The influence of geographic origin and food type on the susceptibility of Callosobruchus maculatus (Fabricius) to Piper guineense (Schum and Thonn)

The tolerance of Callosobruchus maculatus from different geographical locations reared on two cowpea varieties, pale brown Ife Brown (IFBV) and dark brown IAR48 (IAR48V), to seed powder of Piper guineense (Schum and Thonn) was investigated. C. maculatus populations were collected from nine different locations across Osun state in the South Western part of Nigeria. The main and interactive effects of cowpea variety, population origin and dose on C. maculatus tolerance to P. guineense were explored. It was observed that bruchids that emerged from IAR48V had greater tolerance of P. guineense than bruchids reared on IFBV. There were significant effects (P < 0.001) of cowpea variety, population and dose, and significant interactions among these factors (except variety � dose, P > 0.05) on the response of bruchids to P. guineense. When reared on IAR48V, bruchid populations from the North-Eastern part of the state show greater tolerance to P. guineense than their counterparts from the SoutheWest. This study underscores the importance of knowledge of the origin of the population and the cowpea variety on which C. maculatus developed when managing bruchids damage using P. guineense

Different tools to trace geographic origin and seasonality of croaker (Micropogonias furnieri)

The aim of this study was to use proximate chemical composition, macro and trace elements, fatty acid profile and stable isotopes as traceability tools to assess geographic origin and seasonality of croaker (Micropogonicts fumieri). Croaker from Parnaiba contained higher ash in July and lower fat content than croaker from Santos. In contrast, croaker from Santos had statistically higher proportion of 16:1n-9+16:1n-7, 20:1n-11, 20:1n-9, MUFA and n-3/n-6 ratio than croaker from Parnaiba. Concerning seasonality, croaker caught in July had significantly higher amounts of 14:0, 15:0, 16:1n-9+16:1n-7 and saturated fatty acids than fish caught in December. Concerning elements, significant differences were also detected between seasons for Cl, Ca, Fe, Sr and S, whereas differences between geographic origins were only observed with K. delta C-13 and delta N-15 were statistically different between geographic origins, whereas differences between seasons were only detected in delta N-15 ratio of croaker from Santos. Fatty acids, minerals and stable isotope are effective methods to trace geographic origin and seasonality of croaker. Nonetheless, further investigation is still required with larger samples of croaker to enable the implementation of fatty acids, elements or stable isotope as authenticity tools by food control agencies. (C) 2014 Elsevier Ltd. All rights reserved.

Multi-element determination in Brazilian honey samples by inductively coupled plasma mass spectrometry and estimation of geographic origin with data mining techniques

Multi-element analysis of honey samples was carried out with the aim of developing a reliable method of tracing the origin of honey. Forty-two chemical elements were determined (Al, Cu, Pb, Zn, Mn, Cd, Tl, Co, Ni, Rb, Ba, Be, Bi, U, V, Fe, Pt, Pd, Te, Hf, Mo, Sn, Sb, P, La, Mg, I, Sm, Tb, Dy, Sd, Th, Pr, Nd, Tm, Yb, Lu, Gd, Ho, Er, Ce, Cr) by inductively coupled plasma mass spectrometry (ICP-MS). Then, three machine learning tools for classification and two for attribute selection were applied in order to prove that it is possible to use data mining tools to find the region where honey originated. Our results clearly demonstrate the potential of Support Vector Machine (SVM), Multilayer Perceptron (MLP) and Random Forest (RF) chemometric tools for honey origin identification. Moreover, the selection tools allowed a reduction from 42 trace element concentrations to only 5. (C) 2012 Elsevier Ltd. All rights reserved.

