Searching biomarker candidates in serum using multidimensional native chromatography. II Method evaluation with Alport syndrome and severe inflammation

Biomarker search using multidimensional native liquid fractionation of serum in microplates was evaluated. From different donors, homologous sample fractions with UV absorbance depending on state of illness were selected, and their constituents were identified and quantitated by MS. Analysis of sera of patients with Alport syndrome and severe inflammation proved the reliability of the method by confirming characteristic alterations. Moreover, 23 new marker candidates were detected for Alport syndrome, some of them being involved in matrix degradation and repair, and 33 new candidates for severe inflammation, among them alpha1B-glycoprotein cysteine-rich secretory protein and an apparently low molecular-weight albumin variant.     

Visual monitoring of post-translational lipid modifications using EGFP-GTPase probes in live cells

Modification of small GTPases by lipids is required for their proper subcellular localization and biological activity. Lipids added post-translationally include both farnesyl and geranylgeranyl isoprenoids and the fatty acid palmitate. Thus, specific small molecule inhibitors of these processes cause mislocalization of small GTPases and impair their biological activity. Common biochemical methods of determining the lipid modification status or inhibitor sensitivity of small GTPases, such as in vitro prenylation assays, SDS-PAGE mobility shifts or metabolic labeling, although highly useful in their own right, cannot distinguish differences among specific subpopulations of cells, link lipid modification status with other properties of interest, or provide spatio-temporal information. An alternative method takes advantage of the tight link between small GTPase lipid modification and subcellular localization. The innate localization pattern of the enhanced green fluorescent protein, a common epitope tag frequently used in live cell imaging, is altered by fusion to modified but not unmodified small GTPases. We describe here a technique that takes advantage of these properties to monitor post-translational modifications of these proteins in a rapid, visual manner in live cells.     

Identifying modulators of hERG channel activity using the PatchXpress planar patch clamp

The authors used the PatchXpress 7000A system to measure compound activity at the hERG channel using procedures that mimicked the "gold-standard" conventional whole-cell patch clamp. A set of 70 compounds, including hERG antagonists with potencies spanning 3 orders of magnitude, were tested on hERG302-HEK cells using protocols aimed at either identifying compound activity at a single concentration or obtaining compound potency from a cumulative concentration dependence paradigm. After exposure to compounds and subsequent washout of the wells to determine reversibility of the block, blockade by a reference compound served as a quality control. Electrical parameters and voltage dependence were similar to those obtained using a conventional whole-cell patch clamp. Rank order of compound potency was also comparable to that determined by conventional methods. One exception was flunarizine, a particularly lipophilic compound. The PatchXpress accurately identified the activity of 29 moderately potent antagonists, which only weakly displace radiolabeled astemizole and are false negatives in the binding assay. Finally, no false hits were observed from a collection of relatively inactive compounds. High-quality data acquisition by PatchXpress should help accelerate secondary screening for ion channel modulators and the drug discovery process.     

Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation

We report that the halophilic archaeon Halobacterium sp. strain NRC-1 is highly resistant to desiccation, high vacuum and ⁶⁰Co gamma irradiation. Halobacterium sp. was able to repair extensive double strand DNA breaks (DSBs) in its genomic DNA, produced both by desiccation and by gamma irradiation, within hours of damage induction. We propose that resistance to high vacuum and ⁶⁰Co gamma irradiation is a consequence of its adaptation to desiccating conditions. Gamma resistance in Halobacterium sp. was dependent on growth stage with cultures in earlier stages exhibiting higher resistance. Membrane pigments, specifically bacterioruberin, offered protection against cellular damages induced by high doses (5 kGy) of gamma irradiation. High-salt conditions were found to create a protective environment against gamma irradiation in vivo by comparing the amount of DSBs induced by ionizing radiation in the chromosomal DNA of Halobacterium sp. to that of the more radiation-sensitive Escherichia coli that grows in lower-salt conditions. No inducible response was observed after exposing Halobacterium sp. to a nonlethal dose (0.5 kGy) of gamma ray and subsequently exposing the cells to either a high dose (5 kGy) of gamma ray or desiccating conditions. We find that the hypersaline environment in which Halobacterium sp. flourishes is a fundamental factor for its resistance to desiccation, damaging radiation and high vacuum.     

A molecular map of mesenchymal tumors

Background

Bone and soft tissue tumors represent a diverse group of neoplasms thought to derive from cells of the mesenchyme or neural crest. Histological diagnosis is challenging due to the poor or heterogenous differentiation of many tumors, resulting in uncertainty over prognosis and appropriate therapy.

Results

We have undertaken a broad and comprehensive study of the gene expression profile of 96 tumors with representatives of all mesenchymal tissues, including several problem diagnostic groups. Using machine learning methods adapted to this problem we identify molecular fingerprints for most tumors, which are pathognomonic (decisive) and biologically revealing.

Conclusion

We demonstrate the utility of gene expression profiles and machine learning for a complex clinical problem, and identify putative origins for certain mesenchymal tumors.     

