Validation of the periodicity of growth zone formation in the otoliths of four fish species from the Upper Zambezi ecoregion,southern Africa

In the Upper Zambezi and Okavango ecoregions, Brycinus lateralis, Hepsetus cuvieri, Schilbe intermedius and Serranochromis macrocephalus are important in subsistence fisheries, while S. intermedius and S. macrocephalus are often caught in commercial catches. Despite their importance, there is little information on their age and growth and age validation. Growth zone deposition rate in otoliths of B. lateralis, H. cuvieri, S. intermedius and S. macrocephalus was validated as annual using edge analysis in this study. Annual deposition of growth zones was corroborated by a fluorochrome marking experiment. Both methods demonstrated that one growth zone was deposited annually. Edge analysis demonstrated that the highest proportion of opaque zones was detected between August and December, most likely as a result of slow growth during lower temperature water during the preceding winter. With growth zone deposition validated as annual, future research should focus on determining the growth, maturity and mortality rates of these species, parameters which are important for their management.     

Correction to: Coupling landscape graph modeling and biological data: a review

Landscape Ecology - In the original publication of the article, the sixth author name has been misspelt. The correct name is given in this Correction. The original article has been corrected.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.

     

The spatial structure of spontaneous epidemics of different diseases in a groundnut plot

Spontaneous epidemics of rust, early leaf spot, late leaf spot, andRhizoctonia blight simultaneously developed in a groudnut plot. Geostatistical techniques were used to describe and compare the spatial patterns of epidemics.Rhizoctonia blight exhibited a strong aggregative structure, contrasting with leaf spots and rust. The latter disease developed a general epidemic, in combination with local intensification. A strong negative interaction between rust and early leaf spot, and a close correspondence between rust intensification andRhizoctonia blight development were indicated.     

Enquête sur les maladies fongiques de l'arachide (Arachis hypogaea) en Côte-d'Ivoire. I. Méthodes d'enquête et étude descriptive: les conditions culturales et les principales maladies

Groundnut diseases were surveyed in the various traditional cropping regions of Ivory Coast during 1982, 1983 and 1984. The methods used during the survey are described. A preliminary analysis of the results aimed at a characterization of a complex, multiple pathosystem is presented. The analysis especially focuses upon some foliar diseases, and particularly on rust, caused byPuccinia arachidis. The results show the great variability of the climates and of the agricultural techniques which are associated to groundnut cropping. The list of the fungal pathogens which affect groundnut is long: 16 have been identified during the survey, of which 6 are omnipresent in the various regions. A correspondence analysis was performed, allowing to describe the average development of the multiple pathosystem: groundnut-rust-leafsport-wilting fungi. Endemicity in tropical pathosystems is also analyzed in the case of the main foliar diseases (rust and Cercospora leafspots). More specifically, the epidemiology of groundnut rust in southern Ivory Coast is interpreted as regular, explosive epidemics developping on an endemic background. Every year epidemics develop in the northern and central areas too, most of their primary inoculum supposedly originating from the infested southern crops. Probably, intensification of agriculture will strongly favour rust disease.     

Exploring Patterns of Exotic Earthworm Distribution in a Temperate Hardwood Forest in South-Central New York, USA

Exotic earthworms invading forests in Canada and northeastern United States that were naturally devoid of large detritivores cause major changes in ecosystem function. To assess their long-term impacts, studies are needed to elucidate the factors that control the patterns of earthworm invasion at the landscape level. We analyzed the distribution patterns of exotic earthworms in a northern hardwood forest in south-central New York (USA), as explained by landscape variables thought to be important in determining earthworm distribution. Forest type, slope angle, elevation, and the distance to agricultural clearings and wet refugia were significant predictors of earthworm presence, whereas local wetness index and the distance to streams and roads were not. Forest type and distance to agricultural clearings were the two most significant predictors. Our data suggest that areas close to agricultural clearings, dominated by mixed hardwoods, and located towards valley bottoms or on gentle slopes are very likely to support communities of exotic earthworms. Steeper slopes, areas dominated by American beech or eastern hemlock, and locations in the core of extensive forest landscapes have lower probabilities of invasion by exotic earthworms. When applied to a nearby area, our statistical model correctly predicted earthworm presence for 67% of 377 sampling points. Most of the mistakes were incorrect predictions of earthworm absence, suggesting that our statistical model slightly underestimated earthworm presence, possibly because of the pervasive influence of active agricultural fields adjacent to the test site.     

