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Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis  [cached]
Zehr Emilie S,Tabatabai Louisa B,Bayles Darrell O
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-331
Abstract: Background Haemophilus parasuis, the causative agent of Gl sser’s disease, is prevalent in swine herds and clinical signs associated with this disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia. Six to eight week old pigs in segregated early weaning herds are particularly susceptible to the disease. Insufficient colostral antibody at weaning or the mixing of pigs with heterologous virulent H. parasuis strains from other farm sources in the nursery or grower-finisher stage are considered to be factors for the outbreak of Gl sser’s disease. Previously, a Mu-like bacteriophage portal gene was detected in a virulent swine isolate of H. parasuis by nested polymerase chain reaction. Mu-like bacteriophages are related phyologenetically to enterobacteriophage Mu and are thought to carry virulence genes or to induce host expression of virulence genes. This study characterizes the Mu-like bacteriophage, named SuMu, isolated from a virulent H. parasuis isolate. Results Characterization was done by genomic comparison to enterobacteriophage Mu and proteomic identification of various homologs by mass spectrometry. This is the first report of isolation and characterization of this bacteriophage from the Myoviridae family, a double-stranded DNA bacteriophage with a contractile tail, from a virulent field isolate of H. parasuis. The genome size of bacteriophage SuMu was 37,151 bp. DNA sequencing revealed fifty five open reading frames, including twenty five homologs to Mu-like bacteriophage proteins: Nlp, phage transposase-C-terminal, COG2842, Gam-like protein, gp16, Mor, peptidoglycan recognition protein, gp29, gp30, gpG, gp32, gp34, gp36, gp37, gpL, phage tail tube protein, DNA circulation protein, gpP, gp45, gp46, gp47, COG3778, tail fiber protein gp37-C terminal, tail fiber assembly protein, and Com. The last open reading frame was homologous to IS1414. The G + C content of bacteriophage SuMu was 41.87% while its H. parasuis host genome’s G + C content was 39.93%. Twenty protein homologs to bacteriophage proteins, including 15 structural proteins, one lysogeny-related and one lysis-related protein, and three DNA replication proteins were identified by mass spectrometry. One of the tail proteins, gp36, may be a virulence-related protein. Conclusions Bacteriophage SuMu was characterized by genomic and proteomic methods and compared to enterobacteriophage Mu.
Intermediate Scales, Mu Parameter, and Fermion Masses from String Models  [PDF]
G. Cleaver,M. Cvetic,J. R. Espinosa,L. Everett,P. Langacker
Physics , 1997, DOI: 10.1103/PhysRevD.57.2701
Abstract: We address intermediate scales within a class of string models. The intermediate scales occur due to the SM singlets S_i acquiring non-zero VEVs due to radiative breaking; the mass-square (m_i)^2 of S_i is driven negative at mu_{RAD} due to order(1) Yukawa couplings of S_i to exotic particles (calculable in a class of string models). The actual VEV of S_i depends on the relative magnitude of the non-renormalizable terms of the type (S_i)^{K+3}/M^K in the superpotential. We mainly consider the case in which the S_i are charged under an additional non-anomalous U(1) gauge symmetry and the VEVs occur along F- and D-flat directions. We explore various scenarios in detail, depending on the type of Yukawa couplings to the exotic particles and on the initial boundary values of the soft SUSY breaking parameters. We then address the implications of these scenarios for the mu parameter and the fermionic masses of the standard model.
Optimized baseplate geometry for ball swaging process by using finite element analysis
Pattaramon Jongpradist,Rattharong Rojbunsongsri,Chatchapol Sukkana
Songklanakarin Journal of Science and Technology , 2009,
Abstract: A ball swaging process is commonly used in the hard disk drive manufacturing process to attach a suspension arm to an actuator arm via a part known as the baseplate. The geometry of the baseplate affects the contact pressure profile between the baseplate and the arm, torque retention of the swaged connection, and deformation of the assembly parts. In the current study, the effects of altering the baseplate geometric parameters on its characteristics are studied. A large-deformation dynamic finite element analysis of a ball swaging process is performed by using a commercial program ABAQUS. Theproducts of combining several geometric parameters are also investigated so as to obtain the baseplate geometry with improved torque retention and reduced tilt angle. It is concluded that a proper design of the baseplate is in such way that the baseplate boss and the arm possess the largest contact area and that the stress concentration at the baseplate neck is minimal.
