An easy,accurate and efficient procedure to create forest fire risk maps using the SEXTANTE plugin Modeler

To prevent, detect, and protect against forest fires, forest personnel need to define rules for determining forest fire risk. In Portugal, all municipalities must annually produce forest fire risk(FFR) maps. To produce more reliable FFR maps more easily, we developed an open source model using the Modeler plugin of SEXTANTE in the program QGIS version 2.0 Dufour. The model provides all the maps involved in the FFR model(susceptibility map, hazard map, vulnerability map, economic value map,and potential loss map) and was produced according to Portuguese Forest Authority's(AFN, Autoridade Florestal Nacional) rules for determining the FFR. This model was tested for the Portuguese municipality Santa Maria da Feira, where 40 % of the total municipality area falls in the category ‘‘very high' or ‘‘high' fire risk. The ‘‘very high'fire risk area is mainly classified as broad-leaved forest and has the steepest slopes(15 %). The distance of burned areas to roads was also analyzed; the proportion of burned areas increased with increasing distance to the main roads.In addition, 92.6 % of the ‘‘high' and ‘‘very high' risk zones were located in areas with lower elevation. These results confirmed that forest fire is strongly influenced not only by environmental factors but also by anthropogenic factors. The procedure implemented here was compared with our open source application already available in QGIS and also to the same procedure implemented in GIS proprietary software. Although the results were obviously the same, the model developed here presents several advantages over the other two approaches. Besides being faster,it is easy to change the model parameters according to user needs(i.e., to the rules of different countries), and can be modified and adapted to other variables and other areas to create risk maps for different natural phenomena(e.g.,floods, earthquakes, landslides). The model is easy to use and to create risk and hazard maps rapidly in a free, open source environment that does not require any programming knowledge.     

Physical forcing on fish abundance in the southern California Current System

The California Current System (CCS) is an eastern boundary current system with strong biological productivity largely due to seasonal wind‐driven upwelling and transport of the California Current (CC). Two independent, yet complementary time series, CalCOFI ichthyoplankton surveys and sampling of southern California power plant cooling‐water intakes, have indicated that an assemblage of predominantly cool‐water affinity fishes spanning nearshore to oceanic environments in the southern CCS has declined dramatically from the 1970s to the 2000s. We examined potential oceanographic drivers behind this decline both within and north of the CalCOFI survey area in order to capture upstream processes as well. Empirical orthogonal function (EOF) analyses using output from a data‐assimilative regional ocean model revealed significant relationships between the fish time series and spatial patterns of upwelling, upper ocean heat content and eddy kinetic energy in the CCS. Correlation and linear regression analyses indicated that the declining trend in fish abundance was correlated with a suite of factors: reduced offshore and increased inshore upwelling; a long term warming trend combined with more recent interannual variability in ocean temperature; weaker eddy kinetic energy north of Point Conception (35°N), potentially indicating reduced transport of the California Current (CC); increased influence of the California Undercurrent (CUC); and a decline in zooplankton displacement volume across the southern CCS. Understanding how changes in oceanography affect fish populations will offer insights into managing fisheries in a changing climate.     

Interference elimination of PCB and its ramification in determining trace PBBs/PBDEs by GC/MS

The normal method to determine the trace brominated flame retardants such as polybrominated biphenyls (PBBs) and polybrominated diphenylethers (PBDEs) contained in the electronic and electrical products is gas chromatography/mass spectrometry (GC/MS). However, the method is based on the determinations of the persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs), and polychlorinated naphthalene (PCNs) etc. The interferences of those compounds are inevitable. Therefore, in order to overcome this problem, two methods e.g. 1) The combination use of gas chromatography negative ion chemical ionization mass spectrometry (GC-NICI-MS) and gas chromatography-electron impact-mass spectrometry (GC-EI-MS) is employed, 2) a matrix solid-phase dispersion (MSPD) method with YMC ODS-C18 as carrier is developed. The result show that, by the former method, the brominated isomers or ramifications are distinguished remarkably from other halogen compounds because that anion fragment retention peaks of ［Br］-, ［HBr2］- and molecule chain fragment retention peaks of ［M+2］+,［M+4］+,［M+6］+,［M+8］+ are observed simultaneously, and thus the selectivity to determine bromine-containing retardant flames is greatly improved. Using the latter method, the gas chromatographic peaks of multiple polychlorinated biphenyls and polybrominated diphenylethers can be efficiently separated. Thus provides a project to solve interferences of POPs in brominated flame retardants’ determinations. The standard addition experimental results of 10 kinds of BDEs/PCBs belonging to 8 sorts of electronic and electrical equipment show this method has a high precision and reliability due to 60%～98% recovery and <9.5% relative error, which meet the needs regulated by the IEC Commission. It provides a technical support for electronic and eletrical industries in China to further comply with RoHS directive.     

‘Candidatus Phytoplasma australiense’ is the phytoplasma associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases

Sequence comparisons and phylogenetic analysis of the 16S rRNA genes and the 16S/23S spacer regions of the phytoplasmas associated with Australian grapevine yellows, papaya dieback and Phormium yellow leaf diseases revealed minimal nucleotide differences between them resulting in the formation of a monophyletic group. Therefore, along with Australian grapevine yellows, the phytoplasmas associated with Phormium yellow leaf and papaya dieback should also be considered as Candidatus Phytoplasma australiense.     

