Power of QTL detection by either fixed or random models in half-sib designs

The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL variance to total genetic variance (λ = 0.1), marker spacing (10 cM), and QTL allele frequency (0.5). A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ) of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log₁₀ of type I error profiles were quite flat at close marker spacing (1 cM), confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.     

Effects of neighbouring vegetation on eucalypt seedlings at two sites subject to different levels of abiotic stress

Abstract In spite of numerous studies on the effect of nutrient levels and/or standing crop on the intensity of resource competition the debate has not been resolved. Field studies that have used natural productivity gradients have generally supported the argument that competitive intensity and resource availability are positively correlated, whereas studies that have used artificial resource gradients have generally refuted the same argument. Here we report the results from study in which both approaches were used within the same system. We studied two species of eucalypt that occupy contrasting parts of the same landscape: Eucalyptus camaldulensis, found mostly along creek lines and in valleys with deep alluvial soils, and Eucalyptus microcarpa, found on hillsides and ridges with shallow soils. We studied the response of seedlings of the two species to the combined effects of competition and manipulated nutrient levels in a glasshouse experiment, and also investigated their responses to removal of neighbouring plants in the field. Eucalyptus microcarpa was less responsive to increased resource availability, which is consistent with one of the principal assumptions of Grime’s C‐S‐R model. In the glasshouse experiment both species of eucalypt responded in a qualitatively similar fashion to the combined effects of resource availability and competition: release from competition resulted in increased growth, but only in pots that received additional resources. In the field we found that neighbouring vegetation could severely limit the establishment of E. camaldulensis but the removal of neighbouring vegetation did not affect the performance of E. microcarpa seedlings. Eucalyptus camaldulensis seedlings suffered high levels of damage from herbivores. Our results thus generally support the predications of the C‐S‐R model, however, they indicate that the effects of competition and herbivory may be heavily confounded.     

New method for rapid assessment of the functional composition of herbaceous plant communities

Abstract We propose a rapid sampling method to assess the functional composition of herbaceous plant communities without prior knowledge of the floristic composition. To determine the community‐level value of traits (‘aggregated trait values’) for a plant community, a standardized population‐centred method exists, but requires substantial manpower and reliable botanical knowledge. We tested an alternative method, the trait transect, using four subalpine pastures in the Beaufortain region (Northern French Alps) selected along a fertility gradient. We applied both methods to measure five commonly used ‘soft traits’ known to be responsive to soil nutrient availability: plant vegetative and reproductive height, specific leaf area, leaf dry matter and nitrogen contents. We tested whether the variation of these traits along the gradient detected with the population‐centred method was also detected with the trait transect. Both methods detected expected trends in the traits in response to the fertility gradient. The trait transect method was as efficient as the population‐centred method and is recommended as an appropriate tool for monitoring ecosystem changes in response to environmental conditions and management, especially in species‐rich communities.     

Percutaneous liver core biopsy in rats: an alternative to minilaparotomy

Sampling of rat hepatic tissue for histomorphological analysis is usually performed in two different ways: either by killing the animals or by minilaparotomy.In this study we describe a percutaneous core biopsy technique which has been used on day 7, 14 and 21 after allogeneic rat liver transplantation (DA → LEW) in order to examine grafts for rejection in different treatment groups. Fifty-two liver biopsies were performed in 24 animals using a 16-gauge intravenous cannula. Forty-five provided usable specimens which were sufficient for both light or electron microscopy and immunohistochemical analyses to determine the degree of graft rejection. In 7 cases (13.5%) sampling was unsuccessful, especially on day 21 after transplantation, as the plastic cannula could not penetrate the hardened tissue. In 3 animals (5.8%) puncture was immediately followed by death due to perforation of the diaphragm or ether intoxication.In conclusion, this technique is a reliable method for providing ample tissue samples from the rat liver with a low risk of complications.     

Root discoloration and shoot symptoms in silver birch after Phytophthora infection in vitro

• There are no records of established plant pathogenic Phytophthora species in Finnish forests, but they are likely in the future. Therefore, the effects of Phytophthora inoculations on young, ca. 2‐month‐old silver birch (Betula pendula) seedling roots and shoots were investigated.
• Visual inspection of dark discoloration, direct PCR and re‐isolation, and detailed root morphology analyses were used to evaluate the effects of Phytophthora inoculation on roots. Symptoms in leaves and stems were also recorded.
• Phytophthora was successfully re‐isolated from 67% of the surface‐sterilized roots of inoculated seedlings, but not from the non‐inoculated control seedlings. Dark discolorations were found more often in the root segments of inoculated seedlings than in control seedlings. In the Phytophthora‐treated seedlings, discoloured root segments were usually linked and found primarily in the main root or lateral roots attached to it, whereas in the control seedlings a few single discoloured root segments were scattered throughout the root systems. The number of root segments was lower in the inoculated than in the control seedlings, indicating root loss after Phytophthora inoculation. In the shoots of inoculated birches, leaf and shoot wilting was observed.
• The appearance of wilting in shoots without visible dark discoloration in the base of stems indicated that symptoms originated from roots inoculated with Phytophthora.

     

Developing a tool for noninvasive monitoring of renal allografts

Renal transplantation has emerged as the therapy of choice for many patients with end-stage renal disease. One of the major goals is to tailor immunosuppressive therapy to the individual needs of every patient at every time point post transplant, balancing the risk for rejection and over-immunosuppression. Such individualized treatment will require assays that can detect harmful processes in the allograft early and that can be measured repeatedly. In this review, advantages and disadvantages of current assays to monitor renal allografts noninvasively and how proteomic technology might contribute to the development of novel biomarkers to improve patient management will be discussed.     

Early post-fire tree regeneration in a Picea-Vaccinium forest in northern Sweden

Abstract. Age and size structure of saplings of Picea abies, Pinus sylvestris and Betula pubescens were examined in a 26-yr old forest fire area in a Picea abies-Vaccinium myrtillus forest in northern Sweden. Picea, which is a shade-tolerant species, had its maximum regeneration prior to the shade-intolerant Pinus. The shift from Picea to Pinus regeneration in the late 1970s, did not seem to be related to variations in summer temperature. Instead, it is suggested that Picea established in the shade created by dead trees, and, that increased reindeer browsing of Betula in combination with a simultaneous thinning of the tree layer, favoured Pinus recruitment. These regeneration patterns do not confirm conventional views of post-fire succession in Sweden.