GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays

Monitoring of marine microalgae is important to predict and manage harmful algae blooms. It currently relies mainly on light-microscopic identification and enumeration of algal cells, yet several molecular tools are currently being developed to complement traditional methods. MIcroarray Detection of Toxic ALgae (MIDTAL) is an FP7-funded EU project aiming to establish a hierarchical multispecies microarray as one of these tools. Prototype arrays are currently being tested with field samples, yet the analysis of the large quantities of data generated by these arrays presents a challenge as suitable analysis tools or protocols are scarce. This paper proposes a two-part protocol for the analysis of the MIDTAL and other hierarchical multispecies arrays: Signal-to-noise ratios can be used to determine the presence or absence of signals and to identify potential false-positives considering parallel and hierarchical probes. In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration curves. Hybridization- and probe-specific detection limits can be calculated to help evaluate negative results. The suggested analyses were implemented in “GPR-Analyzer”, a platform-independent and graphical user interface-based application, enabling non-specialist users to quickly and quantitatively analyze hierarchical multispecies microarrays. It is available online at http://folk.uio.no/edvardse/gpranalyzer.     

Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta)

Phytoflagellates of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta) form blooms in marine coastal waters in northern Europe, Japan, and New Zealand that at times cause fish kills with severe losses for the aquaculture industry. The aim of this study was to develop molecular probes for the detection and identification of Pseudochattonella at the genus and species level. A variety of probes were developed and applied to either dot blot hybridization, (q)PCR, or microarray format. In the dot blot hybridization assay, five different oligonucleotide probes targeting the small subunit (SSU) rDNA were tested against DNA from 18 microalgal strains and shown to be specific to the genus Pseudochattonella. A genus-specific PCR assay was developed by identifying an appropriate primer pair in the SSU—internal transcribed spacer 1 (ITS1) rDNA region. Its specificity was tested by screening against both target and non-target strains, and the assay was used to confirm the presence or absence of Pseudochattonella species in environmental samples. In order to distinguish between the two species of the genus, two PCR primer pairs each biased towards one of the species were designed in the large subunit (LSU) rDNA D1 domain and used for quantitative real-time PCR. Five selected probes (three SSU and two LSU rDNA) were adapted for the use on microarrays and included on a prototype multi-species microarray for the detection of harmful algae (http://www.midtal.com). Finally, microarrays and qPCR were used for the monthly monitoring of a sampling site in outer Oslofjorden during a 1-year period. Members of Pseudochattonella are difficult to identify by light microscopy in Lugol’s preserved samples, and the two species Pseudochattonella verruculosa and Pseudochattonella farcimen can be morphologically distinguished only by transmission electron microscopy. The molecular probes designed in this study will be a valuable asset to microscopical detection methods in the monitoring of harmful algae and for biogeographical and ecological studies of this genus.     

developing a practical dispersion model for an air quality region

A series of computer models have been developed to predict air quality in the New York/New Jersey/Connecticut Air Quality Region. Efforts have been directed at models which have a shorter time scale than climatological models, and which are capable of providing better recommendations for effective abatement and planning, but use input data presently available.

The basic dispersion model for these investigations is a steady-state,nondivergent Gaussian-type model. A modified inventory of SO₂ sources,based on published data for the New York/New Jersey/Connecticut Air Quality Region, was prepared for use with the model. The basic model has been subjected to various internal sensitivity analyses, in which was isolated the variation produced in the pollutant concentration by a given change in each of the factors that contribute, e.g., wind speed, wind direction,mixing depth, stability conditions, source strengths, and grid size for the area sources.

To date, validation tests of the model have been made against the July and August 1969 data for the ten telemetering stations of the New York City Aerometric Network. Hourly as well as averaged concentrations were considered. Various sets of meteorological data from the network stations and the three area airports, were compared and tested. Additional tests, particularly for the winter season, are needed to substantiate the preliminary conclusions suggested by the results to date.

Considerable insight into the relative importance of model components has been acquired from the sensitivity studies. Furthermore the validation results lend support to the belief that a reasonably simple, practical dispersion model can be developed for the region.     

The enzymes involved in synthesis and utilization of carbamylphosphate in the deep-sea tube worm Riftia pachyptila

 The obligate symbiosis of the deep-sea tube worm Riftia pachyptila with a sulphur-oxidizing bacterium raises important questions concerning its metabolism and metabolic exchanges. In this study, the presence and properties of the enzymes synthesizing and utilizing carbamylphosphate in the arginine and pyrimidine nucleotide pathways were investigated in this worm. The results show that the ammonium-dependent carbamylphosphate synthetase and ornithine transcarbamylase, enzymes involved in the arginine pathway, are present in all body parts of the worm. In contrast, the glutamine-dependent carbamylphosphate synthetase and aspartate transcarbamylase, enzymes involved in the de novo pathway for pyrimidine nucleotides biosynthesis, are present only in the trophosome, the symbiont-harbouring tissue. Although the bacterial nature of these enzymes is not unambigously established, these results strongly suggest that the de novo biosynthesis of pyrimidine nucleotides is limited to the trophosome, the organ where the production of metabolic energy takes place, while the other parts of the worm's body rely on the salvage pathway for the production of the pyrimidine triphosphate nucleotides. Received: 22 June 1998 / Accepted: 26 October 1999     

Remediation of metalliferous mines,revegetation challenges and emerging prospects in semi-arid and arid conditions

Understanding plant behaviour in polluted soils is critical for the sustainable remediation of metal-polluted sites including abandoned mines. Post-operational and abandoned metal mines particularly in semi-arid and arid zones are one of the major sources of pollution by soil erosion or plant hyperaccumulation bringing ecological impacts. We have selected from the literature 157 species belonging to 50 families to present a global overview of ‘plants under action’ against heavy metal pollution. Generally, all species of plants that are drought, salt and metal tolerant are candidates of interest to deal with harsh environmental conditions, particularly at semi-arid and arid mine sites. Pioneer metallophytes namely Atriplex nummularia, Atriplex semibaccata, Salsola kali, Phragmites australis and Medicago sativa, representing the taxonomic orders Caryophyllales, Poales and Fabales are evaluated in terms of phytoremediation in this review. Phytoremediation processes, microbial and algal bioremediation, the use and implication of tissue culture and biotechnology are critically examined. Overall, an integration of available remediation plant-based technologies, referred to here as ‘integrated remediation technology,’ is proposed to be one of the possible ways ahead to effectively address problems of toxic heavy metal pollution.

