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Michel A.M.,University College Cork | Fox G.,University College Cork | Fox G.,University College Dublin | M. Kiran A.,University College Cork | And 8 more authors.
Nucleic Acids Research | Year: 2014

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. © 2013 The Author(s). Published by Oxford University Press.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP-SICA | Phase: KBBE-2009-2-5-01 | Award Amount: 7.58M | Year: 2010

VEG-i-TRADE provides platforms to identify impacts of anticipated climate change and globalisation on food safety, microbiological and chemical hazards, of fresh produce and derived food products. Control measures of managerial and technological nature will be developed in the supply chain of crop production, post-harvest processing and logistics to minimize food safety risks. The assessment of the performance of horticultural safety management systems by a novel diagnostic instrument at EU level exemplified by several countries in Europe and tailored on a global level including major EU trade partners from various climate zones will lead to recommendations on European and global level on quality assurance and the setting of science-based performance objectives. VEG-i-TRADE will pro-actively invest in problem solving technologies for safe produce investigating aspects of water quality and water treatment, horticultural production practices, disinfection treatment and packaging technologies. These control measures will be exploited in collaboration with SMEs and industrial partners. Baseline studies on the hazards, intervention technologies and best practices in the fresh produce chain will provide input for both microbial and chemical risk assessment to elaborate support to risk-based sampling plans, evaluate the risks of newly identified threats as affected by the global trade system and anticipated climate change. The project output will craft a discussion forum for stakeholders in the global food chain reflecting on issues of acceptable risk, sustainability of fresh produce production and long term strategy of international food trade, while making no compromise in food safety for European consumers and in respectation of food sovereignty. Risk communication to increase awareness of trade partners production systems and the uneven consumer behaviour will provide key conditions for prioritisation of risk management strategies.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: FP7-PEOPLE-2009-NIGHT | Award Amount: 141.06K | Year: 2009

During the night of September 25th, several events will be organized in eight Belgian cities (Brussels (3), Gent, Kortrijk, Lige, Louvain-la-Neuve, Mechelen, Namur and Redu-Transinne) in the frame of the European Researchers Night. So, nine partners are cooperating under the coordination of the Belgian Science Policy Office: six universities (Brussels (French- and Flemish speaking), Lige, Louvain-la-Neuve, Gent, Namur), one high school (Kortrijk), a non-profit body (Flanders Technology International vzw) which will hold its activities in Mechelen (Technopolis) and a private body, Craction (the activities will be held at the EuroSpaceCenter in Redu-Transinne). The Vrije Universiteit Brussel will cooperate with the Erasmushogeschool. Ghent University and Hogeschool West-Vlaanderen will cooperate with their association partners Hogeschool Gent and Arteveldehogeschool. The definition of the programme of activities has been developed by each partner. Each partner is also responsible for his own publicity campaign (local newspapers and / or radios ...) but the template will be common. The overall programme of activities appears thus quite varied, composed of games, quizzes, interactive experiments, demonstrations, on site discoveries, guided tours ... All activities offer the audience an opportunity to directly meet researchers and exchange with them on any topic, whether science-linked or not. Beside all these activities a poster contest will be organised, the launching being planned during this summer. So the artistes en herbe will get enough time to create the poster of the Researchers Night 2010, as asked by the Commission. Projects will be collected and displayed in all the venues and the winners of the competition will be announced just after the Night.


Gonzales G.B.,Ghent University | Gonzales G.B.,West-Flanders College | Raes K.,West-Flanders College | Raes K.,Ghent University | And 4 more authors.
Journal of Chromatography A | Year: 2014

In this paper, a strategy for the detection and structural elucidation of flavonoid glycosides from a complex matrix in a single chromatographic run using U(H)PLC-ESI-IMS-HDMS/MSE is presented. This system operates using alternative low and high energy voltages that is able to perform the task of conventional MS/MS in a data-independent way without re-injection of the sample, which saves analytical time. Also, ion mobility separation (IMS) was employed as an additional separation technique for compounds that are co-eluting after U(H)PLC separation. First, the fragmentation of flavonoid standards were analyzed and criteria was set for structural elucidation of flavonoids in a plant extract. Based on retention times, UV spectra, exact mass, and MS fragment characteristics, such as abundances of daughter ions and the presence of radical ions ([Y0-H]-), a total 19 flavonoid glycosides, of which 8 non-acylated and 11 acylated, were detected and structurally characterized in a cauliflower waste extract. Kaempferol and quercetin were the main aglycones detected while sinapic and ferulic acid were the main phenolic acids. C-glycosides were also found although their structure could not be elucidated. The proposed method can be used as a rapid screening test for flavonoid identification and for routine analysis of plant extracts, such as these derived from cauliflower waste. The study also confirms that agroindustrial wastes, such as cauliflower leaves, could be seen as a valuable source of different bioactive phenolic compounds. © 2013 Elsevier B.V.


