Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development ...and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development.
To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data--variations caused by differential probe affinity--was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/pcfs4 and pcfs4/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation.
We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in pcfs4 mutant plants. The enriched GO term "regulation of flower development" among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Capillary evaporation in pores Roth, R; Kroll, K M
Journal of physics. Condensed matter,
07/2006, Letnik:
18, Številka:
28
Journal Article
Recenzirano
We combine a density functional theory (DFT) treatment of capillary evaporation in a cylindrical pore with the morphometric approach in order to study the formation and breaking of bubbles in a ...hydrophobically lined part of a cone. The morphometric approach, in which the grand potential of a system is described in four geometrical terms with corresponding thermodynamical coefficients, allows extrapolation or scaling from macroscopic system sizes to nanoscales. Since only a small number of fluid particles are involved in bubble formation, it is a pseudo phase transition, and the system is subjected to fluctuations between states with and without a bubble. Fluctuations are not included in a DFT treatment, which makes it possible to explore both states of the system in great detail, in contrast to computer simulations, in which averages might be obscured by fluctuations.
In this paper, quasi-isotropic basalt fiber reinforced polyamide PA6 was joined to aluminum sheets using three different joining technologies. The joints were manufactured by means of nut and bolt ...(NAB) as well as two-piece hollow riveting (TPHR) as current state of the art processes. Furthermore, additional joints were established by the new inductive contact joining (ICJ) technology. The obtained specimens were compared by means of tensile shear tests and by analysis of the fractured surfaces. It was found that the joints produced by ICJ are superior in comparison to joints manufactured by TPHR with regard to joint strength. In addition, during ICJ, the fibers of the polymer material are not damaged and the strength of the base material is maintained. Further optimization potential of the ICJ process was discovered during the investigations, so that potentially higher joint strengths as well as shorter process times can be expected, making the process interesting for future industrial applications.
Cirrhotic cardiomyopathy historically has been confused as alcoholic cardiomyopathy. The key points for diagnosis of cirrhotic cardiomyopathy have been well explained, however this entity was ...neglected for a long time. Nowadays the diagnosis of this entity has become important because it is a factor that contributes significantly to morbidity-mortality in cirrhotic patients. Characteristics of cirrhotic cardiomyopathy are a hyperdynamic circulatory state, altered diastolic relaxation, impaired contractility, and electrophysiological abnormalities, particularity QT interval prolongation. The pathogenesis includes impaired function of beta-receptors, altered transmembrane currents and overproduction of cardiodepressant factors, such as nitric oxide, cytokines and endogenous cannabinoids. In addition to physical signs of hyperdynamic state and heart failure under stress conditions, the diagnosis can be done with dosage of serum markers, electrocardiography, echocardiography and magnetic resonance. The treatment is mainly supportive, but orthotopic liver transplantation appears to improve this condition although the prognosis of liver transplantation in patients with cirrhotic cardiomyopathy is uncertain.
Background: Thrombin induces the activation of the platelet serine/threonine kinase Akt. Akt activation is dependent on its phosphorylation at Thr308 and Ser473. The mechanism by which thrombin ...induces Akt phosphorylation is controversial, as is the role of Akt in platelet function. Objectives: To investigate how protease‐activated receptors (PARs) stimulate Akt and the role that Akt plays in human platelet function. Methods: Platelets were stimulated through PAR1 or PAR4. Specific inhibitors were used to evaluate, by Western blotting, signaling pathways regulating Akt phosphorylation, and the role of activated Akt was evaluated by aggregometry and flow cytometry. Results: Phospholipase C (PLC) controls Akt phosphorylation elicited by PARs. Stimulation of PAR1 or PAR4 resulted in rapid Akt phosphorylation, independently of secreted ADP and phosphatidylinositol‐3‐kinase (PI3K) activation. Akt phosphorylation ∼60 s after PAR1 stimulation became entirely dependent on the purinergic receptor P2Y12 and the activation of PI3K. In contrast, PAR4 partially sustained Akt phosphorylation independently of P2Y12 and PI3K for up to 300 s. Pharmacologic inhibition of Akt reduced P‐selectin expression and fibrinogen binding in platelets stimulated through PAR1, and delayed platelet aggregation in response to submaximal PAR1 or PAR4 stimulation, although aggregation at 300 s was unaffected. Conclusions: Platelet PAR stimulation causes rapid Akt phosphorylation downstream of PLC, whereas with continuous stimulation, ADP and PI3K are required for maintaining Akt phosphorylation. Activated Akt regulates platelet function by modulating secretion and αIIbβ3 activation.