Mu Insertions Are Repaired by the Double-Strand Break Repair Pathway of Escherichia coli  [PDF]
Sooin Jang,Steven J. Sandler,Rasika M. Harshey
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002642
Abstract: Mu is both a transposable element and a temperate bacteriophage. During lytic growth, it amplifies its genome by replicative transposition. During infection, it integrates into the Escherichia coli chromosome through a mechanism not requiring extensive DNA replication. In the latter pathway, the transposition intermediate is repaired by transposase-mediated resecting of the 5′ flaps attached to the ends of the incoming Mu genome, followed by filling the remaining 5 bp gaps at each end of the Mu insertion. It is widely assumed that the gaps are repaired by a gap-filling host polymerase. Using the E. coli Keio Collection to screen for mutants defective in recovery of stable Mu insertions, we show in this study that the gaps are repaired by the machinery responsible for the repair of double-strand breaks in E. coli—the replication restart proteins PriA-DnaT and homologous recombination proteins RecABC. We discuss alternate models for recombinational repair of the Mu gaps.
Distinction of atmospheric neutrino-mu - neutrino-tau and neutrino-mu - neutrino-sterile oscillations using short or intermediate baseline experiments  [PDF]
Achim Geiser
Physics , 1998, DOI: 10.1007/s100529901085
Abstract: The current case for atmospheric $\nu_\mu$ oscillations into active or sterile neutrinos is reviewed. It is argued that neither the study of neutral current events at Super-Kamiokande, nor the information obtained from future long baseline experiments might be sufficient to unambigously decide between these two scenarios. However, a combination of these results with the results from future short or intermediate baseline $\tau$ appearance experiments would clearly resolve most of the remaining ambiguities. This conclusion does not strongly depend on whether the results from LSND will be confirmed or not. In the case that LSND would be confirmed, a negative result in such a short or intermediate baseline experiment would also unambigously exclude the interpretation of LSND as indirect $\nu_\mu-\nu_\tau-\nu_e$ oscillations.
The Technology and Application of the Tree Planting Baseplate in Bare Rock Area  [PDF]
Xiaohan Zhou, Hongkai Chen, Hongmei Tang
World Journal of Engineering and Technology (WJET) , 2016, DOI: 10.4236/wjet.2016.43C001
Abstract:
The ecological greening technology of the bare rock area of the arbor governance be-longs to the field of ecological environment restoration, selection of suitable arbors for vegetation restoration in bare rock area, vegetation recovery is the primary approach to governance the ecological environment of bare rock area. The reconstruction of bare rock area arbor-shrub-grass ecosystems is a global environmental science problem. Paying attention to Geological conditions with rich rock fissures and abundant groundwater in these fissures, following the idea to reconstruct ecosystem from arbor to shrub and grass and the principle one tree in a baseplate, authors develop a baseplate technique for tree planting in bare rock area. The baseplate includes the parent body, the root, and the cover to prevent evaporation. Especially, there are filled in nutritional soil for the parent body and the root, and the composition of nutritional soil are selected by test in laboratory, while optimal mix ratio of the composition is obtained. Then, application method in field is put forward. The technique can guarantee survival at early stage and growth in the later for tree planting in the baseplate. In particular, the root provides a good channel to guide tree roots into fissure rock and absorb groundwater in rock. Test in field shows that the baseplate technique has strong practicality in vegetation recovery of bare rock area. Test in field shows that the baseplate technique has strong practicality in vegetation recovery of bare rock area in the world.
Genome Dynamics of Campylobacter jejuni in Response to Bacteriophage Predation  [PDF]
Andrew E Scott,Andrew R Timms,Phillippa L Connerton,Catherine Loc Carrillo,Khairul Adzfa Radzum,Ian F Connerton
PLOS Pathogens , 2007, DOI: 10.1371/journal.ppat.0030119
Abstract: Campylobacter jejuni is a leading cause of food-borne illness. Although a natural reservoir of the pathogen is domestic poultry, the degree of genomic diversity exhibited by the species limits the application of epidemiological methods to trace specific infection sources. Bacteriophage predation is a common burden placed upon C. jejuni populations in the avian gut, and we show that amongst C. jejuni that survive bacteriophage predation in broiler chickens are bacteriophage-resistant types that display clear evidence of genomic rearrangements. These rearrangements were identified as intra-genomic inversions between Mu-like prophage DNA sequences to invert genomic segments up to 590 kb in size, the equivalent of one-third of the genome. The resulting strains exhibit three clear phenotypes: resistance to infection by virulent bacteriophage, inefficient colonisation of the broiler chicken intestine, and the production of infectious bacteriophage CampMu. These genotypes were recovered from chickens in the presence of virulent bacteriophage but not in vitro. Reintroduction of these strains into chickens in the absence of bacteriophage results in further genomic rearrangements at the same locations, leading to reversion to bacteriophage sensitivity and colonisation proficiency. These findings indicate a previously unsuspected method by which C. jejuni can generate genomic diversity associated with selective phenotypes. Genomic instability of C. jejuni in the avian gut has been adopted as a mechanism to temporarily survive bacteriophage predation and subsequent competition for resources, and would suggest that C. jejuni exists in vivo as families of related meta-genomes generated to survive local environmental pressures.
