Modeling acoustic propagation of airgun array pulses recorded on tagged sperm whales (Physeter macrocephalus)

Author Posting. © Acoustical Society of America, 2006. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 120 (2006): 4100-4114, doi:10.1121/1.2359705.In 2002 and 2003, tagged sperm whales (Physeter macrocephalus) were experimentally exposed to airgun pulses in the Gulf of Mexico, with the tags providing acoustic recordings at measured ranges and depths. Ray trace and parabolic equation (PE) models provided information about sound propagation paths and accurately predicted time of arrival differences between multipath arrivals. With adequate environmental information, a broadband acoustic PE model predicted the relative levels of multipath arrivals recorded on the tagged whales. However, lack of array source signature data limited modeling of absolute received levels. Airguns produce energy primarily below 250 Hz, with spectrum levels about 20–40 dB lower at 1 kHz. Some arrivals recorded near the surface in 2002 had energy predominantly above 500 Hz; a surface duct in the 2002 sound speed profile helps explain this effect, and the beampattern of the source array also indicates an increased proportion of high-frequency sound at near-horizontal launch angles. These findings indicate that airguns sometimes expose animals to measurable sound energy above 250 Hz, and demonstrate the influences of source and environmental parameters on characteristics of received airgun pulses. The study also illustrates that on-axis source levels and simple geometric spreading inadequately describe airgun pulse propagation and the extent of exposure zones.Funding for this work was provided by the Office of Naval Research, the U.S. Department of the Interior Minerals Management Service Cooperative Agreements Nos. 1435-01-02- CA-85186 and NA87RJ0445, and the Industry Research Funding Coalition. S.L.D.R. was supported by a National Science Foundation Graduate Research Fellowship

Red Tides In the Gulf of Mexico: Where, When, and Why?

Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus-rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron-rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen-poor sea water. They and the co-occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near-bottom seed populations to CDOM-rich surface waters of coastal regions, light-inhibition of the small red tide of similar to 1 ug chl l(-1) of ichthytoxic K. brevis is alleviated. Thence, dead fish serve as a supplementary nutrient source, yielding large, self-shaded red tides of similar to 10 ug chl l(-1). The source of phosphorus is mainly of fossil origin off west Florida, where past nutrient additions from the eutrophied Lake Okeechobee had minimal impact. In contrast, the P-sources are of mainly anthropogenic origin off Texas, since both the nutrient loadings of Mississippi River and the spatial extent of the downstream red tides have increased over the last 100 years. During the past century and particularly within the last decade, previously cryptic Karenia spp. have caused toxic red tides in similar coastal habitats of other western boundary currents off Japan, China, New Zealand, Australia, and South Africa, downstream of the Gobi, Simpson, Great Western, and Kalahari Deserts, in a global response to both desertification and eutrophication

Phytoplankton Response to Intrusions of Slope Water on the West Florida Shelf: Models and Observations

Previous hypotheses had suggested that upwelled intrusions of nutrient-rich Gulf of Mexico slope water onto the West Florida Shelf (WFS) led to formation of red tides of Karenia brevis. However, coupled biophysical models of (1) wind- and buoyancy-driven circulation, (2) three phytoplankton groups (diatoms, K. brevis, and microflagellates), (3) these slope water supplies of nitrate and silicate, and (4) selective grazing stress by copepods and protozoans found that diatoms won in one 1998 case of no light limitation by colored dissolved organic matter (CDOM). The diatoms lost to K. brevis during another CDOM case of the models. In the real world, field data confirmed that diatoms were indeed the dominant phytoplankton after massive upwelling in 1998, when only a small red tide of K. brevis was observed. Over a 7-month period of the CDOM-free scenario the simulated total primary production of the phytoplankton community was ∼1.8 g C m−2 d−1 along the 40-m isobath of the northern WFS, with the largest accumulation of biomass on the Florida Middle Ground (FMG). Despite such photosynthesis, these models of the WFS yielded a net source of CO2 to the atmosphere during spring and summer and suggested a small sink in the fall. With diatom losses of 90% of their daily carbon fixation to herbivores the simulation supported earlier impressions of a short, diatom-based food web on the FMG, where organic carbon content of the surficial sediments is tenfold those of the surrounding seabeds. Farther south, the simulated near-bottom pools of ammonium were highest in summer, when silicon regeneration was minimal, leading to temporary Si limitation of the diatoms. Termination of these upwelled pulses of production by diatoms and nonsiliceous microflagellates mainly resulted from nitrate exhaustion in the model, however, mimicking most del15PON observations in the field. Yet, the CDOM-free case of the models failed to replicate the observed small red tide in December 1998, tagged with the del15N signature of nitrogen fixation. A large red tide of K. brevis did form in the CDOM-rich case, when estuarine supplies of CDOM favored the growth of the shade-adapted, ungrazed dinoflagellates. The usual formation of large harmful algal blooms of \u3e1 ug chl L−1 (105 cells L−1) in the southern part of the WFS, between Tampa Bay and Charlotte Harbor, must instead depend upon local aeolian and estuarine supplies of nutrients and CDOM sun screen, not those from the shelf break. In the absence of slope water supplies, local upwelling instead focuses nitrate-poor innocula of co-occurring K. brevis and nitrogen fixers at coastal fronts for both aggregation and transfer of nutrients between these phytoplankton groups

