A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data

The 16S rRNA gene (16S rDNA) is currently the most widely used gene for estimating the evolutionary history of prokaryotes, To date, there are more than 30 000 16S rDNA sequences available from the core databases, GenBank, EMBL and DDBJ, This great number may cause a dilemma when composing datasets for phylogenetic analysis, since the choice and number of reference organisms are known to affect the resulting tree topology. A group of sequences appearing monophyletic in one dataset may not be so in another. This can be especially problematic when establishing the relationships of distantly related sequences at the division (phylum) level. In this study, a multiple-outgroup approach to resolving division-level phylogenetic relationships is suggested using 16S rDNA data. The approach is illustrated by two case studies concerning the monophyly of two recently proposed bacterial divisions, OP9 and OP10.

A decade of Taiwanese migration in Australia: Comparisons with Mainland Chinese and Hong Kong settlers

The arrival of Taiwanese migrants to Australia represents the second major wave of Chinese immigration to this nation. Many who entered Australia did so as business migrants. They were typically well educated, affluent professionals, managers, &/or entrepreneurs who were looking for new business opportunities as well as a lifestyle characterized by open space, clean air, a good education for their children, & personal & political safety. Yet, the settlement experiences of many Taiwanese migrants, despite their affluence & (business) skills, have been typified by stress & hardship, particularly in making adjustments in social, business, & economic relationships. A review of statistical data compiled from census & government reports in Australia has revealed that after a decade Down Under, the Taiwanese settler group was still characterized by high unemployment, even when compared to other Chinese migrant groups from Hong Kong & Mainland China. It is suggested that the Taiwanese migrants' persistent high nonparticipation in Australia's labor force is indicative & poignant of their highly distinctive, albeit not exclusive in the broader Chinese migrant terms, experience of migration settlement. There seems to be an increasing number of Taiwanese settlers returning to resettle in Taiwan in recent years, because of perceived better employment & business opportunities or for family & personal reasons. Recent interviews with Taiwanese settlers have also suggested that the most recent arrivals, being more aware of the obstacles in achieving work or business satisfaction during settlement, seem less likely to commit themselves to lifelong settlement in Australia. 16 Tables, 1 Figure, 37 References. Adapted from the source document.

Using MF-PCR to diagnose multiple defects from single cells: implications for PGD

Single cell genetic analysis is generally performed using PCR and FISH. Until recently, FISH has been the method of choice. FISH however is expensive, has significant misdiagnosis rates, can result in interpretation difficulties and is labour intensive making it unsuitable for high throughput processing. Recently fluorescent PCR reliability has increased to levels at or surpassing FISH whilst maintaining low cost. However, PCR accuracy has been a concern due to allelic dropout. Multiplex PCR can now increase accuracy by using multiple markers for each chromosome to firstly provide diagnosis if markers fail and,or secondly confirm diagnosis. We compare a variety of diagnostic methods and demonstrate for the first time a multiplex PCR system providing simultaneous diagnosis and confirmation of the major aneuploidy chromosomes (21, 18, 13) and sex as well as DNA fingerprint in single cells. We also discuss the implications of using PCR for aneuploidy screening in preimplantation genetic diagnosis. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved.

A simulated annealing algorithm for finding consensus sequences

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new algorithm. For comparison, we also present similar results obtained using ClustalW. The new algorithm outperforms ClustalW in many cases.

Monitoring hotel performance

There is a pressing need to address productivity analysis in the hospitality industry if hotels are to exist as sustainable business entities in rapidly maturing markets. Unfortunately, productivity ratios commonly used by managers are narrowly defined. This study illustrates data envelopment analysis of cross-sectional data that benchmark hotels on observed best performances. Data envelopment analysis enables management to integrate unlike multiple inputs and outputs to make simultaneous comparisons. Findings from the cross-sectional data suggest that some of the hotels have the potential to reduce number of beds and number of part-time staff while increasing revenue.

