900 research outputs found
Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes
No full textBacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution. © 2013 Pope et al
Comparative genomics of Shiga toxin encoding bacteriophages
No full textBackground
Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, lifethreatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as 24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of 24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages.
Results
The genome of the Stx2 encoding phage, 24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however 24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The 24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system.
Conclusions
The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potentia
Genetic variation in individuals from a population of the minimalist bacteriophage Merri-merri-uth nyilam marra-natj driving evolution of the virus
No full textUNLABELLED: In a survey of a waterway on Wurundjeri land, two sub-populations of the bacteriophage Merri-merri-uth nyilam marra-natj (phage MMNM) were isolated on a permissive host, Klebsiella B5055 of capsule-type K2, but were distinguished by minor phenotypic differences. The variant phage MMNM(Ala134) showed an inhibited activity against Klebsiella AJ174-2, and this was used as a basis to select for further variation through experimental evolution. Over the course of an evolution experiment, 20 phages that evolved distinct phenotypes in terms of the morphologies of plaques formed when they infected host Klebsiella were subject to whole-genome sequencing. The evolved phages had mutations in a small set of proteins that contribute to the baseplate portion of the phage virion. Phages MMNM and MMNM(Ala134) are minimalist phages, with baseplates formed from only five predicted subunits, akin to other minimalist phages Pam3 and XM1. The homology between all three minimalist phages provided a structural framework to interpret the two classes of mutations derived through evolution in the presence of the semi-permissive host: those that affect the interfacial surfaces between baseplate subunits, and those in a base-plate associated tail-fiber. This study evidences that multiple small mutations can be fixed into a sub-population of phage to provide a basis for phenotypic variation that we suggest could ultimately provide for a shift of virus properties, as an alternative evolutionary scenario to the major genetic events that result in more well-studied evolutionary mechanism of phage mosaicism. IMPORTANCE: Bacteriophages (phages) are viruses that prey on bacteria. This study sampled natural phage populations to test the hypothesis that untapped genetic variation within a population can be the basis for the selection of phages to diversify their host-range. Sampling of a freshwater site revealed two populations of the phage Merri-merri-uth nyilam marra-natj (phage MMNM), differing by a variant residue (Val134Ala) in the baseplate protein MMNM_26. This sequence variation modulated bacterial killing in plaques, and further evolution of the phages on a semi-permissive bacterial host led to a new generation of phages with more diverse phenotypes in killing the bacterium Klebsiella pneumoniae
Complete genome sequences of 138 mycobacteriophages
No full textBacteriophages are the most numerous biological entities in the biosphere, and although their genetic diversity is high, it remains ill defined. Mycobacteriophages-the viruses of mycobacterial hosts-provide insights into this diversity as well as tools for manipulating Mycobacterium tuberculosis. We report here the complete genome sequences of 138 new mycobacteriophages, which-together with the 83 mycobacteriophages previously reported-represent the largest collection of phages known to infect a single common host, Mycobacterium smegmatis mc 2 155. © 2012, American Society for Microbiology
Mycobacteriophage endolysins: Diverse and modular enzymes with multiple catalytic activities
No full textThe mycobacterial cell wall presents significant challenges to mycobacteriophages - viruses that infect mycobacterial hosts - because of its unusual structure containing a mycolic acid-rich mycobacterial outer membrane attached to an arabinogalactan layer that is in turn linked to the peptidoglycan. Although little is known about how mycobacteriophages circumvent these barriers during the process of infection, destroying it for lysis at the end of their lytic cycles requires an unusual set of functions. These include Lysin B proteins that cleave the linkage of mycolic acids to the arabinogalactan layer, chaperones required for endolysin delivery to peptidoglycan, holins that regulate lysis timing, and the endolysins (Lysin As) that hydrolyze peptidoglycan. Because mycobacterial peptidoglycan contains atypical features including 3→3 interpeptide linkages, it is not surprising that the mycobacteriophage endolysins also have non-canonical features. We present here a bioinformatic dissection of these lysins and show that they are highly diverse and extensively modular, with an impressive number of domain organizations. Most contain three domains with a novel N-terminal predicted peptidase, a centrally located amidase, muramidase, or transglycosylase, and a C-terminal putative cell wall binding domain. © 2012 Payne, Hatfull
Language Engineering in Grammatical Framework (GF)