Biosynthetic Gene Cluster for the Cladoniamides, Bis-Indoles with a Rearranged Scaffold

The cladoniamides are bis-indole alkaloids isolated from Streptomyces uncialis, a lichen-associated actinomycete strain. The cladoniamides have an unusual, indenotryptoline structure rarely observed among bis-indole alkaloids. I report here the isolation, sequencing, and annotation of the cladoniamide biosynthetic gene cluster and compare it to the recently published gene cluster for BE-54017, a closely related indenotryptoline natural product. The cladoniamide gene cluster differs from the BE-54017 gene cluster in gene organization and in the absence of one N-methyltransferase gene but otherwise contains close homologs to all genes in the BE-54017 cluster. Both gene clusters encode enzymes needed for the construction of an indolocarbazole core, as well as flavin-dependent enzymes putatively involved in generating the indenotryptoline scaffold from an indolocarbazole. These two bis-indolic gene clusters exemplify the diversity of biosynthetic routes that begin from the oxidative dimerization of two molecules of l-tryptophan, highlight enzymes for further study, and provide new opportunities for combinatorial engineering

Characterisation of a new family of carboxyl esterases with an OsmC domain

Proteins in the serine esterase family are widely distributed in bacterial phyla and display activity against a range of biologically produced and chemically synthesized esters. A serine esterase from the psychrophilic bacterium Pseudoalteromonas arctica with a C-terminal OsmC-like domain was recently characterized; here we report on the identification and characterization of further putative esterases with OsmC-like domains constituting a new esterase family that is found in a variety of bacterial species from different environmental niches. All of these proteins contained the Ser-Asp-His motif common to serine esterases and a highly conserved pentapeptide nucleophilic elbow motif. We produced these proteins heterologously in Escherichia coli and demonstrated their activity against a range of esterase substrates. Two of the esterases characterized have activity of over two orders of magnitude higher than other members of the family, and are active over a wide temperature range. We determined the crystal structure of the esterase domain of the protein from Rhodothermus marinus and show that it conforms to the classical α/β hydrolase fold with an extended ‘lid’ region, which occludes the active site of the protein in the crystal. The expansion of characterized members of the esterase family and demonstration of activity over a wide-range of temperatures could be of use in biotechnological applications such as the pharmaceutical, detergent, bioremediation and dairy industries

Geology and Ground- Water Resources of the Lower Lodgepole Creek Drainage Basin, Nebraska

The area described is almost wholly in Nebraska and is the drainage basin of Lodgepole Creek from the Wyoming State line to the Colorado State line, a distance along the stream valley of about 95 miles. It covers about 1,950 square miles. The purposes of the study were to ascertain the characteristics, thickness, and extent of the water-bearing formations and to obtain and interpret data on the origin, quality, quantity, movement, availability, and use of ground water in the area. The rocks exposed in the drainage basin are the Brule formation of Oligocene (Tertiary) age, the Ogallala formation of Pliocene (Tertiary) age, and alluvium of Pleistocene and Recent (Quaternary) age. The Brule formation is mainly a siltstone, which yields an average of 950 gallons per minute (gpm) to irrigation wells tapping its fractured zones or reworked material; the maximum reported discharge is 2,200 gpm. The Ogallala formation underlies most of the area. It consists of lenticular beds of clayey, silty, sandy, and gravelly materials and supplies water to all wells on the upland, including a few large-discharge wells, and to many irrigation and public-supply wells in the valley of Lodgepole Creek. The yield of irrigation wells tapping the Ogallala formation ranges from 90 to 1,600 gpm and averages about 860 gpm. The alluvium is present in the valleys of Lodgepole Creek and its tributaries and consists mainly of heterogeneous . mixtures of silt, sand, and gravel, and lenticular bodies of these materials. Between the Colorado State line and Chappell, Nebr., irrigation wells derive most of their water from the alluvium. However, between Chappell and Sidney most of the irrigation wells tap both the alluvium and permeable zones in the underlying Brule formation, and in much of the valley west of Sidney, where the water table is beneath the bottom of the alluvium, irrigation wells derive water from the underlying Brule or Ogallala formations. Irrigation wells obtaining water chiefly from the alluvium have a yield ranging from 130 to 1,200 gpm, averaging about 770 gpm. In the Lodgepole Creek valley below Sidney the depth to water generally is less than 20 feet and, in many places, less than 10. In much of this part of the area the water table extends to the land surface or to the root zone of the vegetation, and discharge by evapotranspiration is high. In the valley of Lodgepole Creek between Sidney and the Wyoming State line, the depth to water generally ranges from less than 10 feet near the stream to more than 100 along the edge of the valley. In the upland the depth to water ranges from about 80 to about 300 feet