Bayesian analysis of serial dilution assays

In a serial dilution assay, the concentration of a compound is estimated by combining measurements of several different dilutions of an unknown sample. The relation between concentration and measurement is nonlinear and heteroscedastic, and so it is not appropriate to weight these measurements equally. In the standard existing approach for analysis of these data, a large proportion of the measurements are discarded as being above or below detection limits. We present a Bayesian method for jointly estimating the calibration curve and the unknown concentrations using all the data. Compared to the existing method, our estimates have much lower standard errors and give estimates even when all the measurements are outside the "detection limits." We evaluate our method empirically using laboratory data on cockroach allergens measured in house dust samples. Our estimates are much more accurate than those obtained using the usual approach. In addition, we develop a method for determining the "effective weight" attached to each measurement, based on a local linearization of the estimated model. The effective weight can give insight into the information conveyed by each data point and suggests potential improvements in design of serial dilution experiments.     

Kinetics of stable isotope and body composition in olive baboons (Papio anubis) estimated by deuterium dilution space: a pilot study

Morphometrics and isotope-labelled water were used to determine body composition [total body water, total body fat and fat-free mass (FFM)] of three captive female olive baboons (Papio anubis). Mean mass was 16.5 kg, comparable with other captive settings but heavier than wild olive baboons. Average water content was 66%; FFM averaged 90.5%. Baboon females have less body fat than human counterparts. Compared with captive or wild baboons, these females were adequately nourished for their energy expenditure. A positive association between total mass and FFM existed, but due to the small sample no general relationship was observed for body fat or FFM and condition or size measures. The kinetics of deuterium equilibration in body fluids for baboons was determined as 3-4 hours after injection, similar to that for humans. Deuterium dilution technique appears to be an appropriate method for studying body composition in baboons, although a larger sample is needed for relationships between morphometric indices and body composition.     

Translocation of amino acids from stem nodules of Sesbania rostrata demonstrated by GC-MS in planta 15N isotope dilution

We report a novel use of the ¹⁵N dilution technique to detail the translocation of amino compounds in the legume Sesbania rostrata . The conventional ¹⁵N dilution technique follows the dilution of ¹⁵N within a labelled plant, as ¹⁴N₂ is fixed by symbiotic bacteria. In our experiments, stem-nodulated Sesbania rostrata were enriched by feeding with ¹⁵N ammonium nitrate for 2 weeks, followed by a 1 week period where the only N available to the plants was via nitrogen fixation of atmospheric N₂. We measured the composition, concentration and ¹⁵N enrichment of amino compounds in various plant tissues, both above and below the stem nodules, using GC-MS and isotopic abundance mass spectrometry techniques. Approximately 28% of the total N in the stem nodules was derived from internal plant sources. The ureides allantoic acid and allantoin were not abundant in xylem, leaf or nodule tissues. The amides asparagine and glutamine were the major export products from stem nodules although a wide range of other amino compounds are also synthesized. Amino acids within the nodules had a low level of enrichment, demonstrating that a small fraction (≈ 11%) was derived from outside the nodules, and significant cycling of N (28% of xylem N) through the root system was revealed by measurements of ¹⁵N distribution and amino acid concentrations.     

Origin and succession of phytoplankton in a river-lake system (Spree,Germany)

