Problem formulation in the environmental risk assessment for genetically modified plants

Problem formulation is the first step in environmental risk assessment (ERA) where policy goals, scope, assessment endpoints, and methodology are distilled to an explicitly stated problem and approach for analysis. The consistency and utility of ERAs for genetically modified (GM) plants can be improved through rigorous problem formulation (PF), producing an analysis plan that describes relevant exposure scenarios and the potential consequences of these scenarios. A properly executed PF assures the relevance of ERA outcomes for decision-making. Adopting a harmonized approach to problem formulation should bring about greater uniformity in the ERA process for GM plants among regulatory regimes globally. This paper is the product of an international expert group convened by the International Life Sciences Institute (ILSI) Research Foundation.     

Ecological Effects of Metals in Streams on a Defense Materials Processing Site in South Carolina,USA

The Savannah River Site (SRS) is a 780 km² U.S. Department of Energy facility near Aiken, South Carolina, established in 1950 to produce nuclear materials. SRS streams are “integrators” that potentially receive water transportable contaminants from all sources within their drainage basins, necessitating a watershed approach to organize contaminant distribution data and characterize the effects of multiple contaminants on aquatic organisms. This study used several lines-of-evidence to assess the ecological effects of metals in SRS streams, including contaminant exposure models for apex predators and bioassessments of fish and macroinvertebrate assemblages. Concentrations of metals in sediments, fish, and water were elevated in streams affected by SRS operations, but contaminant exposure models for the river otter Lontra Canadensis and belted kingfisher Ceryle alcyon indicated that toxicological reference values were exceeded only by Hg and Al. Macroinvertebrate assemblage structure was unrelated to sediment metal concentrations. Fish assemblage data were inconclusive. This study indicated that (1) modeling studies and field bioassessments provide a complementary basis for addressing the individual and cumulative effects of contaminants, (2) habitat effects must be controlled when assessing contaminant impacts, (3) sensitivity analyses of contaminant exposure models can help to apportion sampling effort, and (4) most individual metals in SRS streams are unlikely to have significant ecological effects.     

Zoogeography, taxonomy, and conservation of West Virginia's Ohio River floodplain crayfishes (Decapoda, Cambaridae)

The crayfish fauna of West Virginia consists of 23 species and several undescribed taxa. Most survey efforts documenting this fauna have been conducted in lotic waterways throughout the Appalachian plateau, Allegheny Mountains, and Ridge and Valley physiographic provinces. Bottomland forests, swamps, and marshes associated with large river floodplain such as the Ohio River floodplain historically have been under-surveyed in the state. These habitats harbor the richest primary burrowing crayfish fauna in West Virginia, and are worthy of survey efforts. In an effort to fill this void, the crayfish fauna of West Virginia's Ohio River floodplain was surveyed from 2004 through 2009. From this survey, nine species from four genera were documented inhabiting the floodplain. Zoogeography, biology, and conservation status is provided for all nine crayfishes. The dominant genus along the floodplain is Cambarus, which includes Cambarus (Cambarus) carinirostris, Cambarus (Cambarus) bartonii cavatus, Cambarus (Procambarus) robustus and Cambarus (Tubericambarus) thomai. Cambarus (Tubericambarus) thomai is the most prevalent burrowing species occurring along the floodplain. The genus Orconectes consists of two native species, Orconectes (Cambarus) obscurus and Orconectes (Cambarus) sanbornii; and two invasive taxa, Orconectes (Gremicambarus) virilis and Orconectes (Procambarus) rusticus. Orconectes (Cambarus) obscurus has experienced a range extension to the south and occupies streams formerly occupied by Orconectes (Cambarus) sanbornii. Both invasive taxa were allied with anthropogenic habitats and disturbance gradients. The genera Fallicambarus and Procambarus are represented by a single species. Both Fallicambarus (Cambarus) fodiens and Procambarus (Orconectes) acutus are limited to the historic preglacial Marietta River Valley.     