Van Den Hende S.,West-Flanders College | Van Den Hende S.,Ghent University | Vervaeren H.,West-Flanders College | Boon N.,Ghent University
Biotechnology Advances | Year: 2012

Flue gases are a resource yet to be fully utilised in microalgal biotechnology, not only to moderate the anthropogenic effects on our climate, but also to steer microalgal resource management towards innovative applications of microalgal biomass compounds. These gases, both untreated and treated into current discharge standards, contain CO2, N2, H2O, O2, NOx, SOx, CxHy, CO, particulate matter, halogen acids and heavy metals. To better steer and engineer flue gas-fed microalgal cultures, all these compounds need to be considered. Therefore, here, we review (i) the chemical composition and treatment technologies of flue gas, (ii) the uptake pathways and removal of the different compounds in microalgae reactors, and (iii) the tolerance and effects on microalgae of all flue gas compounds. By emphasising the interactions between microalgae and flue gas compounds, we envisage new pathways for microalgal biomass valorisation such as enzyme production for environmental technology, novel biogas production and biosequestration of minerals. Furthermore, we highlight fundamental and applied research niches that merit further investigation. © 2012 Elsevier Inc.


Ryckebosch E.,Sudan University of Science and Technology | Drouillon M.,Ghent University | Vervaeren H.,West-Flanders College
Biomass and Bioenergy | Year: 2011

Biogas from anaerobic digestion and landfills consists primarily of CH4 and CO2. Trace components that are often present in biogas are water vapor, hydrogen sulfide, siloxanes, hydrocarbons, ammonia, oxygen, carbon monoxide and nitrogen. In order to transfer biogas into biomethane, two major steps are performed: (1) a cleaning process to remove the trace components and (2) an upgrading process to adjust the calorific value. Upgrading is generally performed in order to meet the standards for use as vehicle fuel or for injection in the natural gas grid. Different methods for biogas cleaning and upgrading are used. They differ in functioning, the necessary quality conditions of the incoming gas, the efficiency and their operational bottlenecks. Condensation methods (demisters, cyclone separators or moisture traps) and drying methods (adsorption or absorption) are used to remove water in combination with foam and dust. A number of techniques have been developed to remove H2S from biogas. Air dosing to the biogas and addition of iron chloride into the digester tank are two procedures that remove H2S during digestion. Techniques such as adsorption on iron oxide pellets and absorption in liquids remove H2S after digestion. Subsequently, trace components like siloxanes, hydrocarbons, ammonia, oxygen, carbon monoxide and nitrogen can require extra removal steps, if not sufficiently removed by other treatment steps. Finally, CH4 must be separated from CO2 using pressure swing adsorption, membrane separation, physical or chemical CO2-absorption. © 2011 Elsevier Ltd.


Devos J.,West-Flanders College | Landeghem H.V.,Ghent University | Deschoolmeester D.,Vlerick Leuven Gent Management School
Industrial Management and Data Systems | Year: 2012

Purpose - The purpose of this paper is to critically rethink the concepts and the theoretical foundations of IT governance in small- and medium-sized enterprises (SMEs). Design/methodology/approach - The paper is based on multiple case studies. In total, eight cases of outsourced information system projects where failures occurred were selected. An outsourced information system failure (OISF) is suggested as a failure of governance of the IT in a SME environment. A structure for stating propositions derived from two competing theories is proposed (Agency Theory and Theory of Trust). Findings - The results reveal that trust is slightly more important than control issues such as output-based contracts and structured controls in the governance of IT in SMEs. Practical implications - The world of SMEs is significantly different from that of large companies, and therefore, the concept of IT governance in SMEs needs reconsideration. For researchers and practitioners, it would be more meaningful to focus on actual, working SMEs instead of on a version of their activities derived from those of large companies. Originality/value - The paper offers two contributions. First, it elaborates the limited research on IT in SMEs and second, it brings theoretical foundations for their IT governance. The value of IT governance in SMEs is explained. © 2012 Emerald Group Publishing Limited.


