Perfluoroalkyl acids in the Canadian environment: multi-media assessment of current status and trends.

In Canada, perfluoroalkyl acids (PFAAs) have been the focus of several monitoring programs and research and surveillance studies. Here, we integrate recent data and perform a multi-media assessment to examine the current status and ongoing trends of PFAAs in Canada. Concentrations of perfluorooctane sulfonate (PFOS), perfluorooctanoate (PFOA), and other long-chain perfluorocarboxylates (PFCAs) in air, water, sediment, fish, and birds across Canada are generally related to urbanization, with elevated concentrations observed around cities, especially in southern Ontario. PFOS levels in water, fish tissue, and bird eggs were below their respective Draft Federal Environmental Quality Guidelines, suggesting there is low potential for adverse effects to the environment/organisms examined. However, PFOS in fish and bird eggs tended to exceed guidelines for the protection of mammalian and avian consumers, suggesting a potential risk to their wildlife predators, although wildlife population health assessments are needed to determine whether negative impacts are actually occurring. Long-term temporal trends of PFOS in suspended sediment, sediment cores, Lake Trout (Salvelinus namaycush), and Herring Gull (Larus argentatus) eggs collected from Lake Ontario increased consistently from the start of data collection until the 1990s. However, after this time, the trends varied by media, with concentrations stabilizing in Lake Trout and Herring Gull eggs, and decreasing and increasing in suspended sediment and the sediment cores, respectively. For PFCAs, concentrations in suspended sediment, sediment cores, and Herring Gulls generally increased from the start of data collection until present and concentrations in Lake Trout increased until the late 1990s and subsequently stabilized. A multimedia comparison of PFAA profiles provided evidence that unexpected patterns in biota of some of the lakes were due to unique source patterns rather than internal lake processes. High concentrations of PFAAs in the leachate and air of landfill sites, in the wastewater influent/effluent, biosolids, and air at wastewater treatment plants, and in indoor air and dust highlight the waste sector and current-use products (used primarily indoors) as ongoing sources of PFAAs to the Canadian environment. The results of this study demonstrate the utility of integrating data from different media. Simultaneous evaluation of spatial and temporal trends in multiple media allows inferences that would be impossible with data on only one medium. As such, more co-ordination among monitoring sites for different media is suggested for future sampling, especially at the northern sites. We emphasize the importance of continued monitoring of multiple-media for determining future responses of environmental PFAA concentrations to voluntary and regulatory actions.

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.

Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome.

Occurrence of glyphosate and acidic herbicides in select urban rivers and streams in Canada, 2007.

INTRODUCTION: Public and scientific concern has grown over the last decade in Canada over the cosmetic use of pesticides in urban centers. With this in mind, a national survey was designed to monitor eight commonly used herbicides in urban rivers and streams across Canada. MATERIALS AND METHODS: To coordinate sample collections across the country, samples were collected monthly on one of two predetermined dates from April to September, 2007 from 19 sites within 16 watersheds, including 15 sites downstream of urban lands and two reference sites. Water samples were also collected approximately three times from each watershed during or after precipitation events. All samples were collected using a common sampling protocol and all were analyzed using the same analytical laboratories. RESULTS AND DISCUSSION: The herbicides 2,4-D, mecoprop, dicamba, glyphosate and its major metabolite aminomethylphosphonic acid (AMPA) were most frequently detected. Using either herbicide concentrations upstream/downstream of urban centers or bromoxynil and clopyralid as indictors of agricultural inputs of herbicides to streams, it was clear that environmental concentrations of these herbicides downstream of urban areas were linked to urban use in Canada. Herbicide concentrations in streams draining urban areas were greater during or after significant rainfall events and, with the exception of glyphosate, were significantly greater in the Province of Ontario. Herbicide concentrations were not correlated to the proportion of the watersheds in urban land use. Also, there was no difference in seasonal patterns of herbicide concentrations across urban centers when grouped in five geographic areas. None of the herbicide concentrations measured exceeded existing Canadian Water Quality Guidelines for the protection of aquatic life. CONCLUSIONS: This is the first time a national survey of pesticides in urban rivers has been carried out in a consistent fashion across Canada. Concentrations of 2,4-D, mecoprop, dicamba, glyphosate, and AMPA were linked to urban use and frequently detected in all geographic areas. However, geographic differences in concentration suggested differences in usage or stream connectivity patterns among urban centers. Some jurisdictions in Canada have recently restricted cosmetic use of pesticides and it would be interesting to determine whether such restrictions will lead to reduced pesticide concentrations in urban streams.

Occurrence and distribution of sulfonylurea and related herbicides in central Canadian surface waters 2006-2008.

Surface water sampling in 2006-2008 measured the occurrence of sulfonylureas and related herbicides (SUs) during base flow conditions and wet weather events. Flumetsulam (29.2%), diuron (36.5%) and fomesafen (25.3%) were most frequently detected over the course of the study. Typical SU concentrations were in the low parts per trillion range; however, maximum concentrations of fomesafen (873 ng/L), linuron (856 ng/L) and diuron (2,900 ng/L) approached or exceeded 1 µg/L. The temporal trend in SUs showed a correlation with application periods. In general, detections of SUs were more frequent where rotation of row crops was more intense. Sampling during wet-weather events indicated potential for a range of SUs to be flushed into surface waters at relatively high concentrations.

Evaluation of genes from eIF4E and eIF4G multigenic families as potential candidates for partial resistance QTLs to Rice yellow mottle virus in rice.

QTLs for partial resistance to Rice yellow mottle virus (RYMV) in rice were mapped in two populations of doubled-haploid lines (DHLs) and recombinant inbred lines (RILs) derived from the same cross but evaluated for different resistance criteria (virus content and symptom severity). An integrative map was used to compare the two genetic maps and a global analysis of both populations was performed. Most of the QTLs previously identified in DHL population were confirmed with increased significance and precision. As many recent studies evidenced the role of eukaryotic translation initiation factors (eIF) of 4E and 4G families in plant susceptibility to RNA viruses, we checked if these genes co-locate with QTLs of resistance to RYMV. Their systematic in silico identification was carried out on the rice genome and their physical locations were compared to QTL positions on the integrative map. In order to confirm or not the co-locations observed, the analysis was completed by evaluation of near-isogenic lines, QTL fine mapping and sequencing of candidate genes. Three members from eIF4G family could be retained as reliable candidates whereas eIF4E genes, commonly found to govern resistances in other plant/virus interactions, were discarded. Together with the recent identification of an eIF(iso)4G as a major resistance gene, data suggests an important role of genes from eIF4G family in rice resistance to RYMV but does not exclude the contribution of factors different from the translation initiation complex.

SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus.

Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST-SSRs) with a motif length of 1-6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST-SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST-SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.