Collider signals from slow decays in supersymmetric models with an intermediate-scale solution to the mu problem  [PDF]
Stephen P. Martin
Physics , 2000, DOI: 10.1103/PhysRevD.62.095008
Abstract: The problem of the origin of the mu parameter in the Minimal Supersymmetric Standard Model can be solved by introducing singlet supermultiplets with non-renormalizable couplings to the ordinary Higgs supermultiplets. The Peccei-Quinn symmetry is broken at a scale which is the geometric mean between the weak scale and the Planck scale, yielding a mu term of the right order of magnitude and an invisible axion. These models also predict one or more singlet fermions which have electroweak-scale masses and suppressed couplings to MSSM states. I consider the case that such a singlet fermion, containing the axino as an admixture, is the lightest supersymmetric particle. I work out the relevant couplings in several of the simplest models of this type, and compute the partial decay widths of the next-to-lightest supersymmetric particle involving leptons or jets. Although these decays will have an average proper decay length which is most likely much larger than a typical collider detector, they can occasionally occur within the detector, providing a striking signal. With a large sample of supersymmetric events, there will be an opportunity to observe these decays, and so gain direct information about physics at very high energy scales.
Evolutionary Genomics of a Temperate Bacteriophage in an Obligate Intracellular Bacteria (Wolbachia)  [PDF]
Bethany N. Kent, Lisa J. Funkhouser, Shefali Setia, Seth R. Bordenstein
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024984
Abstract: Genome evolution of bacteria is usually influenced by ecology, such that bacteria with a free-living stage have large genomes and high rates of horizontal gene transfer, while obligate intracellular bacteria have small genomes with typically low amounts of gene exchange. However, recent studies indicate that obligate intracellular species that host-switch frequently harbor agents of horizontal transfer such as mobile elements. For example, the temperate double-stranded DNA bacteriophage WO in Wolbachia persistently transfers between bacterial coinfections in the same host. Here we show that despite the phage's rampant mobility between coinfections, the prophage's genome displays features of constraint related to its intracellular niche. First, there is always at least one intact prophage WO and usually several degenerate, independently-acquired WO prophages in each Wolbachia genome. Second, while the prophage genomes are modular in composition with genes of similar function grouping together, the modules are generally not interchangeable with other unrelated phages and thus do not evolve by the Modular Theory. Third, there is an unusual core genome that strictly consists of head and baseplate genes; other gene modules are frequently deleted. Fourth, the prophage recombinases are diverse and there is no conserved integration sequence. Finally, the molecular evolutionary forces acting on prophage WO are point mutation, intragenic recombination, deletion, and purifying selection. Taken together, these analyses indicate that while lateral transfer of phage WO is pervasive between Wolbachia with occasional new gene uptake, constraints of the intracellular niche obstruct extensive mixture between WO and the global phage population. Although the Modular Theory has long been considered the paradigm of temperate bacteriophage evolution in free-living bacteria, it appears irrelevant in phages of obligate intracellular bacteria.
Can medio-lateral baseplate position and load sharing induce asymptomatic local bone resorption of the proximal tibia? A finite element study
Bernardo Innocenti, Evelyn Truyens, Luc Labey, Pius Wong, Jan Victor, Johan Bellemans
Journal of Orthopaedic Surgery and Research , 2009, DOI: 10.1186/1749-799x-4-26
Abstract: The postoperative radiographs of 500 consecutive TKA patients were analyzed to determine the occurrence of local medial bone resorption under the baseplate. Based on these cases, a 3D FE model was developed. Cemented and cementless technique, seven positions of the baseplate and eleven load sharing conditions were considered. The average VonMises stress was evaluated in the bone-baseplate interface, and the medial and lateral periprosthetic region.Sixteen cases with local bone resorption were identified. In each, bone loss became apparent at 3 months post-op and did not increase after one year. None of these cases were symptomatic and infection screening was negative for all. The FE analysis demonstrated an influence of baseplate positioning, and also of load sharing, on stresses. The average stress in the medial periprosthetic region showed a non linear decrease when the prosthetic baseplate was shifted laterally. Shifting the component medially increased the stress on the medial periprosthetic region, but did not significantly unload the lateral side. The presence of a cement layer decreases the stresses.Local bone resorption of the proximal tibia can occur after TKA and might be attributed to a stress shielding effect. This FE study shows that the medial periprosthetic region of the tibia is more sensitive than the lateral region to mediolateral positioning of the baseplate. Medial cortical support of the tibial baseplate is important for normal stress transfer to the underlying bone. The absence of medial cortical support of the tibial baseplate may lead to local bone resorption at the proximal tibia, as a result of the stress shielding effect. The presence of a complete layer of cement can reduce stress shielding, though. Despite the fact that the local bone resorption is asymptomatic and non-progressive, surgeons should be aware of this phenomenon in their interpretation of follow-up radiographs.One of the major failure mechanisms in total knee arthroplasty (T
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