No full textThis thesis describes a number of practical experiments rather than theoreticalinvestigations in the area of natural language processing. The basis forthe work presented is Grammatical Framework (GF). It is a very complexsystem, which comprises among other things a grammar formalism based ontype theory and its implementation written in Haskell. GF is intended forhigh-quality machine translation (of INTERLINGUA type) in the restrictedlanguage domains.The primary concern of this thesis is however limited to the usage of GFas a piece of software. The main results are: Implementing a syntax editor, which provides a graphical user interface(GUI) for the command-line GF core. Writing a part of code for automatic generation of gramletspure Javaprograms with limited (compared to GF) functionality that can be runon PDA (Portable Device Assistants) and as applets in a browser. Writing the Russian resource grammar that takes care of the most basicmorphological and syntactic rules and serves as a standard libraryfor building application grammars (describing restricted language domains)in Russian.These results contribute to language engineering in GF on two differentlevels: Author level (end-user) constructing sentences in natural languages. Grammarian level building a grammar description, which is laterused on the author level.The last part of the thesis deals with a non-linguistic domain. In thatexperiment we try to apply functional parsing technique to the well-knownproblem of protein secondary structure prediction (bioinformatics)
Language Engineering in Grammatical Framework (GF)
No full textThis thesis describes a number of practical experiments rather than theoreticalinvestigations in the area of natural language processing. The basis forthe work presented is Grammatical Framework (GF). It is a very complexsystem, which comprises among other things a grammar formalism based ontype theory and its implementation written in Haskell. GF is intended forhigh-quality machine translation (of INTERLINGUA type) in the restrictedlanguage domains.The primary concern of this thesis is however limited to the usage of GFas a piece of software. The main results are: Implementing a syntax editor, which provides a graphical user interface(GUI) for the command-line GF core. Writing a part of code for automatic generation of gramletspure Javaprograms with limited (compared to GF) functionality that can be runon PDA (Portable Device Assistants) and as applets in a browser. Writing the Russian resource grammar that takes care of the most basicmorphological and syntactic rules and serves as a standard libraryfor building application grammars (describing restricted language domains)in Russian.These results contribute to language engineering in GF on two differentlevels: Author level (end-user) constructing sentences in natural languages. Grammarian level building a grammar description, which is laterused on the author level.The last part of the thesis deals with a non-linguistic domain. In thatexperiment we try to apply functional parsing technique to the well-knownproblem of protein secondary structure prediction (bioinformatics)
Language Engineering in Grammatial Framework (GF)
No full textThe basis for the work presented is Grammatical Framework (GF)a grammar
formalism based on type theory. It is also a powerful language processor
that provides a convenient framework for various multilingual applications.
The primary concern of this thesis is the usage of GF as a piece of software.
The main results are:
Implementing a syntax editor, which provides a graphical user interface
(GUI) for the command-line GF core.
Writing the Russian resource grammar that takes care of the most
basic morphological and syntactic rules and serves as a standard library
for building application grammars (describing sublanguage domains) in
Russian.
These results contribute to language engineering in GF on two different
levels:
Author level (end-user)constructing documents in natural languages.
Grammarian level building a grammar description, which is later
used on the author level. One can also distinguish between application
and resource grammars. An application grammar focuses of a particular
sub-language domain, while resource grammar is a general-purpose
grammar that forms a basis for application grammars
Internship at GoFoton GF Micro Optics Philippines, Inc.
No full textThis paper is a compilation of the internship of the author in the 1st semester of the academic year 2012-2013. It serves as a documentation of the activities that transpired in the internship of the author in GF Micro Optics Philippines, Inc. from May, 1012 until August, 2012.
Included in this paper are the company profile, experiences of the author in the company, and the tasks assigned while taking the training course. Process flow improvement was the main task of the author as his main role under the Industrial Engineering Department of GF Micro Optics Philippines, Inc.
Furthermore, the paper includes problems encountered and lessons learned by the author throughout the training course. These lessons include time management, co-worker management, task management, and enhancement of the authors whole being and skills such as problem solving. All are explained in this manuscript in order to provide self and academic evaluation of the authors training
Linear complexity profile of sequences over the field GF(Q)
No full textSummary form only given. The author extends Reuppel's concept of the linear complexity profile of binary sequences to sequences over an arbitrary finite field and provides formulas for the expected linear complexity and its variance of sequences Sn of length n over GF(q). He shows that the variance approaches 1/q when q approaches ∞. He presents criteria that could be useful when using the linear complexity profile for investigating the randomness of sequences over GF(q). Finally, the author investigates how useful these criteria are by comparing the results with other randomness tests
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