Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

Social structure in migrating humpback whales (Megaptera novaeangliae)

Although largely solitary, humpback whales exhibit a number of behaviours where individuals co-operate with one another, for example during bubble net feeding. Such cases could be due to reciprocal altruism brought on by exceptional circumstances, for example the presence of abundant shoaling fish. An alternative explanation is that these behaviours have evolved through kin selection. With little restriction to either communication or movement, diffuse groups of relatives could maintain some form of social organization without the need to travel in tight-nit units. To try to distinguish between these hypotheses, we took advantage of the fact that migrating humpback whales often swim together in small groups. If kin selection is important in humpback whale biology, these groups should be enriched for relatives. Consequently, we analysed biopsy samples from 57 groups of humpback whales migrating off Eastern Australia in 1992. A total of 142 whales were screened for eight microsatellite markers. Mitochondrial DNA sequences (371 bp) were also used to verify and assist kinship identification. Our data add support to the notion that mothers travel with their offspring for the first year of the calf's life. However, beyond the presence of mother-calf/yearling pairs, no obvious relatedness pattern was found among whales sampled either in the same pod or on the same day. Levels of relatedness did not vary between migratory phases (towards or away from the breeding ground), nor between the two sexes considered either overall or in the north or south migrations separately. These findings suggest that, if any social organization does exist, it is formed transiently when needed rather than being a constant feature of the population, and hence is more likely based on reciprocal altruism than kin selection.

Shoulder movement after breast cancer surgery: results of a randomised controlled study of postoperative physiotherapy

Breast screening programmes have facilitated more conservative approaches to the surgical and radiotherapy management of women diagnosed with breast cancer. This study investigated changes in shoulder movement after surgery for primary, operable breast cancer to determine the effect of elective physiotherapy intervention. Sixty-five women were randomly assigned to either the treatment (TG) or control group (CG) and assessments were completed preoperatively, at day 5 and at 1 month, 3, 6, 12 and 24 months postoperatively. The CG only received an exercise instruction booklet in comparison to the TG who received the Physiotherapy Management Care Plan (PMCP). Analyses of variance revealed that abduction returned to preoperative levels more quickly in the TG than in the CG. The TG women had 14degrees more abduction at 3 months and 7degrees at 24 months. Functional recovery at 1 month was greater in those randomised to the TG, with a dominant operated arm (OA) or receiving breast-conserving surgery. However, it was not possible to predict recovery over the 2 years postoperatively on the basis of an individual woman's recovery at 1 month postoperatively. The eventual recovery of abduction or flexion range of movement was not related to the dominance of the OA nor to the surgical procedure performed. The PMCP provided in the early postoperative period is effective in facilitating and maintaining the recovery of shoulder movement over the first 2 years after breast cancer surgery.

Ventilatory effects of neurophysiological facilitation and passive movement in patients with neurological injury

Thirteen intubated, high dependency patients with neurological injuries were studied in order to investigate the short term respiratory effects of neurophysiological facilitation and passive movement on tidal volume (V-T), minute ventilation (V-E), respiratory rate (V-R) and oxygen saturation (SpO(2)). The subjects were studied under four conditions: no intervention (control) and during periods of neurophysiological facilitation, passive movement and sensory stimulation. All periods were standardised to three minutes duration and all parameters were recorded before and after each intervention. Neurophysiological facilitation produced significant increases (p < 0.01) in V-E and SpO(2) (p < 0.05) when compared with control values, with an overall mean increase in V-E of 14.6%. Similarly, passive movement increased V-E (p < 0.01) by an average of 9.8% and also increased SpO(2) (p < 0.01). In contrast, sensory stimulation produced significant increases (p < 0.01) in SpO(2) with control levels, with no significant change in V-T or V-E. There was no significant difference in V-R with all treatments. This study provides preliminary evidence of improved short term ventilatory function following neurophysiological facilitation, independent of generalised sensory stimulation, which has not been previously examined in the literature, supporting its use in the management of high dependency neurological patients.

