Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci

Prostate cancer is one of the most common cancers among men and has long been recognized to occur in familial clusters. Brothers and sons of affected men have a 2-3-fold increased risk of developing prostate cancer. However, identification of genetic susceptibility loci for prostate cancer has been extremely difficult. Although the suggestion of linkage has been reported for many chromosomes, the most promising regions have been difficult to replicate. In this study, we compare genome linkage scans using microsatellites with those using single-nucleotide polymorphisms (SNPs), performed in 467 men with prostate cancer from 167 families. For the microsatellites, the ABI Prism Linkage Mapping Set version 2, with 402 microsatellite markers, was used, and, for the SNPs, the Early Access Affymetrix Mapping 10K array was used. Our results show that the presence of linkage disequilibrium (LD) among SNPs can lead to inflated LOD scores, and this seems to be an artifact due to the assumption of linkage equilibrium that is required by the current genetic-linkage software. After excluding SNPs with high LD, we found a number of new LOD-score peaks with values of at least 2.0 that were not found by the microsatellite markers: chromosome 8, with a maximum model-free LOD score of 2.2; chromosome 2, with a LOD score of 2.1; chromosome 6, with a LOD score of 4.2; and chromosome 12, with a LOD score of 3.9. The LOD scores for chromosomes 6 and 12 are difficult to interpret, because they occurred only at the extreme ends of the chromosomes. The greatest gain provided by the SNP markers was a large increase in the linkage information content, with an average information content of 61% for the SNPs, versus an average of 41% for the microsatellite markers. The strengths and weaknesses of microsatellite versus SNP markers are illustrated by the results of our genome linkage scans.     

Prospective study of swimmer's itch incidence and severity

This epidemiologic study reports incidence, severity, and risk factors of swimmer's itch (cercarial dermatitis). Daily diaries about water exposures and swimmer's itch symptoms were completed by 40 riparian households at Douglas Lake, Michigan, for July 2000. Minutes spent in the water, minutes in shallow water, location, time of day, preventive action, age, and gender were recorded for all residents and guests. Incidence of swimmer's itch was 6.8 episodes per 100 water-exposure days. Probability of an episode increased with more days of water use and at locations with onshore winds. Episode severity increased with more time in the water and at the same locations. Age and gender had no effect on incidence or severity. In sum, onset and severity of swimmer's itch are affected by how people interact with the lake, not by their demographic features. More studies of human incidence and severity are needed to convince public health agencies to address this problem at recreational lakes. Study designs that combine epidemiologic and biological data will simultaneously inform public health education and biological control programs.     

Chemical modulation of receptor signaling inhibits regenerative angiogenesis in adult zebrafish

We examined the role of angiogenesis and the need for receptor signaling using chemical inhibition of the vascular endothelial growth factor receptor in the adult zebrafish tail fin. Using a small-molecule inhibitor, we were able to exert precise control over blood vessel regeneration. An angiogenic limit to tissue regeneration was determined, as avascular tissue containing skin, pigment, neuronal axons and bone precursors could regenerate up to about 1 mm. This indicates that tissues can regenerate without direct interaction with endothelial cells and at a distance from blood supply. We also investigated whether the effects of chemical inhibition could be enhanced in zebrafish vascular mutants. We found that adult zebrafish, heterozygous for a mutation in the critical receptor effector phospholipase Cgamma1, show a greater sensitivity to chemical inhibition. This study illustrates the utility of the adult zebrafish as a new model system for receptor signaling and chemical biology.     

Phosphoproteomics strategies for the functional analysis of signal transduction

Protein phosphorylation is a key regulatory mechanism of cellular signalling processes. The analysis of phosphorylated proteins and the characterisation of phosphorylation sites under different biological conditions are some of the most challenging tasks in current proteomics research. Reduction of the sample complexity is one major step for the analysis of low-abundance kinase substrates, which can be achieved by various subcellular fractionation techniques. One strategy is the enrichment of phosphorylated proteins or peptides by immunoprecipitation or chromatography, e.g. immobilised metal affinity chromatography, prior to analysis. 2-DE gels are powerful tools for the analysis of phosphoproteins when combined with new multiplexing techniques like DIGE, phosphospecific stains, autoradiography or immunoblotting. In addition, several gel-free methods combining chromatography with highly sensitive MS have been successfully applied for the analysis of complex phosphoproteomes. Recently developed approaches like KESTREL or 'chemical genetics' and also protein microarrays offer new possibilities for the identification of specific kinase targets. This review summarises various strategies for the analyses of phosphoproteins with a special focus on the identification of novel kinase substrates.     

Biologically inspired sensing: infrared spectroscopic analysis of cell responses to an inhalation health hazard

This work describes the development of a biologically based sensing technique to quantify chemical agents that pose inhalation health hazards. The approach utilizes cultured epithelial cells (A549 human type II pneumocytes) of the lung, exposed to potential toxins and monitored through the noninvasive means of infrared spectroscopy to quantify changes to cell physiology and function. Cell response to Streptolysin O, a cholesterol-binding cytolysin, is investigated here. Infrared spectra display changes in cell physiology indicative of membrane damage, altered proteins, and some nucleic acid damage. Methods to improve cell adhesion through modification of support surface properties are detailed. This spectroscopic approach not only provides a robust means to detect potential toxins but also provides information on modes of damage and mechanisms of cellular response.     

Aminopyridinecarboxamide-based inhibitors: Structure–activity relationship

Series of aminopyridinecarboxamide-based inhibitors were synthesized and tested against human recombinant IKK-2 and in IL-1β stimulated synovial fibroblasts. The 2-amino-5-chloropyridine-4-carboxamides were identified as the most potent inhibitors with improved cellular activity.     