Pyrolysis oil from the slow pyrolysis of German brown coal from Schöningen, obtained at a temperature of 500°C, was separated and analyzed using hyphenation of gas chromatography with an atmospheric ...pressure chemical ionization source operated in negative ion mode and Fourier transform ion cyclotron resonance mass spectrometry (GC-APCI-FT-ICR-MS). Development of this ultrahigh-resolving analysis method is described, that is, optimization of specific GC and APCI parameters and performed data processing. The advantages of GC-APCI-FT-ICR-MS hyphenation, for example, soft ionization, ultrahigh-resolving detection, and most important isomer separation, were demonstrated for the sample liquid. For instance, it was possible to separate and identify nine different propylphenol, ethylmethylphenol, and trimethylphenol isomers. Furthermore, homologous series of different acids, for example, alkyl and alkylene carboxylic acids, were verified, as well as homologous series of alkyl phenols, alkyl dihydroxy benzenes, and alkoxy alkyl phenols.
Since recent studies demonstrate that vascular smooth muscle cells synthesize two distinct guanylate cyclase-stimulatory gases, NO and CO, we examined possible regulatory interactions between these ...two signaling molecules. Treatment of rat aortic smooth muscle cells with the NO donors, sodium nitroprusside, S-nitroso-N-acetyl-penicillamine, or 3-morpholinosydnonimine, increased heme oxygenase-1 (HO-1) mRNA and protein levels in a concentration- and time-dependent manner. Both actinomycin D and cycloheximide blocked NO-stimulated HO-1 mRNA and protein expression. Nuclear run-on experiments demonstrated that NO donors increased HO-1 gene transcription between 3- and 6-fold. In contrast, NO donors had no effect on the stability of HO-1 mRNA. Incubation of vascular smooth muscle cells with the membrane-permeable cGMP analogues, dibutyryl cGMP and 8-bromo-cGMP, failed to induce HO-1 gene expression. Treatment of vascular smooth muscle cells with NO donors also stimulated the production and release of CO, as demonstrated by the CO-dependent increase in intracellular cGMP levels in coincubated platelets. Finally, incubating vascular smooth muscle cells with interleukin-1 beta and tumor necrosis factor-alpha induced NO synthesis and also significantly increased the level of HO-1 protein. The cytokine-stimulated production of both NO and HO-1 protein in smooth muscle cells was blocked by the NO synthase inhibitor methyl-L-arginine. These results demonstrate that exogenously administered or endogenously released NO stimulates HO-1 gene expression and CO production in vascular smooth muscle cells. The ability of NO to induce HO-catalyzed CO release from vascular smooth muscle cells provides a novel mechanism by which NO might modulate soluble guanylate cyclase and, thereby, vascular smooth muscle cell and platelet function. (Circ Res. 1997;80:557-564.)
The combination of a stereoscopic setup for particle tracking velocimetry of small dust clouds combined with holographic techniques gives several benefits over using either method separately. ...However, technical limitations and achievable data quality require sophisticated reconstruction algorithms to gain complete and reliable particle trajectories.
It is well documented that neuroanatomical differences exist between adults who stutter and their fluently speaking peers. Specifically, adults who stutter have been found to have more grey matter ...volume (GMV) in speech relevant regions including inferior frontal gyrus, insula and superior temporal gyrus (Beal et al., 2007; Song et al., 2007). Despite stuttering having its onset in childhood only one study has investigated the neuroanatomical differences between children who do and do not stutter. Chang et al. (2008) reported children who stutter had less GMV in the bilateral inferior frontal gyri and middle temporal gyrus relative to fluently speaking children. Thus it appears that children who stutter present with unique neuroanatomical abnormalities as compared to those of adults who stutter. In order to better understand the neuroanatomical correlates of stuttering earlier in its development, near the time of onset, we used voxel-based morphometry to examine volumetric differences between 11 children who stutter and 11 fluent children. Children who stutter had less GMV in the bilateral inferior frontal gyri and left putamen but more GMV in right Rolandic operculum and superior temporal gyrus relative to fluent children. Children who stutter also had less white matter volume bilaterally in the forceps minor of the corpus callosum. We discuss our findings of widespread anatomic abnormalities throughout the cortical network for speech motor control within the context of the speech motor skill limitations identified in people who stutter (Namasivayam and van Lieshout, 2008; Smits-Bandstra et al., 2006).
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