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• Effect of surfactants on the biofilm of Rhodococcus erythropolis, a potent degrader of aromatic pollutants.

  Authors: Olga Schreiberova, Petra Hedbavna, Alena Cejkova, Vladimir Jirku, Jan Masak

  New biotechnology.

  Bioremediation processes based on biofilms are usually very effective. The presence of (bio)surfactants in such processes can increase bioavailability of hydrophobic pollutants in aqueous phase.Bioremediation processes based on biofilms are usually very effective. The presence of (bio)surfactants in such processes can increase bioavailability of hydrophobic pollutants in aqueous phase. However, surfactants can affect the biofilm as well as individual microbial cells in different ways. Biosurfactants produced by a microbial population can be involved in the final structure of biofilm. An external application of synthetic surfactants or "foreign" biosurfactants often results in partial or complete destruction of the biofilm and their high concentrations also have a toxic effect on microbial cells. Finding a suitable surfactant and its concentration, which would minimize the negative effects mentioned above, would allow to construct effective bioremediation processes using the benefits of both the biofilm and the surfactant. In this context, G(+) bacterium Rhodococcus erythropolis, which has a wide potential for biodegradation of aromatic compounds, was studied. High surface hydrophobicity of its cells, given mainly by the presence of mycolic acids in the cell envelopes, allows formation of stable biofilms. Three synthetic surfactants (Spolapon AOS 146, Novanik 0633A, Tween 80) and rhamnolipid isolated from Pseudomonas aeruginosa were used. Changes in initial adhesion and biofilm formation caused by the surfactants were monitored in a flow cell equipped with hydrophilic/hydrophobic carriers and analyzed by image analysis.

• Do companion diagnostics make economic sense for drug developers?

  Authors: Amit Agarwal

  New biotechnology.

  Drug developers are grappling with the impact of personalized medicine on their portfolios. The combination of molecular diagnostics with targeted biologic therapies has been hailed as a recentDrug developers are grappling with the impact of personalized medicine on their portfolios. The combination of molecular diagnostics with targeted biologic therapies has been hailed as a recent innovation with few historical analogs to guide behavior. However, if the definition of companion diagnostics is broadened to include any drug whose FDA approved label requires diagnostic testing before prescription then over 50 drugs across multiple therapeutic areas arise. Most importantly for current drug developers, these drugs represent a wide variety of market situations and with sufficient historical data to evaluate different commercialization strategies for the combination. Included in these examples are drugs which were not initially launched with companion diagnostics but were required to implement companion diagnostics after they were on the market for a period of time. The historical case studies demonstrate that companion diagnostics are neither a universal panacea nor an unmitigated disaster for drug developers but require an understanding of specific situations to determine the utility of companion diagnostics. Numerous case studies highlight how companion diagnostics have been a boon to drug developers including Iressa, statins, Soriatane, Arthrotec, Promacta, Nplate, Letairis, and Tracleer. Other examples provide lessons on how to avoid pitfalls such as Accutane, Ticlid, Tegretol, Ziagen, Actigall and Clozaril. By carefully evaluating these case studies, drug developers can gain insight on the appropriate companion diagnostic strategy to implement for their specific situation and develop the elements of a successful companion diagnostic strategy.

• Autologous stem cells for personalised medicine.

  Authors: Weerapong Prasongchean, Patrizia Ferretti

  New biotechnology.

  Increasing understanding of stem cell biology, the ability to reprogramme differentiated cells to a pluripotent state and evidence of multipotency in certain adult somatic stem cells has opened theIncreasing understanding of stem cell biology, the ability to reprogramme differentiated cells to a pluripotent state and evidence of multipotency in certain adult somatic stem cells has opened the door to exciting therapeutic advances as well as a great deal of regulatory and ethical issues. Benefits will come from the possibility of modelling human diseases and develop individualised therapies, and from their use in transplantation and bioengineering. The use of autologous stem cells is highly desirable, as it avoids the problem of tissue rejection, and also reduces ethical and regulatory issues. Identification of the most appropriate cell sources for different potential applications, development of appropriate clinical grade methodologies and large scale well controlled clinical trials will be essential to assess safety and value of cell based therapies, which have been generating much hope, but are by and large not yet close to becoming standard clinical practice. We briefly discuss stem cells in the context of tissue repair and regenerative medicine, with a focus on individualised clinical approaches, and give examples of sources of autologous cells with potential for clinical intervention.

• Identification of a quinone dehydrogenase from a Bacillus sp. involved in the decolourization of the lignin-model dye, Azure B.

