A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Quantitative prediction of phase diagrams for polymer partitioning in aqueous two-phase systems

Published polymer distribution data for aqueous poly(ethylene glycol)/dextran mixtures have been reassessed to illustrate the feasibility of their quantitative characterization in terms of the Flory-Huggins theory of polymer thermodynamics. Phase diagrams predicted by this characterization procedure provide better descriptions of the experimental data than those based on an earlier, oversimplified treatment in similar terms. (C) 2003 Wiley Periodicals, Inc.

Turbulence in Hydraulic Jumps: Experimental Measurements

A hydraulic jump is the transition from a supercritical open channel flow to a subcritical regime. It is characterised by a highly turbulent flow with macro-scale vortices, some kinetic energy dissipation and a bubbly two-phase flow structure. New air-water flow measurements were performed in hydraulic jump flows for a range of inflow Froude numbers. The experiments were conducted in a large-size facility using two types of phase-detection intrusive probes: i.e., single-tip and double-tip conductivity probes. These were complemented by some measurements of free-surface fluctuations using ultrasonic displacement meters. The present study was focused on the turbulence characteristics of hydraulic jumps with partially-developed inflow conditions. The void fraction measurements showed the presence of an advective diffusion shear layer in which the void fractions profiles matched closely an analytical solution of the advective diffusion equation for air bubbles. The present results highlighted some influence of the inflow Froude number onto the air bubble entrainment process. At the largest Froude numbers, the advected air bubbles were more thoroughly dispersed vertically, and larger amount of air bubbles were detected in the turbulent shear layer. In the air-water mixing layer, the maximum void fraction and bubble count rate data showed some longitudinal decay function in the flow direction. Such trends were previously reported in the literature. The measurements of interfacial velocity and turbulence level distributions provided new information on the turbulent velocity field in the highly-aerated shear region. The present data suggested some longitudinal decay of the turbulence intensity. The velocity profiles tended to follow a wall jet flow pattern. The air–water turbulent time and length scales were deduced from some auto- and cross-correlation analyses based upon the method of CHANSON (2006,2007). The results provided the integral turbulent time and length scales of the eddy structures advecting the air bubbles in the developing shear layer. The experimental data showed that the auto-correlation time scale Txx was larger than the transverse cross-correlation time scale Txz. The integral turbulence length scale Lxz was a function of the inflow conditions, of the streamwise position (x-x1)/d1 and vertical elevation y/d1. Herein the dimensionless integral turbulent length scale Lxz/d1 was closely related to the inflow depth: i.e., Lxz/d1 = 0.2 to 0.8, with Lxz increasing towards the free-surface. The free-surface fluctuations measurements showed large turbulent fluctuations that reflected the dynamic, unsteady structure of the hydraulic jumps. A linear relationship was found between the normalized maximum free-surface fluctuation and the inflow Froude number.

Dynamic Similarity and Scale Effects Affecting Air Bubble Entrainment in Hydraulic Jumps

In an open channel, the transition from super- to sub-critical flow is a flow singularity (the hydraulic jump) characterised by a sharp rise in free-surface elevation, strong turbulence and air entrainment in the roller. A key feature of the hydraulic jump flow is the strong free-surface aeration and air-water flow turbulence. In the present study, similar experiments were conducted with identical inflow Froude numbers Fr1 using a geometric scaling ratio of 2:1. The results of the Froude-similar experiments showed some drastic scale effects in the smaller hydraulic jumps in terms of void fraction, bubble count rate and bubble chord time distributions. Void fraction distributions implied comparatively greater detrainment at low Reynolds numbers yielding some lesser aeration of the jump roller. The dimensionless bubble count rates were significantly lower in the smaller channel, especially in the mixing layer. The bubble chord time distributions were quantitatively close in both channels, and they were not scaled according to a Froude similitude. Simply the hydraulic jump remains a fascinating two-phase flow motion that is still poorly understood.

The strain-driven pyrochlore to "defect fluorite" phase transition in rare earth sesquioxide stabilized cubic zirconias

The relationship between the ordering characteristic of the pyrochlore structure type and that characteristic of the defect fluorite structure type (immediately on either side of two phase regions separating the two structure types) in a range of rare eath sesquioxide stabilized cubic zirconias is investigated via electron diffraction and imaging. Systematic structural change as a function of composition and relative size of the constituent metal ions is highlighted and a multi-q to single-q = 1/2 [111]* model proposed for the observed pyrochlore to defect fluorite phase transition. Strain introduced into the close-packed {111} metal ion planes of the defect fluorite average structure by the local cation and oxygen vacancy distribution is pointed to as the likely origin of the observed behavior. (C) 2001 Academic Press

Experimental investigation of liquid flow shift due to gas cross flow in non-wetted packed beds