An evaluation of geographic and annual variation in morphometric characters and gill-raker counts of yellowfin tuna, Thunnus albacares, from the Pacific Ocean

ENGLISH: Samples of yellowfin tuna, Thunnus albacares, collected from five areas of the Pacific Ocean (Mexico, Ecuador, Australia, Japan, and Hawaii) between January and May of 1988 and 1990 were examined for spatiotemporal variation in morphometric characters and gill-raker counts. 'Iwo-factor analysis of variance, with area and year treated as grouping factors, indicated a significant difference in the means of the total gill-raker counts among fish from different areas, but no significant difference between fish caught in different years. The morphometric data were adjusted by allometric formulae to remove size effects. The correct classification rates for the five groups, using discriminant function analysis, based on adjusted morphometric characters, were 77.60/0 for the samples from 1988 and 74.40/0 for those from 1990. These are 72.00/0 and 68.00/0 (Cohen's kappa statistic) better than would have occurred chance. The pattern of geographic variability, however, is unstable for these two years, thus requiring separate discriminant functions for each year. Although there is annual variability in the morphometric characters, these results demonstrate that the stocks examined are morphometrically distinguishable and that their phenetic relationships reflect their geographic origin. SPANISH: Se examinaron muestras de atún aleta amarilla, Thunnus albacares, tomadas de cinco áreas del Océano Pacífico (México, Ecuador, Australia, Japón, y Hawaii) entre enero y mayo de 1988 y 1990, para descubrir variaciones espaciotemporales en las características morfométricas y los conteos de branquiespinas. Un análisis de varianza de dos factores, con área y año como factores de agrupación, indicó una diferencia significativa en los promedios de los conteos de branquiespinas totales entre peces de distintas áreas, pero ninguna entre peces capturados en distintos años. Se ajustaron los datos morfométricos con fórmulas alométricas para eliminar los efectos de la talla del pez. En un análisis de función discriminante, las tasas de clasificación correcta de los cinco grupos, basadas en características morfométricas ajustadas, fueron 77.60/0 para las muestras de 1988 y 74.40/0 para aquellas de 1990. Estas cifras son 72.00/0 y 68.00/0 (estadístico de kappa de Cohen) mejores de lo que se hubiera obtenido al azar. Sin embargo, la variabilidad geográfica es inestable en estos dos años, requiriendo por lo tanto funciones discriminantes separadas para cada año. Aunque existe variabilidad anual en las características morfométricas, estos resultados demuestran que los stocks examinados son morfamétricamente distinguibles, y que su relación fenética refleja su origen geográfico. (PDF contains 31 pages.)

Geographic provenancing of unprocessed cotton using elemental analysis and stable isotope ratios

Cotton is the most abundant natural fiber in the world. Many countries are involved in the growing, importation, exportation and production of this commodity. Paper documentation claiming geographic origin is the current method employed at U.S. ports for identifying cotton sources and enforcing tariffs. Because customs documentation can be easily falsified, it is necessary to develop a robust method for authenticating or refuting the source of the cotton commodities. This work presents, for the first time, a comprehensive approach to the chemical characterization of unprocessed cotton in order to provide an independent tool to establish geographic origin. Elemental and stable isotope ratio analysis of unprocessed cotton provides a means to increase the ability to distinguish cotton in addition to any physical and morphological examinations that could be, and are currently performed. Elemental analysis has been conducted using LA-ICP-MS, LA-ICP-OES and LIBS in order to offer a direct comparison of the analytical performance of each technique and determine the utility of each technique for this purpose. Multivariate predictive modeling approaches are used to determine the potential of elemental and stable isotopic information to aide in the geographic provenancing of unprocessed cotton of both domestic and foreign origin. These approaches assess the stability of the profiles to temporal and spatial variation to determine the feasibility of this application. This dissertation also evaluates plasma conditions and ablation processes so as to improve the quality of analytical measurements made using atomic emission spectroscopy techniques. These interactions, in LIBS particularly, are assessed to determine any potential simplification of the instrumental design and method development phases. This is accomplished through the analysis of several matrices representing different physical substrates to determine the potential of adopting universal LIBS parameters for 532 nm and 1064 nm LIBS for some important operating parameters. A novel approach to evaluate both ablation processes and plasma conditions using a single measurement was developed and utilized to determine the "useful ablation efficiency" for different materials. The work presented here demonstrates the potential for an a priori prediction of some probable laser parameters important in analytical LIBS measurement.

