Extensive natural variation for cellular hydrogen peroxide release is genetically controlled

Natural variation in DNA sequence contributes to individual differences in quantitative traits. While multiple studies have shown genetic control over gene expression variation, few additional cellular traits have been investigated. Here, we investigated the natural variation of NADPH oxidase-dependent hydrogen peroxide (H₂O₂ release), which is the joint effect of reactive oxygen species (ROS) production, superoxide metabolism and degradation, and is related to a number of human disorders. We assessed the normal variation of H₂O₂ release in lymphoblastoid cell lines (LCL) in a family-based 3-generation cohort (CEPH-HapMap), and in 3 population-based cohorts (KORA, GenCord, HapMap). Substantial individual variation was observed, 45% of which were associated with heritability in the CEPH-HapMap cohort. We identified 2 genome-wide significant loci of Hsa12 and Hsa15 in genome-wide linkage analysis. Next, we performed genome-wide association study (GWAS) for the combined KORA-GenCord cohorts (n = 279) using enhanced marker resolution by imputation (>1.4 million SNPs). We found 5 significant associations (p<5.00×10−8) and 54 suggestive associations (p<1.00×10−5), one of which confirmed the linked region on Hsa15. To replicate our findings, we performed GWAS using 58 HapMap individuals and ∼2.1 million SNPs. We identified 40 genome-wide significant and 302 suggestive SNPs, and confirmed genome signals on Hsa1, Hsa12, and Hsa15. Genetic loci within 900 kb from the known candidate gene p67phox on Hsa1 were identified in GWAS in both cohorts. We did not find replication of SNPs across all cohorts, but replication within the same genomic region. Finally, a highly significant decrease in H₂O₂ release was observed in Down Syndrome (DS) individuals (p<2.88×10−12). Taken together, our results show strong evidence of genetic control of H₂O₂ in LCL of healthy and DS cohorts and suggest that cellular phenotypes, which themselves are also complex, may be used as proxies for dissection of complex disorders.     

Spatial and temporal patterns of recruitment of the tunicate Ciona intestinalis on a mussel farm in Nova Scotia, Canada

Although possibly indigenous to Nova Scotia, the ascidian Ciona intestinalis has become a problem for local mussel aquaculturists. The local population ecology of the ascidian was studied by recording the depth, distribution, and timing of recruitment of C. intestinalis at four different locations (high wave exposure, low wave exposure, recently fallowed, and historically heavily fouled with tunicates) on a mussel farm at Indian Point, Nova Scotia. Animals were collected weekly from 11 collectors deployed at a depth of 4.5 m over two seasons (June-December 2003 and 2004). Recruitment occurred in two peaks during both seasons: the first peak lasted from late June to late July while the second peak lasted from early September to mid-November. Recruitment was highest in the sheltered and historically fouled location, intermediate in the fallowed site, and lowest in the site with highest wave exposure. Collectors were also deployed at different depths. Recruitment was highest at 4.5 m and to a lesser extent at 8.5 m. Little recruitment was seen at the surface (0.5 m) or in deeper water (12.5 and 16.5 m), except during the second peak in 2004. Overall, these results seem to indicate an abbreviated larval dispersal phase with young recruits settling very close to the pool of adults located on the mussel lines.     

Baseline data for automated acoustic monitoring of Orthoptera in a Mediterranean landscape,the Hymettos,Greece

Acoustic emissions of animals serve communicative purposes and most often contain species-specific and individual information exploitable to listeners, rendering bioacoustics a valuable tool for biodiversity monitoring. Recording bioacoustic signals allows reproducible species identification. There is a great need for increased use and further development of automated animal sound recording and identification to improve monitoring efficiency and accuracy for the benefit of conservation. Greece, with its high number of endemic species, represents a hotspot for European Biodiversity, including Orthopteran insects. Songs of many Orthoptera might be employed for the inventorying and monitoring of individual species and communities. We assessed the regional spatio-temporal composition of Orthoptera species at the Hymettos near Athens, which is a Natura 2000 site under constant threat due to the surrounding megacity. Within the framework of the EU Life Plus funded AmiBio project, we documented the Orthopteran species’ habitat characteristics, their co-occurrence and phenology. We found, in total, 20 species with seven to ten Orthoptera at locations characterised by diverse vegetation patterns of perennial herbs and bushes. For the purposes of implementation of an automated remote monitoring scheme, we identified sampling sites with high Orthopteran diversity, allowing the monitoring of all singing Orthoptera within single localities. By analysing sound depositories and adding recordings from new sample individuals, we established a song library as prerequisites for future automatic song detection. Based on our results, acoustic recording units have been placed at remote sites at the Hymettos. We discuss recommendations for further studies to fully employ the potential of automated acoustic monitoring of Orthoptera. A reliable assessment of singing Orthoptera needs recording units covering ultrasound. Due to high attenuation and absorbance by the vegetation, particularly of the high frequencies characterising Orthopteran songs, positioning of microphones at sites is critical: the microphone sensor network has to be an order of magnitude denser than for monitoring birds.     