Partitioned Bremer support and multiple trees

Partitioned Bremer support (PBS) is a valuable means of assessing congruence in combined data sets, but some aspects require clarification. When more than one equally parsimonious tree is found during the constrained search for trees lacking the node of interest, averaging PBS for each data set across these trees can conceal conflict, and PBS should ideally be examined for each constrained tree. Similarly, when multiple most parsimonious trees (MPTs) are generated during analysis of the combined data, PBS is usually calculated on the consensus tree. However, extra information can be obtained if PBS is calculated on each of the MPTs or even suboptimal trees. (C) 2002 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

RNA trafficking and stabilization elements associate with multiple brain proteins

Two of the best understood somatic cell mRNA cytoplasmic trafficking elements are those governing localization of beta-actin and myelin basic protein mRNAs. These cis-acting elements bind the trans-acting factors fibroblast ZBP-1 and hnRNP A2, respectively. It is not known whether these elements fulfil other roles in mRNA metabolism. To address this question we have used Edman sequencing and western blotting to identify six rat brain proteins that bind the beta-actin element (zipcode). All are known RNA-binding proteins and differ from ZBP-1. Comparison with proteins that bind the hnRNP A2 and AU-rich response elements, A2RE/A2RE11 and AURE, showed that AURE and zipcode bind a similar set of proteins that does not overlap with those that bind A2RE11. The zipcode-binding protein, KSRP, and hnRNP A2 were selected for further study and were shown by confocal immunolluorescence microscopy to have similar distributions in the central nervous system, but they were found in largely separate locations in cell nuclei. In the cytoplasm of cultured oligodendrocytes they were segregated into separate populations of cytoplasmic granules. We conclude that not only may there be families of trans-acting factors for the same cis-acting element, which are presumably required at different stages of mRNA processing and metabolism, but independent factors may also target different and multiple RNAs in the same cell.

Three-dimensional space-borne synthetic aperture radar (SAR) imaging with multiple pass processing

Three-dimensional (3D) synthetic aperture radar (SAR) imaging via multiple-pass processing is an extension of interferometric SAR imaging. It exploits more than two flight passes to achieve a desired resolution in elevation. In this paper, a novel approach is developed to reconstruct a 3D space-borne SAR image with multiple-pass processing. It involves image registration, phase correction and elevational imaging. An image model matching is developed for multiple image registration, an eigenvector method is proposed for the phase correction and the elevational imaging is conducted using a Fourier transform or a super-resolution method for enhancement of elevational resolution. 3D SAR images are obtained by processing simulated data and real data from the first European Remote Sensing satellite (ERS-1) with the proposed approaches.

Cross-national comparison of internal migration: issues and measures

Our objectives are to identify the issues that researchers encounter when measuring internal migration in different countries and to propose key indicators that analysts can use to compare internal migration at the 'national' level. We establish the benefits to be gained by a rigorous approach to cross-national comparisons of internal migration and discuss issues that affect such comparisons. We then distinguish four dimensions of internal migration on which countries can be compared and, for each dimension, identify a series of summary measures. We illustrate the issues and measures proposed by comparing migration in Australia and Great Britain.

Existence of multiple solutions for second-order discrete boundary value problems

We give conditions on f involving pairs of discrete lower and discrete upper solutions which lead to the existence of at least three solutions of the discrete two-point boundary value problem yk+1 - 2yk + yk-1 + f (k, yk, vk) = 0, for k = 1,..., n - 1, y0 = 0 = yn,, where f is continuous and vk = yk - yk-1, for k = 1,..., n. In the special case f (k, t, p) = f (t) greater than or equal to 0, we give growth conditions on f and apply our general result to show the existence of three positive solutions. We give an example showing this latter result is sharp. Our results extend those of Avery and Peterson and are in the spirit of our results for the continuous analogue. (C) 2002 Elsevier Science Ltd. All rights reserved.