Geographic Provenancing of Unprocessed Cotton Using Elemental Analysis and Stable Isotope Ratios

Cotton is the most abundant natural fiber in the world. Many countries are involved in the growing, importation, exportation and production of this commodity. Paper documentation claiming geographic origin is the current method employed at U.S. ports for identifying cotton sources and enforcing tariffs. Because customs documentation can be easily falsified, it is necessary to develop a robust method for authenticating or refuting the source of the cotton commodities. This work presents, for the first time, a comprehensive approach to the chemical characterization of unprocessed cotton in order to provide an independent tool to establish geographic origin. Elemental and stable isotope ratio analysis of unprocessed cotton provides a means to increase the ability to distinguish cotton in addition to any physical and morphological examinations that could be, and are currently performed. Elemental analysis has been conducted using LA-ICP-MS, LA-ICP-OES and LIBS in order to offer a direct comparison of the analytical performance of each technique and determine the utility of each technique for this purpose. Multivariate predictive modeling approaches are used to determine the potential of elemental and stable isotopic information to aide in the geographic provenancing of unprocessed cotton of both domestic and foreign origin. These approaches assess the stability of the profiles to temporal and spatial variation to determine the feasibility of this application. This dissertation also evaluates plasma conditions and ablation processes so as to improve the quality of analytical measurements made using atomic emission spectroscopy techniques. These interactions, in LIBS particularly, are assessed to determine any potential simplification of the instrumental design and method development phases. This is accomplished through the analysis of several matrices representing different physical substrates to determine the potential of adopting universal LIBS parameters for 532 nm and 1064 nm LIBS for some important operating parameters. A novel approach to evaluate both ablation processes and plasma conditions using a single measurement was developed and utilized to determine the “useful ablation efficiency” for different materials. The work presented here demonstrates the potential for an a priori prediction of some probable laser parameters important in analytical LIBS measurement.

Mycobacterium abscessus infection and potable water

Mycobacterium abscessus is a rapidly growing mycobacteria responsible for progressive pulmonary disease, soft tissue and wound infections, and can contaminate clinical specimens. Nontuberculous mycobacteria (NTM) are generally considered environmental organisms though M. abscessus has not featured frequently in environmental studies, particularly those examining potable water. In a study of Brisbane potable water, M. abscessus was isolate from ten different locations. The incidence of disease due to M. abscessus has been increasing in Queensland. Aim: To compare genotypically the M. abscessus isolates obtained from water to those obtained from human clinical specimens. Methods: From a study of Brisbane potable water between 2007 and 2009, ten isolates confirmed as M. abscessus were recovered. In addition, one strain was isolated from a rainwater tank of a patient with disease due to M. avium, and another from the swimming pool of a patient with M. intracellulare disease. A random sample of 74 clinical isolates referred to the QLD Mycobacterial reference laboratory during the same time period was available for comparison using repPCR strain typing (Diversilab). Results: The drinking water isolates formed two distinct strain patterns (A and B) that shared >90% similarity. The tankwater isolate (pattern C) shared >85% similarity with the potable water isolates, but the pool isolate (D) was distinctly different. Fifty-three clinical isolates clustered tightly (>95% similarity) with the Group A potable water isolates, 4 patients with Group B. Thirteen patient isolates clustered with the Rainwater tank isolate. One patient matched the pool isolate. There were a further 3 patient isolates that were unrelated to the water isolates. No differences were found between strain types in terms of geographic origin, gender, age, or site/type of infection. Conclusion: The high degree of similarity between strains of M. abscessus from potable water and strains causing infection in humans from the same area, strengthens the possibility that drinking water may be a source of infection in these patients.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