  Authors: Luaine Bandounas, Martijn Pinkse, Johannes H de Winde, Harald J Ruijssenaars

  New biotechnology.

  In this study we have investigated the molecular background of the previously reported dye decolourization potential of Bacillus sp. LD003. Strain LD003 was previously isolated on Kraft lignin andIn this study we have investigated the molecular background of the previously reported dye decolourization potential of Bacillus sp. LD003. Strain LD003 was previously isolated on Kraft lignin and was able to decolourize various lignin model dyes. Specifically Azure B (AB) was decolourized efficiently. Proteins possibly involved in AB decolourization were partially purified, fractionated by gel electrophoresis and identified via mass spectrometry. Five candidate enzymes were selected and expressed in Escherichia coli. Of these, only a quinone dehydrogenase was shown to decolourize AB. Thus, this quinone dehydrogenase was identified as an AB decolourizing enzyme of Bacillus sp. LD003.

• Protein arraying by cell-free expression and diffusion across a fluid-filled gap.

  Authors: Oda Stoevesandt

  New biotechnology.

  An improved system for cell-free expression of protein arrays based on DNA arrays is presented. Our technology uses an array of DNA constructs for cell-free expression, which acts as a templateAn improved system for cell-free expression of protein arrays based on DNA arrays is presented. Our technology uses an array of DNA constructs for cell-free expression, which acts as a template instructing the generation of the corresponding protein array. Proteins are expressed locally from these templates by a cell-free transcription and translation system, and are immobilised on a separate capture surface overlayed on the DNA array. By simplifying the setup to allow protein diffusion between the slides across a gap filled with the cell-free system, we have markedly improved the evenness of the resulting protein microarrays.

• From morphologic to molecular: established and emerging molecular diagnostics for breast carcinoma.

  Authors: Bryce P Portier, Aaron M Gruver, Michael A Huba, Eugen C Minca, Alison Cheah, Zhen Wang, Raymond R Tubbs

  New biotechnology.

  Diagnostics in the field of breast carcinoma are constantly evolving. The recent wave of molecular methodologies, both microscope and non-microscope based, have opened new ways to gain insight intoDiagnostics in the field of breast carcinoma are constantly evolving. The recent wave of molecular methodologies, both microscope and non-microscope based, have opened new ways to gain insight into this disease process and have moved clinical diagnostics closer to a 'personalized medicine' approach. In this review we highlight some of the advancements that laboratory medicine technology is making toward guiding the diagnosis, prognosis, and therapy selection for patients affected by breast carcinoma. The content of the article is largely structured by methodology, with a distinct emphasis on both microscope based and non-microscope based diagnostic formats. Where possible, we have attempted to emphasize the potential benefits as well as limitations to each of these technologies. Successful molecular diagnostics, applied in concert within the morphologic context of a patient's tumor, are what will lay the foundation for personalized therapy and allow a more sophisticated approach to clinical trial stratification. The future of breast cancer diagnostics looks challenging, but it is also a field of great opportunity. Never before have there been such a plethora of new tools available for disease investigation or candidate therapy selection.

• Molecular diagnostics and personalised medicine.

  Authors: Frank Desiere, Vincenzo Romano Spica

  New biotechnology.

  This special issue of New Biotechnology is focused on molecular diagnostics and personalised medicine and appears at an epochal moment in the development of the field. The practice of medicine isThis special issue of New Biotechnology is focused on molecular diagnostics and personalised medicine and appears at an epochal moment in the development of the field. The practice of medicine is taking a significant and irrevocable turn towards personalisation, due to the great progress in areas such as genomics, pharmacogenomics and molecular diagnosis. It becomes increasingly apparent that to deliver the promise of personalised treatments, more and more novel medicines discovered today will be presented together with innovative companion diagnostics. The contributions to this volume touch on many disciplines, ranging from cell biology to genetics, immunology, molecular diagnostics, pharmaceutics and economic issues. The contributions of clinicians and basic scientists are synergistically presented to underline better the wide spectrum of studies that can contribute to the new field of personalised medicine. The promising perspectives of individualised treatments are related not only to higher effectiveness, but also to increased efficiency. This is relevant not only for the individual patient, but even more so for the general public, within a wider economical perspective where resources are limited and it becomes more and more mandatory to close the gap between social costs and benefits. This approach follows the steps of a stratified and individualised medicine and finds its final goal in an individualised healthcare.

• Predictive markers in early research and companion diagnostic developments in oncology.

  Authors: Marlene Pickl, Elisabeth Ruge, Miro Venturi

  New biotechnology.