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Graphical abstract Integrated remediation technology (IRT) in metal-contaminated semi-arid and arid conditions. The hexagonal red line represents an IRT concept based on remediation decisions by combination of plants and microbial processes.

     

Risk assessment of aquifer storage transfer and recovery with urban stormwater for producing water of a potable quality

The objective of the Parafield Aquifer Storage Transfer and Recovery research project in South Australia is to determine whether stormwater from an urban catchment that is treated in a constructed wetland and stored in an initially brackish aquifer before recovery can meet potable water standards. The water produced by the stormwater harvesting system, which included a constructed wetland, was found to be near potable quality. Parameters exceeding the drinking water guidelines before recharge included small numbers of fecal indicator bacteria and elevated iron concentrations and associated color. This is the first reported study of a managed aquifer recharge (MAR) scheme to be assessed following the Australian guidelines for MAR. A comprehensive staged approach to assess the risks to human health and the environment of this project has been undertaken, with 12 hazards being assessed. A quantitative microbial risk assessment undertaken on the water recovered from the aquifer indicated that the residual risks posed by the pathogenic hazards were acceptable if further supplementary treatment was included. Residual risks from organic chemicals were also assessed to be low based on an intensive monitoring program. Elevated iron concentrations in the recovered water exceeded the potable water guidelines. Iron concentrations increased after underground storage but would be acceptable after postrecovery aeration treatment. Arsenic concentrations in the recovered water continuously met the guideline concentrations acceptable for potable water supplies. However, the elevated concentration of arsenic in native groundwater and its presence in aquifer minerals suggest that the continuing acceptable residual risk from arsenic requires further evaluation.     

Wintering French Mallard and Teal Are Heavier and in Better Body Condition than 30?Years Ago: Effects of a Changing Environment?

Animal populations are exposed to large-scale anthropogenic impact from e.g. climate change, habitat alteration and supplemental stocking. All of these may affect body condition in wintering dabbling ducks, which in turn may affect an individual’s survival and reproductive success. The aim of this study was to assess whether there have been morphometric changes in Mallard (Anas platyrhynchos) and Teal (Anas crecca) over the last 30 years at a major wintering site. Body mass and condition increased from the 1950s–1960s to the 2000s in both species. The increase in body mass amounted to as much as 11.7%, with no corresponding change in body size. Improved body condition was maintained from early to mid-winter, but then converged with historical values for late winter. Our interpretation is that increasingly benign ambient winter conditions permit ducks to maintain better energetic “safety margins” throughout winter, and that converging spring departure values may be related to evolutionary flight energetic optima. The observed changes are consistent with large-scale climate amelioration and local/regional habitat improvement (both anthropogenic).     

Fine‐Sediment Loadings to Lake Tahoe1

Abstract: Over the past 35 years, a trend of decreasing water clarity has been documented in Lake Tahoe, attributable in part to the delivery of fine‐grained sediments emanating from upland and channel sources. The overall objective of the research reported here was to determine the amount of fine sediment delivered to Lake Tahoe from each of the 63 contributing watersheds. The research described in this report used combinations of field‐based observations of channel and bank stability with measured and simulated data on fine‐sediment loadings to estimate fine‐sediment loadings from unmonitored basins throughout the Lake Tahoe Basin. Loadings were expressed in the conventional format of mass per unit time but also in the number of particles finer than 20 μm, the latter for future use in a lake‐clarity model. The greatest contributors of fine sediment happened to be those with measured data, not requiring extrapolation. In descending order, they are as follows: Upper Truckee River [1,010 tonnes per year (T/year)], Blackwood Creek (846 T/year), Trout Creek (462 T/year), and Ward Creek (412 T/year). Summing estimated values from the contributing watersheds provided an average, annual estimate of fine‐sediment (<0.063 mm) loadings to the lake of 5,206 T/year. A total of 7.79E + 19 particles in the 5‐20 μm fraction were calculated to enter Lake Tahoe in an average year with the Upper Truckee River accounting for almost 25% of the total. Contributions from Blackwood, Ward, Trout, and Third creeks account for another 23% of these very fine particles. Thus, these five streams making up about 40% of the basin area, account for almost 50% of all fine‐sediment loadings to the lake. Contribution of fine sediment from streambank erosion were estimated by developing empirical relations between measured or simulated bank‐erosion rates with a field‐based measure of the extent of bank instability along given streams. An average, annual fine‐sediment loading from streambank erosion of 1,305 T/year was calculated. This represents about 25% of the average, annual fine‐sediment load delivered to the lake from all sources. The two largest contributors, the Upper Truckee River (639 T/year) and Blackwood Creek (431 T/year), account for slightly more than 80% of all fines emanating from streambanks, representing about 20% of the fine sediment delivered to Lake Tahoe from all sources. Extrapolations of fine‐sediment loadings to the unmonitored watersheds are based on documented empirical relations, yet contain a significant amount of uncertainty. Except for those values derived directly from measured data, reported results should be considered as estimates.