenges and scopes. Plant Biotechnol J 2011, 9:527-539. 19. Guan Z-j, Guo B, Huo Y–l, Guan Z-p, Dai Y-k, Wei Y-h: Recent advances and safety issues of transgenic plant-derived vaccines. Appl Microbiol Biotechnol 2013, 97:2817-2840.

23. Schenk T, Chen WC, Go¨llner S, Howell L, Jin L, Hebestreit K, Klein HU, Popescu AC, Burnett A, Mills K, Casero RA Jr, Marton L, Woster P, Minden MD, Dugas M, Wang JC, Dick JE, Mu¨llerTidow C, Petrie K, Zelent A, Zelent A: Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukaemia. Nat Med 2012, 18:605-611. 24. Obama B: State of the Union Address. 2013. 25. Kaur JS, Petereit DG: Personalized medicine: challenge and promise. J Cancer Educ 2012, 27(s1):12-17. 26. Hegde MR: Marching towards personalized genomic medicine. J Pediatrics 2013, 162:10-11. 27. Dauber A, Stoler J, Hechter E, Safer J, Hirschhorn JN: Whole exome sequencing reveals a novel mutation in CUL7 in a patient with an undiagnosed growth disorder. J Pediatrics 2013, 162:202-204. 28. Shute N: Personalised medicine. Sci Am 2012, 306:44. 29. Harvey A, Brand A, Holgate ST, Kristiansen LV, Lehrach H, Palotie A, Prainsack B: The future of technologies for personalised medicine. New Biotechnol 2012, 29:625-633. 30. Li-Wan-Po A, Farndon P: Barking up the wrong genome – we are not alone. J Clin Pharm Ther 2012, 36:125-127. 31. Monteiro TP, El-Jaick KB, Jeovanio-Silva AL, Brasil PE, Costa MJ, Rolla VC, de Castro L: The roles of GSTM1 and GSTT1 null genotypes and other predictors in anti-tuberculosis drug induced liver injury. J Clin Pharm Ther 2012, 37:712-718. 32. Stahl SM: Psychotherapy as an epigenetic drug. J Clin Pharm Ther 2012, 37:249-253. 33. Peedicayli J: Role of epigenetics in pharmacotherapy, psychotherapy and nutritional management of mental disorders. J Clin Pharm Ther 2012, 37:499-501. 34. Jones S: A snapshot of the microbiome field. Nat Biotechnol 2013, 31:282-283. 35. Jayaseelan S, Tenenbaum SA: Signalling pathways of fragile X syndrome. Nature 2012, 492:359-360. 36. Wilusz JE, Shap PA: A circuitous route to noncoding RNA. Science 2013, 340:440-441. 37. Gahan PB: Circulating nucleic acids in plasma and serum: applications in diagnostic techniques for non-invasive prenatal diagnosis. Int J Women’s Health 2013, 5:177-186. 38. Tsui NB, Kadir RA, Chan KC, Chi C, Mellars G, Tuddenham EG, Leung TY, Lau TK, Chiu RW, Lo YM: Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood 2011, 117:3684-3691. 39. Barrett AN, McDonnell TC, Chan KC, Chitty LS: Digital PCR analysis of maternal plasma for noninvasive detection of sickle cell anemia. Clin Chem 2012, 58:1026-1032. 40. McKenna M: Shock to the system: researchers struggle to develop new treatments for sepsis. Sci Am 2013, 308:30-32. 41. Cooper R: The battle to discover new antibiotics. Telegraph 2012 http://www.telegraph.co.uk/finance/newsbysector/ pharmaceuticalsandchemicals/9010738/The-battle-to-discovernew-antibiotics.html. 42. Butler M, Cooper M: New antibiotics: what’s in the pipeline? Conversation 2012.

20. Nandedkar TD: Nanovaccines: recent developments in vaccination. J Biosci 2009, 34:995-1003.

43. Huang TD, Berhin C, Bogaerts P, Glupczynski Y: Prevalence and mechanisms of resistance to carbapenems in Enterobacteriaceae isolates from 24 hospitals in Belgium. J Antimicrobial Chemother 2013 http://dx.doi.org/10.1093/jac/ dkt096.

