Automatic selection of representative proteins for bacterial phylogeny

BACKGROUND: Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. RESULTS: We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria"), and another containing Planctomycetes and Chlamydiales. CONCLUSION: Representative proteins provide an effective solution to the problem of selecting phylogenetic characters

Data mining for proteins characteristic of clades

A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and γ-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools

I Wonder Who : Has Taken My Place With You

https://digitalcommons.library.umaine.edu/mmb-vp/3903/thumbnail.jp

Energy Choices Revisited : An Examination of the Costs and Benefits of Maine\u27s Energy Policy

https://digitalmaine.com/mainewatch_publications/1003/thumbnail.jp

Prototyping tangibles : exploring form and interaction

In order to better explore the opportunities for tangible interaction in new areas such as the home or cultural heritage sites, we used multiple rapidly-developed prototypes that take advantage of existing technology. Physical prototypes allow us to give form to ideas and to evaluate the integration of form and function, two core components of tangible interaction. We discuss potentials and pitfalls when using off-the-shelf digital devices (by embedding a device, cracking it open and building on it, or collating board and parts) through six prototypes developed in two studies. Hacking devices to materialize our ideas proved excellent for fast prototyping. Technology imposed constraints and prompted different design solutions than initially intended offering unexpected ways to engage. On the basis of this experience we outline a process and offer guidelines for the fast prototyping of tangible interactions

Psychometric properties of the Stroke and Aphasia Quality of Life Scale (SAQOL-39) in a generic stroke population

Background: We previously developed the Stroke and Aphasia Quality of Life scale (SAQOL-39) and tested it with people with chronic aphasia. A scale allowing comparisons of quality of life between people with versus without aphasia post-stroke would be of value to clinicians. Objectives: To evaluate the psychometrics of the SAQOL-39 in a generic stroke sample. Should this process result in a generic-stroke version of the scale (SAQOL-39g), a further aim is to compare the latter and the SAQOL-39 as tested in chronic aphasia. Design and subjects: Repeated measures psychometric study, evaluating internal consistency, test—retest reliability, construct validity and responsiveness to change. People admitted to hospital with a first stroke were assessed two weeks, three months and six months post stroke. Measures: SAQOL-39, National Institutes of Health Stroke Scale, Barthel, Frenchay Aphasia Screening Test, General Health Questionnaire-12 and Frenchay Activities Index. Results: Of 126 eligible participants, 96 (76%) participated and 87 (69%) were able to self-report and are presented here. Testing the SAQOL-39 in generic stroke resulted in the SAQOL-39g, which has the same items as the SAQOL-39 but three domains: physical, psychosocial, communication. The SAQOL-39g showed good internal consistency (α = 0.95 overall score, 0.92—0.95 domains), test—retest reliability (interclass correlation (ICC) = 0.96 overall, 0.92—0.98 domains), convergent (r = 0.36—0.70 overall, 0.47—0.78 domains) and discriminant validity (r = 0.26 overall, 0.03—0.40 domains). It differentiated people by stroke severity and visual analogue scale (VAS)-defined quality of life. Moderate changes (d = 0.35—0.49; standardized response mean (SRM) = 0.29—0.53) from two weeks to six months supported responsiveness. Conclusions: The SAQOL-39g demonstrated good reliability, validity and responsiveness to change. It can be used to evaluate quality of life in people with and without aphasia post stroke