An experimental study has been carried out for the gas-liquid two-phase flow in a packed bed simulating conditions of the gas and liquid flows in the lower part of blast furnace. The localised liquid flow phenomenon in presence of gas cross flow, which usually occurs around the cohesive zone and raceway in blast furnace, was investigated in detail. Such liquid flow is characterised in terms of liquid shift distance or liquid shift angle that can effectively be measured by the experiments involved in the current study. It is found that liquid shift angle does not significantly increase or decrease with different packing depth. This finding supports the hypothesis of the force balance model where a vectorial relationship among acting forces, i.e. gas drag force, gravitational force and solid-liquid friction force, and liquid shift angle does exist. Liquid shift angle is inversely proportional to particle size and liquid density, and proportional to square of gas superficial velocity, but is almost independent on liquid flowrate and liquid viscosity. The gas-liquid drag coefficient, an important aspect for quantifying the interaction between gas and liquid flows, was conceptually modified based on the discrete feature of liquid flow through a packed bed and evaluated by the combined theoretical and experimental investigation. Experimental measurements suggest that the gas-liquid drag coefficient is approximately a constant (C-DG(')=5.4+/-1.0) and is independent on liquid properties, gas velocity and packing structure. The result shows a good agreement with previous experimental data and prediction of the existing liquid flow model.

Competition and resource availability in an annual plant community dominated by an invasive species, Carrichtera annua (L. Aschers.), in South Australia

The last decade has seen spirited debates about how resource availability affect the intensity of competition. This paper examines the effect that a dominant introduced species, Carrichtera annua, has upon the winter annual community in the arid chenopod shrublands of South Australia. Manipulative field experiments were conducted to assess plant community response to changing below-ground resource levels and to the manipulation of the density of C. annua. Changes in the density of C. annua had little effect on the abundance of all other species in the guild. Nutrient addition produced an increase in the biomass of the most abundant native species, Crassula colorata. An analysis of the root distribution of the main species suggested that the areas of soil resource capture of C. annua and C. colorata are largely segregated. Our results suggest that intraspecific competition may be stronger than interspecific competition, controlling the species responses to increased resource availability. The results are consistent with a two-phase resource dynamics systems, with pulses of high resource availability triggering growth, followed by pulses of stress. Smaller plants were nutrient limited under natural field conditions, suggesting that stress experienced during long interpulse phases may override competitive effects after short pulse phases. The observed differences in root system structure will determine when plants of a different species are experiencing a pulse or an interpulse phase. We suggest that the limitations to plant recruitment and growth are the product of a complex interplay between the length and intensity of the pulse of resource availability, the duration and severity of the interpulse periods, and biological characters of the species.

Analysis of the phase behavior of the aqueous poly(ethylene glycol)-Ficoll system

The PEG-Ficoll polymer phase system is one that has been overlooked in the past for biotechnology applications because of the stability of its emulsions. However, new applications, such as emulsion coating of cells, are appearing that rely on this very property. Ficoll is highly polydisperse and multimodal with three distinct Ficoll peaks in gel permeation chromatography. As a result, the transition between one-phase and two-phase systems is blurred and the binodials obtained through turbidometric titration and tie-line analysis differ significantly. Moreover, since the three Ficoll peaks partition differently, tie-line analysis cannot be described by a simple model of the aqueous two-phase system. A simple modification to the model allowed for excellent fit, and this modification may prove well-suited for the many practical cases where aqueous two-phase systems fail to display parallel tie-lines as implicitly assumed in the simpler model.

Effects of phytase supplementation of diets with two tiers of nutrient specifications on growth performance and protein efficiency ratios of broiler chickens

in two feeding experiments male and mixed-sex broiler chicks were offered diets based on sorghum and a wheat-sorghum blend with two tiers of nutrient specifications, without and with microbial phytase (600 and 800 FTU/kg), from 7-25 and 1-42 days post-hatch, respectively. The nutrient specifications for protein, amino acids, energy density and phosphorus (P) of standard diets were reduced to formulate the modified diets on a least-cost basis. Calculated differences in nutrient specifications between standard and modified diets ranged from 14.3 to 17.1 g/kg crude protein, 0.24 to 0.40 MJ/kg apparent metabolisable energy (AME) and 1.06 to 1.20 g/kg available P. In both experiments, reduced nutrient specifications had a negative impact on growth rates and feed efficiency and phytase supplementation had a positive influence on growth performance and protein efficiency ratios (PER). Phytase addition to the less expensive, modified diets either partially or entirely compensated for reduced growth performance and, consequently, feed costs per kg of live weight gain were reduced. In Experiment 1, phytase increased (p<0.001) nitrogen-corrected AME (AMEn) from 15.39 to 15.89 MJ/kg dry matter. For nitrogen (N) retention there was an interaction (p<0.05) between diet type and phytase as the effects of phytase on N retention were more pronounced in the modified diets, with an increase from 0.512 to 0.561. These results demonstrate the positive effects of phytase on protein and energy utilisation, in addition to its established liberation of phytate-bound P and illustrate the feasibility of assigning nutrient replacement values to the feed enzyme for consideration in least-cost ration formulations. Further work is, however, required to define the most appropriate reductions in nutrient specifications in association with phytase supplementation.