Functional analysis of calcium-binding EF-hand motifs of visinin-like protein-1

Visinin-like protein-1 (VILIP-1), a myristoylated calcium sensor protein with three EF-hand motifs, modulates adenylyl cyclase activity. It translocates to membranes when a postulated "calcium-myristoyl switch" is triggered by calcium-binding to expose its sequestered myristoyl moiety. We investigated the contributions of the EF-hand motifs to the translocation of VILIP-1 to membranes and to the modulation of adenylyl cyclase activity. Mutation of residues crucial for binding calcium within each one of the EF-hand motifs indicated that they all contributed to binding calcium. Simultaneous mutations of all of the three EF-hand motifs completely abolished VILIP-1's ability to bind calcium, attenuated but did not eliminate its modulation of adenylyl cyclase activity, and abolished its calcium-dependence for association with cellular membranes. These results show that the calcium-binding EF-hand motifs of VILIP-1 do not have an essential role in modulating adenylyl cyclase activity but instead have a structural role in activating the "calcium-myristoyl switch" of VILIP-1.     

Oncogenic point mutations in the Myb DNA-binding domain alter the DNA-binding properties of Myb at a physiological target gene

The oncoprotein v-Myb of avian myeloblastosis virus (AMV) transforms myelomonocytic cells by deregulating specific target genes. Previous work has shown that the oncogenic potential of v-Myb was activated by truncation of N- and C-terminal sequences of c-Myb and was further increased by amino acid substitutions in the DNA-binding domain and other parts of the protein. We have analyzed the activation of the chicken lysozyme gene which is strongly activated by c-Myb but not by its oncogenic counterpart v-Myb. We report that Myb acts on two different cis-regulatory elements, the promoter and an enhancer located upstream of the gene. Interestingly, the activation of the enhancer was abolished by the oncogenic amino acid substitutions. We demonstrated that a single Myb-binding site is responsible for the activation of the lysozyme enhancer by Myb and showed that the v-Myb protein of AMV was unable to bind to this site. Our data demonstrate for the first time that oncogenic activation of Myb alters its DNA-binding specificity at a physiological Myb target gene.     

Organelle proteomics of rat synaptic proteins: correlation-profiling by isotope-coded affinity tagging in conjunction with liquid chromatography-tandem mass spectrometry to reveal post-synaptic density specific proteins

Organelle proteomics is the method of choice for global analysis of cellular proteins. However, it is difficult to isolate organelles to homogeneity. Recently, correlation-profiling has been used to filter off the contaminants ad hoc and to disclose the genuine organelle-specific proteins. In the present study, we further extend the method to include subcellular compartments that contain proteins shared by multiple distinct subcellular domains. We performed correlation profiling of proteins contained in synaptic membrane and postsynaptic density (PSD) fractions isolated from rat brain. Proteins were labeled with isotope-coded affinity-tag reagents, digested with trypsin, and resulting peptides were resolved by cation exchange chromatography followed by reversed phase chromatography. Peptides were then subjected to mass spectrometry for quantification and identification. We confirm that the core PSD proteins were enriched in the PSD preparation. Other functional protein groups such as cytoskeleton-associated proteins, protein kinases and phosphatases, signaling components and regulators, as well as proteins involved in energy production partitioned to multiple organelles. When analyzed as groups, they were shown to accumulate to a lesser extent. Mitochondrial proteins and transporters were generally strongly depleted from the PSD fraction confirming that they were contaminants of the PSD preparation. Finally, immunoelectron microscopy was performed on selected proteins to validate the proteomics results, and confirm that synaptophysin that was highly depleted in the PSD preparation is localized in the presynaptic compartment, whereas LASP-1 that was slightly enriched in the PSD preparation is present in the PSD as well as other subdomains within the synapse.