Global dissemination of a multidrug resistant Escherichia coli clone

Escherichia coli sequence type 131 (ST131) is a globally disseminated, multidrug resistant (MDR) clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with several factors, including resistance to fluoroquinolones, high virulence gene content, the possession of the type 1 fimbriae FimH30 allele, and the production of the CTX-M-15 extended spectrum β-lactamase (ESBL). Here, we used genome sequencing to examine the molecular epidemiology of a collection of E. coli ST131 strains isolated from six distinct geographical locations across the world spanning 2000–2011. The global phylogeny of E. coli ST131, determined from whole-genome sequence data, revealed a single lineage of E. coli ST131 distinct from other extraintestinal E. coli strains within the B2 phylogroup. Three closely related E. coli ST131 sublineages were identified, with little association to geographic origin. The majority of single-nucleotide variants associated with each of the sublineages were due to recombination in regions adjacent to mobile genetic elements (MGEs). The most prevalent sublineage of ST131 strains was characterized by fluoroquinolone resistance, and a distinct virulence factor and MGE profile. Four different variants of the CTX-M ESBL–resistance gene were identified in our ST131 strains, with acquisition of CTX-M-15 representing a defining feature of a discrete but geographically dispersed ST131 sublineage. This study confirms the global dispersal of a single E. coli ST131 clone and demonstrates the role of MGEs and recombination in the evolution of this important MDR pathogen.

Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy® or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to 1 infected in 800 samples with pepper but never detecting more than 1 infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

An integrated assessment of the continued spread and potential impacts of the colonial ascidian, Didemnum sp. A, in U.S. waters

Didemnum sp. A is a colonial ascidian or “sea squirt” of unknown geographic origin. Colonies of Didemnum sp. A were first documented in U.S. waters in 1993 at Damariscotta River, Maine and San Francisco Bay, California. An alarming number of colonies have since been found at several locations in New England and along the West Coast of the contiguous continental United States. Originally believed to be restricted to artificial structures in nearshore habitats, such as ports and marinas, colonies of Didemnum sp. A have also been discovered on a gravel-pavement habitat on Georges Bank at depths of 40-65m. The wide distribution of Didemnum sp. A, the presence of colonies on an important offshore fishing ground, and the negative economic impacts that other species of noninidigenous ascidians have had on aquaculture operations have raised concerns about the potential impacts of Didemnum sp. A. We reviewed the available information on the biology and ecology of Didemnum sp. A and potentially closely related species to examine the environmental and socioeconomic factors that may have influenced the introduction, establishment and spread of Didemnum sp. A in U.S. waters, the potential impacts of this colonial ascidian on other organisms, aquaculture, and marine fisheries, and the possibility that it will spread to other U.S. waters. In addition, we present and discuss potential management objectives for minimizing the impacts and spread of Didemnum sp. A. Concern over the potential for Didemnum sp. A to become invasive stems from ecological traits that it shares with other invasive species, including the ability to overgrow benthic organisms, high reproductive and population growth rates, ability to spread by colony fragmentation, tolerance to a wide range of environmental conditions, apparent scarcity of predators, and the ability to survive in human dominated habitats. At relatively small spatial scales, species of Didemnum and other nonindigenous ascidians have been shown to alter the abundance and composition of benthic assemblages. In addition, the Canadian aquaculture industry has reported that heavy infestations of nonindigenous ascidians result in increased handling and processing costs. Offshore fisheries may also suffer where high densities of Didemnum sp. A may alter the access of commercially important fish species to critical spawning grounds, prey items, and refugia. Because colonial ascidian larvae remain viable for only 12–24hrs, the introduction and spread of Didemnum sp. A across large distances is thought to be predominantly human mediated; hull fouling, aquaculture, and ballast water. Recent studies suggest that colony growth rates decline when temperatures exceed 21 ºC for 7 consecutive days. Similarly, water temperatures above 8 to 10 ºC are necessary for colony growth; however, colonies can survive extended periods of time below this temperature threshold as an unidentified overwintering form. A qualitative analysis of monthly mean nearshore water temperatures suggest that new colonies of Didemnum will continue to be found in the Northeast U.S., California Current, and Gulf of Alaska LMEs. In contrast, water temperatures become less favorable for colony establishment in subarctic, subtropical, and tropical areas to the north and south of Didemnum’s current distribution in cool temperate habitats. We recommend that the Aquatic Nuisance Species Task Force serve as the central management authority to coordinate State and Federal management activities. Five objectives for a Didemnum sp. A management and control program focusing on preventing the spread of Didemnum sp. A to new areas and limiting the impacts of existing populations are discussed. Given the difficulty of eradicating large populations of Didemnum sp. A, developing strategies for limiting the access of Didemnum sp. A to transport vectors and locating newly established colonies are emphasized. (PDF contains 70 pages)

