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131.
Boomkens SY de Rave S Pot RG Egberink HF Penning LC Rothuizen J Zondervan PE Kusters JG 《FEMS immunology and medical microbiology》2005,44(2):221-225
Helicobacter species DNA has been detected in liver tissue of patients affected by primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). To investigate a potential causative relation between Helicobacter species and PBC/PSC, we compared the presence of Helicobacter species-specific DNA in liver tissue of patients with PBC/PSC (n=18/n=13) with those of a control group of patients with various liver diseases with known cause (n=29). A PCR with Helicobacter genus-specific 16S rRNA primers was performed on DNA isolated from paraffin embedded liver tissue. Control patients had hepatitis-B (n=9), alcoholic cirrhosis (n=14), or non-cirrhotic metabolic liver disease (n=6). There was no significant difference between the incidence of Helicobacter spp.-specific DNA in PBC/PSC (9/31; 29%) and the control group (10/29; 34%). Sequence analysis confirmed Helicobacter spp. DNA. Because Helicobacter spp. DNA can be found in approximately one-third of all samples tested, it is unlikely that PSC and PBC are caused by Helicobacter infection. 相似文献
132.
Sandhu AP Lam AM Fenske DB Palmer LR Johnston M Cullis PR 《Analytical biochemistry》2005,341(1):156-164
Previous work from this laboratory has shown that plasmid DNA can be encapsulated in small (70-nm-diameter) stabilized plasmid-lipid particles (SPLP) that consist of a single plasmid encapsulated within a bilayer lipid vesicle. SPLP preferentially transfect tumor tissue following intravenous administration. Although the levels of transgene expression in vivo are greater for SPLP than can be achieved with naked DNA or complexes, they are lower than may be required for therapeutic benefit. In the present work we examine whether Ca2+ can enhance the transfection potency of SPLP. It is shown that Ca2+ can enhance SPLP transfection potency in bovine hamster kidney cells by 60- to 100-fold when treated in serum containing medium and an additional 60-fold when serum is absent for the initial 10 min of the transfection period. When cells are treated with SPLP in the presence of Ca2+, there is a fivefold increase in intact plasmid in the cell. It is also shown that this Ca2+ effect involves the formation of calcium phosphate precipitates; however, these precipitates are not directly associated with the SPLP plasmid DNA. The ability of calcium phosphate to facilitate delivery of other macromolecules without direct association is also demonstrated by the release of large-molecular-weight dextrans from endosomal/lysosomal compartments in the presence of calcium phosphate. Finally, it is shown that, unlike naked DNA, SPLP transfection potency in the presence of calcium phosphate is not affected by nuclease activity. 相似文献
133.
Sangkyun Lee J?rg Rahnenführer Michel Lang Katleen De Preter Pieter Mestdagh Jan Koster Rogier Versteeg Raymond L. Stallings Luigi Varesio Shahab Asgharzadeh Johannes H. Schulte Kathrin Fielitz Melanie Schwermer Katharina Morik Alexander Schramm 《PloS one》2014,9(10)
Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org). 相似文献
134.
Pieter Candry Britt Abrahamson David Allan Stahl Mari-Karoliina Henriikka Winkler 《Global Change Biology》2023,29(18):5169-5183
Wetlands are crucial nodes in the carbon cycle, emitting approximately 20% of global CH4 while also sequestering 20%–30% of all soil carbon. Both greenhouse gas fluxes and carbon storage are driven by microbial communities in wetland soils. However, these key players are often overlooked or overly simplified in current global climate models. Here, we first integrate microbial metabolisms with biological, chemical, and physical processes occurring at scales from individual microbial cells to ecosystems. This conceptual scale-bridging framework guides the development of feedback loops describing how wetland-specific climate impacts (i.e., sea level rise in estuarine wetlands, droughts and floods in inland wetlands) will affect future climate trajectories. These feedback loops highlight knowledge gaps that need to be addressed to develop predictive models of future climates capturing microbial contributions. We propose a roadmap connecting environmental scientific disciplines to address these knowledge gaps and improve the representation of microbial processes in climate models. Together, this paves the way to understand how microbially mediated climate feedbacks from wetlands will impact future climate change. 相似文献
135.
Logan T. Berner Pieter S. A. Beck Andrew G. Bunn Scott J. Goetz 《Global Change Biology》2013,19(11):3449-3462
Russia's boreal (taiga) biome will likely contract sharply and shift northward in response to 21st century climatic change, yet few studies have examined plant response to climatic variability along the northern margin. We quantified climate dynamics, trends in plant growth, and growth–climate relationships across the tundra shrublands and Cajander larch (Larix cajanderi Mayr.) woodlands of the Kolyma river basin (657 000 km2) in northeastern Siberia using satellite‐derived normalized difference vegetation indices (NDVI), tree ring‐width measurements, and climate data. Mean summer temperatures (Ts) increased 1.0 °C from 1938 to 2009, though there was no trend (P > 0.05) in growing year precipitation or climate moisture index (CMIgy). Mean summer NDVI (NDVIs) increased significantly from 1982 to 2010 across 20% of the watershed, primarily in cold, shrub‐dominated areas. NDVIs positively correlated (P < 0.05) with Ts across 56% of the watershed (r = 0.52 ± 0.09, mean ± SD), principally in cold areas, and with CMIgy across 9% of the watershed (r = 0.45 ± 0.06), largely in warm areas. Larch ring‐width measurements from nine sites revealed that year‐to‐year (i.e., high‐frequency) variation in growth positively correlated (P < 0.05) with June temperature (r = 0.40) and prior summer CMI (r = 0.40) from 1938 to 2007. An unexplained multi‐decadal (i.e., low‐frequency) decline in annual basal area increment (BAI) occurred following the mid‐20th century, but over the NDVI record there was no trend in mean BAI (P > 0.05), which significantly correlated with NDVIs (r = 0.44, P < 0.05, 1982–2007). Both satellite and tree‐ring analyses indicated that plant growth was constrained by both low temperatures and limited moisture availability and, furthermore, that warming enhanced growth. Impacts of future climatic change on forests near treeline in Arctic Russia will likely be influenced by shifts in both temperature and moisture, which implies that projections of future forest distribution and productivity in this area should take into account the interactions of energy and moisture limitations. 相似文献
136.