A freeze-etch study of the phototactic zoospores ofPhlyctochytrium sp., a marine fungus

Summary The major difference between freeze-etched illuminated and non-illuminatedPhlyctochytrium zoospores was in the plasmalemma. The illuminated spores had abundant 15–18 nm freeze fracture particles on the PF surface of the plasmalemma in a region external to the rumposomal complex. Non-illuminated spores show fewer and smaller (6–12 nm) freeze fracture particles on the PF surface of the plasmalemma external to the rumposomal complex. Both illuminated and non-illuminated zoospores have rumposomal complexes, nuclear caps, mitochondria, nuclei, and a variety of cytoplasmic vesicles. The nuclear pores were not randomly distributed over the surface of the zoospore nucleus. Micrographs of nuclei in developing sporangia indicate pore formation in the region of the nuclear pockets.A portion of this study was carried out at the Virginia Institute of Marine Science, Gloucester Point, Virginia.     

Short read sequence typing (SRST): multi-locus sequence types from short reads

ABSTRACT: BACKGROUND: Multi-locus sequence typing (MLST) has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven) to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. RESULTS: We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST assigns alleles using read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. CONCLUSIONS: SRST is a novel software tool for accurate assignment of sequence types using short read data. Several uses for the tool are demonstrated, including quality control for high-throughput sequencing projects, plasmid MLST and analysis of genomic data during outbreak investigation. SRST is open-source, requires Python, BWA and SamTools, and is available from http://srst.sourceforge.net.     

Spatiotemporal assessment of Sickle Darter (Percina williamsi Page and Near, 2007) distribution in the upper Tennessee River Basin

The Sickle Darter Percina williamsi (Page and Near, 2007) is a species of fish endemic to the upper Tennessee River basin in eastern Tennessee, southwestern Virginia, and western North Carolina. Because of its narrow range and presumed decline in occupied sites over the last half century, it is being proposed for federal listing under the Endangered Species Act. We analyzed the current distribution of the Sickle Darter and temporal trends in its distribution in relation to temporal trends in environmental and habitat covariates for each of the historically occupied sub-basins (upper Clinch, Emory, upper French Broad, Little, Little Pigeon, Middle Fork Holston, North Fork Holston, Powell, South Fork Holston, and Watauga) with multiple linear regression modelling. A total of 154 Sickle Darters were observed at 15 sites throughout the upper Tennessee River Basin. Sickle Darters were observed in the Little River, Emory River, and Middle Fork Holston River sub-basins. A total of 133 unique historical occurrences were used for the spatiotemporal analyses. Sickle Darters have declined in 8 out of 10 historically occupied sub-basins. Our best model for the whole distribution scale (Mallow's Cp = −0.87; Adjusted R² = .92) suggests that habitat fragmentation due to damming has had adverse effects on Sickle Darter populations across its distribution. Models were very similar for the sub-basin specific models as well. The results from this study highlight the drivers of decline in Sickle Darter distribution and outline the future research needs for this species that should be used to inform future conservation decisions regarding this species.     

Protozoan species accrual on artificial islands in differing lentic and wetland systems

In the recently broadened context of insular biogeographic theory, artificial substrates might well be considered as initially barren islands with the surrounding natural community acting as a source pool of potential colonists. In an attempt to relate protozoan communities forming on polyurethane foam (PF) substrates to their environments, a series of field experiments were performed in several aquatic and semi-aquatic (wetlands) systems in Michigan, Virginia, and Colorado. Results were considered in the context of island colonization theory.Given relatively stable environmental conditions and sufficient time to colonize, protozoa formed highly replicable communities on PF substrates; MacArthur & Wilson's equation for noninteractive island colonization, S = Seq ·(l-e^–Gt ), accuratelt described the process of species accrual in most cases. Sites were compared using non-linear regression estimates of the parameter, G, which reflects the rate at which substrates attained equilibrium species numbers. In general, the rate of equilibrium acquisition reflected differences in productivity and structure between the protozoan communities from the various habitats and systems studied.     