Insecticide resistance in Chinese populations of the Culex pipiens complex through esterase overproduction

In most parts of China, mosquitoes have been subjected to organophosphate (OP) insecticide treatments since the mid-1960s, and resistance gene monitoring in the Culex pipiens complex (Diptera: Culicidae) started in only a few locations from the end of the 1980s. Many resistant alleles at the Ester locus have been found in field populations, including those commonly found around the world (Ester(B1) and Ester(2)), and those endemic to China (Ester(B6), Ester(B7), Ester(8), and Ester(9)). This situation is atypical, and may represent a complex situation for the evolution of insecticide resistance genes in China. To increase our understanding of the Chinese situation and our ability to manage resistance in the C. pipiens complex, a large study was performed. Twenty field populations were sampled from Beijing to Guangzhou. Bioassays with five insecticides (dichlorvos, parathion, chlorpyrifos, 2-sec-butylphenyl methyl carbamate, and propoxur) disclosed resistance levels variable according to the geographic origin, and up to 85-fold for dichlorvos. Six overproduced esterases were identified, including two that have not been previously described. Most of them were found in all samples, although at variable frequencies, suggesting variable selection or a transient situation, e.g., each one was recently restricted to a particular geographic area. The results are discussed in the context of recent alterations to insecticide campaigns, and of the evolution of resistance genes in Chinese C. pipiens populations.

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Eighteen isolates of the red algae Chondrus crispus were collected from Northern Atlantic sites, together with C. ocellatus, C. yendoi and C. pinnulatus from the North Pacific. The nuclear rDNA internal transcribed spacer (ITS) was sequenced and compared, spanning both the ITS regions and the 5.8S rRNA gene. Percentage of nucleotide variation for C. crispus ranged from 0.3% to 4.0%. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor-joining (NJ) and minimum evolution methods. They showed that two main clades existed within the C. crispus samples examined and that suggested C. crispus had a single Atlantic origin. The clustering however did not follow the geographic origin. We hypothesized that the current distribution of C. crispus populations might be a result of three main factors: temperature boundaries, paleoclimate and paleoceanography. ITS data exhibited abundant molecular information not only for phylogeographical investigation but also for systematics studies.

Phenotypical characterization in "Plasmopara halstedii" (sunflower downy mildew) isolates of several races

Phenotypic variation (morphological and pathogenic characters), and genetic variability were studied in 50 isolates of seven Plasmopara halstedii (sunflower downy mildew) races 100, 300, 304, 314, 710, 704 and 714. There were significant morphological, aggressiveness, and genetic differences for pathogen isolates. However, there was no relationship between morphology of zoosporangia and sporangiophores and pathogenic and genetic characteristics for the races used in our study. Also, our results provided evidence that no relation between pathogenic traits and multilocus haplotypes may be established in P. halstedii. The hypothesis explaining the absence of relationships among phenotypic and genetic characteristics is discussed.