David W. Thieltges Per‐Arne Amundsen Ryan F. Hechinger Pieter T. J. Johnson Kevin D. Lafferty Kim N. Mouritsen Daniel L. Preston Karsten Reise C. Dieter Zander Robert Poulin 《Oikos》2013,122(10):1473-1482
While the recent inclusion of parasites into food‐web studies has highlighted the role of parasites as consumers, there is accumulating evidence that parasites can also serve as prey for predators. Here we investigated empirical patterns of predation on parasites and their relationships with parasite transmission in eight topological food webs representing marine and freshwater ecosystems. Within each food web, we examined links in the typical predator–prey sub web as well as the predator–parasite sub web, i.e. the quadrant of the food web indicating which predators eat parasites. Most predator– parasite links represented ‘concomitant predation’ (consumption and death of a parasite along with the prey/host; 58–72%), followed by ‘trophic transmission’ (predator feeds on infected prey and becomes infected; 8–32%) and predation on free‐living parasite life‐cycle stages (4–30%). Parasite life‐cycle stages had, on average, between 4.2 and 14.2 predators. Among the food webs, as predator richness increased, the number of links exploited by trophically transmitted parasites increased at about the same rate as did the number of links where these stages serve as prey. On the whole, our analyses suggest that predation on parasites has important consequences for both predators and parasites, and food web structure. Because our analysis is solely based on topological webs, determining the strength of these interactions is a promising avenue for future research. 相似文献
137.
Veltman IM Veltman JA Arkesteijn G Janssen IM Vissers LE de Jong PJ van Kessel AG Schoenmakers EF 《BioTechniques》2003,35(5):1066-1070
Despite the recent completion of the human genome project, the mapping of disease-related chromosomal translocation breakpoints and genes has remained laborious. Here, we describe a novel and rapid procedure to map such translocation breakpoints using flow-sorted chromosomes in combination with array-based comparative genomic hybridization (arrayCGH). To test the feasibility of this approach, we used a t(12;15)(q13;q25)-positive cell line with known breakpoint positions as a model. The derivative 12 chromosomes were flow-sorted, labeled, and hybridized to a genome-wide array containing 3648 well-characterized human genomic clones. The exact locations of the breakpoints on both chromosome 12 and 15 could be determined in a single hybridization experiment. In addition, we have tested the minimal amount of material necessary to perform these experiments and show that it is possible to obtain highly reliable profiles using as little as 10,000 flow-sorted chromosomes. 相似文献
138.
Synergistic Actions of Nisin, Sublethal Ultrahigh Pressure, and Reduced Temperature on Bacteria and Yeast 总被引:5,自引:3,他引:5 下载免费PDF全文
Nisin in combination with ultrahigh-pressure treatment (UHP) showed strong synergistic effects against Lactobacillus plantarum and Escherichia coli at reduced temperatures (<15°C). The strongest inactivation effects were observed when nisin was present during pressure treatment and in the recovery medium. Elimination (>6-log reductions) of L. plantarum was achieved at 10°C with synergistic combinations of 0.5 μg of nisin per ml at 150 MPa and 0.1 μg of nisin per ml at 200 MPa for 10 min. Additive effects of nisin and UHP accounted for only 1.2- and 3.7-log reductions, respectively. Elimination was also achieved for E. coli at 10°C with nisin present at 2 μg/ml, and 10 min of pressure at 200 MPa, whereas the additive effect accounted for only 2.6-log reductions. Slight effects were observed even against the yeast Saccharomyces cerevisiae with nisin present at 5 μg/ml and with 200 MPa of pressure. Combining nisin, UHP, and lowered temperature may allow considerable reduction in time and/or pressure of UHP treatments. Kill can be complete without the frequently encountered survival tails in UHP processing. The slightly enhanced synergistic kill with UHP at reduced temperatures was also observed for other antimicrobials, the synthetic peptides MB21 and histatin 5. The postulated mode of action was that the reduced temperature and the binding of peptides to the membrane increased the efficacy of UHP treatment. The increases in fatty acid saturation or diphosphatidylglycerol content and the lysylphosphatidyl content of the cytoplasm membrane of L. plantarum were correlated with increased susceptibility to UHP and nisin, respectively. 相似文献
139.
140.
Willize E. van der Starre Cees van Nieuwkoop Uginia Thomson Marleen S. M. Zijderveld-Voshart Jan Pieter R. Koopman Tanny J. K. van der Reijden Jaap T. van Dissel Esther van de Vosse 《PloS one》2015,10(3)