  Predictive biomarkers are discovered and used in oncology research to formulate hypotheses aimed at the identification of patients benefiting from specific therapeutic intervention(s). They pave thePredictive biomarkers are discovered and used in oncology research to formulate hypotheses aimed at the identification of patients benefiting from specific therapeutic intervention(s). They pave the way to the development of companion diagnostic tests which are tools readily implemented in the clinic and serve to qualify a patient for treatment with a particular targeted drug or the continued use of a particular drug, thus maximizing the benefit to risk ratio of the medical intervention to the patient. Predictive biomarkers are defined by biological characteristics of the patient's or tumor status that can be measured objectively and correlated with clinical outcome: these can be molecular, cellular or biochemical features. Predictive markers need extensive analytical validation - specific for the tool utilized for their assessment - as well as rigorous clinical qualification in the context of the drug treatment for which they define clinical utility. The process of companion diagnostic development is a highly interdisciplinary and complex one, driven by key crucial milestones and accompanying the same and typical process of a whole drug discovery and development continuum, from marker discovery and validation, assay development, clinical qualification until test approval and commercialization.

• Synthetic biology: an EFB Microbial Physiology Section initiative.

  Authors: Jeff Cole

  New biotechnology.

• A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory.

  Authors: Leroy Hood, Mauricio Flores

  New biotechnology.

  Systems biology and the digital revolution are together transforming healthcare to a proactive P4 medicine that is predictive, preventive, personalized and participatory. Systems biology - holistic,Systems biology and the digital revolution are together transforming healthcare to a proactive P4 medicine that is predictive, preventive, personalized and participatory. Systems biology - holistic, global and integrative in approach - has given rise to systems medicine, a systems approach to health and disease. Systems medicine promises to (1) provide deep insights into disease mechanisms, (2) make blood a diagnostic window for viewing health and disease for the individual, (3) stratify complex diseases into their distinct subtypes for a impedance match against proper drugs, (4) provide new approaches to drug target discovery and (5) generate metrics for assessing wellness. P4 medicine, the clinical face of systems medicine, has two major objectives: to quantify wellness and to demystify disease. Patients and consumers will be a major driver in the realization of P4 medicine through their participation in medically oriented social networks directed at improving their own healthcare. P4 medicine has striking implications for society - including the ability to turn around the ever-escalating costs of healthcare. The challenge in bringing P4 medicine to patients and consumers is twofold: first, inventing the strategies and technologies that will enable P4 medicine and second, dealing with the impact of P4 medicine on society - including key ethical, social, legal, regulatory, and economic issues. Managing the societal problems will pose the most significant challenges. Strategic partnerships of a variety of types will be necessary to bring P4 medicine to patients.

• Public-private collaborations and partnerships in stratified medicine: making sense of new interactions.

  Authors: Joanna Chataway, Caroline Fry, Sonja Marjanovic, Ohid Yaqub

  New biotechnology.

  The field of personalised or stratified medicine is evolving alongside the formation of a plethora of public/private partnerships and collaborations. These new institutional forms, or 'socialThe field of personalised or stratified medicine is evolving alongside the formation of a plethora of public/private partnerships and collaborations. These new institutional forms, or 'social technologies', are varied and emerge in response to several drivers, including the need to draw on a broader base of data inputs relating to genomics, patient behaviour and healthcare system differentiation. This paper discusses some of these drivers of partnerships and collaborations. Although the number of such partnerships is growing, their rationale and basis for collaboration remains unclear. Public-private collaborations are at the core of the set of new life sciences policies in the UK but there is little indication in the policy documents of clear boundaries for these partnerships. In part, this is due to the lack of empirical evidence at the system level for conceptualising what is still a relatively new approach. The collection of evidence in the form of broad evaluations, rather than tightly focused theoretical studies, is more likely to be related back to systems and be of more use for formulating policy rationales.

• Practical perspectives of personalized healthcare in oncology.

  Authors: Darren R Hodgson, Robert Wellings, Christopher Harbron

  New biotechnology.