Determinants of physical activity in middle school children

Objective: To evaluate the theory of reasoned action (TRA) and planned behavior (TPB) in predicting moderate-to-vigorous physical activity (MVPA) in sixth-grade youth. Methods: One hundred ninety-eight students completed a questionnaire measuring attitudes, subjective norms, perceived behavioral control, and intentions to be active. MVPA was measured using the CSA 7,164 accelerometer. Results: Although demonstrating an acceptable fit, the TRA and TPB accounted for only a small percentage of the variance in MVPA. In support of the TPB: the addition: of control perceptions to the reasoned! action model! added to the prediction of intentions and MVPA. Conclusion: Within our sample of sixth graders, the utility of the, TRA or TPB;as a framework for activity interventions appears to be limited.

Role of peripheral afference during acquisition of a complex coordination task

It has long been supposed that the interference observed in certain patterns of coordination is mediated, at least in part, by peripheral afference from the moving limbs. We manipulated the level of afferent input, arising from movement of the opposite limb, during the acquisition of a complex coordination task. Participants learned to generate flexion and extension movements of the right wrist, of 75degrees amplitude, that were a quarter cycle out of phase with a 1-Hz sinusoidal visual reference signal. On separate trials, the left wrist either was at rest, or was moved passively by a torque motor through 50degrees, 75degrees or 100degrees, in synchrony with the reference signal. Five acquisition sessions were conducted on successive days. A retention session was conducted I week later. Performance was initially superior when the opposite limb was moved passively than when it was static. The amplitude and frequency of active movement were lower in the static condition than in the driven conditions and the variation in the relative phase relation across trials was greater than in the driven conditions. In addition, the variability of amplitude, frequency and the relative phase relation during each trial was greater when the opposite limb was static than when driven. Similar effects were expressed in electromyograms. The most marked and consistent differences in the accuracy and consistency of performance (defined in terms of relative phase) were between the static condition and the condition in which the left wrist was moved through 50degrees. These outcomes were exhibited most prominently during initial exposure to the task. Increases in task performance during the acquisition period, as assessed by a number of kinematic variables, were generally well described by power functions. In addition, the recruitment of extensor carpi radialis (ECR), and the degree of co-contraction of flexor carpi radialis and ECR, decreased during acquisition. Our results indicate that, in an appropriate task context, afferent feedback from the opposite limb, even when out of phase with the focal movement, may have a positive influence upon the stability of coordination.

Neural compensation for compliant loads during rhythmic movement

An experiment was performed to characterise the movement kinematics and the electromyogram (EMG) during rhythmic voluntary flexion and extension of the wrist against different compliant (elastic-viscous-inertial) loads. Three levels of each type of load, and an unloaded condition, were employed. The movements were paced at a frequency of I Hz by an auditory metronome, and visual feedback of wrist displacement in relation to a target amplitude of 100degrees was provided. Electro-myographic recordings were obtained from flexor carpi radialis (FCR) and extensor carpi radialis brevis (ECR). The movement profiles generated in the ten experimental conditions were indistinguishable, indicating that the CNS was able to compensate completely for the imposed changes in the task dynamics. When the level of viscous load was elevated, this compensation took the form of an increase in the rate of initial rise of the flexor and the extensor EMG burst. In response to increases in inertial load, the flexor and extensor EMG bursts commenced and terminated earlier in the movement cycle, and tended to be of greater duration. When the movements were performed in opposition to an elastic load, both the onset and offset of EMG activity occurred later than in the unloaded condition. There was also a net reduction in extensor burst duration with increases in elastic load, and an increase in the rate of initial rise of the extensor burst. Less pronounced alterations in the rate of initial rise of the flexor EMG burst were also observed. In all instances, increases in the magnitude of the external load led to elevations in the overall level of muscle activation. These data reveal that the elements of the central command that are modified in response to the imposition of a compliant load are contingent, not only upon the magnitude, but also upon the character of the load.