21. Burridge S: Drugging the epigenome. Nat Rev Drug Discov 2013, 12:92-93.

44. Moir DT, Opperman TJ, Butler MM, Bowlin T: New classes of antibiotics. Curr Opin Pharmacol 2012, 12:535-544.

22. Arrowsmith CH, Boutra C, Fish PV, Lee K, Schapira M: Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 2012, 11:384-400.

45. Garmendia L, Hernandez A, Sanchez MB, Martinez L: Metagenomics and antibiotics. Clin Microbiol Infect 2012, 18:27-31.

Current Opinion in Biotechnology 2013, 24S:S6–S13

www.sciencedirect.com

Progress towards the ‘Golden Age’ of biotechnology Gartland et al.

46. Chung K, Wallace J, Kim S-Y, Kalyanasundaram S, Andalmn AS: Structural and molecular interrogation of intact biological systems. Nature 2013 http://dx.doi.org/10.1038/nature12107. 47. Parr C: At the heart of the higher education debate: Obama’s research boost welcomed by US universities. Times Higher Education 2013. 48. Baker M: Gene editing nucleases. Nat Methods 2012, 9:23-26. 49. Lei Y, Lee CL, Joo KI, Zarzar J, Liu Y, Dai B, Fox V, Wang P: Gene editing of human embryonic stem cells via an engineered baculoviral vector carrying zinc-finger nucleases. Mol Ther 2011, 19:942-950.

S13

for microRNAs in plants. Plant Physiol 2013. h*ttp://dx.doi.org/ 10.1104/pp.113.215962. 66. Chen Q, Tao S, Bi X, Xu X, Wang L, Li X: Research progress in physiological and molecular biology mechanism of drought resistance in rice. Am J Mol Biol 2013, 3:102-107. 67. Strauss SH, Viswanath V: Field trials of GM trees in the USA: activity and regulatory environments. BMC Proc 2011, 5(s7):061. 68. Arborgen: Freeze Tolerant Eucalyptus. 2011:. http:// www.arborgen.us/index.php/products/product-pipeline/freezetolerant-eucalyptus.

50. Papaioannou I, Simons JP, Owen JS: Oligonucleotide-directed gene-editing technology: mechanisms and future prospects. Expert Opin Biol Ther 2012, 12:329-342.

69. Bonawitz ND, Chapple C: Can genetic engineering of lignin deposition be accomplished without an unacceptable yield penalty? Curr Opin Biotechnol 2013, 24:336-343.

51. Chang N, Changhong S, Gao L, Zhu D, Xu X, Zhu X, Xiong J-W, Xi JJ: Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Res 2013, 23:465-472.

70. Patrascoiu M, Rathbauer J, Negrea M, Zeller R: Perspectives of safflower oil as a biodiesel source for South Eastern Europe (comparative study: safflower, soybean and rapeseed). Fuel 2013. ht*tp://dx.doi.org/10.1016/j.fuel.2013.04.012.

