"Die dreiteilige Grundkonzeption der Reihe (Darstellung - Grundprobleme und Tendenzen der Forschung - Quellen und Literatur) muss hier nicht diskutiert werden. Das Konzept ist so bestechend und ...praktikabel, dass sich die Oldenbourg-Reihe seit Langem mühelos gegen andere Studienbuchreihen behauptet, die es mittlerweile bekanntlich in großer Zahl gibt. Neben der konzeptionellen Grundstruktur hat zu dieser Führungsposition der Reihe auch die Tatsache beigetragen, dass es gelungen ist, als Bandautoren durchweg ausgewiesene Fachleute zu gewinnen, denen es eben möglich ist, im Rahmen der engen Umfangsvorgaben eine konzise Gesamtdarstellung und eine auf die wesentlichen Probleme konzentrierte Sichtung der Forschungsdiskussion zu bieten." Enno Bün, in: sehepunkte Ausführliche Informationen unter www.geschichte-lehrbuch.de
Ischemia/reperfusion injury is a major cause of acute kidney injury (AKI). AKI is characterized by a sudden decrease in kidney function, systemic inflammation, oxidative stress, and dysregulation of ...the sodium, potassium, and water channels. While AKI leads to uremic encephalopathy, epidemiological studies have shown that AKI is associated with a subsequent risk for developing stroke and dementia. To get more insights into kidney-brain crosstalk, we have created an in vitro co-culture model based on human kidney cells of the proximal tubule (HK-2) and brain microvascular endothelial cells (BMEC). The HK-2 cell line was grown to confluence on 6-well plates and exposed to oxygen/glucose deprivation (OGD) for 4 h. Control HK-2 cells were grown under normal conditions. The BMEC cell line cerebED was grown to confluence on transwells with 0.4 μm pores. The transwell filters seeded and grown to confluence with cereEND were inserted into the plates with HK-2 cells with or without OGD treatment. In addition, cerebEND were left untreated or treated with uremic toxins, indole-3-acetic acid (IAA) and indoxyl sulfate (IS). The protein and mRNA expression of selected BBB-typical influx transporters, efflux transporters, cellular receptors, and tight junction proteins was measured in BMECs. To validate this in vitro model of kidney-brain interaction, we isolated brain capillaries from mice exposed to bilateral renal ischemia (30 min)/reperfusion injury (24 h) and measured mRNA and protein expression as described above. Both in vitro and in vivo systems showed similar changes in the expression of drug transporters, cellular receptors, and tight junction proteins. Efflux pumps, in particular Abcb1b, Abcc1, and Abcg2, have shown increased expression in our model. Thus, our in vitro co-culture system can be used to study the cellular mechanism of kidney and brain crosstalk in renal ischemia/reperfusion injury.
Timing common and specific modulators of disease progression is crucial for treatment, but the understanding of the underlying complex system of interactions is limited. While attempts at elucidating ...this experimentally have produced enormous amounts of phenotypic data, tools that are able to visualize and analyze them are scarce and the insight obtained from the data is often unsatisfactory. Linking and visualizing processes from genes to phenotypes and back, in a temporal context, remains a challenge in systems biology. We introduce PhenoTimer, a 2D/3D visualization tool for the mapping of time-resolved phenotypic links in a genetic context. It uses a novel visualization approach for relations between morphological defects, pathways or diseases, to enable fast pattern discovery and hypothesis generation. We illustrate its capabilities of tracing dynamic motifs on cell cycle datasets that explore the phenotypic order of events upon perturbations of the system, transcriptional activity programs and their connection to disease. By using this tool we are able to fine-grain regulatory programs for individual time points of the cell cycle and better understand which patterns arise when these programs fail. We also illustrate a way to identify common mechanisms of misregulation in diseases and drug abuse.
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Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular biology. To fully understand this connection, it is necessary to consider the underlying networks and ...the time factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link discovery between processes. It uses a layered display to separate different levels of information while emphasizing the connections between them. We present novel developments of the tool for the visualization and analysis of dynamic genotype-phenotype landscapes.
Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells. Dynamic cluster analysis suggests alternative indirect links between Nanog and other proteins in the core stem cell network. Moreover, recurrent correlations from the epigenetic to the translational level are identified. Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. Here, a potential new role for the gene lsm14a in cytokinesis is suggested. We also show how phenotypic patterning allows for extensive comparison and identification of high impact knockdown targets.
We present a new visualization approach for perturbation screens with multiple phenotypic outcomes. The novel functionality implemented in Arena3D enables effective understanding and comparison of temporal patterns within morphological layers, to help with the system-wide analysis of dynamic processes. Arena3D is available free of charge for academics as a downloadable standalone application from: http://arena3d.org/.
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Acute kidney injury (AKI) is a postoperative complication after cardiac surgery with a high impact on mortality and morbidity. Nephrocheck® TIMP-2*IGFBP7 determines markers of tubular stress, which ...occurs prior to tubular damage. It is unknown at which time-point TIMP-2*IGFBP7 measurement should be performed to ideally predict AKI. We investigated the association of TIMP-2*IGFBP7 at various time-points with the incidence of AKI in patients undergoing elective cardiac surgery including cardio-pulmonary bypass.
In a prospective cohort study, serial blood and urine samples were collected from 150 patients: pre-operative, at ICU-admission, 24h and 48h post-surgery. AKI was defined as Serum-Creatinine rise >0.3 mg/dl within 48hrs. Urinary TIMP-2*IGFBP7 was measured at pre-operative, ICU-admission and 24h post-surgery; medical staff was kept blinded to these results.