  There is an increasing prevalence of drug-diagnostic combinations in oncology. This has placed diagnostic stakeholders directly into the complex benefit-risk, cost, value and uncertainty-drivenThere is an increasing prevalence of drug-diagnostic combinations in oncology. This has placed diagnostic stakeholders directly into the complex benefit-risk, cost, value and uncertainty-driven development paradigm traditionally the preserve of the drug development community. In this review we focus on the delivery of the clinical data required to advance such drug-diagnostic combination development programmes and ultimately satisfy regulators and payors of the value of contemporaneous changes in diagnostic and treatment practice. Ideally all stakeholders would like to initially estimate, and ultimately specify, the comparative benefit-risk for a new treatment option with and without changing diagnostic practice. Hence, in an ideal world clinical trial design is focused on acquiring biomarker treatment interaction data. In this review we describe the key scientific and feasibility inputs required to design and deliver such trials and the drivers, advantages and disadvantages associated with departing from this model. We do not discuss the discovery of new biomarkers nor the analytical validation and marketing of diagnostic products. Following on from trial design we describe how subsequent success then depends upon the concepts that guide trial design being driven into the complex world of large, multinational clinical trial delivery. For every aspect of a traditional clinical drug trial such as supply, recruitment and adherence, there is a corresponding concept for the diagnostic element. In practice, this means that each patient's contribution to the decision making data-set is subject to double jeopardy (attrition on clinical outcome and biomarker status). Historically, this has led to significantly reduced power for detecting biomarker-treatment interactions, reduced decision making confidence and a waste of valuable human and financial resources. We describe recent practice changes and experience that have led to the successful delivery of such trials focusing on both pre- and on trial aspects. The former includes the pivotal role of tissue banks in accurate estimation of evaluability and prevalence for biomarker assays and the latter several practices designed to engage and incentivize key stakeholders particularly CRAs and pathologists. The result is that in the new world of developing personalized treatments for cancer patients the real-time acquisition and monitoring of biomarker data receives similar support to that traditionally reserved for clinical outcome data and far more patients contribute to the testing of personalized medicine hypotheses.

• Signal enhancement in polysaccharide based sensors for infections by incorporation of chemically modified laccase.

  Authors: Konstantin P Schneider, Ulrike Gewessler, Teresa Flock, Andrea Heinzle, Verena Schenk, Franz Kaufmann, Eva Sigl, Georg M Guebitz

  New biotechnology.

  Bioresponsive polymers (BRPs) allow the detection of potentially pathogenic microorganisms. Here, peptidoglycan and cellulose based hydrogels were constructed with potential for diagnosis of woundBioresponsive polymers (BRPs) allow the detection of potentially pathogenic microorganisms. Here, peptidoglycan and cellulose based hydrogels were constructed with potential for diagnosis of wound infection or, for example, Aspergillosis, respectively. These systems respond to extracellular enzymes from microbes or enzymes secreted from the human immune system in case of infection. Laccases as 'enhanzymes' were incorporated into these devices for signal and stability enhancement when compared to simple dye release based systems. To retain the enhanzymes within the BRPs, they were either PEGylated laccase (Laccase_PEG) to increase size or methacrylated laccase (Laccase_MA) to allow covalent attachment to the polysaccharide matrices. PEGylation of Trametes hirsuta laccase led to a fivefold increase in size to 270kDa according to size exclusion chromatography (SEC). Likewise, successful methacrylation of the laccase was demonstrated by using reversed phase chromatography while SEC analysis proved covalent attachment of the enzyme to the methacrylated polysaccharide matrix. Upon incubation of peptidoglycan based BRPs with fluid from infected wounds, the difference to controls was four times higher for Laccase_PEG based signalling when compared to simple dye release. Similarly, the control signals (i.e. leaching) were considerably reduced in case of Laccase_MA incorporated in crosslinked peptidoglycan (PG) and carboxymethylcellulose (CMC) hydrogels for signalling. In addition, Laccase_MA catalysed colour formation enhanced the signal dramatically with factors between 100- and 600-fold. Laccase_MA was demonstrated to oxidise silica gel immobilised ferulic acid incorporated into the BRP with clearly visible colour changes of 4.5 ΔE units according the CIELab concept upon incubation by trigger enzymes as well as infected wound fluids.

• Pharmacogenomics and personalized medicine: wicked problems, ragged edges and ethical precipices.

  Authors: Leonard M Fleck

  New biotechnology.

