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.     

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.

     

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.     

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.     

Use of the pisces database: Power plant aqueous stream compositions

The Power Plant Integrated Systems: Chemical Emissions Studies (PISCES) Database sponsored by the Electric Power Research Institute is a powerful tool for evaluating and comparing the level of trace substances in power plant process streams. In this paper, data are presented on the level of several selected trace metals found in a few of the aqueous streams present in power plants. In addition, a brief discussion of other features of the Database is presented.     

Amelioration of a hardsetting Alfisol through deep mouldboard ploughing, gypsum application and double cropping. III. Crop production and profitability

Deep mouldoard ploughing to 0.45 m, gypsum application (5 t ha⁻¹), and double cropping were evaluated, alone and combined, as ameliorants for a hardsetting red-brown earth (Alfisol). The double cropped treatment consisted of winter wheat (Triticum aestivum) and a summer forage crop consisting of sudax (Sorghum sudanese) intersown with cowpea (Vigna unguiculata). This paper describes the effect of these treatments on crop development, yield, crop-water relations and economic returns. Crop emergence was not affected by any treatment. Mouldboard ploughing significantly increased wheat grain yield from 1.86 to 2.15 t ha⁻¹, in 1984, but not in 1985. Yield was also increased from 5.18 to 5.68 t ha⁻¹ as a result of gypsum addition in 1985—after no significant difference in 1984. Double cropping significantly increased yield (by 0.6 t ha⁻¹) in 1985. Greater increases were obtained with the summer cropping phase where higher evaporative demand during the summer would have aggravated soil structural problems associated with hardsetting. Sudax-cowpea dry matter yields were increased from 13.6 to 17 t ha⁻¹ and from 13.0 to 17.5 t ha⁻¹ during summer 1984–1985 by gypsum and mouldboard ploughing, respectively. The higher yields are attributed to increased water storage and depletion, and reduced soil strength for the mouldboard ploughed and gypsum main treatments. No interactions were found between the main treatments, except at the end of the 1985 winter cropping phase when there was a negative interaction between mouldboard ploughing and gypsum application for dry matter, equivalent root length and yield. The yield increases associated with mouldboard ploughing did not persist beyond the second year of the experiment. Double cropping combined with mouldboard ploughing (Mb+DC) was the most profitable treatment, whereas mouldboard ploughing with gypsum (Mb+G) was the least profitable for the crops grown in this experiment.     

Identification of a putative regulator of early T cell activation genes

Molecules involved in the antigen receptor-dependent regulation of early T cell activation genes were investigated with the use of functional sequences of the T cell activation-specific enhancer of interleukin-2 (IL-2). One of these sequences forms a protein complex, NFAT-1, specifically with nuclear extracts of activated T cells. This complex appeared 10 to 25 minutes before the activation of the IL-2 gene. Studies with inhibitors of protein synthesis indicated that the time of synthesis of the activator of the IL-2 gene in Jurkat T cells corresponds to the time of appearance of NFAT-1. NFAT-1, or a very similar protein, bound functional sequences of the long terminal repeat (LTR) of the human immunodeficiency virus type 1; the LTR of this virus is known to be stimulated during early T cell activation. The binding site for this complex activated a linked promoter after transfection into antigen receptor-activated T cells but not other cell types. These characteristics suggest that NFAT-1 transmits signals initiated at the T cell antigen receptor.     

Human c-Ki-ras2 proto-oncogene on chromosome 12

A human colonic adenocarcinoma transforming gene, recently identified as a cellular homolog of the Kirsten sarcoma gene (v-ras), was used to assign the human cellular Kirsten ras2 gene to chromosome 12 by the Southern hybridization method. A single 640 base-pair Eco RI--Hind III fragment of the transforming gene, isolated by DNA transfection and molecular cloning, can detect a single Eco RI fragment (2.9 kilobase pairs) of DNA from phenotypically normal cells. The data suggest a constant chromosomal location of c-Ki-ras2.     

Spatial Variability of Turbulent Mixing in the Abyssal Ocean

Ocean microstructure data show that turbulent mixing in the deep Brazil Basin of the South Atlantic Ocean is weak at all depths above smooth abyssal plains and the South American Continental Rise. The diapycnal diffusivity there was estimated to be less than or approximately equal to 0.1 x 10(-4) meters squared per second. In contrast, mixing rates are large throughout the water column above the rough Mid-Atlantic Ridge, and the diffusivity deduced for the bottom-most 150 meters exceeds 5 x 10(-4) meters squared per second. Such patterns in vertical mixing imply that abyssal circulations have complex spatial structures that are linked to the underlying bathymetry.