Kinetics of propranolol uptake in muscle, skin, and fat of the isolated perfused rat hindlimb

The tissue distribution kinetics of a highly bound solute, propranolol, was investigated in a heterogeneous organ, the isolated perfused limb, using the impulse-response technique and destructive sampling. The propranolol concentration in muscle, skin, and fat as well as in outflow perfusate was measured up to 30 min after injection. The resulting data were analysed assuming (1) vascular, muscle, skin and fat compartments as well mixed (compartmental model) and (2) using a distributed-in-space model which accounts for the noninstantaneous intravascular mixing and tissue distribution processes but consists only of a vascular and extravascular phase (two-phase model). The compartmental model adequately described propranolol concentration-time data in the three tissue compartments and the outflow concentration-time curve (except of the early mixing phase). In contrast, the two-phase model better described the outflow concentration-time curve but is limited in accounting only for the distribution kinetics in the dominant tissue, the muscle. The two-phase model well described the time course of propranolol concentration in muscle tissue, with parameter estimates similar to those obtained with the compartmental model. The results suggest, first that the uptake kinetics of propranolol into skin and fat cannot be analysed on the basis of outflow data alone and, second that the assumption of well-mixed compartments is a valid approximation from a practical point of view las, e.g., in physiological based pharmacokinetic modelling). The steady-state distribution volumes of skin and fat were only 16 and 4%, respectively, of that of muscle tissue (16.7 ml), with higher partition coefficient in fat (6.36) than in skin (2.64) and muscle (2.79. (C) 2000 Elsevier Science B.V. All rights reserved.

Target similarity effects: Support for the parallel distributed processing assumptions

Recent research has begun to provide support for the assumptions that memories are stored as a composite and are accessed in parallel (Tehan & Humphreys, 1998). New predictions derived from these assumptions and from the Chappell and Humphreys (1994) implementation of these assumptions were tested. In three experiments, subjects studied relatively short lists of words. Some of the Lists contained two similar targets (thief and theft) or two dissimilar targets (thief and steal) associated with the same cue (ROBBERY). AS predicted, target similarity affected performance in cued recall but not free association. Contrary to predictions, two spaced presentations of a target did not improve performance in free association. Two additional experiments confirmed and extended this finding. Several alternative explanations for the target similarity effect, which incorporate assumptions about separate representations and sequential search, are rejected. The importance of the finding that, in at least one implicit memory paradigm, repetition does not improve performance is also discussed.

Feed intake and liveweight responses to nitrogen and/or protein supplements by steers of Bos taurus, Bos indicus and Bos taurus x Bos indicus breed types offered a low quality grass hay

Thirty steers were used in two pen experiments (Expts 1 and 2). and 27 of these in a third (Expt 3), to quantify their responses of hay intake, rumen ammonia nitrogen (RAN) concentrations, and liveweight to inputs of rumen soluble nitrogen (urea) and rumen undegradable protein (formaldehyde-treated casein; F-casein) when added to a basal diet of low quality hays. The hays were made From unimproved native pastures typical of those grazed by cattle in the subtropics of Australia and contained 7.8 g N/kg dry matter (DM) with coefficient of organic matter digestibility of 0.503 in Expts 1 and 2, and 5.2 g N/kg DM with a digestibility range from 0.385 to 0.448 in Expt 3. The steers (15 months old) were either Brahman (B), Hereford (H) or the F-1 Brahman x Hereford (BH) cross. Steers were offered supplementary minerals with the hays in each experiment. In Expt 1 (35 days) urea was sprayed on part of the hay, allowing for daily urea intakes (g/steer) of either 0, 5, 11, 16 or 26. In Expt 2 (42 days), F-casein was offered daily (g/steer) at either 0, 75, 150, 225 or 300 and in Expt 3 (56 days) discrete offerings were made of soluble casein (225 g/day), of urea (18 g/day) + F-casein (225 g/day) or of nil. There were significant linear effects of urea intake upon hay intake and liveweight change of steers. However, B steers had smaller increases in intake and liveweight change than did H steers, and B steers did not have a linear increase in RAN concentrations with increasing urea intake as did H and SH steers. In Expt 2 there were significant linear effects of F-casein supplements on hay intake and liveweight change of steers and a significant improvement in their feed conversion ratio (i.e. DM intake:liveweight change). The B steers did not differ from H and BH steers in liveweight change but had significantly lower hay intakes and non-significantly smaller increases in RAN with increasing F-casein intake. In Expt 3, hay intake of the steers increased with soluble casein (by 16.8 %) and with urea + F-casein (24.5 %). Only steers given urea + F-casein had a high RAN concentration (94 mg/l) and a high liveweight gain. The B steers had a liveweight loss and a lower hay intake than H or BH steers in Expt 3 but a higher RAN concentration. These studies have indicated the importance of the form and quantity of additional N required by cattle of differing breed types to optimize their feed intake and liveweight gain when offered low-N, low-digestible hays.