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91.
Azadeh?BadieeEmail author Hans?Geir?Eiken Vidar?M?Steen Roger?L?vlie 《BMC biotechnology》2003,3(1):23
Background
Several different cDNA labeling methods have been developed for microarray based gene expression analysis. We have examined the accuracy and reproducibility of such five commercially available methods in detection of predetermined ratio values from target spike mRNAs (A. thaliana) in a background of total RNA. The five different labeling methods were: direct labeling (CyScribe), indirect labeling (FairPlay? – aminoallyl), two protocols with dendrimer technology (3DNA® Array 50? and 3DNA® submicro?), and hapten-antibody enzymatic labeling (Micromax? TSA?). Ten spike controls were mixed to give expected Cy5/Cy3 ratios in the range 0.125 to 6.0. The amounts of total RNA used in the labeling reactions ranged from 5 – 50 μg.Results
The 3DNA array 50 and CyScribe labeling methods performed best with respect to relative deviation from the expected values (16% and 17% respectively). These two methods also displayed the best overall accuracy and reproducibility. The FairPlay method had the lowest total experimental variation (22%), but the estimated values were consistently higher than the expected values (36%). TSA had both the largest experimental variation and the largest deviation from the expected values (45% and 48% respectively).Conclusion
We demonstrate the usefulness of spike controls in validation and comparison of cDNA labeling methods for microarray experiments.92.
93.
Overeem S Kok SW Lammers GJ Vein AA Frölich M Meinders AE Roelfsema F Pijl H 《American journal of physiology. Endocrinology and metabolism》2003,284(3):E641-E647
Narcolepsy is a sleep disorder caused by impaired hypocretin (orexin) neurotransmission. Growth hormone (GH) secretion may be altered in narcolepsy for various reasons. Slow-wave sleep episodes, which are closely associated with GH-secretory events, are more randomly dispersed over 24 h in narcoleptics. Furthermore, hypocretins may inhibit pituitary GH release. We assessed the function of the somatotropic axis in narcolepsy by deconvolving 24-h (10-min sampling interval) plasma GH concentration profiles in seven hypocretin-deficient narcoleptic patients and in seven healthy controls matched for age, sex, and body weight. Both basal and pulsatile GH secretion rate and secretagogue-induced GH release were similar in patients and controls. However, narcoleptics secreted approximately 50% of their total production during the daytime, whereas controls secreted only 25% during the day. Also, the GH output pattern of narcoleptics was significantly less regular. We propose that hypocretin deficiency disrupts the circadian distribution of hypothalamic GH-releasing hormone release in narcoleptic patients to simultaneously cause daytime GH release and promote their propensity to fall asleep during the day. 相似文献
94.
The heterofermentative lactic acid bacterium Oenococcus oeni requires pantothenic acid for growth. In the presence of sufficient pantothenic acid, glucose was converted by heterolactic fermentation stoichiometrically to lactate, ethanol and CO2. Under pantothenic acid limitation, substantial amounts of erythritol, acetate and glycerol were produced by growing and resting bacteria. Production of erythritol and glycerol was required to compensate for the decreasing ethanol production and to enable the synthesis of acetate. In ribose fermentation, there were no shifts in the fermentation pattern in response to pantothenate supply. In the presence of pantothenate, growing O. oeni contained at least 10.2 microM HSCoA, whereas the HSCoA content was tenfold lower after growth in pantothenate-depleted media. HSCoA and acetyl-CoA are cosubstrates of phosphotransacetylase and acetaldehyde dehydrogenase from the ethanol pathway. Both enzymes were found with activities commensurate with their function in ethanol production during heterolactic fermentation. From the kinetic data of the enzymes and the HSCoA and acetyl-CoA contents, it can be calculated that, under pantothenate limitation, phosphotransacetylase, and in particular acetaldehyde dehydrogenase activities become limiting due to low levels of the cosubstrates. Thus HSCoA deficiency represents the major limiting factor in heterolactic fermentation of glucose under pantothenate deficiency and the reason for the shift to erythritol, acetate, and glycerol fermentation. 相似文献
95.
