Delft University of Technology

About: Delft University of Technology is a education organization based out in Delft, Zuid-Holland, Netherlands. It is known for research contribution in the topics: Computer science & Catalysis. The organization has 37681 authors who have published 94404 publications receiving 2741710 citations. The organization is also known as: TU-Delft & Technische Hogeschool Delft.

Anaerobic ammonium oxidation by anammox bacteria in the Black Sea

Abstract: The availability of fixed inorganic nitrogen (nitrate, nitrite and ammonium) limits primary productivity in many oceanic regions. The conversion of nitrate to N2 by heterotrophic bacteria (denitrification) is believed to be the only important sink for fixed inorganic nitrogen in the ocean. Here we provide evidence for bacteria that anaerobically oxidize ammonium with nitrite to N2 in the world's largest anoxic basin, the Black Sea. Phylogenetic analysis of 16S ribosomal RNA gene sequences shows that these bacteria are related to members of the order Planctomycetales performing the anammox (anaerobic ammonium oxidation) process in ammonium-removing bioreactors. Nutrient profiles, fluorescently labelled RNA probes, 15N tracer experiments and the distribution of specific 'ladderane' membrane lipids indicate that ammonium diffusing upwards from the anoxic deep water is consumed by anammox bacteria below the oxic zone. This is the first time that anammox bacteria have been identified and directly linked to the removal of fixed inorganic nitrogen in the environment. The widespread occurrence of ammonium consumption in suboxic marine settings indicates that anammox might be important in the oceanic nitrogen cycle.

Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

Abstract: X-linked SCID (SCID-X1) is amenable to correction by gene therapy using conventional gammaretroviral vectors. Here, we describe the occurrence of clonal T cell acute lymphoblastic leukemia (T-ALL) promoted by insertional mutagenesis in a completed gene therapy trial of 10 SCID-X1 patients. Integration of the vector in an antisense orientation 35 kb upstream of the protooncogene LIM domain only 2 (LMO2) caused overexpression of LMO2 in the leukemic clone. However, leukemogenesis was likely precipitated by the acquisition of other genetic abnormalities unrelated to vector insertion, including a gain-of-function mutation in NOTCH1, deletion of the tumor suppressor gene locus cyclin-dependent kinase 2A (CDKN2A), and translocation of the TCR-β region to the STIL-TAL1 locus. These findings highlight a general toxicity of endogenous gammaretroviral enhancer elements and also identify a combinatorial process during leukemic evolution that will be important for risk stratification and for future protocol design.

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Abstract: The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Tomographic particle image velocimetry

Abstract: This paper describes the principles of a novel 3D PIV system based on the illumination, recording and reconstruction of tracer particles within a 3D measurement volume The technique makes use of several simultaneous views of the illuminated particles and their 3D reconstruction as a light intensity distribution by means of optical tomography The technique is therefore referred to as tomographic particle image velocimetry (tomographic-PIV) The reconstruction is performed with the MART algorithm, yielding a 3D array of light intensity discretized over voxels The reconstructed tomogram pair is then analyzed by means of 3D cross-correlation with an iterative multigrid volume deformation technique, returning the three-component velocity vector distribution over the measurement volume The principles and details of the tomographic algorithm are discussed and a parametric study is carried out by means of a computer-simulated tomographic-PIV procedure The study focuses on the accuracy of the light intensity field reconstruction process The simulation also identifies the most important parameters governing the experimental method and the tomographic algorithm parameters, showing their effect on the reconstruction accuracy A computer simulated experiment of a 3D particle motion field describing a vortex ring demonstrates the capability and potential of the proposed system with four cameras The capability of the technique in real experimental conditions is assessed with the measurement of the turbulent flow in the near wake of a circular cylinder at Reynolds 2,700