Synergistic Cooperation between Two ClpB Isoforms in Aggregate Reactivation

Bacterial AAA⁺ ATPase ClpB cooperates with DnaK during reactivation of aggregated proteins. The ClpB-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric ClpB. Two isoforms of ClpB are produced in vivo: the full-length ClpB95 and ClpB80, which does not contain the substrate-interacting N-terminal domain. The biological role of the truncated isoform ClpB80 is unknown. We found that resolubilization of aggregated proteins in Escherichia coli after heat shock and reactivation of aggregated proteins in vitro and in vivo occurred at higher rates in the presence of ClpB95 with ClpB80 than with ClpB95 or ClpB80 alone. Combined amounts of ClpB95 and ClpB80 bound to aggregated substrates were similar to the amounts of either ClpB95 or ClpB80 bound to the substrates in the absence of another isoform. The ATP hydrolysis rate of ClpB95 with ClpB80, which is linked to the rate of substrate translocation, was not higher than the rates measured for the isolated ClpB95 or ClpB80. We postulate that a reaction step that takes place after substrate binding to ClpB and precedes substrate translocation is rate-limiting during aggregate reactivation, and its efficiency is enhanced in the presence of both ClpB isoforms. Moreover, we found that ClpB95 and ClpB80 form hetero-oligomers, which are similar in size to the homo-oligomers of ClpB95 or ClpB80. Thus, the mechanism of functional cooperation of the two isoforms of ClpB may be linked to their heteroassociation. Our results suggest that the functionality of other AAA⁺ ATPases may be also optimized by interaction and synergistic cooperation of their isoforms.     

Regulation of Vascular Endothelial Growth Factor (VEGF) Splicing from Pro-angiogenic to Anti-angiogenic Isoforms: A NOVEL THERAPEUTIC STRATEGY FOR ANGIOGENESIS*

Vascular endothelial growth factor (VEGF) is produced either as a pro-angiogenic or anti-angiogenic protein depending upon splice site choice in the terminal, eighth exon. Proximal splice site selection (PSS) in exon 8 generates pro-angiogenic isoforms such as VEGF₁₆₅, and distal splice site selection (DSS) results in anti-angiogenic isoforms such as VEGF₁₆₅b. Cellular decisions on splice site selection depend upon the activity of RNA-binding splice factors, such as ASF/SF2, which have previously been shown to regulate VEGF splice site choice. To determine the mechanism by which the pro-angiogenic splice site choice is mediated, we investigated the effect of inhibition of ASF/SF2 phosphorylation by SR protein kinases (SRPK1/2) on splice site choice in epithelial cells and in in vivo angiogenesis models. Epithelial cells treated with insulin-like growth factor-1 (IGF-1) increased PSS and produced more VEGF₁₆₅ and less VEGF₁₆₅b. This down-regulation of DSS and increased PSS was blocked by protein kinase C inhibition and SRPK1/2 inhibition. IGF-1 treatment resulted in nuclear localization of ASF/SF2, which was blocked by SPRK1/2 inhibition. Pull-down assay and RNA immunoprecipitation using VEGF mRNA sequences identified an 11-nucleotide sequence required for ASF/SF2 binding. Injection of an SRPK1/2 inhibitor reduced angiogenesis in a mouse model of retinal neovascularization, suggesting that regulation of alternative splicing could be a potential therapeutic strategy in angiogenic pathologies.     

Tetratricopeptide repeats are essential for PcrH chaperone function in Pseudomonas aeruginosa type III secretion

The type III secretion system (T3SS) is a specialized apparatus evolved by Gram-negative bacteria to deliver effector proteins into host cells, thus facilitating the establishment of an infection. Effector translocation across the target cell plasma membrane is believed to occur via pores formed by at least two secreted translocator proteins, the functions of which are dependent upon customized class II T3SS chaperones. Recently, three internal tetratricopeptide repeats (TPRs) were identified in this class of chaperones. Here, defined mutagenesis of the class II chaperone PcrH of Pseudomonas aeruginosa revealed these TPRs to be essential for chaperone activity towards the translocator proteins PopB and PopD and subsequently for the translocation of exoenzymes into host cells.     

Differential community development of fouling species on the pearl oysters Pinctada fucata, Pteria penguin and Pteria chinensis (Bivalvia, Pteriidae)

A field experiment documented the development of fouling communities on two shell regions, the lip and hinge, of the pearl oyster species Pinctada fucata, Pteria penguin and Pteria chinensis. Fouling communities on the three species were not distinct throughout the experiment. However, when each species was analysed separately, fouling communities on the lip and hinge of P. penguin and P. chinensis were significantly different during the whole sampling period and after 12 weeks, respectively, whereas no significant differences could be detected for P. fucata. There was no significant difference in total fouling cover between shell regions of P. fucata and P. chinensis after 16 weeks; however, the hinge of P. penguin was significantly more fouled than the lip. The most common fouling species (the hydroid Obelia bidentata, the bryozoan Parasmittina parsevalii, the bivalve Saccostrea glomerata and the ascidian Didemnum sp.) showed species-specific fouling patterns with differential fouling between shell regions for each species. The role of the periostracum in determining the community development of fouling species was investigated by measuring the presence and structure of the periostracum at the lip and hinge of the three pearl oyster species. The periostracum was mainly present at the lip of the pearl oysters, while the periostracum at the hinge was absent and the underlying prismatic layer eroded. The periostracum of P. fucata lacked regular features, whereas the periostracum of P. penguin and P. chinensis consisted of a regular strand-like structure with mean amplitudes of 0.84 microm and 0.65 microm, respectively. Although the nature and distribution of fouling species on the pearl oysters was related to the presence of the periostracum, the periostracum does not offer a fouling-resistant surface for these pearl oyster species.