Development of fusion and duplication finder BLAST (fdfBLAST): a systematic tool to detect differentially distributed gene fusions and resolve trifurcations in the tree of life

The construction of a tree of life and the placing of taxa into their correct phylogenetic context is the underpinning of modern evolutionary biology. However, many parts of the tree are currently unresolved due to conflicts within the sequence data. These sources of conflict include: horizontal gene transfer (HGT), hidden paralogy, and the effects of methodological artefacts such as Long Branch attraction (LBA). These limitations are further compounded by absence of key taxa that are yet to be sampled. Therefore, whilst phylogenetic methods are fundamentally useful for the reconstruction of the tree of life, given their current limitations, additional strategies are needed in order to fully resolve the tree of life. Gene fusions represent a potential source of evolutionary synapomorphies useful for resolving contentious branching relationships in the tree of life. I therefore, built a program to analyse whole genome datasets for the presence of differentially distributed gene fusion events (shared derived characters - SDCs). These putative SDCs can then be polarised with the help of traditional phylogenetic techniques and used as synapomorphies on the tree of life. Having constructed this program and tested it on established fusion datasets, I analysed five sets of four genomes from across the tree of life (the Deuterostomia, Fungi, Vertebrata, Viridiplantae and Discicristata). I used this data to identify the relative rates of gene fusion events. Previous studies have suggested that fission events occurred more often than gene fusion events. However, our analysis broadly suggests the opposite (albeit with a higher rate of fissions in the Deuterostomia). This result has direct implications for the use of gene fusions as evolutionary informative synapomorphies because the identification of a lower rate of reversion suggests that these characters are less likely to be homoplasious and therefore represent useful tools for polarising evolutionary relationships. Six phylogenetically informative synapomorphies were recovered, three in the Discicristata which resolve the monophyly of the Kinetoplastida and four in the Fungi, one of which represented a HGT event and was independently discovered and previously published. Thus, this thesis reports the development and testing of a new tool to identify differentially distributed gene fusion events. The datasets analysed demonstrate that the program can be used to find phylogenetically informative gene fusion characters that can help resolve the tree of life in conjunction with traditional phylogenetic methods

REFGEN and TREENAMER: automated sequence data handling for phylogenetic analysis in the genomic era.

Published onlineJournal ArticleThe phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends.Leverhulm

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends

A comparative study of the church attendance habits of a selected group of naval personnel before and after their entry into the naval service.

http://www.archive.org/details/comparativestudy00leo

An Aboriginal Perspective on the Remediation of Mid-Canada Radar Line Sites in the Subarctic: A Partnership Evaluation

The Mid-Canada Radar Line (MCRL) was built during the 1950s in response to the perceived threat of a Soviet nuclear attack over the Arctic. The MCRL was an entirely Canadian project, consisting of 98 radar stations that stretched across the 55th parallel from Dawson Creek, British Columbia, to Hopedale, Labrador. Seventeen MCRL sites were located in Ontario, and by 1965, all had been closed for strategic and economic reasons. Since these sites were improperly decommissioned, they have become point sources of contaminants in northern Canada. In 2001, MCRL Site 050 was remediated. The Fort Albany First Nation (located near Site 050), the Department of National Defence, and the Ontario Ministry of Natural Resources had formed a “partnership” to undertake this. We determined that from an Aboriginal perspective, a true partnership (as we define it) did exist between these organizations; a partnership based on the essential elements of respect, equity, and empowerment. We show that these cornerstones of a true partnership were present in the initial documents that discussed remediation of this site. This evaluation will provide insight, guidance, and a potential framework to benefit future partnership endeavours, helping to foster stronger collaborative relationships between Aboriginal organizations and governments at all levels, especially with respect to the remediation of abandoned radar line sites.Le réseau mitoyen d’alerte radar du Canada a été aménagé dans les années 1950 en réaction à une menace perçue d’attaque nucléaire soviétique qui passerait par l’Arctique. Ce réseau mitoyen était un projet entièrement canadien. Il consistait en 98 postes de radar répartis à la hauteur du 55e parallèle, de Dawson Creek, en Colombie-Britannique, à Hopedale, au Labrador. Dix-sept postes de radar avaient été installés en Ontario, et vers 1965, ils avaient tous fermé leurs portes et ce, pour des raisons stratégiques et économiques. Puisque ces postes n’ont pas été désaffectés dans les règles de l’art, ils sont devenus des sources ponctuelles de contaminants dans le nord du Canada. En 2001, le poste 050 du réseau mitoyen a fait l’objet d’une biorestauration. La Première Nation de Fort Albany (située près du poste 050), le ministère de la Défense nationale et le ministère des Richesses naturelles de l’Ontario avaient formé un « partenariat » pour s’acquitter de cette tâche. Nous avons déterminé que du point de vue des Autochtones, un vrai partenariat (comme nous le définissons) a existé entre ces organismes. Il s’agissait d’un partenariat reposant sur des éléments essentiels de respect, d’équité et d’habilitation. Nous montrons que ces éléments essentiels d’un vrai partenariat étaient présents dans les premiers documents ayant trait aux efforts de biorestauration de ce poste de radar. La présente évaluation a pour but de fournir une perspective, une orientation et un cadre de référence éventuel pouvant servir de modèles à d’autres partenariats et ce, dans le but de favoriser des relations de collaboration plus étroites entre les organismes autochtones et les gouvernements de tous les échelons, surtout en ce qui a trait aux travaux de biorestauration des postes de radar abandonnés