52. Joung JK, Sander JD: TALENS: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 2013, 14:49-55. 53. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF: Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 2011, 39:e82. 54. Ledford L: Targeted gene editing enters clinic. Nature 2011, 471:16. 55. Allers K, Hutter G, Hofmann J, Loddenkemper C, Rieger K, Thiel E, Schneider T: Evidence for the cure of HIV infection by CCR5D32/D32 stem cell transplantation. Blood 2011, 117:2791-2799. 56. Whyte JJ, Prather RS: Cell Biology Symposium: zinc-finger nucleases to create custom-designed modifications in the swine (Sus scrofa) genome. J Anim Sci 2012, 90:1111-1117. 57. USFDA: FDA Extends Comment Period on Aqua-Advantage Salmon Documents. 2013:. http://www.fda.gov/AnimalVeterinary/ NewsEvents/CVMUpdates/ucm339270.htm. 58. DEFRA (UK): Method verification of the LOD associated with the DEFRA/FSA study protocol for the detection of horse DNA in food samples. DEFRA Research Report. 2013:. FAO134. 59. Arun OO, Yilmaz F, Muratogolu K: PCR detection of genetically modified maize and soy in mildly and highly processed foods. Food Control 2013, 32:525-531. 60. Kamle S, Ali S: Genetically modified crops: detection strategies and biosafety issues. Gene 2013. ht*tp://dx.doi.org/10.1016/ j.gene.2013.107. 61. Anonymous: GM crops: a story in numbers. Nature 2013, 497:22-23. 62. Fermin G, Keith RC, Suzuki JY, Ferreira SA, Gaskil DA, Pitz KY, Manshardt RM, Gonsalves D, Tripathi S: Allergenicity assessment of the papaya ringspot virus coat protein expressed in transgenic rainbow papya. J Agric Food Chem 2011, 59:10006-10012. 63. Abbas Z, Zafar Y, Khan SA, Mukhtar Z: A chimeric protein encoded by synthetic genes shows toxicity to Helicoverpa armigera and Spodotera littoralis larvae. Int J Agric Biol 2013, 15:325-330. 64. Sharma VK, Sanghera GS, Kashyap PL, Sharma BB, Chandel C: RNA interference: a novel tool for plant disease management. African J Biotechnol 2013, 12:2303-2312. 65. Wu H-J, Wang Z-M, Wang M, Wang X-J: Wide-spread long noncoding RNAs (IncRNAs) as endogenous target mimics (eTMs)

www.sciencedirect.com

71. Lo´pez JA, Naranjo JM, Higuita JC, Cubitto MA, Cardona CA, Villar MA: Biosynthesis of PHB from a new isolated Bacillus megaterium strain: outlook on future developments with endospore forming bacteria. Biotechnol Bioprocess Eng 2012, 17:250-258. 72. Pan W, Perrotta JA, Stipanovic AJ, Nomura CT, Nakas JP: Production of polyhydroxyalkanoates by Burkholderia cepacia ATCC 17759 using a detoxified sugar maple hemicellulosic hydrolysate. J Ind Microbiol Biotechnol 2012, 39:459-469. 73. Schnell JA, Treyvaud-Amiguet V, Arnason JT, Johnson DA: Expression of polyhydroxybutyric acid as a model for metabolic engineering of soybean seed coats. Transgenic Res 2012, 21:895-899. 74. Su T-T, Lin C-W, Y-P I, Wu C-H: Biodegradation of semiconductor volatile organic compounds by four novel bacterial strains: a kinetic analysis. Bioprocess Biosyst Eng 2012, 35:1117-1124. 75. Nielsen PH, Mielczerek AT, Kragelund C, Nielsen JL, Saunders AM, Kong Y, Hansen AA, Vollertsen J: A conceptual ecosystem model of microbial communities in enhanced biological phosphorous removal plants. Water Res 2010, 44:5070-5088. 76. Albertsen M, Hansen LBS, Saunders AM, Nielsen PH, Nielsen KL: A metagenome of a full-scale microbial community carrying out enhanced biological phosphorous removal. ISME J 2012, 6:1094-1106. 77. Nielsen PH, Saunders AM, Hansen AA, Larsen P, Nielsen JL: Microbial communities involved in enhanced biological phosphorus removal from wastewater – a model system in environmental biotechnology. Curr Opin Biotechnol 2012, 23:452-459. 78. Salwan R, Chand R: Purification and characterisation of an extracellular low temperature-active and alkaline stable peptidase from psychotrophic Acinetobacter sp., MN12 MTCC (10786). Ind J Microbiol 2013, 53:63-69. 79. Palma-Rodriguez HM, Agama-Acevedo E, Gonzalez-Soto RA, Vernon-Carter EJ, Alvarez-Ramirez J, Bello-Perez LA: Ascorbic acid microencapsulation by spray-drying in native and acidmodified starches from different botanical sources. Starch J 2013 http://dx.doi.org/10.1002/star.201200200. 80. Jubril I, Muazu J, Mohammed GT: Effects of phosphate modified and pregelatinized sweet potato starches on disintegrant property of paracetamol tablet formulations. J Appl Pharmaceut Sci 2012:32-36.

Current Opinion in Biotechnology 2013, 24S:S6–S13