Evolution of chromosome Y in primates

We have investigated, by fluorescence in situ hybridization (FISH), the cytogenetic evolution of the Y chromosome in primates using 17 yeast artificial chromosomes, representative of the Y-specific euchromatic region of the human chromosome Y. The FISH experiments were performed on great apes (Homo sapiens, Pan troglodytes, Gorilla gorilla and Pongo pygmaeus pygmaeus), and on two Old World monkeys species as an outgroup (Cercopitecidae Macaca fascicularis and Papio anubis). The results showed that this peculiar chromosome has undergone rapid and unconstrained evolution both in sequence content and organization. Received: 16 January 1998; in revised form: 29 May 1998 / Accepted: 24 June 1998     

The application of acoustic Doppler current profilers to measure the timing and patterns of coral larval dispersal

An experiment was conducted along the reefs off west Maui, Hawaii, during the summer of 2003 to monitor the spawning of the reef-building coral Montipora capitata and to determine the role of ocean currents in dispersing the larvae from the natal reef. Instruments documented the environmental forcing during the coral spawning season; drifters were deployed on three successive nights following direct observations of coral spawning. Both the timing and relative magnitude of the coral spawning were identifiable in acoustic backscatter data and correlated to plankton tow data. Each drifter track showed that the surface water containing coral eggs and planula larvae were transported rapidly offshore and not locally retained. Wind and current patterns during the previous year and during subsequent coral spawning events later in the summer were similar to those observed during the drifter releases. This suggests that the trajectories observed during the focused experiment are representative of the general pattern of larval dispersal off west Maui. These findings demonstrate the application of acoustic profilers for remotely imaging coral spawning and predicting their initial dispersal patterns.     

Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer

The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array, fluorescent in situ hybridization and polymerase chain reaction-based techniques, we inferred the fine structure of MYC-containing dmin/hsr amplicons harboring sequences from several different chromosomes in seven tumor cell lines, and characterized an unprecedented number of hsr insertion sites. Local chromosome shattering involving a single-step catastrophic event (chromothripsis) was recently proposed to explain clustered chromosomal rearrangements and genomic amplifications in cancer. Our bioinformatics analyses based on the listed criteria to define chromothripsis led us to exclude it as the driving force underlying amplicon genesis in our samples. Instead, the finding of coexisting heterogeneous amplicons, differing in their complexity and chromosome content, in cell lines derived from the same tumor indicated the occurrence of a multi-step evolutionary process in the genesis of dmin/hsr. Our integrated approach allowed us to gather a complete view of the complex chromosome rearrangements occurring within MYC amplicons, suggesting that more than one model may be invoked to explain the origin of dmin/hsr in cancer. Finally, we identified PVT1 as a target of fusion events, confirming its role as breakpoint hotspot in MYC amplification.     

Historic impact of watershed change and sedimentation to reefs along west-central Guam

Using coral growth parameters (extension, density, calcification rates, and luminescence) and geochemical measurements (barium to calcium rations; Ba/Ca) from coral cores collected in west-central Guam, we provide a historic perspective on sediment input to coral reefs adjacent to the Piti-Asan watershed. The months of August through December are dominated by increased coral Ba/Ca values, corresponding to the rainy season. With river water enriched in barium related to nearshore seawater, coral Ba/Ca ratios are presented as a proxy for input of fine-grained terrigenous sediment to the nearshore environment. The century-long Ba/Ca coral record indicates that the Asan fore reef is within the zone of impact from discharged sediments transported from the Piti-Asan watershed and has experienced increased terrestrial sedimentation since the 1940s. This abrupt shift in sedimentation occurred at the same time as both the sudden denudation of the landscape by military ordinance and the immediate subsequent development of the Asan area through the end of the war, from 1944 through 1945. In response to rapid input of sediment, as determined from coral Ba/Ca values, coral growth rates were reduced for almost two decades, while calcification rates recovered much more quickly. Furthermore, coral luminescence is decoupled from the Ba/Ca record, which is consistent with degradation of soil organic matter through disturbance by forest fires, suggesting a potential index of fire history and degradation of soil organic matter. These patterns were not seen in the cores from nearby reefs associated with watersheds that have not undergone the same degree of landscape denudation. Taken together, these records provide a valuable tool for understanding the compounding effects of land-use change on coral reef health.     

End of the chain? Rugosity and fine-scale bathymetry from existing underwater digital imagery using structure-from-motion (SfM) technology

The rugosity or complexity of the seafloor has been shown to be an important ecological parameter for fish, algae, and corals. Historically, rugosity has been measured either using simple and subjective manual methods such as ‘chain-and-tape’ or complicated and expensive geophysical methods. Here, we demonstrate the application of structure-from-motion (SfM) photogrammetry to generate high-resolution, three-dimensional bathymetric models of a fringing reef from existing underwater video collected to characterize the seafloor. SfM techniques are capable of achieving spatial resolution that can be orders of magnitude greater than large-scale lidar and sonar mapping of coral reef ecosystems. The resulting data provide finer-scale measurements of bathymetry and rugosity that are more applicable to ecological studies of coral reefs than provided by the more expensive and time-consuming geophysical methods. Utilizing SfM techniques for characterizing the benthic habitat proved to be more effective and quantitatively powerful than conventional methods and thus might portend the end of the ‘chain-and-tape’ method for measuring benthic complexity.     

The spliceosomal intron of the rolA gene of agrobacterium rhizogenes is a prokaryotic promoter

Agrobacterium rhizogenes transfers DNA (T-DNA) from its Ri plasmid to plant cells. All T-DNA genes are expressed in plant cells. The rolA gene is the only T-DNA gene that contains an intron in the untranslated leader region of its mRNA. This paper shows that (i) the rolA gene is also transcribed in bacteria; (ii) the 85 bp corresponding to the spliceosomal intron drives prokaryotic gene expression in agrobacteria, in free-living rhizobia and in bacteroids within root nodules; and (iii) promoter activity is abolished by the deletion of 63 bp from its 5' end and is reduced by mutations changing its sequence near the putative -10 region. The expression pattern of a chimeric reporter gene shows that, in free-living bacteria, gene expression takes place during the exponential phase of growth and increases at the onset of the stationary phase. Within root nodules, reporter gene expression occurs in the invasion, nitrogen fixing and senescent zones.     

Sediment resuspension and transport patterns on a fringing reef flat,Molokai, Hawaii

Corals are known to flourish in various turbid environments around the world. The quantitative distinction between clear and turbid water in coral habitats is not well defined nor are the amount of sediment in suspension and rates of sedimentation used to evaluate the condition of reef environments well established. This study of sediment resuspension, transport, and resulting deposition on a fringing reef flat off Molokai, Hawaii, uses a year of time-series data from a small, instrumented tripod. It shows the importance of trade winds and ocean wave heights in controlling the movement of sediment. Sediment is typically resuspended daily and the dominant controls on the magnitude of events (10–25 mg/l) are the trade-wind-generated waves and currents and tidal elevation on the reef flat. The net flux of sediment on this reef is primarily along the reef flat in the direction of the prevailing trade winds (to the west), with a secondary direction of slightly offshore, towards a zone of low coral abundance.These results have application to reef studies and reef management in other areas in several ways. First, the observed resuspension and turbidity results from fine-grained terrigenous sediment that appears to be trapped and recycled on the reef flat. Thus corals are subjected to light attenuation by the same particles repeatedly, however small the amount. Secondly, the measurements show high temporal variability (from daily to seasonal scales) of sediment resuspension, indicating that single measurements are inadequate to accurately describe conditions on a reef flat.Communicated by: P.K. Swart