  In the age of genomic medicine we can often now do the genetic testing that will permit more accurate personal tailoring of medications to obtain the best therapeutic results. This is certainly aIn the age of genomic medicine we can often now do the genetic testing that will permit more accurate personal tailoring of medications to obtain the best therapeutic results. This is certainly a medically and morally desirable result. However, in other areas of medicine pharmacogenomics is generating consequences that are much less ethically benign and much less amenable to a satisfactory ethical resolution. More specifically, we will often find ourselves left with 'wicked problems,' 'ragged edges,' and well-disguised ethical precipices. This will be especially true with regard to these extraordinarily expensive cancer drugs that generally yield only extra weeks or extra months of life. Our key ethical question is this: Does every individual faced with cancer have a just claim to receive treatment with one of more of these targeted cancer therapies at social expense? If any of these drugs literally made the difference between an unlimited life expectancy (a cure) and a premature death, that would be a powerful moral consideration in favor of saying that such individuals had a strong just claim to that drug. However, what we are beginning to discover is that different individuals with different genotypes respond more or less positively to these targeted drugs with some in a cohort gaining a couple extra years of life while others gain only extra weeks or months. Should only the strongest responders have a just claim to these drugs at social expense when there is no bright line that separates strong responders from modest responders from marginal responders? This is the key ethical issue we address. We argue that no ethical theory yields a satisfactory answer to this question, that we need instead fair and respectful processes of rational democratic deliberation.

• Analysing stratified medicine business models and value systems: innovation-regulation interactions.

  Authors: James Mittra, Joyce Tait

  New biotechnology.

  Stratified medicine offers both opportunities and challenges to the conventional business models that drive pharmaceutical R&D. Given the increasingly unsustainable blockbuster model of drugStratified medicine offers both opportunities and challenges to the conventional business models that drive pharmaceutical R&D. Given the increasingly unsustainable blockbuster model of drug development, due in part to maturing product pipelines, alongside increasing demands from regulators, healthcare providers and patients for higher standards of safety, efficacy and cost-effectiveness of new therapies, stratified medicine promises a range of benefits to pharmaceutical and diagnostic firms as well as healthcare providers and patients. However, the transition from 'blockbusters' to what might now be termed 'niche-busters' will require the adoption of new, innovative business models, the identification of different and perhaps novel types of value along the R&D pathway, and a smarter approach to regulation to facilitate innovation in this area. In this paper we apply the Innogen Centre's interdisciplinary ALSIS methodology, which we have developed for the analysis of life science innovation systems in contexts where the value creation process is lengthy, expensive and highly uncertain, to this emerging field of stratified medicine. In doing so, we consider the complex collaboration, timing, coordination and regulatory interactions that shape business models, value chains and value systems relevant to stratified medicine. More specifically, we explore in some depth two convergence models for co-development of a therapy and diagnostic before market authorisation, highlighting the regulatory requirements and policy initiatives within the broader value system environment that have a key role in determining the probable success and sustainability of these models.

• The triad of success in personalised medicine: pharmacogenomics, biotechnology and regulatory issues from a Central European perspective.

  Authors: Bertalan Mesko, Gabor Zahuczky, Laszlo Nagy

  New biotechnology.

  The population of the world has recently passed the 7 billion milestone and as the cost of human genome sequencing is rapidly declining, sequence data of billions of people should be accessible muchThe population of the world has recently passed the 7 billion milestone and as the cost of human genome sequencing is rapidly declining, sequence data of billions of people should be accessible much sooner than anyone would have predicted 10years ago. This will form the basis of personalised medicine. However it is still not clear, even in principle, whether these data, combined with data of the expression of one's genome in various cells and tissues relevant to different diseases, could be used effectively in clinical medicine and healthcare, or in predicting responses to different therapies. Therefore this is an important issue which needs to be addressed before more resources are wasted on less than informative studies and surveys simply because technologies exist. As a typical example, we have selected and summarise here key studies from the biomedical literature that focus on gene expression profiling of the response to biologic therapies in peripheral blood and biopsy samples in autoimmune diseases such as rheumatoid arthritis, spondylarthropathy, inflammatory bowel diseases and psoriasis. We also present the state of the biotechnology market from a European perspective, discuss how spin-offs leverage the power of genomic technologies and describe how they might contribute to personalised medicine. As ethical, legal and social issues are essential in the area of genomics, we analysed these aspects and present here the European situation with a special focus on Hungary. We propose that the synergy of these three issues: pharmacogenomics, biotechnology and regulatory issues should be considered a triad necessary to succeed in personalised medicine.

• Glycan variability on a recombinant IgG antibody transiently produced in HEK-293E cells.

  Authors: Sophie Nallet, Luca Fornelli, Simone Schmitt, Julien Parra, Lucia Baldi, Yury O Tsybin, Florian M Wurm

  New biotechnology.

  In this study, a recombinant monoclonal IgG antibody was produced by transient gene expression (TGE) in suspension-adapted HEK-293E cells. The objective of the study was to determine the variation inIn this study, a recombinant monoclonal IgG antibody was produced by transient gene expression (TGE) in suspension-adapted HEK-293E cells. The objective of the study was to determine the variation in recombinant IgG yield and glycosylation in ten independent transfections. In a ten-day batch process, the variation in transient IgG yield in the ten batches was less than 30% with the specific productivity averaging 20.2±2.6pg/cell/day. We characterized the N-glycosylation profile of each batch of affinity-purified IgG by intact protein and bottom-up mass spectrometry. Four major glycans were identified at Asn(297) in the ten batches with the maximum relative deviation for a single glycoform being 2.5%. In addition, within any single transfection there was little variation in glycoforms over the ten-day culture. Our experimental data indicate that with TGE, the production of recombinant IgG with little batch-to-batch variation in volumetric yield and protein glycosylation is feasible, even in a non-instrumented cultivation system as described here.

• Co-development of a companion diagnostic for targeted cancer therapy.

  Authors: Suzanne Cheng, Walter H Koch, Lin Wu

  New biotechnology.

  Oncology drug development is a long and costly process associated with a success rate of 5-10%. The parallel development of companion diagnostic tests that will identify patients most likely toOncology drug development is a long and costly process associated with a success rate of 5-10%. The parallel development of companion diagnostic tests that will identify patients most likely to receive benefit has the potential to increase the success rate for oncology drugs and decrease development time and associated costs. Metastatic melanoma is a challenging disease that has been associated with poor survival. Identification of a mutated BRAF kinase gene in many cases of melanoma provided a promising therapeutic target. Here we describe the successful co-development of vemurafenib, a first-in-class selective inhibitor of oncogenic BRAF kinase, and its companion diagnostic, the cobas(®) 4800 BRAF V600 Mutation Test. Key success factors in the development process included early identification of the BRAF V600E biomarker, early development of the diagnostic test, and early and close collaboration between the pharmaceutical and diagnostic development teams. This focused and integrated process resulted in the first personalized medicine for the treatment of metastatic melanoma less than five years after the Investigational New Drug Application, a remarkably short time.

• Overcoming regulatory and economic challenges facing pharmacogenomics.

  Authors: Joshua P Cohen

  New biotechnology.

  The number of personalized medicines and companion diagnostics in use in the United States has gradually increased over the past decade, from a handful of medicines and tests in 2001 to several dozenThe number of personalized medicines and companion diagnostics in use in the United States has gradually increased over the past decade, from a handful of medicines and tests in 2001 to several dozen in 2011. However, the numbers have not reached the potential hoped for when the human genome project was completed in 2001. Significant clinical, regulatory, and economic barriers exist and persist. From a regulatory perspective, therapeutics and companion diagnostics are ideally developed simultaneously, with the clinical significance of the diagnostic established using data from the clinical development program of the corresponding therapeutic. Nevertheless, this is not (yet) happening. Most personalized medicines are personalized post hoc, that is, a companion diagnostic is developed separately and approved after the therapeutic. This is due in part to a separate and more complex regulatory process for diagnostics coupled with a lack of clear regulatory guidance. More importantly, payers have placed restrictions on reimbursement of personalized medicines and their companion diagnostics, given the lack of evidence on the clinical utility of many tests. To achieve increased clinical adoption of diagnostics and targeted therapies through more favorable reimbursement and incorporation in clinical practice guidelines, regulators will need to provide unambiguous guidance and manufacturers will need to bring more and better clinical evidence to the market place.

• High hydrostatic pressure treatment for the inactivation of Staphylococcus aureus in human blood plasma.

  Authors: Nolwennig Rivalain, Jean Roquain, Jean-Michel Boiron, Jean-Paul Maurel, Alain Largeteau, Zoran Ivanovic, Gérard Demazeau

  New biotechnology. 29(3):409-14.

  For the past 30years, pressure inactivation of microorganisms has been developed in biosciences, in particular for foods and more recently for biological products, including pharmaceutical ones. InFor the past 30years, pressure inactivation of microorganisms has been developed in biosciences, in particular for foods and more recently for biological products, including pharmaceutical ones. In many past studies, the effect of high hydrostatic pressure (HHP) processes on pathogens focused mainly on the effect of an increase of the pressure value. To assure the safety of pharmaceutical products containing fragile therapeutic components, development of new decontamination processes at the lowest pressure value is needed to maintain their therapeutic properties. The aim of this study was therefore to evaluate the impact of the process parameters characterizing high-pressure treatments [such as the pressurization rate (PR) and the application mode (AM)] on the inactivation of pathogens, in particular to determine how these parameters values could help decrease the pressure value necessary to reach the same inactivation level. The effect of these physical parameters was evaluated on the inactivation of Staphylococcus aureus ATCC 6538 which is an opportunistic pathogen of important relevance in the medical, pharmaceutical and food domains. Human blood plasma was chosen as the suspension medium because of its physiological importance in the transfusion field. It was shown that the optimization of all the selected parameters could lead to a high inactivation level (≈5log(10) decrease of the initial bacterial load) at a pressure level as low as 200MPa, underlining some synergistic effects among these parameters. Complete inactivation of the initial bacterial population was achieved for the following conditions: PR=50MPas(-1), AM=5×2min, T≈-5°C and P=300MPa.

