Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes

Bacteriophages 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

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

Background: Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.Results: We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.Conclusions: Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes. © 2011 Cresawn et al; licensee BioMed Central Ltd

In vitro influence of stem surface finish and mantle conformity on pressure generation in cemented hip arthroplasty

Background and purpose Under physiological loads, debonded cemented femoral stems have been shown to move within their cement mantle and generate a fluid pump that may facilitate peri-prosthetic osteolysis by pressurizing fluid and circulating wear debris. The long-term physiological loading of rough and polished tapered stems in vitro has shown differences in performance, with greater interface pressures generated by the rough stems. In this study we investigated the individual effects of stem surface finish, degree of mantle wear, and mode of loading on the stem pump mechanism

A Shigella boydii bacteriophage which resembles Salmonella phage ViI

<p>Abstract</p> <p>Background</p> <p>Lytic bacteriophages have been applied successfully to control the growth of various foodborne pathogens. Sequencing of their genomes is considered as an important preliminary step to ensure their safety prior to food applications.</p> <p>Results</p> <p>The lytic bacteriophage, ΦSboM-AG3, targets the important foodborne pathogen, <it>Shigella</it>. It is morphologically similar to phage ViI of <it>Salmonella enterica </it>serovar Typhi and a series of phages of <it>Acinetobacter calcoaceticus </it>and <it>Rhizobium meliloti</it>. The complete genome of ΦSboM-AG3 was determined to be 158 kb and was terminally redundant and circularly permuted. Two hundred and sixteen open reading frames (ORFs) were identified and annotated, most of which displayed homology to proteins of <it>Salmonella </it>phage ViI. The genome also included four genes specifying tRNAs.</p> <p>Conclusions</p> <p>This is the first time that a Vi-specific phage for <it>Shigella </it>has been described. There is no evidence for the presence of virulence and lysogeny-associated genes. In conclusion, the genome analysis of ΦSboM-AG3 indicates that this phage can be safely used for biocontrol purposes.</p

Diffuse idiopathic skeletal hyperostosis in ancient clergymen

Diffuse idiopathic skeletal hyperostosis (DISH) is a common but often unrecognized systemic disorder observed mainly in the elderly. DISH is diagnosed when the anterior longitudinal ligament of the spine is ossified on at least four contiguous spinal levels or when multiple peripheral enthesopathies are present. The etiology of DISH is unknown but previous studies have shown a strong association with obesity and insulin-independent diabetes mellitus. DISH can lead to back pain, dysphagia, myelopathy, musculoskeletal impairment and grossly unstable spine fractures after minor trauma. In archeological studies a high prevalence of DISH has been demonstrated in ancient clergymen. The present study describes the pathological changes of human remains excavated from the abbey court (Pandhof) in the city of Maastricht, The Netherlands. Human remains of 51 individuals buried between 275 and 1795 ce were excavated and examined. The remains were investigated according to a standardized physical anthropological report and individuals demonstrating ossification of spinal ligaments and/or multiple peripheral enthesopathies were included in the study group. The authors reviewed all available material and after reaching consensus, each abnormality found was given a diagnosis and subsequently recorded. After examination, 28 individuals were considered to be adult males; 11 adult females; three adults of indeterminate sex and nine individuals were of sub adult age. The mean age at death for adults was 36.8 years. Seventeen adult individuals (40.4% of all adults), displayed ossifications of at least four contiguous spinal levels and/or multiple enthesopathies of the appendicular skeleton and were therefore, assigned the diagnosis DISH. The mean age of these individuals was 49.5 ± 13.0 years. In at least three of these individuals, DISH had led to extensive ossification and subsequent ankylosis of axial and peripheral skeletal structures. In this population of (presumably) clergymen and high-ranking citizens, DISH was observed in unusual high numbers at a relatively young age. Some of the examined cases suggest that DISH may be a seriously incapacitating disorder when the more advanced stages of the disease have been reached. It is hypothesized that “a monastic way of life” can predispose to DISH. Present demographic trends in obesity and diabetes mellitus as potential co-factors for the development of DISH warrant further study to investigate its future prevalence

Quantitative analysis of the anterolateral ossification mass in diffuse idiopathic skeletal hyperostosis of the thoracic spine