Christensen Steen; Tokuoka Yoko; Silverthorne Jane; Wada Masamitsu 《Plant & cell physiology》1998,39(6):647-654
Light regulates development in the fern Adiantum capillus-venerisduring both the haploid gametophyte and diploid sporophyte phases.In this study, we have investigated the role of the photoreceptorphytochrome in haploid spore germination and regulation of expressionof mRNA encoding the major light-harvesting polypeptides ofphotosystem II {Lhcb mRNAs). Both of these responses appearto be induced by phytochrome and inhibited by blue light, acting.throughseparate photoreceptor(s). Characteristics of phytochrome actionwere similar for both responses, showing no induction in thevery low fluence range and an escape from far-redreversal for 50% of the response by 6 h. Overall, these resultsshow that phytochrome regulates both a morphological and a molecularprocess in haploid fern spores, and that these processes mayshare a common signal transduction pathway. (Received February 4, 1998; Accepted April 8, 1998) 相似文献
96.
Analysis of mannose selection used for transformation of sugar beet 总被引:39,自引:0,他引:39
Joersbo Morten Donaldson Iain Kreiberg Jette Petersen Steen Guldager Brunstedt Janne Okkels Finn T. 《Molecular breeding : new strategies in plant improvement》1998,4(2):111-117
Various factors affecting mannose selection for the production of transgenic plants were studied using Agrobacterium tumefaciens-mediated transformation of sugar beet (Beta vulgaris L.) cotyledonary explants. The selection system is based on the Escherichia coli phosphomannose isomerase (PMI) gene as selectable gene and mannose as selective agent. Transformation frequencies were about 10-fold higher than for kanamycin selection but were only obtained at low selection pressures (1.0–1.5 g/l mannose) where 20–30% of the explants produced shoots. The non-transgenic shoots were eliminated during the selection procedure by a stepwise increase in the mannose concentration up to 10 g/l. Analysis of the transformed shoots showed that the PMI activity varied from 2.4 mU/mg to 350 mU/mg but the expression level was independent of the selection pressure. Complete resistance to mannose of transformed shoots was observed already at low PMI activities (7.5 mU/mg). Genomic DNA blot analysis confirmed the presence of the PMI gene in all transformants analysed. The possible mode of action of mannose selection compared to other selection methods is discussed. 相似文献
97.
H?kon Dahle Ingeborg ?kland Ingunn H Thorseth Rolf B Pederesen Ida H Steen 《The ISME journal》2015,9(7):1593-1606
Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki''s Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition. 相似文献
98.
Silvia Pineda Francisco X. Real Manolis Kogevinas Alfredo Carrato Stephen J. Chanock Núria Malats Kristel Van Steen 《PLoS genetics》2015,11(12)
Omics data integration is becoming necessary to investigate the genomic mechanisms involved in complex diseases. During the integration process, many challenges arise such as data heterogeneity, the smaller number of individuals in comparison to the number of parameters, multicollinearity, and interpretation and validation of results due to their complexity and lack of knowledge about biological processes. To overcome some of these issues, innovative statistical approaches are being developed. In this work, we propose a permutation-based method to concomitantly assess significance and correct by multiple testing with the MaxT algorithm. This was applied with penalized regression methods (LASSO and ENET) when exploring relationships between common genetic variants, DNA methylation and gene expression measured in bladder tumor samples. The overall analysis flow consisted of three steps: (1) SNPs/CpGs were selected per each gene probe within 1Mb window upstream and downstream the gene; (2) LASSO and ENET were applied to assess the association between each expression probe and the selected SNPs/CpGs in three multivariable models (SNP, CPG, and Global models, the latter integrating SNPs and CPGs); and (3) the significance of each model was assessed using the permutation-based MaxT method. We identified 48 genes whose expression levels were significantly associated with both SNPs and CPGs. Importantly, 36 (75%) of them were replicated in an independent data set (TCGA) and the performance of the proposed method was checked with a simulation study. We further support our results with a biological interpretation based on an enrichment analysis. The approach we propose allows reducing computational time and is flexible and easy to implement when analyzing several types of omics data. Our results highlight the importance of integrating omics data by applying appropriate statistical strategies to discover new insights into the complex genetic mechanisms involved in disease conditions. 相似文献
99.
