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21.
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.22.
A case of intracellular systemic infection with the diplomonad flagellate Spironucleus barkhanus in farmed Arctic char Salvelinus alpinus is described. The parasites were widely disseminated throughout the vasculature and in most organs. Aggregates of the parasites were seen within well-defined structures regarded as host cells in capillaries and sinusoids of the liver, spleen and head kidney. Intracellular infection with Spironucleus spp. has never previously been reported. The prevalence of infection and mortality in the affected farm was low. In contrast to systemic spironucleosis in farmed Atlantic salmon, and despite huge numbers of flagellates in the vasculature, the tissues of the organs were remarkably unaffected. The relatively few gross and histopathological lesions may indicate that Arctic char are more tolerant to this parasite than Atlantic salmon. 相似文献
23.
Brinkhuis H Klinkenberg E Williams GL Fensome RA 《Review of Palaeobotany and Palynology》2000,110(1-2):93-110
Maastrichtian and Danian deposits from the Bunde Borehole in the Maastrichtian type area contain the morphologically unusual dinoflagellate species Spumadinium felderorum gen. et sp. nov. and Lasagniella herngreenii gen. et sp. nov., both of which have archeopyles formed by the loss of several paraplates. In S. felderorum the paraplates forming the operculum or opercular pieces appear to be the third and fourth precingulars (3"-4") plus the first and second anterior intercalaries (1a-2a). This suggests that Spumadinium, although having a wall resembling some cribroperidinioids, is a cladopyxiinean. L. herngreenii is unique in having up to eight wall layers, separated and supported by buttresses. The archeopyle is also a combination type but formed by loss of one apical (3'), three anterior intercalary (1a-3a) and three precingular (3"-5") paraplates. Thus, Lasagniella is assignable to the Peridiniales. The distinctive morphology and restricted ranges of the two genera make them useful stratigraphic markers for the Upper Maastrichtian-Danian. 相似文献
24.
Our ability to model spatial distributions of fish populations is reviewed by describing the available modelling tools. Ultimate models of the individual's motivation for behavioural decisions are derived from evolutionary ecology. Mechanistic models for how fish sense and may respond to their surroundings are presented for vision, olfaction, hearing, the lateral line and other sensory organs. Models for learning and memory are presented, based both upon evolutionary optimization premises and upon neurological information processing and decision making. Functional tools for modelling behaviour and life histories can be categorized as belonging to an optimization or an adaptation approach. Among optimization tools, optimal foraging theory, life history theory, ideal free distribution, game theory and stochastic dynamic programming are presented. Among adaptation tools, genetic algorithms and the combination with artificial neural networks are described. The review advocates the combination of evolutionary and neurological approaches to modelling spatial dynamics of fish. 相似文献
25.
Vito A. G. Ricigliano Adam E. Handel Geir K. Sandve Viviana Annibali Giovanni Ristori Rosella Mechelli M. Zameel Cader Marco Salvetti 《PloS one》2015,10(4)
Epstein-Barr virus (EBV) is a non-heritable factor that associates with multiple sclerosis (MS). However its causal relationship with the disease is still unclear. The virus establishes a complex co-existence with the host that includes regulatory influences on gene expression. Hence, if EBV contributes to the pathogenesis of MS it may do so by interacting with disease predisposing genes. To verify this hypothesis we evaluated EBV nuclear antigen 2 (EBNA2, a protein that recent works by our and other groups have implicated in disease development) binding inside MS associated genomic intervals. We found that EBNA2 binding occurs within MS susceptibility sites more than expected by chance (factor of observed vs expected overlap [O/E] = 5.392-fold, p < 2.0e-05). This remains significant after controlling for multiple genomic confounders. We then asked whether this observation is significant per se or should also be viewed in the context of other disease relevant gene-environment interactions, such as those attributable to vitamin D. We therefore verified the overlap between EBNA2 genomic occupancy and vitamin D receptor (VDR) binding sites. EBNA2 shows a striking overlap with VDR binding sites (O/E = 96.16-fold, p < 2.0e-05), even after controlling for the chromatin accessibility state of shared regions (p <0.001). Furthermore, MS susceptibility regions are preferentially targeted by both EBNA2 and VDR than by EBNA2 alone (enrichment difference = 1.722-fold, p = 0.0267). Taken together, these findings demonstrate that EBV participates in the gene-environment interactions that predispose to MS. 相似文献
26.
