Chemical Ecology of Marine Cyanobacterial Secondary Metabolites: a Mini-review

More than 300 nitrogen-containing secondary metabolites have been reported from the procaryotic marinecyanobacteria. A majority of these compounds are of the polypeptide or mixed polyketide-polypeptidestructural class and they are a potential source of novel pharmaceuticals. In spite of the chemical richnessof marine cyanobacteria, not much is known regarding their ecological functions. To date only a handful ofmarine cyanobacterial compounds have been examined for their involvement in predator-prey interactions.This mini-review surveys the various chemical ecology studies conducted on marine cyanobacterialcompounds. From these ecological studies, many marine cyanobacterial compounds are known to deterfeeding by several species of marine predators. Such chemical defense may be crucial in maintaining thepopulation of marine cyanobacterial bloom in nature. In addition, a series of ecological studies from ourlaboratory revealed the anti-settlement properties of a number of benthic marine cyanobacterialcompounds. These studies suggested marine cyanobacteria as a potential source of natural antifoulants forthe control of fouling organisms

Chemical Ecology of Marine Cyanobacterial Secondary Metabolites: a Mini-review

More than 300 nitrogen-containing secondary metabolites have been reported from the procaryotic marinecyanobacteria. A majority of these compounds are of the polypeptide or mixed polyketide-polypeptidestructural class and they are a potential source of novel pharmaceuticals. In spite of the chemical richnessof marine cyanobacteria, not much is known regarding their ecological functions. To date only a handful ofmarine cyanobacterial compounds have been examined for their involvement in predator-prey interactions.This mini-review surveys the various chemical ecology studies conducted on marine cyanobacterialcompounds. From these ecological studies, many marine cyanobacterial compounds are known to deterfeeding by several species of marine predators. Such chemical defense may be crucial in maintaining thepopulation of marine cyanobacterial bloom in nature. In addition, a series of ecological studies from ourlaboratory revealed the anti-settlement properties of a number of benthic marine cyanobacterialcompounds. These studies suggested marine cyanobacteria as a potential source of natural antifoulants forthe control of fouling organisms

Diversity, Distribution and Biological Activity of Soft Corals (Octocorallia, Alcyonacea) in Singapore

The Southern Islands of Singapore are known to contain coral reefs which are high in biodiversity. However, the diversity of soft corals had received little attention to date. This study was conducted to determine the soft coral diversity in Singapore reefs as well as to conduct preliminary bioactivity tests on the organic extracts from these soft corals. A 100-meter line transect was used to survey soft corals at a 3m depth at ten different sample sites. Sclerites from samples were used to identify the soft corals to the generic level. This study uncovered the following genera of soft corals: Carijoa spp., Cladiella spp., Sinularia spp., Lobophytum spp., Sarcophyton spp., Stereonephthya spp., and Nephthea spp. In addition, an unidentified genus of soft coral was observed at Kusu Island. Cladiella spp. yielded the highest number of colonies, and Sarcophyton spp. had the highest coverage in terms of total colony diameter. The brine shrimp (Artemia salina) toxicity assay was carried out to screen for toxicity of the soft coral extracts at concentrations of 10, 100, and 1000 ppm. Results showed high levels of toxicity in extracts of Sarcophyton spp. and Cladiella spp., indicating that these soft corals are potentially good sources of bioactive compounds for drug discovery

Empirical comparison of cross-platform normalization methods for gene expression data

<p>Abstract</p> <p>Background</p> <p>Simultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the combination and comparison of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, software for the selected method must be obtained and incorporated into a data analysis workflow.</p> <p>Results</p> <p>Using two publicly available cross-platform testing data sets, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data. Scatter and ROC-like plots are produced and new statistics based on those plots are introduced to measure the effectiveness of each method. Bootstrapping is employed to obtain distributions for those statistics. The consistency of platform effects across studies is explored theoretically and with respect to the testing data sets.</p> <p>Conclusions</p> <p>Our comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. We provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. The package can be downloaded at <url>http://alborz.sdsu.edu/conor</url> and is available from CRAN.</p

The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes — Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes — quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an “accidental pathogen”, where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts