Root respiratory characteristics associated with plant adaptation to high soil temperature for geothermal and turf-type Agrostis species

Respiration is a major avenue of carbohydrates loss. The objective of the present study was to examine root respiratory characteristics associated with root tolerance to high soil temperature for two Agrostis species: thermal Agrostis scabra, a species adapted to high-temperature soils in geothermal areas in Yellowstone National Park, and two cultivars ('L-93' and 'Penncross') of a cool-season turfgrass species, A. stolonifera (creeping bentgrass), that differ in their heat sensitivity. Roots of thermal A. scabra and both creeping bentgrass cultivars were exposed to high (37 degrees C) or low soil temperature (20 degrees C). Total root respiration rate and specific respiratory costs for maintenance and ion uptake increased with increasing soil temperatures in both species. The increases in root respiratory rate and costs for maintenance and ion uptake were less pronounced for A. scabra than for both creeping bentgrass cultivars (e.g. respiration rate increased by 50% for A. scabra upon exposure to high temperature for 28 d, as compared with 99% and 107% in 'L-93' and 'Penncross', respectively). Roots of A. scabra exhibited higher tolerance to high soil temperature than creeping bentgrass, as manifested by smaller decreases in relative growth rate, cell membrane stability, maximum root length, and nitrate uptake under high soil temperature. The results suggest that acclimation of respiratory carbon metabolism plays an important role in root survival of Agrostis species under high soil temperatures, particularly for the thermal grass adaptation to chronically high soil temperatures. The ability of roots to tolerate high soil temperatures could be related to the capacity to control respiratory rates and increase respiratory efficiency by lowering maintenance and ion uptake costs.     

Conversion of alloantigen-specific CD8+ T cell anergy to CD8+ T cell priming through in vivo ligation of glucocorticoid-induced TNF receptor

In this study, we investigated the effect of an agonistic mAb (DTA-1) against glucocorticoid-induced TNF receptor (GITR) in a murine model of systemic lupus erythematosus-like chronic graft-vs-host disease (cGVHD). A single dose of DTA-1 inhibited the production of anti-DNA IgG1 autoantibody and the development of glomerulonephritis, typical symptoms of cGVHD. DTA-1-treated mice showed clinical and pathological signs of acute GVHD (aGVHD), such as lymphopenia, loss of body weight, increase of donor cell engraftment, and intestinal damage, indicating that DTA-1 shifted cGVHD toward aGVHD. The conversion of cGVHD to aGVHD occurred because DTA-1 prevented donor CD8+ T cell anergy. Functionally active donor CD8+ T cells produced high levels of IFN-gamma and had an elevated CTL activity against host Ags. In in vitro MLR, anergic responder CD8+ T cells were generated, and DTA-1 stimulated the activation of these anergic CD8+ T cells. We further confirmed in vivo that donor CD8+ T cells, but not donor CD4+ T cells, were responsible for the DTA-1-mediated conversion of cGVHD to aGVHD. These results indicate that donor CD8+ T cell anergy is a restriction factor in the development of aGVHD and that in vivo ligation of GITR prevents CD8+ T cell anergy by activating donor CD8+ T cells that otherwise become anergic. In sum, our data suggest GITR as an important costimulatory molecule regulating cGVHD vs aGVHD and as a target for therapeutic intervention in a variety of related diseases.     

Machine Learning for Detecting Gene-Gene Interactions

Complex interactions among genes and environmental factors are known to play a role in common human disease aetiology. There is a growing body of evidence to suggest that complex interactions are 'the norm' and, rather than amounting to a small perturbation to classical Mendelian genetics, interactions may be the predominant effect. Traditional statistical methods are not well suited for detecting such interactions, especially when the data are high dimensional (many attributes or independent variables) or when interactions occur between more than two polymorphisms. In this review, we discuss machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases. We focus on the following machine-learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction. We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics.     

Interleukin 2 regulation following semi-allogeneic bone marrow transplantation in mice

Success of allogeneic and autologous bone marrow transplantation (BMT) is hampered by susceptibility to infection during the first two post-treatment years. Further, in treating malignant diseases, impaired anti-host reactivity for donor cells may contribute to a high rate of relapse. Both complications are a consequence of immune deficiency involving B and T lymphocytes. The present study evaluates several key parameters of the immunologic reconstitution mechanism in mice subjected to myeloablative total body irradiation following semi-allogeneic (parental) BMT. This resulted in a gradual reduction of splenic CD3, CD4 and CD8 cells until day 45 post-BMT. Concomitantly, there was an increase in monocytes and CD4⁺/CD8⁺ (double positive) cells, accompanied by a persistent elevation in the percentage of B lymphocytes. The total thymic and splenic T cell populations were reduced until day +30. The cellular reduction correlated with the poor proliferative response of the thymic and splenic cells. A decrease occurred in IL-2 mRNA expression in thymic cells during days 15–20 post-transplant, corresponding with the low level of IL-2 secretion in the spleen and thymus of the transplanted mice. In conclusion, following semi-allogeneic BMT, there was an overall immune down-regulation in the cells, gene and protein levels. Reduced immunological responsiveness following BMT reinforces the need for improving the immune dysfunction by immunotherapy post-BMT.     

Assimilation and allocation of carbon and nitrogen of thermal and nonthermal Agrostis species in response to high soil temperature

We studied whether changes in the assimilation and allocation of carbon and nitrogen are associated with plant tolerance to high soil temperatures. Two Agrostis species, thermal Agrostis scabra, a species adapted to high-temperature soils in geothermal areas in Yellowstone National Park (USA), and two cultivars of a cool-season species, Agrostis stolonifera, L-93 and Penncross, were exposed to soil temperatures of 37 or 20 degrees C, while shoots were exposed to 20 degrees C. Net photosynthesis rate, photochemical efficiency, NO(3) (-)-assimilation rate and root viability decreased with increasing soil temperatures in both species. However, the decreases were less pronounced for A. scabra than for both A. stolonifera cultivars. Carbon investment in growth of plants exposed to 37 degrees C decreased more dramatically in both A. stolonifera cultivars than in A. scabra. Nitrogen allocation to shoots was greater in A. scabra than in both creeping bentgrass cultivars at 37 degrees C soil temperature. Our results demonstrate that plant tolerance to high soil temperature is related to efficient expenditure and adjustment of C- and N-allocation patterns between growth and respiration.     

Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance

Optimum allocation of resources is of fundamental importance for the efficiency of breeding programs. The objectives of our study were to (1) determine the optimum allocation for the number of lines and test locations in hybrid maize breeding with doubled haploids (DHs) regarding two optimization criteria, the selection gain ΔG _k and the probability P _k of identifying superior genotypes, (2) compare both optimization criteria including their standard deviations (SDs), and (3) investigate the influence of production costs of DHs on the optimum allocation. For different budgets, number of finally selected lines, ratios of variance components, and production costs of DHs, the optimum allocation of test resources under one- and two-stage selection for testcross performance with a given tester was determined by using Monte Carlo simulations. In one-stage selection, lines are tested in field trials in a single year. In two-stage selection, optimum allocation of resources involves evaluation of (1) a large number of lines in a small number of test locations in the first year and (2) a small number of the selected superior lines in a large number of test locations in the second year, thereby maximizing both optimization criteria. Furthermore, to have a realistic chance of identifying a superior genotype, the probability P _k of identifying superior genotypes should be greater than 75%. For budgets between 200 and 5,000 field plot equivalents, P _k > 75% was reached only for genotypes belonging to the best 5% of the population. As the optimum allocation for P _k (5%) was similar to that for ΔG _k , the choice of the optimization criterion was not crucial. The production costs of DHs had only a minor effect on the optimum number of locations and on values of the optimization criteria. C. Friedrich H. Longin and H. Friedrich Utz contributed equally to this work.     