Spectrum of topics for world congresses and other activities of the International Society for Physical and Rehabilitation Medicine (ISPRM) : a first proposal

Background: One of the objectives of the International Society for Physical and Rehabilitation Medicine is to improve the continuity of World Congresses. This requires the development of an abstract topic list for use in congress announcements and abstract submissions. Methods: An abstract topic list was developed on the basis of the definitions of human functioning and rehabilitation research, which define 5 main areas of research (biosciences in rehabilitation, biomedical rehabilitation sciences and engineering, clinical Physical and Rehabilitation Medicine (PRM) sciences, integrative rehabilitation sciences, and human functioning sciences). For the abstract topic list, these research areas were grouped according to the proposals of congress streams. In a second step, the first version of the list was systematically compared with the topics of the 2003 ISPRM World Congress. Results: The resulting comprehensive abstract topic list contains 5 chapters according to the definition of human functioning and rehabilitation research. Due to the high significance of clinical research, clinical PRM sciences were placed at the top of the list, comprising all relevant health conditions treated in PRM services. For congress announcements a short topic list was derived. Discussion: The ISPRM topic list is sustainable and covers a full range of topics. It may be useful for congresses and elsewhere in structuring research in PRM

AVCAL reduction analysis model

This thesis provides decision makers with a model to analyze the impact of an Aviation Consolidated Allowance List (AVCAL) reduction onboard aircraft carriers (CVs). The Department of Defense in currently down-sizing its forces by 25 percent from FY1991 to FY1995 due to the reduction in funding caused by the significant change in the threat assessment. The implications of the current down-sizing of forces are wide-ranging throughout DoD, including the possibility of reducing a CV's AVCAL from 90 to 60 days. Both analytical and simulation models (RP-FOR and RP-SIM, respectively) have been developed. The model measure the impact of reducing an AVCAL from 90 to 60 days by comparing the benefits of savings gained from a reduction of AVCAL, versus the penalties of reduced operational availability of the aircraft.http://archive.org/details/avcalreductionan00leopLieutenant, United States NavyApproved for public release; distribution is unlimited

The Secreted Proteins of \u3cem\u3eAchlya hypogyna\u3c/em\u3e and \u3cem\u3eThraustotheca clavata\u3c/em\u3e Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer

Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the “secretome” and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here,we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle

A Mixture of Manhattan Frames: Beyond the Manhattan World

Objects and structures within man-made environments typically exhibit a high degree of organization in the form of orthogonal and parallel planes. Traditional approaches to scene representation exploit this phenomenon via the somewhat restrictive assumption that every plane is perpendicular to one of the axes of a single coordinate system. Known as the Manhattan-World model, this assumption is widely used in computer vision and robotics. The complexity of many real-world scenes, however, necessitates a more flexible model. We propose a novel probabilistic model that describes the world as a mixture of Manhattan frames: each frame defines a different orthogonal coordinate system. This results in a more expressive model that still exploits the orthogonality constraints. We propose an adaptive Markov-Chain Monte-Carlo sampling algorithm with Metropolis-Hastings split/merge moves that utilizes the geometry of the unit sphere. We demonstrate the versatility of our Mixture-of-Manhattan-Frames model by describing complex scenes using depth images of indoor scenes as well as aerial-LiDAR measurements of an urban center. Additionally, we show that the model lends itself to focal-length calibration of depth cameras and to plane segmentation.United States. Office of Naval Research. Multidisciplinary University Research Initiative (Award N00014-11-1-0688)United States. Defense Advanced Research Projects Agency (Award FA8650-11-1-7154)Technion, Israel Institute of Technology (MIT Postdoctoral Fellowship Program