| 1. |
- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 2. |
- Nielsen, Jens B, 1962
(författare)
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Engineering yeast metabolism for production of fuels and chemicals
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 33:Supplement: S Meeting Abstract: PL3, s. S66-S66
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Metabolic engineering relies on the Design-Build-Test cycle. This cycle includes technologies like mathematical modeling of metabolism, genome editing and advanced tools for phenotypic characterization. In recent years there have been advances in several of these technologies, which has enabled faster development of metabolically engineered strains that can be used for production of fuels and chemicals.The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel industrial processes have been developed over the last 10 years. Besides its wide industrial use, S. cerevisiae also serves as an eukaryal model organism, and many systems biology tools have therefore been developed for this organism. These tools can be used for detailed phenotypic characterization as well as for metabolic design.In this lecture it will be demonstrated how the Design-Build-Test cycle of metabolic engineering has allowed for development of yeast cell factories for production of a range of different fuels and chemicals. Some examples of different technologies will be presented together with examples of metabolic engineering designs, in particular for development of platform strains that can be used for production of a fatty acid derived products, e.g. fatty alcohols and alkanes. It will be argued that with advancement in genome-editing technologies and novel methods for rapid phenotypic screening, advancement in the field is hampered by our design abilities, i.e. to predict genotype–phenotype connections. For this genome-scale metabolic modeling is a strong technology, and in the presentation recent advancements in mathematical modeling for cell factory design will be presented. Finally, the presentation will also demonstrate how the Design-Build-Test cycle can be expanded to incorporate adaptive laboratory evolution to identify targets for engineering complex traits, such as improved tolerance to toxic metabolites like elevated temperatures or low pH.
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| 3. |
- Ewing, Andrew, 1957
(författare)
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Mass spectrometry imaging of lipids and metabolites: from fruit fly brains to single nanometer vesicles
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 33:Supplement: S Meeting Abstract: O5-1, s. S21-S21
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Tidskriftsartikel (refereegranskat)abstract
- We have been developing mass spectrometry imaging methods to study the process of neurocommunication at the system and cellular level. We focus on PC12 cells as a model of exocytosis and the fly model (Drosophila melanogaster) providing a unique system to examine neurotransmitter release and drug dependence mechanisms in a small, but complete system.Mass spectrometry imaging with ion beams allows spatial resolution of a few micrometers down to 40 nanometers in favorable cases. We have been using secondary ion mass spectrometry (SIMS) with a unique 40-kV argon cluster ion source and the NanoSIMS to measure the lipids across the fly brain and catecholamine in nanometer vesicles, respectively. Here, we have focused on the effect of the drug, methylphenidate, on lipid composition in the brain and find that it varies in a way that might affect learning and memory. We have also used NanoSIMS to measure transmitter in subregions of nanometer vesicles. Combined with other new methods to measure the content of the interior of vesicles, we have begun to investigate the details and implications of open and closed exocytosis on regulation of how the brain works.
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| 4. |
- Pedersen, Anders, 1976, et al.
(författare)
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Rational improvement of cell-free protein synthesis.
- 2011
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 28:3, s. 218-224
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Tidskriftsartikel (refereegranskat)abstract
- Experimental design principles were applied on cell-free protein synthesis to optimize performance with regard to the expression yield and the incorporation efficiency of amino acid precursors. A versatile screening platform based on batch-mode cell-free expression and central composite design was used. The performance of different extracts (S12 and S30), the concentration dependence of key components and the effect of different additives were investigated. We find that the initial expression yield can be enhanced twofold to threefold in this manner. The improved conditions comprise a modified S12 extract, optimized concentrations of creatine phosphate and key amino acids, as well as introduction of ketoacid additives. Our results show that current cell-free expression technology is far from optimal and that higher yields and increased utilization of the provided precursors are attainable with further optimization.
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| 5. |
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| 6. |
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| 7. |
- Klingström, Tomas, et al.
(författare)
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Workshop on laboratory protocol standards for the molecular methods database
- 2013
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Ingår i: New Biotechnology. - : Elsevier BV. - 1871-6784 .- 1876-4347. ; 30:2, s. 109-113
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Tidskriftsartikel (refereegranskat)abstract
- Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
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| 8. |
- Wenning, Leonie, 1986, et al.