• Wave characterization for mammalian cell culture: residence time distribution.

  Authors: Maria Elisa Rodrigues, Ana Rita Costa, Mariana Henriques, Joana Azeredo, Rosário Oliveira

  New biotechnology. 29(3):402-8.

  The high dose requirements of biopharmaceutical products led to the development of mammalian cell culture technologies that increase biomanufacturing capacity. The disposable Wave bioreactor is oneThe high dose requirements of biopharmaceutical products led to the development of mammalian cell culture technologies that increase biomanufacturing capacity. The disposable Wave bioreactor is one of the most promising technologies, providing ease of operation and no cross-contamination, and using an innovative undulation movement that ensures good mixing and oxygen transfer without cell damage. However, its recentness demands further characterization. This study evaluated the residence time distribution (RTD) in Wave, allowing the characterization of mixing and flow and the comparison with ideal models and a Stirred tank reactor (STR) used for mammalian cell culture. RTD was determined using methylene blue with pulse input methodology, at three flow rates common in mammalian cell culture (3.3×10(-5)m(3)/h, 7.9×10(-5)m(3)/h, and 1.25×10(-4)m(3)/h) and one typical of microbial culture (5×10(-3)m(3)/h). Samples were taken periodically and the absorbance read at 660nm. It was observed that Wave behavior diverted from ideal models, but was similar to STR. Therefore, the deviations are not related to the particular Wave rocking mechanism, but could be associated with the inadequacy of these reactors to operate in continuous mode or to a possible inability of the theoretical models to properly describe the behavior of reactors designed for mammalian cell culture. Thus, the development of new theoretical models could better characterize the performance of these reactors.

• Comparative high-throughput RNAi screening methodologies in C. elegans and mammalian cells.

  Authors: Kaylene J Simpson, Gregory M Davis, Peter R Boag

  New biotechnology.

  The discovery of RNAi in Caenorhabditis elegans has generated a paradigm shift in how research is performed. Targeted gene knockdown using high throughput screening approaches is becoming a routineThe discovery of RNAi in Caenorhabditis elegans has generated a paradigm shift in how research is performed. Targeted gene knockdown using high throughput screening approaches is becoming a routine feature of the scientific landscape, and researchers can now evaluate the function of each gene in the genome in a relatively short period of time. This review compares and contrasts high throughput screening methodologies in C. elegans and mammalian cells and highlights the breadth of applications of this technology.

• In situ fabrication of a microfluidic device for immobilised metal affinity sensing.

  Authors: Abhishek G Deshpande, Nicholas J Darton, Kamran Yunus, Adrian C Fisher, Nigel K H Slater

  New biotechnology.

  In this work a novel microfluidic device was constructed in situ containing the smallest microscopic co-polymeric immobilised metal affinity (IMA) adsorbent yet documented. This device has for theIn this work a novel microfluidic device was constructed in situ containing the smallest microscopic co-polymeric immobilised metal affinity (IMA) adsorbent yet documented. This device has for the first time allowed the microlitre scale chromatographic assay of histidine-tagged proteins in a biological sample. To enable this approach, rather than using a high capacity commercial packed bed column which requires large sample volumes and would be susceptible to occlusion by cell debris, a microgram capacity co-polymeric chromatographic substrate suitable for analytical applications was fabricated within a microfluidic channel. This porous co-polymeric IMA micro-chromatographic element, only 27μl in volume, was assessed for the analytical capture of two different histidine-tagged recombinant fusion proteins. The micro-chromatographic adsorber was fabricated in situ by photo-polymerising an iminodiacetic acid (IDA) functionalised polymer matrix around a template of fused 100μm diameter NH(4)Cl particles entirely within the microfluidic channel and then etching away the salt with water to form a network of interconnected voids. The surface of the micro-chromatographic adsorber was chemically functionalised with a chelating agent and loaded with Cu(2+) ions. FTIR and NMR analysis verified the presence of the chelating agent on the adsorbent surface and its Cu(2+) ion binding capacity was determined to be 2.4μmol Cu(2+) (ml of adsorbent)(-1). Micro-scale equilibrium adsorption studies using the two different histidine-tagged proteins, LacI-His(6)-GFP and α-Synuclein-His(8)-YFP, were carried out and the protein binding capacity of the adsorbent was determined to be 0.370 and 0.802mg(g of adsorbent)(-1), respectively. The dynamic binding capacity was determined at four different flow rates and found to be comparable to the equilibrium binding capacity at low flow rates. The sensing platform was also used to adsorb LacI-His(6)-GFP protein from crude cell lysate. During adsorption, laser scanning confocal microscopy identified locations within the adsorbent where protein adsorption and desorption occurred. The findings indicate that minimal channelling, selective product capture and near quantitative elution of the captured (adsorbed) product could be achieved, supporting the application of this new device as a high-throughput process analytical tool (PAT) for the in-process monitoring of histidine-tagged proteins in manufacturing.

