851 research outputs found
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 âpartnershipâ 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 rĂ©seau mitoyen dâalerte radar du Canada a Ă©tĂ© amĂ©nagĂ© dans les annĂ©es 1950 en rĂ©action Ă une menace perçue dâattaque nuclĂ©aire soviĂ©tique qui passerait par lâArctique. Ce rĂ©seau mitoyen Ă©tait un projet entiĂšrement canadien. Il consistait en 98 postes de radar rĂ©partis Ă la hauteur du 55e parallĂšle, de Dawson Creek, en Colombie-Britannique, Ă Hopedale, au Labrador. Dix-sept postes de radar avaient Ă©tĂ© installĂ©s en Ontario, et vers 1965, ils avaient tous fermĂ© leurs portes et ce, pour des raisons stratĂ©giques et Ă©conomiques. Puisque ces postes nâont pas Ă©tĂ© dĂ©saffectĂ©s dans les rĂšgles de lâart, ils sont devenus des sources ponctuelles de contaminants dans le nord du Canada. En 2001, le poste 050 du rĂ©seau mitoyen a fait lâobjet dâune biorestauration. La PremiĂšre Nation de Fort Albany (situĂ©e prĂšs du poste 050), le ministĂšre de la DĂ©fense nationale et le ministĂšre des Richesses naturelles de lâOntario avaient formĂ© un « partenariat » pour sâacquitter de cette tĂąche. Nous avons dĂ©terminĂ© que du point de vue des Autochtones, un vrai partenariat (comme nous le dĂ©finissons) a existĂ© entre ces organismes. Il sâagissait dâun partenariat reposant sur des Ă©lĂ©ments essentiels de respect, dâĂ©quitĂ© et dâhabilitation. Nous montrons que ces Ă©lĂ©ments essentiels dâun vrai partenariat Ă©taient prĂ©sents dans les premiers documents ayant trait aux efforts de biorestauration de ce poste de radar. La prĂ©sente Ă©valuation a pour but de fournir une perspective, une orientation et un cadre de rĂ©fĂ©rence Ă©ventuel pouvant servir de modĂšles Ă dâautres partenariats et ce, dans le but de favoriser des relations de collaboration plus Ă©troites entre les organismes autochtones et les gouvernements de tous les Ă©chelons, surtout en ce qui a trait aux travaux de biorestauration des postes de radar abandonnĂ©s
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 âsecretomeâ 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
Fiber Pulling Apparatus
The fiber optics industry has grown into a multi-billion marketplace that will continue to grow into the 21st century. Optical fiber communications is currently dominated by silica glass technology. Successful efforts to improve upon the low loss transmission characteristics of silica fibers have propelled the technology into the forefront of the communications industry. However, reaching the theoretical transmission capability of silica fiber through improved processing has still left a few application areas in which other fiber systems can provide an influential role due to specific characteristics of high theoretical transmission in the 2 - 3 micron wavelength region. One of the other major materials used for optical fibers is the systems based upon Heavy Metal Fluoride Glass (HMFG). Commercial interest is driven primarily by the potential for low loss repeaterless infrared fibers. An example of the major communications marketplace which would benefit from the long distance repeaterless capability of infrared fibers is the submarine cables which link the continents. When considering commercial interests, optical fiber systems provide a healthy industrial position which continues to expand. Major investments in the systems used for optical fiber communications have continued to increase each year and are predicted to continue well into the next century. Estimates of 8.5% compounded annually are predicted through 1999 for the North American market and 1 1 % worldwide. The growth for the optical fiber cable itself is expected to continue between 44 and 50 per cent of the optical fiber communications budget through 1999. The total budget in 1999 world-wide is expected to be in the neighborhood of 8.5 billion through 1993 and another $13 billion planned through 1998. A large portion of the future activity (34%) is planned for Southeast Asia and the Pacific Region. Other examples of the commercial utility of optical fiber networks is given in a recent scientific symposium in which the outlook for HMFG infrared fiber was determined to be very bright.Another area of interest lies in the use of fiber optics for laser surgery delivery systems
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