Site-Specific Derivation of the Acute Copper Criteria for the Clinch River,Virginia

Previous studies indicated that inputs from the Clinch River Plant (CRP), a coal-burning, power-generating facility in Carbo, Virginia, caused impairment to transplanted freshwater mussels. These findings necessitated the examination of instream biological responses to CRP effluents. Therefore, our objective was to derive a site-specific Criterion Maximum Concentration (CMC) for copper (Cu), the toxic constituent of the effluent. This was accomplished by conducting acute toxicity tests with Cu using 17 different genera native to or currently residing in the Clinch River watershed. Four native unionids and a mayfly (Isonychia bicolor) had genus mean acute values of 60?µJ.g/L or lower (ranging from 37 to 60?µJ,g/L). With a GMAV of 88?µJ,g/L, Ceriodaphnia dubia ranked sixth among the 17 genera tested, and the fathead minnow, Pimephales promelas, ranked fourteenth with a GMAV of 310?µJ.g/L. Despite the sensitivity of the indigenous mussels tested, the site-specific CMC of 18?µJg/L was not substantially lower than the national CMC for Cu (20?µJ,g/L, hardness = 150?mg/L as CaCO3). While we conducted acute exposure tests, future investigations should incorporate both biomarker and population or community-level studies to determine low-level contaminant impacts on freshwater mussels.     

In-Situ Remediation of TCE in Clayey Soils

The remediation of solvent contaminated low permeable soils poses a significant problem for many facilities. A consortium of industrial partners (Monsanto, DuPont and General Electric), the USEPA and the DOE jointly developed a technology that integrates electrokinetics with in-situ treatment of chlorinated organics to address this problem. The process, called Lasagna^TM, utilizes a DC electric field to move pore water and contaminants uniformly through the soil mass to treatment zones emplaced within the contaminated area. The emplacement is performed using common piling technologies and results in little or no wastes. The treatment materials emplaced are typically iron, coke and kaolin. After two in-field demonstrations, a full-scale Lasagna remediation system was implemented at the DOE facility in Paducah, KY for the remediation of TCE contaminated clay soils. The system was installed and operated over a two-year period. The process was shut down in December 2001 after meeting the cleanup target of 5.6 mg/kg specified by the Record of Decision (ROD) for the site. The final results show an average TCE concentration of 0.38 mg/kg.     

The Southern Churchill, Petrocephalus Wesselsi, a New Species of Mormyrid from South Africa defined by Electric Organ Discharges, Genetics, and Morphology

East African and south African churchills (Petrocephalus, Mormyridae) were synonymised in 1959 to become members of a single species of subcontinental, southern African distribution, Petrocephalus catostoma (Günther, 1866). By comparison with the type material for P. catostoma from the Ruvuma River and P. stuhlmanni from the Ruvu River, both of East African origin, we confirm the South African form of churchill to represent a new species, P. wesselsi, ranging from the northern Limpopo and Incomati systems south to the Pongola River (Natal) as its southern limit. We also compared churchills from the Sabie River (25° S, South Africa, Incomati system) with churchills from the Upper Zambezi River (17° S, Namibia), using electric organ discharges (EODs) and morphology. The duration of an EOD pulse of the South African form (N = 39; 943.2±S.E. 18.82µs) is, on average, more than twice that of the Upper Zambezi form (N = 37; 436.6±15.1µs), and the amplitude of the second head-positive phase (P2 phase relative to P1 = 1) significantly weaker (0.133 ± 0.0005 vs. 0.472 ± 0.002 for Upper Zambezi males, 0.363 ± 0.03 for Upper Zambezi females). In contrast to the Upper Zambezi form, the EOD of the South African form exhibits no difference between the sexes. Fish from the two origins differ significantly in 11 out of 14 anatomical characters studied, confirming molecular genetic differentiation on the species level.     