• Global transcriptional changes of Clostridium acetobutylicum cultures with increased butanol:acetone ratios.

  Authors: Daniel Hönicke, Holger Janssen, Christina Grimmler, Armin Ehrenreich, Tina Lütke-Eversloh

  New biotechnology.

  Artificial electron carriers have been widely used to shift the solvent ratio toward butanol in acetone-butanol-ethanol (ABE) fermentation of solventogenic clostridia according to decreased hydrogenArtificial electron carriers have been widely used to shift the solvent ratio toward butanol in acetone-butanol-ethanol (ABE) fermentation of solventogenic clostridia according to decreased hydrogen production. In this study, first insights on the molecular level were gained to explore the effect of methyl viologen addition to cultures of Clostridium acetobutylicum. Employing batch fermentation in mineral salts medium, the butanol:acetone ratio was successively increased from 2.3 to 12.4 on a 100-ml scale in serum bottles and from 1.4 to 16.5 on a 1300-ml scale in bioreactors, respectively. The latter cultures were used for DNA microarray analyses to provide new information on the transcriptional changes referring to methyl viologen exposure and thus, exhibit gene expression patterns according to the manipulation of the cellular redox balance. Methyl viologen-exposed cultures revealed lower expression levels of the sol operon (CAP0162-0164) and the adjacent adc gene (CAP0165) responsible for solvent formation as well as iron and sulfate transporters and the CAC0105-encoded ferredoxin. On the contrary, genes for riboflavin biosynthesis, for the butyrate/butanol metabolic pathway and genes coding for sugar transport systems were induced. Interestingly, the adhE2-encoded bifunctional NADH-dependent aldhehyde/alcohol-dehydrogenase (CAP0035) was upregulated up to more than 100-fold expression levels as compared to the control culture without methyl viologen addition. The data presented here indicate a transcriptional regulation for decreased acetone biosynthesis and the redox-dependent substitution of adhE1 (CAP0162) by adhE2.

• Continuous steroid biotransformations in microchannel reactors.

  Authors: Marco P C Marques, Pedro Fernandes, Joaquim M S Cabral, Polona Znidaršič-Plazl, Igor Plazl

  New biotechnology. 29(2):227-34.

  The use of microchannel reactor based technologies within the scope of bioprocesses as process intensification and production platforms is gaining momentum. Such trend can be ascribed a particularThe use of microchannel reactor based technologies within the scope of bioprocesses as process intensification and production platforms is gaining momentum. Such trend can be ascribed a particular set of characteristics of microchannel reactors, namely the enhanced mass and heat transfer, combined with easier handling and smaller volumes required, as compared to traditional reactors. In the present work, a continuous production process of 4-cholesten-3-one by the enzymatic oxidation of cholesterol without the formation of any by-product was assessed. The production was carried out within Y-shaped microchannel reactors in an aqueous-organic two-phase system. Substrate was delivered from the organic phase to aqueous phase containing cholesterol oxidase and the product formed partitions back to the organic phase. The aqueous phase was then forced through a plug-flow reactor, containing immobilized catalase. This step aimed at the reduction of hydrogen peroxide formed as a by-product during cholesterol oxidation, to avoid cholesterol oxidase deactivation due to said by-product. This setup was compared with traditional reactors and modes of operation. The results showed that microchannel reactor geometry outperformed traditional stirred tank and plug-flow reactors reaching similar conversion yields at reduced residence time. Coupling the plug-flow reactor containing catalase enabled aqueous phase reuse with maintenance of 30% catalytic activity of cholesterol oxidase while eliminating hydrogen peroxide. A final production of 36 m of cholestenone was reached after 300 hours of operation.

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