Heterogeneity of the aerial concentration and deposition of ascospores of <Emphasis Type="Italic">Venturia inaequalis</Emphasis> within a tree canopy during the rain

Scab is an important disease of apple and its control depends almost exclusively on frequent use of fungicides. Primary scab infection in the spring assumes several steps: ascospore maturation, liberation of ascospores that become airborne, deposition on susceptible tissues, and infection. However, the spatial heterogeneity of ascospores within the tree canopy is unknown. Aerial concentration of ascospore (ACA), ascospore concentration in rain water (ACR) and ascospore deposition (AD) were therefore measured at six heights (20–257 cm from the ground) with rotating-arm air samplers, funnels, and greased glass slides, respectively, during five rain events in 2001 and in 2002. In addition, ACR and AD were measured at eight locations within tree canopy at 196 cm height. Apple scab was assessed at the end of the primary infection period in each sampling location within the apple tree. A similar experimental design was used in 2003 to study the spatial heterogeneity of both AD and primary scab lesions. ACA and AD decreased with increasing height, while ACR increased with increasing height. Based on both variance to mean ratio and the power law relationship in both years, the ACR was heterogeneous, while AD was heterogeneous only during the peaks of ascospore release. The ACR was significantly higher at the centre of the trees and the AD was significantly higher at the centre and at the western edge of the trees. Only the cumulative AD was significantly correlated with apple scab lesions at the same location (r = 0.83). In 2003, a similar pattern of spatial heterogeneity within the tree canopy was observed for AD and primary scab lesion counts and there was a linear relationship (R ² = 0.84) between these two variables. It was concluded that ACR and AD within the tree canopy are not randomly distributed at least during peaks of ascospore release and that AD is a good estimate of primary scab lesion development. This spatial heterogeneity should be considered when estimating ascospore deposition using mathematical models or when quantifying ascosporic inoculum using spore samplers.     

SCINTIGRAPHIC TRACKING OF MESENCHYMAL STEM CELLS AFTER PORTAL,SYSTEMIC INTRAVENOUS AND SPLENIC ADMINISTRATION IN HEALTHY BEAGLE DOGS

Mesenchymal stem cells have been proposed to treat liver disease in the dog. The objective of this study was to compare portal, systemic intravenous and splenic injections for administration of mesenchymal stem cells to target the liver in healthy beagle dogs. Four healthy beagle dogs were included in the study. Each dog received mesenchymal stem cells via all three delivery methods in randomized order, 1 week apart. Ten million fat‐derived allogeneic mesenchymal stem cells labeled with Technetium‐99m (99mTc)‐hexamethyl‐propylene amine oxime(HMPAO) were used for each injection. Right lateral, left lateral, ventral, and dorsal scintigraphic images were obtained with a gamma camera equipped with a low‐energy all‐purpose collimator immediately after injection and 1, 6, and 24 h later. Mesenchymal stem cells distribution was assessed subjectively using all four views. Pulmonary, hepatic, and splenic uptake was quantified from the right lateral view, at each time point. Portal injection resulted in diffuse homogeneous high uptake through the liver, whereas the systemic intravenous injection led to mesenchymal stem cell trapping in the lungs. After splenic injection, mild splenic retention and high homogeneous diffuse hepatic uptake were observed. Systemic injection of mesenchymal stem cells may not be a desirable technique for liver therapy due to pulmonary trapping. Splenic injection represents a good alternative to portal injection. Scintigraphic tracking with 99mTc‐HMPAO is a valuable technique for assessing mesenchymal stem cells distribution and quantification shortly after administration. Data obtained at 24 h should be interpreted cautiously due to suboptimal labeling persistence.     

Enzymatic modification of pectin to increase its calcium sensitivity while preserving its molecular weight

A commercial high-methoxy citrus pectin was treated with a purified salt-independent pectin methylesterase (PME) isozyme isolated from Valencia orange peel to prepare a series of deesterified pectins. A series of alkali-deesterified pectins was also prepared at pH 10 under conditions permitting beta-elimination. Analysis of these pectins using high-performance size exclusion chromatography (HPSEC) with on-line multiangle laser light-scattering, differential viscometer, and refractive index (RI) detectors revealed no reduction in weight-average molecular weight (M(w); 150000) in the PME-treated pectin series, whereas a 16% reduction in intrinsic viscosity (IV) occurred below a degree of esterification (DE) of 47%. In contrast, alkali deesterification rapidly reduced both M(w) and IV to less than half of that observed for untreated pectin. PME treatment of a non-calcium-sensitive citrus pectin introduced calcium sensitivity with only a 6% reduction in the DE. Triad blocks of unesterified galacturonic acid were observed in (1)H nuclear magnetic resonance spectra of this calcium-sensitive pectin (CSP). These results demonstrate that the orange salt-independent PME isozyme utilizes a blockwise mode of action. This is the first report of the preparation of a CSP by PME treatment without significant loss of the pectin's M(w) due to depolymerization.