EphA receptors and ephrin-A ligands exhibit highly regulated spatial and temporal expression patterns in the developing olfactory system

The spatiotemporal expression patterns of the chemorepulsive EphA receptors, EphA4 and EphA7, and three ephrins-A2, A4 and A5, were examined in the developing rat primary olfactory system. Unlike the visual system that has simple and stable gradients of Ephs and ephrins, the olfactory system demonstrates complex spatiotemporal expression patterns of these molecules. Using immunohistochemistry, we demonstrate that expression of these molecules is dynamic and tightly regulated both within and between different cell types. We reveal restricted targeting of these proteins within subcellular compartments of some neurons. EphA4, ephrin-A2 and ephrin-A5 were expressed by primary olfactory axons during the embryonic formation of the olfactory nerve. There were no gradients in expression along the rostrocaudal or ventrodorsal axes in the nasal cavity and olfactory bulb. However, during the early neonatal period, axons expressing different levels of ephrin-A5 sorted out and terminated in a subpopulation of glomeruli that were mosaically dispersed throughout the bulb. The expression of EphA4 and ephrin-A2 was dramatically down-regulated on all axons during the early neonatal period of glomerular formation. The uniform co-expression of receptors and ligands before glomerular formation suggests they play a generic role in axon-axon interactions in the olfactory nerve and nerve fibre layer. In contrast, loss of EphA4 from axons during glomerular formation may facilitate the interaction of ephrin-A5 with Eph receptors on target cells in the bulb. While EphA4, EphA5 and EphA7 are not mosaically expressed by bulbar neurons, other Eph receptors may have expression patterns complementary to the ephrin-A5-positive subpopulation of glomeruli. (C) 2002 Elsevier Science B.V. All rights reserved.

Spoilage patterns of skim and whole milks

The reason for the reported difference in spoilage behaviour of skim and whole pasteurised milks was investigated The rates of growth of psychrotrophic bacteria were not significantly different in the two milks and the bacterial types. till pseudomonad, present at spoilage were also similar. However. when representative spoilage organisms were cultured into freshly pasteurised skim and whole milks, skim milks exhibited predominantly bitter flavours while whole milk showed mostly sour flavours. The different spoilage, behaviours can be largely explained by greater proteolysis in skim milk than in whole milk. caused by, higher production of protease and greater susceptibility of the protein to protease attack. In addition, lipolysis in whole milk, caused by the substantial quantities of lipase produced by spoilage pseudomonads in this milk. also contributes to the different flavours produced during cold storage of these milk types.

Patterns of lipid storage and mobilisation in the female green sea turtle (Chelonia mydas)

Reproductive data from southern Queensland indicate that vitellogenesis in female Chelonia mydas takes approximately 8 months and is followed by a migration to a breeding area. At Heron Island, females lay multiple clutches over approximately 3 months. To investigate how females mobilise and store lipid during the breeding season we collected plasma, yolk, and fat tissue samples from females at a variety of stages during the nesting season. In breeding females, concentrations of plasma triglyceride increased seasonally. They reached peak concentrations during vitellogenesis and courtship, remained high throughout the nesting season, and then declined to a nadir after the last clutch. Plasma protein concentration increased throughout the breeding season, peaking following the last clutch for the season. Yolk lipids were highest during courtship and were similar throughout the nesting season, suggesting that uptake of lipid by ovarian follicles is completed prior to the beginning of the nesting season. Plasma triglyceride decreases in females with prolonged periods of unsuccessful nesting, and total lipid levels in adipose tissue and follicle yolks were significantly lower in atretic females. It appears that: (1) endogenous energy reserves can be reduced by stochastic environmental events (such as those reducing nesting success), and (2) a metabolic shift signalling the end of the nesting season is characterised by a drop in plasma triglycerides and slight increase in total plasma protein.

Patterns of resistance to angular leaf spot, anthracnose and common bacterial blight in common bean germplasm

Diseases and insect pests are major causes of low yields of common bean (Phaseolus vulgaris L.) in Latin America and Africa. Anthracnose, angular leaf spot and common bacterial blight are widespread foliar diseases of common bean that also infect pods and seeds. One thousand and eighty-two accessions from a common bean core collection from the primary centres of origin were investigated for reaction to these three diseases. Angular leaf spot and common bacterial blight were evaluated in the field at Santander de Quilichao, Colombia, and anthracnose was evaluated in a screenhouse in Popayan, Colombia. By using the 15-group level from a hierarchical clustering procedure, it was found that 7 groups were formed with mainly Andean common bean accessions (Andean gene pool), 7 groups with mainly Middle American accessions (Middle American gene pool), while 1 group contained mixed accessions. Consistent with the theory of co-evolution, it was generally observed that accessions from the Andean gene pool were resistant to Middle American pathogen isolates causing anthracnoxe, while the Middle American accessions were resistant to pathogen isolates from the Andes. Different combinations of resistance patterns were found, and breeders can use this information to select a specific group of accessions on the basis of their need.