Medium term planning of biopharmaceutical manufacture using mathematical programming

Regulatory pressures and capacity constraints are forcing the biopharmaceutical industry to consider employing multiproduct manufacturing facilities running on a campaign basis. The need for such flexible and cost-effective manufacture poses a significant challenge for planning and scheduling. This paper reviews the problem of planning and scheduling of biopharmaceutical manufacture and presents a methodology for the planning of multiproduct biopharmaceutical manufacturing facilities. The problem is formulated as a mixed integer linear program (MILP) to represent the relevant decisions required within the planning process and is tested on two typical biopharmaceutical industry planning problems. The proposed formulation is compared with an industrial rule based approach, which it outperforms in terms of profitability. The results indicate that the developed formulation offers an effective representation of the planning problem and would be a useful decision tool for manufacturers in the biopharmaceutical industry particularly at times of limited manufacturing capacity.     

Light,temperature and flow regimes of the Vaal River at Balkfontein,South Africa

A detailed investigation into light, temperature and flow regimes of the Vaal River was done for the first time. The Vaal River is ecologically and economically one of the most important rivers in South Africa. In a South African context, the Vaal River, with an average Secchi disk depth (Z _sd) of 0.41 m and an average euphotic zone depth (Z _eu) of 1.3 m, is a moderately turbid system. Red light (approx. 670 nm) penetrated Vaal River water to a greater degree than other components of the light spectrum. Water temperature in the Vaal River (min. = 10, max. = 27 °C at midday), closely followed seasonal changes in average atmospheric temperatures. The water-column shows little temperature stratification. The Vaal River is a highly regulated system with relatively high discharge rates at Balkfontein (average 112 m³ s^–1), but relatively low current velocity (approx. 0.35 m s^–1). Discharge was the most important variable to influence transparency of Vaal River water. Higher discharge resulted in higher total suspended solids (TSS) concentration and higher extinction coefficient (k) values as well as in higher turbidity and thus in lower Z _eu and Z _sd. From the mean TSS (141 mg l^–1) it was calculated that the Vaal River (mean annual run-off of 3532 million m³) transported 498016 tonnes of suspended solids per annum.     

Formulation and Release Behavior of Doxycycline–Alginate Hydrogel Microparticles Embedded into Pluronic F127 Thermogels as a Potential New Vehicle for Doxycycline Intradermal Sustained Delivery

The aim of this work was the formulation and characterization of alginate (ALG)–doxycycline (DOX) hydrogel microparticles (MPs) embedded into Pluronic F127 thermogel for DOX intradermal sustained delivery. ALG–DOX MPs were formed by adding a solution of the drug into a 1.5% polymer solution while stirring. The MPs were cross-linked by dispersion into a 1.2% CaCl₂ solution. Free MPs were characterized in terms of size, drug content, and release behavior by HPLC and UV–vis. DOX and hydrogel MPs were embedded into PF127, PF127-HPMC, and PF127-Methocel thermogels. The thermogels were characterized in terms of gelling time, morphology, and release behavior. A target release period of 4–7 days was considered optimal. The hydrogel MPs were about 20 μm in size with 90% of the population <59 μm. Drug content was about 35% (w/w). DOX released rapidly from the MPs, 90% within 2 days. An expected faster release was observed for free DOX from the thermogels with 80–90% of drug released after 3.5–4 h even in the presence of 1% HPMC or Methocel. The release was sustained after embedding the MPs into PF127 and PF127-HPMC thermogels. In particular, the PF127-HPMC thermogel showed an almost linear release, reaching 80% after 3 days and 90% up to 6 days. Although a further characterization and formulation assessment is required to optimize MP characteristics, ALG/DOX-loaded hydrogel MPs, when embedded into a PF127-HPMC thermogel, show a potential for achieving a 7-day sustained release formulation for DOX intradermal delivery.     

