Search results for "sequence data"
showing 10 items of 1952 documents
Serological and molecular characteristics of Vibrio vulnificus biotype 3: evidence for high clonality.
2007
Vibrio vulnificus biotype 3 has been implicated as the causative pathogen of an ongoing disease outbreak that erupted in Israel in 1996. Recent work based on multi-locus sequence typing (MLST) showed that V. vulnificus biotype 3 is genetically homogeneous. The aim of this study was to investigate the existence of subpopulations within this homogeneous biotype by characterizing the surface antigens and analysing the sequence diversity of selected outer-membrane protein (OMP)-encoding genes. Rabbit antisera were prepared against biotype 1, 2 and 3 strains. The results of the slide-agglutination test, dot-blot assay (using fresh and boiled cells), and immunoblotting of lipopolysaccharides (LPS…
S-type lectins occur also in invertebrates: high conservation of the carbohydrate recognition domain in the lectin genes from the marine sponge Geodi…
1993
The marine sponge Geodia cydonium contains several lectins. The main component, called lectin-1, is composed of three to four identical subunits. The subunits of the lectins were cloned from a cDNA library; two clones were obtained. From the deduced aa sequence of one clone, LECT-1, a mol. wt of 15,313 Da is calculated; this value is in good agreement with mass spectrometric analysis of 15,453 +/- 25 Da. The sequence of another clone, LECT-2, was analysed and the aa sequence was deduced (15,433 Da). The two subunits have a framework sequence of 38 conserved aa which are characteristic for the carbohydrate-binding site of vertebrate S-type lectins. Clustering of lectin sequences of various s…
Analysing Complex Life Sequence Data with Hidden Markov Modelling
2016
When analysing complex sequence data with multiple channels (dimensions) and long observation sequences, describing and visualizing the data can be a challenge. Hidden Markov models (HMMs) and their mixtures (MHMMs) offer a probabilistic model-based framework where the information in such data can be compressed into hidden states (general life stages) and clusters (general patterns in life courses). We studied two different approaches to analysing clustered life sequence data with sequence analysis (SA) and hidden Markov modelling. In the first approach we used SA clusters as fixed and estimated HMMs separately for each group. In the second approach we treated SA clusters as suggestive and …
Light induces expression of a dehydrin-encoding gene during seedling de-etiolation in sunflower (Helianthus annus L.)
2007
The effects of light quality on the expression of a sunflower dehydrin-encoding gene, HaDhn1, were studied during seedling de-etiolation. Seeds were germinated in the dark and, after 5 days, seedlings were maintained well watered and de-etiolated under different lights for 3, 6, 12, and 24h. Exposure to white light stimulated HaDhn1 transcript accumulation in the cotyledons of these seedlings, contrary to seedlings grown in the dark. HaDhn1 transcripts increased also treating plantlets with monochromatic lights, especially red light. The increase of HaDhn1 transcripts is provoked by the formation of the active form of phytochrome. Further experiments, performed saturating active phytochrome…
Investigation and control of a Norovirus outbreak of probable waterborne transmission through a municipal groundwater system
2014
During March 2011 an outbreak of gastroenteritis occurred in Santo Stefano di Quisquina, Agrigento, Sicily, Italy. Within two weeks 156 cases were identified among the 4,965 people living in the municipality. An epidemiological investigation was conducted to characterize the outbreak and target the control measures. A case was defined as a person developing diarrhea or vomiting during February 27–March 13, 2011. Stool specimens were collected from 12 cases. Norovirus (NoV) genotype GII.4 variant New Orleans 2009 was identified in stool samples from 11 of 12 cases tested (91.7%). Epidemiological investigations suggested a possible association with municipal drinking water consumption. Water …
Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora
2011
Abstract Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three dist…
Design and experimental validation of a generic model for combinatorial assembly of DNA tiles into 1D-structures.
2010
Abstract Background Quantitative modeling of the self-assembly of DNA tiles leading either to defined end-products or distribution of biopolymers is of practical importance for biotechnology and synthetic biology. Methods The combinatorial process describing tile assembly was implemented into a generic algorithm allowing quantitative description of the population of significant species accumulating during the reaction course. Experimental formation and characterization by optical and electrophoresis approaches of copolymers resulting from the self-assembly of a limited number of half-complementary tiles were used to define and validate generic rules allowing definition of model parameters. …
The endopolygalacturonase 1 from botrytis cinerea activates grapevine defense reactions unrelated to its enzyumatic activity
2003
A purified glycoprotein from Botrytis cinerea(strain T4), identified as endopolygalacturonase 1 (T4BcPG1) by mass spectrometry analysis, has been shown to activate defense reactions in grapevine (Vitis vinifera cv. Gamay). These reactions include calcium influx, production of active oxygen species, activation of two mitogen-activated protein kinases, defense gene transcript accumulation, and phytoalexin production. Most of these defense reactions were also activated in grapevine in response to purified oligogalacturonides (OGA) with a degree of polymerization of 9 to 20. In vivo, these active OGA might be a part of the released products resulting from endopolygalacturonase activity on plan…
Identification and characterization of autoantibodies against catalase and α-enolase in patients with primary sclerosing cholangitis
1998
SUMMARY Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology. Recent studies have shown that genetic factors and both cellular and humoral immunological abnormalities are important in the pathogenesis of PSC. The most prominent autoantibodies in PSC are anti-neutrophil cytoplasmic antibodies (ANCA). The autoepitopes of ANCA in PSC are not well defined. The aim of this study was to identify corresponding ANCA autoantigens in patients with PSC. A biochemical approach with enrichment and partial purification of soluble neutrophil proteins, detection of autoantibodies by Western blot and partial amino acid sequencing were used. Two new autoantigen/aut…
De novo CCND2 mutations leading to stabilization of cyclin D2 cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome
2014
Activating mutations in genes encoding phosphatidylinositol 3-kinase (PI3K)-AKT pathway components cause megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome (MPPH, OMIM 603387)(1-3). Here we report that individuals with MPPH lacking upstream PI3K-AKT pathway mutations carry de novo mutations in CCND2 (encoding cyclin D2) that are clustered around a residue that can be phosphorylated by glycogen synthase kinase 313 (GSK-3 beta)(4). Mutant CCND2 was resistant to proteasomal degradation in vitro compared to wild-type CCND2. The PI3K-AKT pathway modulates GSK-3 beta activity(4), and cells from individuals with PIK3CA, PIK3R2 or AKT3 mutations showed similar CCND2 accumulation. CCND…