(författare)
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Biosynthesis of very long-chain fatty alcohols and wax esters in metabolically engineered strains of Saccharomyces cerevisiae
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 33:Supplement: S Meeting Abstract: O18-3, s. S54-S54
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Tidskriftsartikel (refereegranskat)abstract
- The objective of our research is the biosynthesis of very long-chain fatty alcohols (VLCFAlcs) and wax esters (WEs) in S. cerevisiae . VLCFAlcs and WEs have a broad application range and can be used for many commercial purposes. The applications of WEs include personal care products, lubricants, varnishes, inks, detergents, resins & plastics. WEs can also be used for coatings (for fruits & pills) and as an oil phase in formulas containing active compounds to enhance the efficiency of topical drugs.VLCFAlcs, like docosanol, are used as an emollient, emulsifier and thickener in cosmetics as well as a nutritional supplement. Unfortunately, at present most of the possible applications are limited to cosmetic and medical products due to the high price for WE isolation from their natural host, the plant Simmondsia chinensis . Because of this fact, a renewable approach for low-cost production of VLCFAlcs and WEs in a well-studied organism like S. cerevisiae is desirable. The in vitro and in vivo synthesis of different WEs up to C36 has already been shown in S. cerevisiae , but these WEs do not show the mentioned desired properties for commercial use. The in vivo synthesis of WE up to C44 in S. cerevisiae has so far only been achieved after substrate feeding. In our approach we demonstrate that the heterologous expression of specific fatty acyl-CoA reductases (FARs), enzymes required for alcohol synthesis, and wax synthases (WSs), enzymes responsible for WE synthesis, allow the in vivo synthesis of VLCFAlcs up to C22 and VLCWEs up to C42.
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| 9. |
- Yan, Ruoyu, et al.
(författare)
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Structural characterization of the family GH115 α-glucuronidase from Amphibacillus xylanus yields insight into its coordinated action with α-arabinofuranosidases
- 2021
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 62, s. 49-56
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Tidskriftsartikel (refereegranskat)abstract
- The coordinated action of carbohydrate-active enzymes has mainly been evaluated for the purpose of complete saccharification of plant biomass (lignocellulose) to sugars. By contrast, the coordinated action of accessory hemicellulases on xylan debranching and recovery is less well characterized. Here, the activity of two family GH115 α-glucuronidases (SdeAgu115A from Saccharophagus degradans, and AxyAgu115A from Amphibacillus xylanus) on spruce arabinoglucuronoxylan (AGX) was evaluated in combination with an α-arabinofuranosidase from families GH51 (AniAbf51A, aka E-AFASE from Aspergillus niger) and GH62 (SthAbf62A from Streptomyces thermoviolaceus). The α-arabinofuranosidases boosted (methyl)-glucuronic acid release by SdeAgu115A by approximately 50 % and 30 %, respectively. The impact of the α-arabinofuranosidases on AxyAgu115A activity was comparatively low, motivating its structural characterization. The crystal structure of AxyAgu115A revealed increased length and flexibility of the active site loop compared to SdeAgu115A. This structural difference could explain the ability of AxyAgu115A to accommodate more highly substituted arabinoglucuronoxylan, and inform enzyme selections for improved AGX recovery and use.
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| 10. |
- Azizi, Tamir, et al.
(författare)
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A COST Action on microbial responses to low pH : Developing links and sharing resources across the academic-industrial divide
- 2022
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Ingår i: New Biotechnology. - : Elsevier BV. - 1871-6784 .- 1876-4347. ; 72, s. 64-70
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Tidskriftsartikel (refereegranskat)abstract
- We present work of our COST Action on "Understanding and exploiting the impacts of low pH on micro-or-ganisms". First, we summarise a workshop held at the European Federation of Biotechnology meeting on Mi-crobial Stress Responses (online in 2020) on "Industrial applications of low pH stress on microbial bio-based production", as an example of an initiative fostering links between pure and applied research. We report the outcomes of a small survey on the challenging topic of developing links between researchers working in academia and industry that show that, while people in different sectors strongly support such links, barriers remain that obstruct this process. We present the thoughts of an expert panel held as part of the workshop above, where people with experience of collaboration between academia and industry shared ideas on how to develop and maintain links. Access to relevant information is essential for research in all sectors, and because of this we have developed, as part of our COST Action goals, two resources for the free use of all researchers with interests in any aspects of microbial responses to low pH. These are (1) a comprehensive database of references in the literature on different aspects of acid stress responses in different bacterial and fungal species, and (2) a database of research expertise across our network. We invite the community of researchers working in this field to take advantage of these resources to identify relevant literature and opportunities for establishing collaborations.
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