Fruit fly liquid larval diet technology transfer and update

Since October 2006, the US Department of Agriculture–Agricultural Research Service (USDA–ARS) has been implementing a fruit fly liquid larval diet technology transfer, which has proceeded according to the following steps: (1) recruitment of interested groups through request; (2) establishment of the Material Transfer Agreement with agricultural research service; (3) fruit fly liquid larval diet starter kit sent to the requestor for preliminary evaluation; (4) problem‐solving through email or onsite demonstration; (5) assessment on feedback from the participants to decide whether to continue the project. Up to date, the project has involved 35 participants from 29 countries and 26 species of fruit flies. Fourteen participants have concluded their evaluation of the process, and 11 of these 14, have deemed it to be successful. One participant has decided to implement the project on a larger scale. The 14 participants were, Argentina (Ceratitis capitata and Anastrepha fraterculus), Bangladesh (Bactrocera cucurbitae, C. capitata, and Bactrocera dorsalis), China (Fujia province) (B. dorsalis), Italy (C. capitata), Fiji (Bactrocera passiflorae), Kenya (Bactrocera invadens, Ceratitis cosyra), Mauritius (Bactrocera zonata and B. cucurbitae), Mexico (Anastrepha species), Philippines (Bactrocera philippinese), Thailand (Bactrocera correcta), Austria (C. capitata, Vienna 8 and A. fraterculus), Israel (Dacus ciliatus and C. capitata), South Africa (C. capitata, Vienna 8) and Australia (C. capitata). The Stellenbosch medfly mass‐rearing facility in South Africa and the CDFA in Hawaii were two mass‐scale rearing facilities that allowed us to demonstrate onsite rearing in a larger scale. Demonstrations were performed in CDFA in 2007, and in Stellenbosch, South Africa in 2008; both were found to be successful. The Stellenbosch medfly mass‐rearing facility in South Africa decided to adopt the technology and is currently evaluating the quality control of the flies that were reared as larvae on a liquid diet.     

NEW DISTRIBUTION RECORD FOR CHILOGLANIS BIFURCUS JUBB AND LE ROUX, 1969 IN A TRIBUTARY OF THE CROCODILE RIVER,MPUMALANGA PROVINCE,SOUTH AFRICA

Summary

A new distribution record for the South African Red Data fish species Chiloglanis bifurcus was found in the Nels River at an altitude of 830 m a.m.s.l. in the Mpumalanga province, South Africa. Previously this species was known to occur between altitudes 900 m and 1200 m a.m.s.l. in the Elands and Crocodile Rivers of the Inkomati River system, as well as in tributaries of these rivers, namely the Gladdespruit, Stadspruit and Ngodwana River. It was also found to occur in the Komati River of the same river system.     

Hydrilla verticillata (Hydrocharitaceae), a recent invader threatening Brazil’s freshwater environments: a review of the extent of the problem

Hydrilla verticillata (Hydrocharitaceae) is a highly prolific, rooted submerged macrophyte native to Asia that has invaded aquatic systems worldwide, causing many ecological and human-related problems. Hydrilla recently invaded the Paraná River basin in Brazil, making other ecologically and socially important Brazilian watersheds more susceptible to invasion by this plant. Here, I summarize the relevant information about Hydrilla, focusing on its biotic attributes, abiotic tolerance and effects on ecosystems. The aim of this review is to provide background information to assist with planning for the potential impacts of this species in the Neotropical region (particularly in Brazil) and the development of research, monitoring and management strategies. A wide ecological amplitude, resistance organs, and high growth rates and dispersion ability provide Hydrilla with great potential to invade and infest a variety of habitats, often resulting in important physico-chemical and biotic effects on the environment. Hydrilla is similar in its morphological and ecological aspects to Egeria najas and Egeria densa (South American Hydrocharitaceae), but this non-native species is a superior competitor and can be expected to exert significant pressure in habitats colonized by these native Hydrocharitaceae. Socially important rivers (such as the S?o Francisco River) have a high risk of being infested with Hydrilla, especially in stretches affected by dams, which could prejudice important human activities like hydropower generation. Important wetlands for biodiversity conservation (such as the Pantanal) may also be invaded, but they seem to be more resistant to infestations as long as their natural hydrologies are preserved. Before investing substantial effort to control Hydrilla, managers should weigh the potential costs and benefits of available techniques and consider the potential benefits of Hydrilla in providing ecosystem services.     