Multiple shoot formation in lentil (Lens culinaris) seeds

A protocol based on seed culture was developed for efficient in vitro propagation of lentil (Lens culinaris Medik). Benzyladenine (BA), thidiazuron (TDZ), and kinetin all induced multiple shoot formation. In terms of the number of long shoots (>2.0 cm) produced per seed, BA and TDZ at optimum concentrations (0.2-0.4 and 0.1 mg/litre, respectively) had similar efficiency, whereas kinetin produced less shoots. Murashige and Skoog (MS) salt composition was better than that of Gamborge (B5) for shoot induction. Increasing calcium (Ca) concentration was necessary to overcome shoot-tip necrosis. For shoot elongation, fresh medium of the same composition of shoot induction medium could be used for stumps from medium with low BA (

Absorption and dispersion by a multiple driven two-level atom

We investigate the absorption and dispersion properties of a two-level atom driven by a polychromatic field. The driving field is composed of a strong resonant (carrier) frequency component and a large number of symmetrically detuned sideband fields (modulators). A rapid increase in the absorption at the central frequency and the collapse of the response of the system from multiple frequencies to a single frequency are predicted to occur when the Rabi frequency of the modulating fields is equal to the Rabi frequency of the carrier field. These are manifestations of the undressing or a disentanglement of the atomic and driving field states, that leads to a collapse of the atom to its ground state. Our calculation permits consideration of the question of the undressing of the driven atom by a multiple-modulated field and the predicted spectra offer a method of observing undressing. Moreover, we find that the absorption and dispersion spectra split into multiplets whose structures depend on the Rabi frequency of the modulating fields. The spectral features can jump between different resonance frequencies by changing the Rabi frequency of the modulating fields or their initial phases, which can have potential applications as a quantum frequency filter.

Multiple axon guidance cues establish the olfactory topographic map: how do these cues interact?

Each primary olfactory neuron stochastically expresses one of similar to1000 odorant receptors. The total population of these neurons therefore consists of similar to1,000 distinct subpopulations, each of which are mosaically dispersed throughout one of four semi-annular zones in the nasal cavity. The axons of these different subpopulations are initially intermingled within the olfactory nerve. However, upon reaching the olfactory bulb, they sort out and converge so that axons expressing the same odorant receptor typically target one or two glomeruli. The spatial location of each of these 1800 glomeruli are topographically-fixed in the olfactory bulb and are invariant from animal to animal. Thus, while odorant receptors are expressed mosaically by neurons throughout the olfactory neuroepithelium their axons sort out, converge and target the same glomerulus within the olfactory bulb. How is such precise and reproducible topographic targeting generated? While some of the mechanisms governing the growth cone guidance of olfactory sensory neurons are understood, the cues responsible for homing axons to their target site remain elusive.

Development of a measure of coping with multiple sclerosis caregiving

Development of a self-report measure of coping specific to multiple sclerosis (MS) caregiving is needed to advance our understanding of the role of coping in adaptation to caring for a person with MS and to contribute to a lack of empirical data on MS caregiving. A total of 213 MS caregivers and their care recipients completed a Coping with MS Caregiving Inventory (CMSCI) and measures of adjustment (psychological distress), appraisal and illness. A subsample (n = 64) also completed the Ways of Coping Checklist (WCC) and additional adjustment measures (depression, caregiving impact. dyadic adjustment, and relationship conflict and reciprocity). Factor analyses revealed 5 factors: Supportive Engagement, Criticism and Coercion, Practical Assistance, Avoidance, and Positive Reframing. Subscales had internal reliabilities comparable to similar scales and were empirically distinct. Preliminary construct validation data are consistent with recent MS caregiving research that links passive avoidant emotion-focused coping with poorer adjustment, and relationship-focused coping caregiving research that links greater reliance on positive relationship-focused coping and less reliance on criticism with better adjustment. Results extend this research by revealing new relations between coping and adaptation to MS caregiving. Convergent validation data suggest that although the inventory differs from the WCC, it does share certain conceptual similarities with this scale.