The effect of an imprecise map on interval mapping QTLs

The statistical analysis of quantitative trait locus (QTL) experiments relies on the use of a linkage map of the markers genotyped. Such a map is, at best, a good estimate of the true map. Resources might be diverted into developing better marker maps or improved maps become available after the analysis, raising concerns over the original analysis. It is therefore important to understand the sensitivity of QTL analysis to map inaccuracy. We have used simulation methods to investigate the consequences of an incorrect map on the results of a QTL analysis using interval mapping. Backcross data sets were generated with a particular map and then analysed with both the correct map and incorrect maps. If the incorrect maps maintained the true linkage groups (i.e. no markers were incorrectly assigned to another linkage group), the accuracy of the map had little or no impact on the ability to detect QTLs, the true significance levels of the tests or the relative placement of QTLs. When a marker was incorrectly placed on another linkage group, there was a small increase in the level of the test. After adjusting for this increase, there was a decrease in power to detect a QTL near the misplaced marker. This decrease was of a similar magnitude to that found when using a single-marker analysis compared with interval mapping. These results mean that QTL analyses can proceed without the need for very accurate marker maps, and that estimated QTL positions can be translated onto updated maps without the need for reanalysis.     

A portable flow chamber for in situ determination of benthic metabolism

1. Many stream ecologists are interested in determining the metabolic rates of benthic organisms, particularly those of production and respiration. It is often necessary to make these measurements on fresh material in the field at remote sites. Recirculating chambers are commonly used for this purpose.
2. A broad variety of recirculating chambers are described in the literature, but each design has inherent limitations. The most common are inability to control flow in the chamber and match it with external flow rates, and a lack of the power required to do this for extended periods. Alteration of spectral irradiance, temperature rise and elevated internal chamber pressures are additional limitations that have received little attention.
3. We have designed and constructed a flow chamber that eliminates some of these problems. The chamber utilizes a DC motor-driven propeller as an efficient recirculator (axial impeller), minimizing power requirements and it is constructed of UVB transparent acrylic to allow a full spectral complement of solar irradiance in the interior. Modular components allow the chamber to be taken apart quickly for cleaning and replacement of parts, making it more functional than some previous designs.
4. The axial impeller chamber was compared to a similar sized conventional chamber that had a small diameter return line and a high capacity centrifugal pump. The axial impeller chamber had less of a temperature rise during field incubations, lower power consumption and less internal pressure in the return line when producing equivalent water velocities.
5. The reported axial impeller design had relatively homogeneous velocity across the working section relative to other chambers and was capable of water velocities in excess of 1 m s^–1.     

Factors affecting ammonium uptake in streams – an inter-biome perspective

1. The Lotic Intersite Nitrogen eXperiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter‐biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and from desert to rainforest. Measurements at each site included physical, hydraulic and chemical characteristics, biological parameters, whole‐stream metabolism and ammonium uptake. Ammonium uptake was measured by injection of ¹⁵N‐ammonium and downstream measurements of ¹⁵N‐ammonium concentration. 3. We found no general, statistically significant relationships that explained the variability in ammonium uptake among sites. However, this approach does not account for the multiple mechanisms of ammonium uptake in streams. When we estimated biological demand for inorganic nitrogen based on our measurements of in‐stream metabolism, we found good correspondence between calculated nitrogen demand and measured assimilative nitrogen uptake. 4. Nitrogen uptake varied little among sites, reflecting metabolic compensation in streams in a variety of distinctly different biomes (autotrophic production is high where allochthonous inputs are relatively low and vice versa). 5. Both autotrophic and heterotrophic metabolism require nitrogen and these biotic processes dominate inorganic nitrogen retention in streams. Factors that affect the relative balance of autotrophic and heterotrophic metabolism indirectly control inorganic nitrogen uptake.     

PHOTOSYNTHESIS OF TWO MORPHOLOGIES OF NOSTOC PARMELIOIDES (CYANOBACTERIA) AS RELATED TO CURRENT VELOCITIES AND DIFFUSION PATTERNS1

Colonies of the stream-inhabiting cyanobacterium Nostoc parmelioides Kützing often contain a single endosymbiotic dipteran larva Cricotopus nostocicola (Wirth), which induces a morphological change from small, spherical colonies to larger, ear-shaped colonies. At a current velocity of 0 cm · s^?1, whole colonies containing the midge showed overall rates of ¹⁴CO₂ uptake and nitrogenase activity that were higher than those when the midge was absent (sphere-shaped colonies). Spherical colonies incubated at current velocities of 5-10 cm · s^?1did not show higher rates of ¹⁴CO₂ or ¹⁵N₂ incorporation than those with the larvae (ear-shaped colonies). Ear-shaped colonies extended well into regions of higher current velocity, whereas spherical colonies did not. Photosynthesis of ear-shaped colonies was stimulated by increased current velocity, increased inorganic C and decreased O₂ concentrations. Moreover, levels of O₂ at the surface of midge-inhabited colonies decreased with increased current velocity. The morphological change induced by the larva is detrimental (lowers photosynthesis and N₂ fixation) in quiescent water but not at current velocities above 10 cm · s^?1. This is probably a result of higher diffusion of O₂ and CO₂ associated with the midge-induced morphology.     