The River Spree (Germany) flows through an impoundment and several shallow lakes in its middle and lower course. In this river-lake system, the seasonal and longitudinal dynamics of dominant phytoplankton populations were studied in relation to retention time of water, mixing conditions and nutrient supply from 1988–92. Some phytoplankton species populated the same river section for weeks or months each year at their season. Such stable populations have to origin from river zones functioning like mixed reactors. In the Spree system, centric diatoms originated from an impoundment and filamentous cyanobacteria from a flushed lake with longer retention time of water. Downstream, biomass and composition of phytoplankton altered nearly simultaneously along the system.The fate of planktonic organisms washed from mixed reactors into the flow depended on the conditions at the zones of origin. During spring, populations dominating phytoplankton communities of the well-mixed lakes grew further under river conditions. However the biomass of summer species, adapted to intermittent stratification, was halved along the river course. These seasonal differences were probably caused by lower maximum growth rates of summer species and enhanced losses (photorespiration, sedimentation or grazing of benthic filter feeders, but not of zooplankton) of algal populations under river conditions in summer.Phytoplankton assimilation, settlement of diatoms, or denitrification caused declining (probably growth limiting) concentrations of dissolved inorganic phosphorus (spring), silicon (early summer) or nitrogen (summer) along the river course, respectively. The minimum content of DRP was often followed by a clear-water phase. Reduced DSi supply selected against diatoms and additional DIN shortage favoured N₂-fixing cyanobacteria in the last lake of the system.R-strategists (sensu Reynolds) were selected in both the flushed, shallow lakes and the lowland river. In general, the biomass of cyanobacteria increased within the lakes and declined along the river course. Some diatom populations grew in the river, but were grazed or settled down in the lakes. Beside this general picture, different populations from the same phylogenetic group did not necessarily perform in similar ways.     

Biological nitrogen fixation in four Gliricidia sepium genotypes

A field experiment was conducted at the Coconut Research Institute in Sri Lanka to examine the biological nitrogen fixation potential of three Gliricidia sepium provenances (OFI 14/84, 17/84, 12/86) and a local landrace (designated LL), using the ¹⁵N isotope dilution method. There was marked variation in dry matter, total N, nodulation and ¹⁵N enrichment among the Gliricidia genotypes (=0.001), and the dry matter yield of Cassia siamea (syn. Senna siamea), the non-N₂ fixing reference plant was higher than for G. sepium. In all cases, highest biomass and total N were aboveground, with roots on average accounting for < 20 % of total dry matter or the total N in plants. Atom % ¹⁵N excess was highest in C. siamea, and lowest in OFI 14/84. Although atom % ¹⁵N excess was lower in Gliricidia leaves than in the other organs (all of which had similar ¹⁵N enrichments), values of % N derived from atmospheric N₂ fixation (% Ndfa) calculated for any individual organ or for the whole plant were similar. This was because the relative distribution of ¹⁵N in the different parts of the fixing plant followed the same trend as in the reference plant. There were significant differences (p=0.01) in N₂ fixation between the Gliricidia genotypes. The values ranged from 17.8 g N tree^-1 (equivalent to 86 kg N ha^-1 at 5000 trees ha^-1) in OFI 12/86 to 61.7g N tree^-1 (equivalent to 309 kg N ha^-1) in OFI 14/84. Although most of this variability was due to differences in both % Ndfa and total N in plant, amount of N fixed was more correlated with total N in plant (r=0.935) than with % Ndfa (r=0.707). On average, % Ndfa in all three G. sepium provenances and LL was about 55 % or 34.6 g N tree^-1 (equivalent to some 166 kg N ha^-1) in the 9 months within which N₂ fixation was measured. This represents a substantial contribution of N into the soil-plant system.     

Re-dating the Early Upper Paleolithic Levels of Le Trou Magrite (Pont-à-Lesse,Belgium)

All but one of the published radiocarbon dates from the 1991–1992 excavations of Strata 3 and 2 at le Trou Magrite are considered too recent because the dating was done with then-standard chemical pretreatment protocols. This study re-dates Stratum 2 using the same, then-pioneering, XAD-2 purification method on bone collagen as had been used for the 44,650 cal BP date from Stratum 3. The results are two averaged dates that are in stratigraphic order between themselves and in relation to the Stratum 3 date: 43,400 and 43,500 cal BP, according to the IntCal20 curve. These dates are very similar to recently published dates for the earliest Aurignacian in SW Germany and the latest Neanderthal remains in Belgium and they are associated with artifact assemblages that, without obvious evidence of mixture (other than that which was highly localized), include Upper Paleolithic stone tools and blades/bladelets together with numerous sidescrapers, denticulates and notches which are not exclusively Mousterian artifacts. Nineteenth-century excavations in the cave of le Trou Magrite yielded unambiguously diagnostic Aurignacian artifacts and works of portable art that could conceivably have been from a deposit equivalent in age to these strata on the contiguous terrace. It is clear that the first blade(let)-rich assemblages in the site were created on the cusp of the transition from the Middle-to-Upper Paleolithic transition and replacement of the Neanderthals in NW Europe.     