Matthijs van der Steen Tjalling Leenstra Jan A. J. W. Kluytmans Akke K. van der Bij ISIS-AR study group 《PloS one》2015,10(9)
We investigated time trends in extended-spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates from different patient settings in The Netherlands from 2008–2012. E. coli and K. pneumoniae isolates from blood and urine samples of patients > = 18 years were selected from the Dutch Infectious Disease Surveillance System-Antimicrobial Resistance (ISIS-AR) database. We used multivariable Poisson regression to study the rate per year of blood stream infections by susceptible and resistant isolates, and generalized estimating equation (GEE) log-binomial regression for trends in the proportion of extended-spectrum cephalosporin-resistant isolates. Susceptibility data of 197,513 E. coli and 38,244 K. pneumoniae isolates were included. The proportion of extended-spectrum cephalosporin-resistant E. coli and K. pneumoniae isolates from urine and blood samples increased in all patient settings, except for K. pneumoniae isolates from patients admitted to intensive care units. For K. pneumoniae, there was a different time trend between various patient groups (p<0.01), with a significantly higher increase in extended-spectrum cephalosporin-resistant isolates from patients attending a general practitioner than in isolates from hospitalized patients. For E. coli, the increasing time trends did not differ among different patient groups. This nationwide study shows a general increase in extended-spectrum cephalosporin-resistant E. coli and K. pneumoniae isolates. However, differences in trends between E. coli en K. pneumoniae underline the importance of E. coli as a community-pathogen and its subsequent influence on hospital resistance level, while for K. pneumoniae the level of resistance within the hospital seems less influenced by the resistance trends in the community. 相似文献
100.
The stress hormone corticosterone in a marine top predator reflects short‐term changes in food availability
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Robert T. Barrett Kjell E. Erikstad Hanno Sandvik Mari Myksvoll Susi Jenni‐Eiermann Ditte L. Kristensen Truls Moum Tone K. Reiertsen Frode Vikebø 《Ecology and evolution》2015,5(6):1306-1317
In many seabird studies, single annual proxies of prey abundance have been used to explain variability in breeding performance, but much more important is probably the timing of prey availability relative to the breeding season when energy demand is at a maximum. Until now, intraseasonal variation in prey availability has been difficult to quantify in seabirds. Using a state‐of‐the‐art ocean drift model of larval cod Gadus morhua, an important constituent of the diet of common guillemots Uria aalge in the southwestern Barents Sea, we were able to show clear, short‐term correlations between food availability and measurements of the stress hormone corticosterone (CORT) in parental guillemots over a 3‐year period (2009–2011). The model allowed the extraction of abundance and size of cod larvae with very high spatial (4 km) and temporal resolutions (1 day) and showed that cod larvae from adjacent northern spawning grounds in Norway were always available near the guillemot breeding colony while those from more distant southerly spawning grounds were less frequent, but larger. The latter arrived in waves whose magnitude and timing, and thus overlap with the guillemot breeding season, varied between years. CORT levels in adult guillemots were lower in birds caught after a week with high frequencies of southern cod larvae. This pattern was restricted to the two years (2009 and 2010) in which southern larvae arrived before the end of the guillemot breeding season. Any such pattern was masked in 2011 by already exceptionally high numbers of cod larvae in the region throughout chick‐rearing period. The findings suggest that CORT levels in breeding birds increase when the arrival of southern sizable larvae does not match the period of peak energy requirements during breeding. 相似文献