Van Haute S.,Ghent University | Van Haute S.,West-Flanders College | Sampers I.,West-Flanders College | Holvoet K.,Ghent University | And 2 more authors.
Applied and Environmental Microbiology | Year: 2013

Chlorine was assessed as a reconditioning agent and wash water disinfectant in the fresh-cut produce industry. Artificial freshcut lettuce wash water, made from butterhead lettuce, was used for the experiments. In the reconditioning experiments, chlorine was added to artificial wash water inoculated with Escherichia coli O157 (6 log CFU/ml). Regression models were constructed based on the inactivation data and validated in actual wash water from leafy vegetable processing companies. The model that incorporated chlorine dose and chemical oxygen demand (COD) of the wash water accurately predicted inactivation. Listeria monocytogenes was more resistant to chlorine reconditioning in artificial wash water than Salmonella spp. and Escherichia coli O157. During the washing process with inoculated lettuce (4 log CFU/g), in the absence of chlorine, there was a rapid microbial buildup in the water that accumulated to 5.4±0.4 log CFU/100 ml after 1 h. When maintaining a residual concentration of 1 mg/liter free chlorine, wash water contamination was maintained below 2.7, 2.5, and 2.5 log CFU/100 ml for tap water and artificial process water with COD values of 500 and 1,000 mg O2/liter, respectively. A model was developed to predict water contamination during the dynamic washing process. Only minor amounts of total trihalomethanes were formed in the water during reconditioning. Total trihalomethanes accumulated to larger amounts in the water during the wash water disinfection experiments and reached 124.5±13.4 μg/liter after 1 h of execution of the washing process in water with a COD of 1,000 mg O2/liter. However, no total trihalomethanes were found on the fresh-cut lettuce after rinsing. © 2013, American Society for Microbiology.


Audenaert W.T.M.,Ghent University | Audenaert W.T.M.,West-Flanders College | Vandierendonck D.,West-Flanders College | Van Hulle S.W.H.,Ghent University | And 2 more authors.
Water Research | Year: 2013

This study experimentally examined the impact of oxidation on the properties of effluent organic matter (EfOM) using two different oxidation techniques: ozonation and UV/H2O2 treatment. Multiple surrogates for EfOM related to its spectral properties, molecular size, concentration, polarity and biodegradability were used to study the oxidant induced conversions. Spectral calculations as differential absorbance spectra (DAS) and absorbance slope index (ASI) were applied for the first time to describe EfOM oxidation and proved to be useful to unravel differences in working mechanism between ozone and hydroxyl radical (HO) induced transformation of EfOM. Effluent ozonation inherently led to significant HO production as a result of electron transfers between ozone and electron rich moieties of EfOM. HO production increased as function of ozone dose and was strongly correlated to UV absorption at 254 nm (UV254). During the UV moderated process, pseudo steady-state behaviour of the HO concentration was observed. Ozone decomposition was extremely sensitive to EfOM reactivity. Most likely, the degree of dissociation of EfOM controlled its reactivity towards ozone. The pH effect was quantified by calculating the pseudo-first order decay constant for ozone as function of reaction time and pH. Treatment with both processes led to more oxygen rich, less hydrophobic and more biodegradable EfOM. © 2013 Elsevier Ltd.


Grant
Agency: European Commission | Branch: FP7 | Program: CSA-SA | Phase: FP7-2008-PEOPLE-NIGHT | Award Amount: 226.18K | Year: 2008

During the night of September 26th, six events will be organised in five Belgian cities (Brussels, Antwerp, Kortrijk, Lige and Louvain-la-neuve) in the frame of the European Researchers Night. Six partners have joined their forces by the Belgian Science Policy Office (Belspo) : 3 universities, 2 high schools and one Federal Scientific Institute. All partners agreed on a common publicity campaign, a commom communication and, last but not least, a common theme : The Year of the Planet Earth. Next to this common theme, freedom has been given to the partners to develop thier point of view. So there will be a science caf in each city, a huge city game in Antwerp and Kortrijk, a concert in Brussels, ... All partners will intend to get this evening funny and serious at the same time. \ concours photo

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