Postural control and movement performance during upper limb tasks in children with developmental co-ordination disorder (DCD)

At least 6% of primary school aged children present with DCD, where co-ordination is substantially below the normal range for the child’s age and intelligence. Motor skill difficulties negatively affect academic achievement, recreation and activities of daily living. Poor upper-limb co-ordination is a common difficulty for children with DCD. A possible cause of this problem is deviant muscle timing in proximal muscle groups, which results in poor postural and movement control. While studies have been published investigating postural control in response to external perturbations, detail about postural muscle activity during voluntary movement is limited even in children with normal motor development. No studies have investigated the relationship between muscle timing, resultant arm motion and upper-limb coordination deficits. Objectives: To investigate the relationship between functional difficulties with upper-limb motor skills and neuromuscular components of postural stability and coordination. Specifically, to investigate onset-timing of muscle activity, timing of arm movement, and resultant three-dimensional (3D) arm co-ordination during rapid, voluntary arm movement and to analyse differences arising due to the presence of DCD. This study is part of a larger research program investigating postural stability and control of upper limb movement in children. Design: A controlled, cross-sectional study of differences between children with and without DCD. Methods: This study included 50 children aged eight to 10 years (25 with DCD and 25 without DCD). Children participated in assessment of motor skills according to the Movement ABC Test and a laboratory study of rapid, voluntary arm movements. Parameters investigated included muscle activation timing of shoulder and trunk muscles (surface electromyography), arm movement timing (light sensor) and resultant 3D arm motion (Fastrak). Results: A MANOVA is being used to analyse between-group differences. Preliminary results indicate children with DCD demonstrate altered muscle timing during a rapid arm raise when compared with the control group of children. Conclusion: Differences in proximal muscle timing in children with DCD support the hypothesis that altered proximal muscle activity may contribute to poor proximal stability and consequently poor arm movement control. This has implications for clinical physiotherapy.

Spatial and temporal patterns in Australian wheat yield and their relationship with ENSO

Spatial and temporal variability in wheat production in Australia is dominated by rainfall occurrence. The length of historical production records is inadequate, however, to analyse spatial and temporal patterns conclusively. In this study we used modelling and simulation to identify key spatial patterns in Australian wheat yield, identify groups of years in the historical record in which spatial patterns were similar, and examine association of those wheat yield year groups with indicators of the El Nino Southern Oscillation (ENSO). A simple stress index model was trained on 19 years of Australian Bureau of Statistics shire yield data (1975-93). The model was then used to simulate shire yield from 1901 to 1999 for all wheat-producing shires. Principal components analysis was used to determine the dominating spatial relationships in wheat yield among shires. Six major components of spatial variability were found. Five of these represented near spatially independent zones across the Australian wheatbelt that demonstrated coherent temporal (annual) variability in wheat yield. A second orthogonal component was required to explain the temporal variation in New South Wales. The principal component scores were used to identify high- and low-yielding years in each zone. Year type groupings identified in this way were tested for association with indicators of ENSO. Significant associations were found for all zones in the Australian wheatbelt. Associations were as strong or stronger when ENSO indicators preceding the wheat season (April-May phases of the Southern Oscillation Index) were used rather than indicators based on classification during the wheat season. Although this association suggests an obvious role for seasonal climate forecasting in national wheat crop forecasting, the discriminatory power of the ENSO indicators, although significant, was not strong. By examining the historical years forming the wheat yield analog sets within each zone, it may be possible to identify novel climate system or ocean-atmosphere features that may be causal and, hence, most useful in improving seasonal forecasting schemes.