A total of 35 patients (23.5%) experienced AKI, with a higher incidence in those with high TIMP-2*IGFBP7 values at ICU admission (57.1% vs. 10.1%, p<0.001). In logistic regression TIMP-2*IGFBP7 at ICU admission was independently associated with the occurrence of AKI (Odds Ratio 11.83; p<0.001, C-statistic= 0.74) after adjustment for EuroSCORE II and CBP-time.
Early detection of elevated TIMP-2*IGFBP7 at ICU admission was strongly predictive for postoperative AKI and appeared to be more precise as compared to subsequent measurements.
The hexagonal ferrite h-YbFeO3 grown on YSZ(111) by pulsed laser deposition is foreseen as a promising single multiferroic candidate where ferroelectricity and antiferromagnetism coexist for future ...applications at low temperatures. We studied in detail the microstructure as well as the temperature dependence of the magnetic properties of the devices by comparing the heterostructures grown directly on YSZ(111) (i.e., YbPt_Th0nm) with h-YbFeO3 films deposited on substrates buffered with platinum Pt/YSZ(111) and in dependence on the Pt underlayer film thickness (i.e., YbPt_Th10nm, YbPt_Th40nm, YbPt_Th55nm, and YbPt_Th70nm). The goal was to deeply understand the importance of the crystal quality and morphology of the Pt underlayer for the h-YbFeO3 layer crystal quality, surface morphology, and the resulting physical properties. We demonstrate the relevance of homogeneity, continuity, and hillock formation of the Pt layer for the h-YbFeO3 microstructure in terms of crystal structure, mosaicity, grain boundaries, and defect distribution. The findings of transmission electron microscopy and X-ray diffraction reciprocal space mapping characterization enable us to conclude that an optimum film thickness for the Pt bottom electrode is ThPt = 70 nm, which improves the crystal quality of h-YbFeO3 films grown on Pt-buffered YSZ(111) in comparison with h-YbFeO3 films grown on YSZ(111) (i.e., YbPt_Th0nm). The latter shows a disturbance in the crystal structure, in the up-and-down atomic arrangement of the ferroelectric domains, as well as in the Yb–Fe exchange interactions. Therefore, an enhancement in the remanent and in the total magnetization was obtained at low temperatures below 50 K for h-YbFeO3 films deposited on Pt-buffered substrates Pt/YSZ(111) when the Pt underlayer reached ThPt = 70 nm.
The morphology and crystal structure of Pt films grown by pulsed laser deposition (PLD) on yttria-stabilized zirconia (YSZ)at high temperatures
= 900 °C was studied for four different film ...thicknesses varying between 10 and 70 nm. During the subsequent growth of the capping layer, the thermal stability of the Pt was strongly influenced by the Pt film's thickness. Furthermore, these later affected the film morphology, the crystal structure and hillocks size, and distribution during subsequent growth at
= 900 °C for a long duration. The modifications in the morphology as well as in the structure of the Pt film without a capping layer, named also as the as-grown and encapsulated layers in the bilayer system, were examined by a combination of microscopic and scattering methods. The increase in the thickness of the deposited Pt film brought three competitive phenomena into occurrence, such as 3D-2D morphological transition, dewetting, and hillock formation. The degree of coverage, film continuity, and the crystal quality of the Pt film were significantly improved by increasing the deposition time. An optimum Pt film thickness of 70 nm was found to be suitable for obtaining a hillock-free Pt bottom electrode which also withstood the dewetting phenomena revealed during the subsequent growth of capping layers. This achievement is crucial for the deposition of functional bottom electrodes in ferroelectric and multiferroic heterostructure systems.
Background: Recently, we gained evidence that impairment of rOat1 and rOat3 expression induced by ischemic acute kidney injury (AKI) is mediated by COX metabolites and this suppression might be ...critically involved in renal damage. Methods: (i) Basolateral organic anion uptake into proximal tubular cells after model ischemia and reperfusion (I/R) was investigated by fluorescein uptake. The putative promoter sequences from hOAT1 (SLC22A6) and hOAT3 (SCL22A8) were cloned into a reporter plasmid, transfected into HEK cells and (ii) transcriptional activity was determined after model ischemia and reperfusion as a SEAP reporter gen assay. Inhibitors or antagonists were applied with the beginning of reperfusion. Results: By using inhibitors of PKA (H89) and PLC (U73122), antagonists of E prostanoid receptor type 2 (AH6809) and type 4 (L161,982), we gained evidence that I/R induced down regulation of organic anion transport is mediated by COX1 metabolites via E prostanoid receptor type 4. The latter signaling was confirmed by application of butaprost (EP2 agonist) or TCS2510 (EP4 agonist) to control cells. In brief, the latter signaling was verified for the transcriptional activity in the reporter gen assay established. Therein, selective inhibitors for COX1 (SC58125) and COX2 (SC560) were also applied. Conclusion: Our data show (a) that COX1 metabolites are involved in the regulation of renal organic anion transport(ers) after I/R via the EP4 receptor and (b) that this is due to transcriptional regulation of the respective transporters. As the promoter sequences cloned were of human origin and expressed in a human renal epithelial cell line we (c) hypothesize that the regulatory mechanisms described after I/R is meaningful for humans as well.
Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different ...data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies-data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI); which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations (EFPIA) and the European Commission (EC).
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