Diffuse idiopathic skeletal hyperostosis (DISH) is a systemic condition leading to ossification of spinal ligaments and has been shown to behave similarly to ankylosing spondylitis (AS) often leading to unstable hyperextension fractures. Currently, no quantitative data are available on the spatial relationship between the bridging anterolateral ossification mass (ALOM) and the vertebral body/intervertebral disc to explain the propensity in DISH to fracture through the vertebral body instead of through the intervertebral disc as more often seen in AS. Furthermore, no reasonable explanation is available for the typical flowing wax morphology observed in DISH. In the current study, a quantitative analysis of computed tomography (CT) data from human cadaveric specimens with DISH was performed to better understand the newly formed osseous structures and fracture biomechanics. Additionally, the results were verified using computed tomography angiography data from ten patients with DISH and ten controls. Transverse CT images were analyzed to obtain ALOM area and centroid angle relative to the anteroposterior axis; intervertebral disc and adjacent cranial and caudal levels. The ALOM area at the mid-vertebral body level averaged 57.9 ± 50.0 mm2; at the mid-intervertebral disc space level it averaged 246.4 ± 95.9 mm2. The mean ALOM area at the adjacent level caudal to the mid-vertebral body level was 169.6 ± 81.3 mm2; at the adjacent cranial level, it was 161.7 ± 78.2 mm2. The main finding was the significant difference between mean ALOM area at the mid-vertebral body level and other three levels (p < 0.0001). The subsequent verification study showed the presence of vertebral segmental arteries at the mid-vertebral body level in nearly all images irrespective of the presence of DISH. A larger area of ALOM seemed associated with increased counter-clockwise rotation (away from the aorta) of the centroid relative to the anteroposterior axis. The results from the present study suggest a predisposition for fractures through the vertebral body and a role for the arterial system in the inhibition of soft tissue ossification

Specific detection of Salmonella enterica and Escherichia coli strains by using ELISA with bacteriophages as recognition agents

The use of bacteriophages, instead of antibodies, in the ELISA-based detection of bacterial strains was tested. This procedure appeared to be efficient, and specific strains of Salmonella enterica and Escherichia coli could be detected. The sensitivity of the assay was about 105 bacterial cells/well (106/ml), which is comparable with or outperforms other ELISA tests detecting intact bacterial cells without an enrichment step. The specificity of the assay depends on the kind of bacteriophage used. We conclude that the use of bacteriophages in the detection and identification of bacteria by an ELISA-based method can be an alternative to the use of specific antibodies. The advantages of the use of bacteriophages are their environmental abundance (and, thus, a possibility to isolate various phages with different specificities) and the availability of methods for obtaining large amounts of phage lysates, which are simple, rapid, cheap, and easy

The λ Red Proteins Promote Efficient Recombination between Diverged Sequences: Implications for Bacteriophage Genome Mosaicism

Genome mosaicism in temperate bacterial viruses (bacteriophages) is so great that it obscures their phylogeny at the genome level. However, the precise molecular processes underlying this mosaicism are unknown. Illegitimate recombination has been proposed, but homeologous recombination could also be at play. To test this, we have measured the efficiency of homeologous recombination between diverged oxa gene pairs inserted into λ. High yields of recombinants between 22% diverged genes have been obtained when the virus Red Gam pathway was active, and 100 fold less when the host Escherichia coli RecABCD pathway was active. The recombination editing proteins, MutS and UvrD, showed only marginal effects on λ recombination. Thus, escape from host editing contributes to the high proficiency of virus recombination. Moreover, our bioinformatics study suggests that homeologous recombination between similar lambdoid viruses has created part of their mosaicism. We therefore propose that the remarkable propensity of the λ-encoded Red and Gam proteins to recombine diverged DNA is effectively contributing to mosaicism, and more generally, that a correlation may exist between virus genome mosaicism and the presence of Red/Gam-like systems

DNA Barcoding Reveals Cryptic Diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826)

The widely studied and invasive earthworm, Lumbricus terrestris L., 1758 has been the subject of nomenclatural debate for many years. However these disputes were not based on suspicions of heterogeneity, but rather on the descriptions and nomenclatural acts associated with the species name. Large numbers of DNA barcode sequences of the cytochrome oxidase I obtained for nominal L. terrestris and six congeneric species reveal that there are two distinct lineages within nominal L. terrestris. One of those lineages contains the Swedish population from which the name-bearing specimen of L. terrestris was obtained. The other contains the population from which the syntype series of Enterion herculeum Savigny, 1826 was collected. In both cases modern and old representatives yielded barcode sequences allowing us to clearly establish that these are two distinct species, as different from one another as any other pair of congeners in our data set. The two are morphologically indistinguishable, except by overlapping size-related characters. We have designated a new neotype for L. terrestris. The newly designated neotype and a syntype of L. herculeus yielded DNA adequate for sequencing part of the cytochrome oxidase I gene (COI). The sequence data make possible the objective determination of the identities of earthworms morphologically identical to L. terrestris and L. herculeus, regardless of body size and segment number. Past work on nominal L. terrestris could have been on either or both species, although L. herculeus has yet to be found outside of Europe