Can the acoustic adaptation hypothesis predict the structure of Australian birdsong?

The acoustic adaptation hypothesis (AAH) predicts that long-distance signals will be structured so as to maximize their transmission fidelity. Previous studies testing the hypothesis on birdsong have provided equivocal support. The best support comes from large-scale comparative studies and those studies where habitat is characterized as open versus densely vegetated. In the first case, sufficient statistical power is present to detect even small effects on song structure, whereas in the later case the effect size of the habitat may be sufficiently large. Most studies have focused on Holarctic or Neotropical species, which may ultimately share a common evolutionary history. In this study, Australian birds were chosen for a phylogenetically independent test of key predictions of the AAH. Specifically, birds in open habitats were predicted to sing songs with higher frequencies, greater bandwidth, have a greater probability of having overtones, and be emitted at a quicker rate than birds inhabiting densely forested habitats. Acoustic measurements were made on commercially available recordings of 121 species of Australian birds from 41 different families. Analyses controlled for variation explained by body mass (using ANCOVA), and phylogeny (using genus pairs analyses). We found only modest support for the AAH. Our finding that birds in open habitats produced higher frequency vocalizations and greater bandwidth vocalizations is also consistent with hypotheses about signal structure facilitating auditory distance assessment. Forest birds may therefore rely on cues other than frequency-dependent attenuation for ranging.     

Differences in cell death induction by Phytophthora Elicitins are determined by signal components downstream of MAP kinase kinase in different species of Nicotiana and cultivars of Brassica rapa and Raphanus sativus

Elicitins are small, secreted proteins produced by species of the plant-pathogenic oomycete Phytophthora. They induce hypersensitive cell death in most Nicotiana species and in some cultivars of Brassica rapa and Raphanus sativus. In this study, two true-breeding Fast Cycling B. rapa lines were established that showed severe necrosis (line 7-R) or no visible response (line 18-NR) after treatment with elicitin. Unexpectedly, microscopic examination revealed localized cell death in line 18-NR plants, and expression levels of various defense-marker genes were comparable in both lines. These results suggested that both “responsive” and “nonresponsive” plants responded to elicitin but differed in the extent of the cell death response. Expression of a constitutively active form of Arabidopsis (Arabidopsis thaliana) MAP kinase kinase 4 (AtMEK4^DD) also induced rapid development of confluent cell death in line 7-R, whereas line 18-NR showed no visible cell death. Similarly, elicitin-responsive Nicotiana species and R. sativus cultivars showed significantly stronger cell death responses following expression of AtMEK4^DD compared with nonresponsive species/cultivars. Line 7-R also showed higher sensitivity to toxin-containing culture filtrates produced by Alternaria brassicicola, and toxin sensitivity cosegregated with elicitin responsiveness, suggesting that the downstream responses induced by elicitin and Alternaria toxin share factors that control the extent of cell death. Interestingly, elicitin responsiveness was shown to correlate with greater susceptibility to A. brassicicola (a necrotroph) in B. rapa but less susceptibility to Phytophthora nicotianae (a hemibiotroph) in Nicotiana, suggesting a more extensive cell death response could cause opposite effects on the outcomes of biotrophic versus necrotrophic plant-pathogen interactions.     

Aperture pattern ontogeny in angiosperms

Pollen grains display a wide range of variation in aperture number and arrangement (pattern) in angiosperms. Apertures are well-defined areas of the pollen wall surface that permit pollen tube germination. For low aperture numbers, aperture patterns are characteristic of the major taxonomic divisions of angiosperms. This paper presents a developmental model that explains most of the aperture patterns that are recorded in angiosperms. It is based on the analysis of the different events that occur during meiosis and lead to microspore differentiation. It demonstrates that variation occurring during meiosis in angiosperms is sufficient to produce the core morphological set of the most commonly observed pollen morphologies.     

Correlated variation in microtubule distribution, callose deposition during male post-meiotic cytokinesis, and pollen aperture number across Nicotiana species (Solanaceae)

In most flowering plants, a single cytokinesis follows the two meiotic divisions during pollen-grain ontogeny. Aperture pattern (i.e., aperture number and distribution on pollen surface) ontogeny could be linked to the processes ensuring the apportionment of the cytoplasm to the four microspores.This apportionment is achieved by radial arrays of microtubules organized around the nuclei. The cleavage planes are defined in the overlapping regions of opposing arrays extending from different nuclei. We followed the establishment of these arrays in two different lines of plants belonging to the genus Nicotiana that produce pollen grains with different aperture numbers. Different distributions of the microtubules have been observed, which can be interpreted as resulting from variation in the interactions between nuclei; these distributions appear to be correlated with aperture number.As a consequence, we propose that simultaneous cytokinesis allows the formation of multiple pollen morphologies. This mechanism is consistent with aperture number distribution within angiosperms and provides clues to help our understanding of the evolution of aperture number.