A new test for family-based association mapping with inbred lines from plant breeding programs

Association mapping holds great promise for the detection of quantitative trait loci (QTL) in plant breeding populations. The main objectives of this study were to (1) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs, (2) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) with the commonly employed logistic regression ratio test (LRRT), with respect to the power and type I error rate of QTL detection, and (3) demonstrate the use of the QIPDT by applying it to flowering data of European elite maize inbreds. QIPDT and LRRT were compared based on computer simulations modeling 55 years of hybrid maize breeding in Central Europe. Furthermore, we applied QIPDT to a cross-section of 49 European elite maize inbred lines genotyped with 722 amplified fragment length polymorphism markers and phenotyped in four environments for days to anthesis. Compared to LRRT, the power to detect QTL was higher with QIPDT when using data collected routinely in plant breeding programs. Application of QIPDT to the 49 European maize inbreds resulted in a significant (P < 0.05) association located at a position for which a consensus QTL was detected in a previous study. The results of our study suggested that QIPDT is a promising QTL detection method for data collected routinely in plant breeding programs.     

Hematologic, biochemical, and cytologic findings from apparently healthy atlantic bottlenose dolphins (Tursiops truncatus) inhabiting the Indian River Lagoon, Florida, USA

The objective of this study was to establish reference baseline data for hematologic, biochemical, and cytologic findings in apparently healthy Atlantic bottlenose dolphins (Tursiops truncatus) inhabiting the Indian River Lagoon, Florida, USA. Sixty-two dolphins were captured, examined, and released during June 2003 and June 2004. Mean, standard deviation, and range were calculated for each parameter, and values for which published data were available, were close to or within the ranges previously reported for free-ranging bottlenose dolphins. No pathologic abnormalities were found in fecal and blowhole cytologic specimens. However, 24% (7/29) of the dolphins examined in 2003 had evidence of gastritis, which was graded as severe in 14% (4/29) of the cases. In 2004, only 4% (1/24) of dolphins sampled had evidence of mild or moderate gastritis; no severe inflammation was present. Dolphins with evidence of gastritis were 8 yr of age or older and predominantly male. Several statistically significant differences were found between males and females, between pregnant and nonpregnant animals, and between juveniles (<6 yr) and adults (> or =6 yr). However, the values remained within the established ranges for this species, and the differences were not likely to be of clinical significance.     

New Rapid and Simple Methods for Detection of Bacteria and Determination of Their Antibiotic Susceptibility by Using Phage Mutants

Three new methods applying a novel approach for rapid and simple detection of specific bacteria, based on plaque formation as the end point of the phage lytic cycle, are described. Different procedures were designed to ensure that the resulting plaques were derived only from infected target bacteria (“infectious centers”). (i) A pair of amber mutants that cannot form plaques at concentrations lower than their reversion rate underwent complementation in the tested bacteria; the number of plaques formed was proportional to the concentration of the bacteria that were coinfected by these phage mutants. (ii) UV-irradiated phages were recovered by photoreactivation and/or SOS repair mediated by target bacteria and plated on a recA uvrA bacterial lawn in the dark to avoid recovery of noninfecting phages. (iii) Pairs of temperature-sensitive mutants were allowed to coinfect their target bacteria at the permissive temperature, followed by incubation of the plates at the restrictive temperature to avoid phage infection of the host cells. This method allowed the omission of centrifuging and washing the infected cells. Only phages that recovered by recombination or complementation were able to form plaques. The detection limit was 1 to 10 living Salmonella or Escherichia coli O157 cells after 3 to 5 h. The antibiotic susceptibility of the target bacteria could also be determined in each of these procedures by preincubating the target bacteria with antibiotic prior to phage infection. Bacteria sensitive to the antibiotic lost the ability to form infectious centers.