Search results for " array"
showing 10 items of 895 documents
The focal plane assembly for the Athena X-ray Integral Field Unit instrument
2016
This paper summarizes a preliminary design concept for the focal plane assembly of the X-ray Integral Field Unit on the Athena spacecraft, an imaging microcalorimeter that will enable high spectral resolution imaging and point-source spectroscopy. The instrument's sensor array will be a ~ 3840-pixel transition edge sensor (TES) microcalorimeter array, with a frequency domain multiplexed SQUID readout system allowing this large-format sensor array to be operated within the thermal constraints of the instrument's cryogenic system. A second TES detector will be operated in close proximity to the sensor array to detect cosmic rays and secondary particles passing through the sensor array for off…
Aneuploid IMR90 cells induced by depletion of pRB, DNMT1 and MAD2 show a common gene expression signature
2019
Chromosome segregation defects lead to aneuploidy which is a major feature of solid tumors. How diploid cells face chromosome mis-segregation and how aneuploidy is tolerated in tumor cells are not completely defined yet. Thus, an important goal of cancer genetics is to identify gene networks that underlie aneuploidy and are involved in its tolerance. To this aim, we induced aneuploidy in IMR90 human primary cells by depleting pRB, DNMT1 and MAD2 and analyzed their gene expression profiles by microarray analysis. Bioinformatic analysis revealed a common gene expression profile of IMR90 cells that became aneuploid. Gene Set Enrichment Analysis (GSEA) also revealed gene-sets/pathways that are …
New Trends in Molecular Techniques to Identify Microorganisms in Dairy Products
2018
International audience; Dairy products constitute one of the most important types of functional foods. Most of these functional properties have been attributed to their complex microbial ecosystem. Moreover, microorganisms are responsible for the broad diversity of tastes, aromas, and textures of dairy products. For instance, many bacteria make a positive contribution to the organoleptic quality of cheeses or fermented milk. However, some other bacteria may have adverse effects, or may even present a health risk from a safety point of view. Thus, it is of a paramount importance to control microbial ecosystem of dairy products. Traditionally culture-based methods have been used for the ident…
Plasmonic nanosensor array for multiplexed DNA-based pathogen detection
2019
In this research we introduce a plasmonic nanoparticle based optical biosensor for monitoring of molecular binding events. The sensor utilizes spotted gold nanoparticle arrays as sensing platform. The nanoparticle spots are functionalized with capture DNA sequences complementary to the analyte (target) DNA. Upon incubation with the target sequence, it will bind on the respectively complementary functionalized particle spot. This binding changes the local refractive index, which is detected spectroscopically as the resulting changes of the localized surface plasmon resonance (LSPR) peak wavelength. In order to increase the signal, a small gold nanoparticle label is introduced. The binding ca…
Evaluation of the DNA microarray “AMR Direct Flow Chip Kit” for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bact…
2019
Abstract Introduction The AMR Direct Flow Chip assay allows the simultaneous detection of a large variety of antibiotic resistance genetic markers. To assess this kit's performance, we use isolated colonies as starting material. The assay has been approved by the European Economic Area as a suitable device for in vitro diagnosis (CE IVD) using clinical specimens. Methods A total of 210 bacterial isolates harbouring either one or more antimicrobial resistance genes including plasmid-encoded extended-spectrum β-lactamases (SHV, CTX-M) and carbapenemases (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP, and OXA), mecA, vanA and vanB, and 30 controls were included. Results The assay displa…
LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli
2002
The function of the LysR-type regulator LrhA of Escherichia coli was defined by comparing whole-genome mRNA profiles from wild-type E. coli and an isogenic lrhA mutant on a DNA microarray. In the lrhA mutant, a large number (48) of genes involved in flagellation, motility and chemotaxis showed relative mRNA abundances increased by factors between 3 and 80. When a representative set of five flagellar, motility and chemotaxis genes was tested in lacZ reporter gene fusions, similar factors for derepression were found in the lrhA mutant. In gel retardation experiments, the LrhA protein bound specifically to flhD and lrhA promoter DNA (apparent K-D approximate to 20 nM), whereas the promoters of…
Digital image processing for rapid analysis of differentially expressed transcripts on high-density cDNA arrays.
1999
Usage of filter arrays is becoming increasingly attractive for many research laboratories involved in determination of gene-expression profiles. However, analysis of numerous spots, representing genes or partial gene sequences (ESTs), is still tedious work involving the ordered analysis of vast amounts of numerical tabular data. We present a rapid and efficient method for the visual identification of differentially expressed targets on high-density cDNA filter arrays using standard laboratory equipment and standard software, which is available for free. The method we introduce provides an inexpensive alternative, and no changes in the experimental set up are required. Our results were veri…
Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression al…
2002
AbstractGenomic aberrations in a series of paired biopsy samples from patients who presented initially with follicle center lymphoma (FCL) and subsequently transformed to diffuse large B-cell lymphoma (DLBCL) were measured by array comparative genomic hybridization (CGH). The consequences of these aberrations on gene expression were determined by comparison with expression analysis on these specimens using cDNA microarrays. A heterogeneous pattern of acquired genomic abnormalities was observed upon transformation, some of which were recurrent in small subsets of patients. Some of the genomic aberration acquired upon transformation, such as gain/amplification of 1q21-q24, 2p16 (REL/BCL11A ge…
Development-dependent changes in the tight DNA-protein complexes of barley on chromosome and gene level
2008
Abstract Background The tightly bound to DNA proteins (TBPs) is a protein group that remains attached to DNA with covalent or non-covalent bonds after its deproteinisation. The functional role of this group is as yet not completely understood. The main goal of this study was to evaluate tissue specific changes in the TBP distribution in barley genes and chromosomes in different phases of shoot and seed development. We have: 1. investigated the TBP distribution along Amy32b and Bmy1 genes encoding low pI α-amylase A and endosperm specific β-amylase correspondingly using oligonucleotide DNA arrays; 2. characterized the polypeptide spectrum of TBP and proteins with affinity to TBP-associated D…
Context matters-consensus molecular subtypes of colorectal cancer as biomarkers for clinical trials
2019
Abstract The Colorectal Cancer Subtyping Consortium identified four gene expression consensus molecular subtypes, CMS1 (immune), CMS2 (canonical), CMS3 (metabolic), and CMS4 (mesenchymal), using multiple microarray or RNA-sequencing datasets of primary tumor samples mainly from early stage colon cancer patients. Consequently, rectal tumors and stage IV tumors (possibly reflective of more aggressive disease) were underrepresented, and no chemo- and/or radiotherapy pretreated samples or metastatic lesions were included. In view of their possible effect on gene expression and consequently subtype classification, sample source and treatments received by the patients before collection must be ca…