Species composition,distribution, and abundance of oligochaetes in the Kanawha River,West Virginia

Species composition, distribution, and abundance of oligochaetes in the Kanawha River, West Virginia, were investigated. Eighteen taxa of oligochaetes including 7 tubificids, 8 naidids, and representatives of the families Enchytraeidae, Lumbriculidae, and Aelosomatidae were collected. While most of the species collected are cosmopolitan, Pristina synclites and Stephensoniana sp. previously reported only from Asia and Africa were collected in the Kanawha. Other peculiarities of the Kanawha oligochaete fauna included the common occurrence of specimens of Limnodrilus cervix and Limnodrilus hoffmeisteri with atypical penis sheaths. The dominant and most widely distributed of the Kanawha River oligochaetes were immature tubificids lacking capilliform chaetae, Branchiura sowerbyi, Dero cf. obtusa, Limnodrilus hoffmeisteri, and Aulodrilus pigueti.Oligochaete densities ranged from 401–2403 individuals/m² in areas presumed to be nonpolluted, to 1–671 individual/m² at sites with suspected toxicity. The highest density of oligochaetes (2835 individuals/m²) occurred at a site of organic enrichment.     

Quarantine host range studies with Lophyrotoma zonalis, an Australian sawfly of interest for biological control of melaleuca, Melaleuca quinquenervia, in Florida, U.S.A.

The Australian melaleuca tree, Melaleuca quinquenervia (Cav.) S. T. Blake (Myrtaceae), has naturalized in southern Florida,U.S.A., and is now one of that regions most important weeds.Primarily a weed of wetlands, it also infests neighboring drierareas. Current efforts to restore the South Florida ecosystem arethreatened by the continuing range expansion of melaleuca andother weeds. In an effort to supplement the current chemical andcultural control methods for melaleuca, a search for potentialbiological control agents was begun in Australia in 1986. Thesawfly, Lophyrotoma zonalis, was determined after extensive fieldand laboratory studies to have potential as a biological controlagent. Larvae of L. zonalis eat leaves and occasionally defoliatelarge trees in Australia. Host range studies were conducted in aFlorida quarantine facility with native and cultivated plantspecies. Multi-choice and no-choice oviposition tests wereconducted with 36 species in the Myrtaceae and with 18 species inother families. Larvae developed to prepupae and adults from theeggs oviposited on 23 species of Myrtaceae only on 3 species ofbottlebrushes, Callistemon. Medium-sized larvae were tested forfeeding on bouquets of plant cuttings and on potted plants. Theyare the stage that might wander from defoliated trees. Noticeablefeeding, but much less than on melaleuca, was restricted to theMyrtaceae, except for a few individual larvae that fed on waxmyrtle, Myrica cerifera. Medium-sized larvae became prepupae onlyon Melaleuca decora (73%) and on wax myrtle (10%). However,neither species received eggs in the oviposition tests. Thesestudies confirmed the narrow host range of L. zonalis aspreviously reported from field and laboratory studies inAustralia.     

The abundance of an invasive freshwater snail Tarebia granifera (Lamarck, 1822) in the Nseleni River,South Africa

The invasive freshwater snail Tarebia granifera (Lamarck, 1822) was first reported in South Africa in 1999 and it has become widespread across the country, with some evidence to suggest that it reduces benthic macroinvertebrate biodiversity. The current study aimed to identify the primary abiotic drivers behind abundance patterns of T. granifera, by comparing the current abundance of the snail in three different regions, and at three depths, of the highly modified Nseleni River in KwaZulu-Natal, South Africa. Tarebia granifera was well established throughout the Nseleni River system, with an overall preference for shallow waters and seasonal temporal patterns of abundance. Although it is uncertain what the ecological impacts of the snail in this system are, its high abundances suggest that it should be controlled where possible and prevented from invading other systems in the region.