In Vitro Ceramic Scaffold Mineralization: Comparison Between Histological and Micro-Computed Tomographical Analysis

The porous structure of beta-tricalcium phosphate (β-TCP) scaffolds was assessed by conventional histomorphometry and micro-computed tomography (micro-CT) to evaluate the substitutability of time-consuming histomorphometry by rapid micro-CT. Extracellular matrix mineralization on human mesenchymal stem cell seeded β-TCP scaffolds was scanned by means of micro-CT after 6weeks in cultivation and evaluated morphometrically. For the histomorphometric analysis, undecalcified sections were prepared in the mediosagittal plane of the cylindrical tissue-engineered constructs. The sections were scanned at a nominal resolution of 8μm and stained with von Kossa and Toluidine Blue. Pores were analyzed with both methods for morphometrical parameters such as horizontal/vertical diameter and pore/mineralized tissue area. Results showed highly significant correlations between histomorphometry and micro-CT for pore horizontal length (r=0.95), pore vertical length (r=0.96), pore area (r=0.97), and mineralized tissue area (r=0.82). Mean percentage differences between histomorphometry and micro-CT measurements ranged from 1.4% (pore vertical diameter) to 14.0% (area of mineralized tissue). With its high image precision, micro-CT qualifies as an additional tool for endpoint evaluation measurements of mineralized tissue development within tissue-engineered constructs also in ceramic scaffold

The Re-Establishment of Desiccation Tolerance in Germinated Arabidopsis thaliana Seeds and Its Associated Transcriptome

The combination of robust physiological models with “omics” studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. Here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (DT) in Arabidopsis thaliana seeds. We show that the incubation of desiccation sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution re-induces the mechanisms necessary for expression of DT. Based on a SNP-tile array gene expression profile, our data indicates that the re-establishment of DT, in this system, is related to a programmed reversion from a metabolic active to a quiescent state similar to prior to germination. Our findings show that transcripts of germinated seeds after the PEG-treatment are dominated by those encoding LEA, seed storage and dormancy related proteins. On the other hand, a massive repression of genes belonging to many other classes such as photosynthesis, cell wall modification and energy metabolism occurs in parallel. Furthermore, comparison with a similar system for Medicago truncatula reveals a significant overlap between the two transcriptomes. Such overlap may highlight core mechanisms and key regulators of the trait DT. Taking into account the availability of the many genetic and molecular resources for Arabidopsis, the described system may prove useful for unraveling DT in higher plants

PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs. PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis. PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at . CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms

Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity

Comparing Methods of Characterizing Energetic Disorder in Organic Solar Cells

The energetic disorder has been known for decades to limit the performance of structurally disordered semiconductors such as amorphous silicon and organic semiconductors. However, in the past years, high-performance organic solar cells have emerged showing a continuously reduced amount of energetic disorder. While searching for future high-efficiency material systems, it is therefore important to correctly characterize this energetic disorder. While there are several techniques in the literature, the most common approaches to probe the density of defect states are using optical excitation as in external quantum efficiency measurements, or sequential filling of the tail states by applying an external voltage as in admittance spectroscopy. A metanalysis of available literature, as well as the experiments using four characterization techniques on two material systems, reveal that electrical, voltage-dependent measurements frequently yield higher values of energetic disorder than optical measurements. With drift-diffusion simulations, it is demonstrated that the approaches probe different energy ranges of the subband-gap density of states. The limitations of the techniques are further explored and it is found that extraction of information from a capacitance-voltage curve can be inhibited by internal series resistance. Thereby, the discrepancies between measurement techniques with sensitivity to different energy ranges and electronic parameters are explained

In Vitro Ceramic Scaffold Mineralization: Comparison Between Histological and Micro-Computed Tomographical Analysis

ISSN:1573-9686ISSN:0191-5649ISSN:0090-696

The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula

Tellstroem V, Usadel B, Thimm O, Stitt M, Kuester H, Niehaus K. The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula. Plant Physiology. 2007;143(2):825-837.In the establishment of symbiosis between Medicago truncatula and the nitrogen-fixing bacterium Sinorhizobium meliloti, the lipopolysaccharide (LPS) of the microsymbiont plays an important role as a signal molecule. It has been shown in cell cultures that the LPS is able to suppress an elicitor-induced oxidative burst. To investigate the effect of S. meliloti LPS on defense-associated gene expression, a microarray experiment was performed. For evaluation of the M. truncatula microarray datasets, the software tool MapMan, which was initially developed for the visualization of Arabidopsis (Arabidopsis thaliana) datasets, was adapted by assigning Medicago genes to the ontology originally created for Arabidopsis. This allowed functional visualization of gene expression of M. truncatula suspension-cultured cells treated with invertase as an elicitor. A gene expression pattern characteristic of a defense response was observed. Concomitant treatment of M. truncatula suspension-cultured cells with invertase and S. meliloti LPS leads to a lower level of induction of defense-associated genes compared to induction rates in cells treated with invertase alone. This suppression of defense-associated transcriptional rearrangement affects genes induced as well as repressed by elicitation and acts on transcripts connected to virtually all kinds of cellular processes. This indicates that LPS of the symbiont not only suppresses fast defense responses as the oxidative burst, but also exerts long-term influences, including transcriptional adjustment to pathogen attack. These data indicate a role for LPS during infection of the plant by its symbiotic partner