?ivind ?rstavik Ornella Manfra Kjetil Wessel Andressen Geir ?ystein Andersen Tor Skomedal Jan-Bj?rn Osnes Finn Olav Levy Kurt Allen Krobert 《PloS one》2015,10(3)
Aims
We recently published that the positive inotropic response (PIR) to levosimendan can be fully accounted for by phosphodiesterase (PDE) inhibition in both failing human heart and normal rat heart. To determine if the PIR of the active metabolite OR-1896, an important mediator of the long-term clinical effects of levosimendan, also results from PDE3 inhibition, we compared the effects of OR-1896, a representative Ca2+ sensitizer EMD57033 (EMD), levosimendan and other PDE inhibitors.Methods
Contractile force was measured in rat ventricular strips. PDE assay was conducted on rat ventricular homogenate. cAMP was measured using RII_epac FRET-based sensors.Results
OR-1896 evoked a maximum PIR of 33±10% above basal at 1 μM. This response was amplified in the presence of the PDE4 inhibitor rolipram (89±14%) and absent in the presence of the PDE3 inhibitors cilostamide (0.5±5.3%) or milrinone (3.2±4.4%). The PIR was accompanied by a lusitropic response, and both were reversed by muscarinic receptor stimulation with carbachol and absent in the presence of β-AR blockade with timolol. OR-1896 inhibited PDE activity and increased cAMP levels at concentrations giving PIRs. OR-1896 did not sensitize the concentration-response relationship to extracellular Ca2+. Levosimendan, OR-1896 and EMD all increased the sensitivity to β-AR stimulation. The combination of either EMD and levosimendan or EMD and OR-1896 further sensitized the response, indicating at least two different mechanisms responsible for the sensitization. Only EMD sensitized the α1-AR response.Conclusion
The observed PIR to OR-1896 in rat ventricular strips is mediated through PDE3 inhibition, enhancing cAMP-mediated effects. These results further reinforce our previous finding that Ca2+ sensitization does not play a significant role in the inotropic (and lusitropic) effect of levosimendan, nor of its main metabolite OR-1896. 相似文献27.
Ida Johansson Vivi Talstad Monsen Kristine Pettersen Jennifer Mildenberger Kristine Misund Kai Kaarniranta Svanhild Sch?nberg Geir Bj?rk?y 《Autophagy》2015,11(9):1636-1651
Accumulation and aggregation of misfolded proteins is a hallmark of several diseases collectively known as proteinopathies. Autophagy has a cytoprotective role in diseases associated with protein aggregates. Age-related macular degeneration (AMD) is the most common neurodegenerative eye disease that evokes blindness in elderly. AMD is characterized by degeneration of retinal pigment epithelial (RPE) cells and leads to loss of photoreceptor cells and central vision. The initial phase associates with accumulation of intracellular lipofuscin and extracellular deposits called drusen. Epidemiological studies have suggested an inverse correlation between dietary intake of marine n-3 polyunsaturated fatty acids (PUFAs) and the risk of developing neurodegenerative diseases, including AMD. However, the disease-preventive mechanism(s) mobilized by n-3 PUFAs is not completely understood. In human retinal pigment epithelial cells we find that physiologically relevant doses of the n-3 PUFA docosahexaenoic acid (DHA) induce a transient increase in cellular reactive oxygen species (ROS) levels that activates the oxidative stress response regulator NFE2L2/NRF2 (nuclear factor, erythroid derived 2, like 2). Simultaneously, there is a transient increase in intracellular protein aggregates containing SQSTM1/p62 (sequestosome 1) and an increase in autophagy. Pretreatment with DHA rescues the cells from cell cycle arrest induced by misfolded proteins or oxidative stress. Cells with a downregulated oxidative stress response, or autophagy, respond with reduced cell growth and survival after DHA supplementation. These results suggest that DHA both induces endogenous antioxidants and mobilizes selective autophagy of misfolded proteins. Both mechanisms could be relevant to reduce the risk of developing aggregate-associate diseases such as AMD. 相似文献
28.
Halfdan Rydbeck Geir Kjetil Sandve Egil Ferkingstad Boris Simovski Morten Rye Eivind Hovig 《PloS one》2015,10(4)
Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering is routinely applied to gene expression data, there is a lack of appropriate general methodology for clustering of sequence-level genomic and epigenomic data, e.g. ChIP-based data. We here introduce a general methodology for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. By defining appropriate feature extraction approaches and similarity measures, we allow biologically meaningful clustering to be performed for genomic tracks using standard clustering algorithms. An implementation of the methodology is provided through a tool, ClusTrack, which allows fine-tuned clustering analyses to be specified through a web-based interface. We apply our methods to the clustering of occupancy of the H3K4me1 histone modification in samples from a range of different cell types. The majority of samples form meaningful subclusters, confirming that the definitions of features and similarity capture biological, rather than technical, variation between the genomic tracks. Input data and results are available, and can be reproduced, through a Galaxy Pages document at http://hyperbrowser.uio.no/hb/u/hb-superuser/p/clustrack. The clustering functionality is available as a Galaxy tool, under the menu option "Specialized analyzis of tracks", and the submenu option "Cluster tracks based on genome level similarity", at the Genomic HyperBrowser server: http://hyperbrowser.uio.no/hb/. 相似文献
29.
30.
Henrik Sundh Bjørn Olav Kvamme Frode Fridell Rolf Erik Olsen Tim Ellis Geir Lasse Taranger Kristina Sundell 《BMC physiology》2010,10(1):22