Covalent binding properties of the human complement protein C4 and hydrolysis rate of the internal thioester upon activation.

The complement proteins C3 and C4 have an internal thioester. Upon activation on the surface of a target cell, the thioester becomes exposed and reactive to surface-bound amino and hydroxyl groups, thus allowing covalent deposition of C3 and C4 on these targets. The two human C4 isotypes, C4A and C4B, which differ by only four amino acids, have different binding specificities. C4A binds more efficiently than C4B to amino groups, and C4B is more effective than C4A in binding to hydroxyl groups. By site-directed mutagenesis, the four residues in a cDNA clone of C4B were modified. The variants were expressed and their binding properties studied. Variants with a histidine residue at position 1106 showed C4B-like binding properties, and those with aspartic acid, alanine, or asparagine at the same position were C4A-like. These results suggest that the histidine is important in catalyzing the reaction of the thioester with water and other hydroxyl group-containing compounds. When substituted with other amino acids, this reaction is not catalyzed and the thioester becomes apparently more reactive with amino groups. This interpretation also predicts that the stability of the thioester in C4A and C4B, upon activation, will be different. We measured the time course of activation and binding of glycine to C4A and C4B. The lag in the binding curve behind the activation curve for C4A is significantly greater than that for C4B. The hydrolysis rates (k0) of the thioester in the activated proteins were estimated to be 0.068 s-1 (t1/2 of 10.3 s) for C4A and 1.08 s-1 (t1/2 of 0.64 s) for C4B. These results indicate that the difference in hydrolysis rate of the thioester accounts, at least in part, for the difference in the binding properties of C4A and C4B.     

The effects of diet on the esterification of glycerol phosphate, dihydroxyacetone phosphate and 2-hexadecylglycerol by homogenates of rat adipose tissue.

1. Male rats were fed for 5 weeks after weaning on a diet containing (by weight) 59% of starch or on diets that contained 39% of starch and 20% of either sucrose, beef tallow or corn oil. 2. The rats fed on the beef tallow consumed more energy than did the rats fed on the starch and sucrose diets. The rats fed on the corn oil drank less water than did the other groups of rats. 3. There were no significant differences between the four groups in terms of body-weight gain, epididymal-fat-pad weight and in the size, number and triacylglycerol content of the adipocytes in the fat-pads. 4. There was a significant correlation (P less than 0.001) between the activities of glycerol phosphate acyltransferase and monoacylglycerol acyltransferase in individual rats. Both of these activities were highest in the group fed on the high-starch diet and both correlated with the consumption of glucose by individual rats in the four groups. 5. The percentage of glycerol phosphate converted into diacylglycerol and triacylglycerol was positively correlated with the mean diameters, surface area and triacylglycerol content of the adipocytes for individual rats and was greates in the sucrose-fed rats. 6. The specific activity of dihydroxyacetone phosphate acyltransferase was highest in the rats fed on beef tallow. This activity was positively correlated with the energy intake for all dietary groups over the 5-week feeding period. 7. The results are discussed in terms of the functions of the three routes of glycerolipid synthesis in adipose tissue.     

Disease-Driven Amphibian Declines Alter Ecosystem Processes in a Tropical Stream

Predicting the ecological consequences of declining biodiversity is an urgent challenge, particularly in freshwater habitats where species declines and losses are among the highest. Small-scale experiments suggest potential ecosystem responses to losses of species, but definitive conclusions require verification at larger scales. We measured ecosystem metabolism and used whole-ecosystem stable isotope tracer additions to quantify nitrogen cycling in a tropical headwater stream before and after the sudden loss of amphibians to the fungal pathogen Batrachochytrium dendrobatidis. Tadpoles are normally dominant grazers in such streams, where greater than 18 species may co-occur and densities often exceed 50 individuals m^?2. Loss of 98% of tadpole biomass corresponded with greater than 2× increases in algae and fine detritus biomass in the stream and a greater than 50% reduction in nitrogen uptake rate. Nitrogen turnover rates in suspended and deposited organic sediments were also significantly lower after the decline. As a consequence, the stream cycled nitrogen less rapidly, and downstream exports of particulate N were reduced. Whole stream respiration was significantly lower following the decline, indicating less biological activity in the stream sediments. Contrary to our predictions, biomass of grazing invertebrates, or any invertebrate functional groups, did not increase over 2 years following loss of tadpoles. Thus, reductions in ecosystem processes linked to the amphibian decline were not compensated for by other, functionally redundant consumers. Declining animal biodiversity has ecosystem-level consequences that may not be offset by ecological redundancy, even in biologically diverse regions such as the Neotropics.