An investigation of Salmonella Fluntern illnesses linked to leopard geckos—United States, 2018

Reptile contact can result in zoonotic non‐typhoidal salmonellosis. In April 2018, Oregon Public Health Division contacted CDC about a cluster of four Salmonella serovar Fluntern (SF) illnesses in four states (OR, CA, IA, NY); patients reported contact with geckos, a popular reptile pet. PulseNet, the national molecular subtyping network of food‐borne disease surveillance, subsequently identified additional SF clinical isolates. Twelve cases in 11 states were identified; median age was 5 years (range: <1–58 years). Three patients were hospitalized; no deaths were reported. Of those with exposure information (n = 10), all reported reptile exposure; 9 (90%) specified contact with leopard geckos. No common source of geckos was identified from reported purchase locations. Los Angeles County (LAC) health officials isolated SF from one patient's leopard gecko. Five reptile/gecko isolates were identified from the USDA National Veterinary Services Laboratories (NVSL) from 2015 to 2018. Five countries responded to an Epidemic Intelligence Information System post by PulseNet; reptile isolate sequence data were received from Czech Republic. A clinical case from England was identified through the National Center for Biotechnology Information pathogen detection pipeline; the patient did not report contact with leopard geckos. Whole genome sequencing analysis revealed substantial genetic diversity between clinical and animal isolates; however, gecko and clinical isolates from LAC were highly related (1 allele difference). This investigation linking SF illnesses to leopard geckos highlights an important public health risk from pets. A better understanding of how geckos are distributed by the pet industry in the United States could improve traceability to points of origin and mitigate Salmonella transmission at gecko breeders. Earlier NVSL reports of SF isolates from geckos suggest the risk of human SF infection from geckos is not new. This investigation demonstrates a need to educate gecko breeders, retailers and gecko owners about the continued Salmonella infection risk from pet geckos.     

New insights into the morphology, molecular characterization and identification of Baylisascaris transfuga (Ascaridida, Ascarididae)

Species ranked within the genus Baylisascaris (Ascaridida, Ascarididae) have been implicated in clinical and subclinical intestinal diseases in their natural hosts (e.g., raccoons and bears) as well as in life-threatening larva migrans syndromes in a number of incidental hosts, including humans. Following the diagnosis of Baylisascaris transfuga infestation in two captive polar bears, living in the zoo park of Pistoia (Tuscany, Italy), nematodes (n=300; both sexes) have been characterized by morphological and molecular methods by sequencing and analysing ribosomal (large ribosomal DNA (28S) and internal transcribed spacer region 1 and 2 (ITSs)) and mitochondrial (cytochrome c oxidase subunit 1 (cox1) and cytochrome c oxidase subunit 2 (cox2)) target regions. In addition, seven faecal samples were collected from the animal enclosure and submitted to copromicroscopic and molecular examination. All nematodes were morphologically identified as B. transfuga and their main distinctive features are here presented. No variation in size and nucleotide polymorphisms was detected within each target sequence among all samples analysed. These data contribute to facilitate an accurate diagnosis of this little known nematode infestation in order to apply appropriate anthelmintic strategies.     

First reports of Trichinella pseudospiralis in wild boars (Sus scrofa) of Italy

Trichinella pseudospiralis is a non-encapsulated species infecting both mammals and birds. In Italy, this parasite was reported only in two night-birds of prey of Central Italy. In January 2010, Trichinella larvae were detected in three wild boars (Sus scrofa) of two regions of Northern Italy by enzymatic digestion. The parasites were identified as T. pseudospiralis by multiplex-PCR. The first infected wild boar was hunted in the Emilia Romagna region and the other two infected wild boars were bred outdoors in a small family farm of the Friuli Venezia Giulia region. These new epidemiological data reinforce the role of the wild boar as the main reservoir of T. pseudospiralis in Europe.     

Positive Streptobacillus moniliformis PCR in guinea pigs likely due to Leptotrichia spp

Streptobacillus moniliformis is a zoonotic bacterium. We obtained positive S. moniliformis PCR results in oral swab samples from guinea pigs from an experimental colony and the breeding colony of origin. Comparison of the DNA sequence of an amplicon with deposited 16S rDNA sequences revealed that Leptotrichia sp. can be the source of a false positive S. moniliformis PCR outcome.     

The effect of column purification on cDNA indirect labelling for microarrays

Background

The success of the microarray reproducibility is dependent upon the performance of standardized procedures. Since the introduction of microarray technology for the analysis of global gene expression, reproducibility of results among different laboratories has been a major problem. Two of the main contributors to this variability are the use of different microarray platforms and different laboratory practices. In this paper, we address the latter question in terms of how variation in one of the steps of a labelling procedure affects the cDNA product prior to microarray hybridization.

Results

We used a standard procedure to label cDNA for microarray hybridization and employed different types of column chromatography for cDNA purification. After purifying labelled cDNA, we used the Agilent 2100 Bioanalyzer and agarose gel electrophoresis to assess the quality of the labelled cDNA before its hybridization onto a microarray platform. There were major differences in the cDNA profile (i.e. cDNA fragment lengths and abundance) as a result of using four different columns for purification. In addition, different columns have different efficiencies to remove rRNA contamination. This study indicates that the appropriate column to use in this type of protocol has to be experimentally determined. Finally, we present new evidence establishing the importance of testing the method of purification used during an indirect labelling procedure. Our results confirm the importance of assessing the quality of the sample in the labelling procedure prior to hybridization onto a microarray platform.

Conclusion

Standardization of column purification systems to be used in labelling procedures will improve the reproducibility of microarray results among different laboratories. In addition, implementation of a quality control check point of the labelled samples prior to microarray hybridization will prevent hybridizing a poor quality sample to expensive micorarrays.