Proteomic analysis of cardiac metabolic enzymes in asphyxiated newborn piglets

Hypoxia/reoxygenation (H/R) creates an energetic deficiency in the heart, which may contribute to myocardial dysfunction. We hypothesized that H/R-induced impairment of cardioenergetic enzymes occurs in asphyxiated newborn animals. After hypoxia for 2 h (10-15% oxygen), newborn piglets were resuscitated with 100% oxygen for 1 h, followed by 21% oxygen for 3 h. Sham-operated control piglets had no H/R. Hemodynamic parameters in the piglets were continuously measured. At the end of experiment, hearts were isolated for proteomic analysis. In asphyxiated hearts, the level of isocitrate dehydrogenase and malate dehydrogenase was reduced compared to controls. Inverse correlations between the level of myocardial malate dehydrogenase and cardiac function were observed in the control, but not the H/R hearts. We conclude that reoxygenation of asphyxiated newborn piglets reduces the level of myocardial isocitrate dehydrogenase and malate dehydrogenase. While the cause is not clear, it may be related to the impaired tricarboxylic acid cycle pathway and energy production in the heart.     

The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus

Seven of nine pericentric inversions that distinguish human (HSA) and chimpanzee karyotypes are chimpanzee-specific. In this study we investigated whether the two extant chimpanzee species, Pan troglodytes (common chimpanzee) and Pan paniscus (bonobo), share exactly the same pericentric inversions. The methods applied were FISH with breakpoint-spanning BAC/PAC clones and PCR analyses of the breakpoint junction sequences. Our findings for the homologues to HSA 4, 5, 9, 12, 16, and 17 confirm for the first time at the sequence level that these pericentric inversions have identical breakpoints in the common chimpanzee and the bonobo. Therefore, these inversions predate the separation of the two chimpanzee species 0.86-2 Mya. Further, the inversions distinguishing human and chimpanzee karyotypes may be regarded as early acquisitions, such that they are likely to have been present at the time of human/chimpanzee divergence. According to the chromosomal speciation theory the inversions themselves could have promoted human speciation.     

Vacuolization of HeLa cells by a partially purified Clostridium histolyticum cytotoxin

Clostridium histolyticum vacuolating cytotoxin was partially purified from culture broth using ammonium sulfate precipitation, gel filtration and hydrophobic interaction chromatography. The toxin caused vacuolization of HeLa cells visible under a light microscope after 2 h and distinct after 8 h. Transmission electron microscopy revealed the presence of numerous vacuoles, condensation of the mitochondrial matrix, increased cytoplasm density and increased amounts of heterochromatin. Apoptosis was not detected either by electron microscopy or by an apoptosis/necrosis discrimination assay with fluorescein-labeled annexin V and propidium iodide, or DNA fragmentation assay. Calcium ion influx was detected by flow cytometry after labeling cells with Fluo-4 AM. Vacuolation of HeLa cells by C. histolyticum cytotoxin was inhibited by bafilomycin A1, suggesting involvement of H+ -ATPase in the formation of vacuoles.     

Structural characterization and binding properties of the hemopexin-like domain of the matrixmetalloproteinase-19

The matrixmetalloproteinase-19 (MMP-19) belongs to the superfamily of the zinc-dependent endopeptidases, which are secreted by cells and are involved in the remodeling of the extracellular matrix. The full-length protein consists of a signal peptide, a propeptide, a catalytic domain and a C-terminal hemopexin-like domain. For other members of this superfamily, the hemopexin-like domain has been described to be involved in substrate recognition. In this study, the hemoxpexin domain of MMP-19 was expressed in Escherichia coli, refolded, and purified. For structural characterization, circular dichroism and NMR spectroscopy were used. We show that the hemopexin-like domain of MMP-19 is able to bind calcium and this binding induces a conformational change and an increase in the thermal stability of the domain. MMP-19 promotes proliferation of keratinocytes by cleaving the insulin-like-growth factor binding protein-3, thereby causing the release of IGF-1, which is a potent growth factor for these cells. By plasmon resonance experiments, we show that the isolated hemopexin-like domain is able to bind to the insulin-like-growth factor binding protein-3. These results provide a basis for further structural investigations that could be used for the rational design of potential agonists and antagonists.     

Parasites in hybridizing communities: the Red Queen again?

Over the past two decades, infection levels in hybrids have frequently been compared with those in their progenitor species to find out whether parasites favour or penalize hybridization. Four static infection scenarios are possible, depending on whether hybrid resistance differs from that of one or both parental species. All four alternatives have been supported by some empirical data, but any potential dynamics might have been overlooked because of limited sampling or experimental designs. However, coevolutionary oscillations generated by frequency-dependent selection might provide a better explanation for the observed results than does a static genetic perspective of host resistance.     

Cancer stem cells: the theory and perspectives in cancer therapy

The cancer stem cell theory elucidates not only the issue of tumour initiation and development, tumour's ability to metastasise and reoccur, but also the ineffectiveness of conventional cancer therapy. This review examines stem cell properties, such as self-renewal, heterogeneity, and resistance to apoptosis. The 'niche' hypothesis is presented, and mechanisms of division, differentiation, self-renewal and signalling pathway regulation are explained. Epigenetic alterations and mutations of genes responsible for signal transmission may promote the formation of cancer stem cells. We also present the history of development of the cancer stem cell theory and discuss the experiments that led to the discovery and confirmation of the existence of cancer stem cells. Potential clinical applications are also considered, including therapeutic models aimed at selective elimination of cancer stem cells or induction of their proper differentiation.     

Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression

Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.     

Influence of the separation of the charged groups and aromatic ring on interaction of tyrosine and phenylalanine analogues and derivatives with beta-cyclodextrin

Interactions of tyrosine and phenylalanine analogues with beta-cyclodextrin have been examined in terms of structural features of the ligand such as the separation of the charged amino group and aromatic ring, the presence of additional functional group attached to the amino or phenyl ring, and the presence of a charge on amino or carboxyl group, and steric effects using steady-state and time-resolved fluorescence spectroscopy and microcalorimetry. The studied aromatic amino acids possess low binding constant to beta-cyclodextrin, diversified with respect to the presence or absence of a substituent in para position of the phenyl ring. However, calculated, based on the global analysis of the fluorescence intensity decays, binding constants do not allow to estimate unequivocally the influence of the distance between the charged groups and phenol/phenyl ring on the inclusion complex stability because of their low diversification.     

The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function

A new microarray method, the isotope array approach, for identifying microorganisms which consume a (14)C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [(14)C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of (14)C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO(2) fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [(14)C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO(2) fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by (14)C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of (14)C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.