Yield and biological nitrogen fixation of common bean (Phaseolus vulgaris L.) in Peru

Two field experiments were performed to evaluate the nitrogen fixation potential of twenty common bean cultivars and breeding lines during summer and winter seasons of 1986 and 1988, respectively. The ¹⁵N isotope dilution method was used to quantify N₂ fixation. The cultivars and breeding lines were variable in terms of their N₂ fixation. The cv. Caballero was very efficient, with more than 50% N derived from the atmosphere and 60–80 kg N ha^–1 fixed in both seasons. Other cultivars were less efficient, since the poorest ones derived less than 30% of their nitrogen from the atmosphere and fixed less than 20 kg N ha^–1. After additional testing the best cultivars may be used directly by the farmers for cultivation. The experiments have provided information about which genotypes may be used to breed for enhanced fixation in common bean.     

Early seedling and seasonal N2-fixing symbiotic activity of two soybean [Glycine max (L.) Merr.] cultivars inoculated with Bradyrhizobium strains of diverse origin

In areas with a short growing season the poor adaptability of soybean [Glycine max Meer. (L.)] to cool soil conditions is considered the primary yield limiting factor. Soybean requires temperatures in the 25 to 30°C range for optimum N₂-fixation and yield. Field studies were conducted in 1990 and 1991 at Montreal, Quebec to determine whether adaptability to cool soil conditions, with respect to earlier symbiosis establishment and function, existed among either Bradyrhizobium strains or soybean genotypes. An early maturing isoline of the soybean cultivar Evans and the cultivar Maple Arrow were inoculated with one of four strains isolated from the cold soils of Hakkaido, northern Japan, or the commercially used strains 532C or USDA110, at two planting dates. Plot biomass and nodulation were assessed at seedling (V2), and flowering(R2) growth stages and harvest maturity. Soybean genotypes did not differ for pre-flowering nodulation or N₂-fixation in the cool spring conditions of the first year. Seasonal N₂-fixation rates were also determined at the final harvest by the N-balance and ¹⁵N-isotope dilution methods. Significantly higher symbiotic activity was found for two of the four Hakkaido strains and was reflected in higher final soybean seed yield and total N₂-fixation for the growing season, as compared to the two commercial strains. Planting 14 days earlier resulted in greater early vegetative and total seasonal N₂ fixation and yield in the second year when soil temperatures were warmer, emphasizing the need for the development of soybean-Bradyrhizobium combinations superior in nodule development and function under cool soil conditions.     

Methods for enhancing symbiotic nitrogen fixation

Biological nitrogen fixation of leguminous crops is becoming increasingly important in attempts to develop sustainable agricultural production. However, these crops are quite variable in their effectiveness in fixing nitrogen. By the use of the ¹⁵N isotope dilution method some species have been found to fix large proportions of their nitrogen, while others like common bean have been considered rather inefficient. Methods for increasing N₂ fixation are therefore of great importance in any legume work. Attempts to enhance nitrogen fixation of grain legumes has been mainly the domain of microbiologists who have selected rhizobial strains with superior effectiveness or competitive ability. Few projects have focused on the plant symbiont with the objective of improving N₂ fixation as done in the FAO/IAEA Co-ordinated Research Programme which is being reported in this volume. The objective of the present paper is to discuss some possibilities available for scientists interested in enhancing symbiotic nitrogen fixation in grain legumes. Examples will be presented on work performed using agronomic methods, as well as work on the plant and microbial symbionts. There are several methods available to scientists working on enhancement of N₂ fixation. No one approach is better than the others; rather work on the legume/Rhizobium symbiosis combining experience from various disciplines in inter-disciplinary research programmes should be pursued.