Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species

Cluster k mycobacteriophages: Insights into the evolutionary origins of mycobacteriophage tm4

Five newly isolated mycobacteriophages -Angelica, CrimD, Adephagia, Anaya, and Pixie - have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them - with the exception of TM4 - form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species. © 2011 Pope et al.Fil: Pope, Welkin H.. University of Pittsburgh; Estados UnidosFil: Ferreira, Christina M.. University of Pittsburgh; Estados UnidosFil: Jacobs Sera, Deborah. University of Pittsburgh; Estados UnidosFil: Benjamin, Robert C.. University of North Texas; Estados UnidosFil: Davis, Ariangela J.. Calvin College; Estados UnidosFil: DeJong, Randall J.. Calvin College; Estados UnidosFil: Elgin, Sarah C. R.. Washington University in St. Louis; Estados UnidosFil: Guilfoile, Forrest R.. University of Pittsburgh; Estados UnidosFil: Forsyth, Mark H.. The College Of William And Mary; Estados UnidosFil: Harris, Alexander D.. Calvin College; Estados UnidosFil: Harvey, Samuel E.. The College Of William And Mary; Estados UnidosFil: Hughes, Lee E.. University of North Texas; Estados UnidosFil: Hynes, Peter M.. Washington University in St. Louis; Estados UnidosFil: Jackson, Arrykka S.. The College Of William And Mary; Estados UnidosFil: Jalal, Marilyn D.. University of North Texas; Estados UnidosFil: MacMurray, Elizabeth A.. The College Of William And Mary; Estados UnidosFil: Manley, Coreen M.. University of North Texas; Estados UnidosFil: McDonough, Molly J.. The College Of William And Mary; Estados UnidosFil: Mosier, Jordan L.. University of North Texas; Estados UnidosFil: Osterbann, Larissa J.. Calvin College; Estados UnidosFil: Rabinowitz, Hannah S.. Washington University in St. Louis; Estados UnidosFil: Rhyan, Corwin N.. Washington University in St. Louis; Estados UnidosFil: Russell, Daniel A.. University of Pittsburgh; Estados UnidosFil: Saha, Margaret S.. The College Of William And Mary; Estados UnidosFil: Shaffer, Christopher D.. Washington University in St. Louis; Estados UnidosFil: Simon, Stephanie E.. University of North Texas; Estados UnidosFil: Sims, Erika F.. Washington University in St. Louis; Estados UnidosFil: Tovar, Isabel G.. University of North Texas; Estados UnidosFil: Weisser, Emilie G.. Washington University in St. Louis; Estados UnidosFil: Wertz, John T.. Calvin College; Estados UnidosFil: Weston-Hafer, Kathleen A.. Washington University in St. Louis; Estados UnidosFil: Williamson, Kurt E.. The College Of William And Mary; Estados UnidosFil: Zhang, Bo. Washington University in St. Louis; Estados UnidosFil: Cresawn, Steven G.. James Madison University; Estados UnidosFil: Jain, Paras. Albert Einstein College Of Medicine Of Yeshiva University; Estados UnidosFil: Piuri, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Pittsburgh; Estados UnidosFil: Jacobs, William R.. Albert Einstein College Of Medicine Of Yeshiva University; Estados UnidosFil: Hendrix, Roger W.. University of Pittsburgh; Estados UnidosFil: Hatfull, Graham F.. University of Pittsburgh; Estados Unido

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Searches for 25 rare and forbidden decays of D+D^{+} and Ds+ {D}_s^{+} mesons

International audienceA search is performed for rare and forbidden charm decays of the form ${D}_{(s)}^{+}\to {h}^{\pm }{\mathrm{\ell}}^{+}{\mathrm{\ell}}^{\left(\prime \right)\mp }$, where h$^{±}$ is a pion or kaon and ℓ$^{(′)±}$ is an electron or muon. The measurements are performed using proton-proton collision data, corresponding to an integrated luminosity of 1.6 fb$^{−1}$, collected by the LHCb experiment in 2016. No evidence is observed for the 25 decay modes that are investigated and 90 % confidence level limits on the branching fractions are set between 1.4 × 10$^{−8}$ and 6.4 × 10$^{−6}$. In most cases, these results represent an improvement on existing limits by one to two orders of magnitude.[graphic not available: see fulltext

Observation of new excited Bs0{B} ^0_{s} states

International audienceA structure is observed in the ${B} ^{\pm }{K} ^{\mp }$ mass spectrum in a sample of proton–proton collisions at centre-of-mass energies of 7, 8, and 13 TeV, collected with the LHCb detector and corresponding to a total integrated luminosity of 9$\,\text {fb} ^{-1}$. The structure is interpreted as the result of overlapping excited ${B} ^0_{s}$ states. With high significance, a two-peak hypothesis provides a better description of the data than a single resonance. Under this hypothesis the masses and widths of the two states, assuming they decay directly to ${B} ^{\pm }{K} ^{\mp }$, are determined to be $\begin{aligned} m_1&= 6063.5 \pm 1.2 \text { (stat)} \pm 0.8\text { (syst)}\,\text {Me}\text {V}, \\ \Gamma _1&= 26 \pm 4 \text { (stat)} \pm 4\text { (syst)}\,\text {Me}\text {V}, \\ m_2&= 6114 \pm 3 \text { (stat)} \pm 5\text { (syst)}\,\text {Me}\text {V}, \\ \Gamma _2&= 66 \pm 18 \text { (stat)} \pm 21\text { (syst)}\,\text {Me}\text {V}. \end{aligned}$Alternative values assuming a decay through ${B} ^{*\pm }{K} ^{\mp }$, with a missing photon from the $B^{*\pm } \rightarrow B^{\pm }\gamma$ decay, which are shifted by approximately 45$\,\text {Me}$V, are also determined. The possibility of a single state decaying in both channels is also considered. The ratio of the total production cross-section times branching fraction of the new states relative to the previously observed $B_{s2}^{*0}$ state is determined to be $0.87 \pm 0.15 \text { (stat)} \pm 0.19 \text { (syst)}$

Evidence of a J/ψΛJ/\psi\Lambda structure and observation of excited Ξ−\Xi^- states in the Ξb−→J/ψΛK−\Xi^-_b \to J/\psi\Lambda K^- decay

First evidence of a structure in the $J/\psi{\Lambda}$ invariant mass distribution is obtained from an amplitude analysis of $\Xi_b^-{\rightarrow}J/\psi{\Lambda}K^-$ decays. The observed structure is consistent with being due to a charmonium pentaquark with strangeness with a significance of $3.1\sigma$ including systematic uncertainties and look-elsewhere effect. Its mass and width are determined to be $4458.8\pm2.9^{+4.7}_{-1.1}$ MeV and $17.3\pm6.5^{+8.0}_{-5.7}$ MeV, respectively, where the quoted uncertainties are statistical and systematic. The structure is also consistent with being due to two resonances. In addition, the narrow excited $\Xi^-$ states, $\Xi(1690)^-$ and $\Xi(1820)^-$, are seen for the first time in a $\Xi^-_b$ decay, and their masses and widths are measured with improved precision. The analysis is performed using $pp$ collision data corresponding to a total integrated luminosity of 9 fb$^{-1}$, collected with the LHCb experiment at centre-of-mass energies of 7, 8 and 13 TeV

Branching Fraction Measurements of the Rare Bs0→ϕμ+μ−B^0_s\rightarrow\phi\mu^+\mu^- and Bs0→f2′(1525)μ+μ−B^0_s\rightarrow f_2^\prime(1525)\mu^+\mu^- Decays

The branching fraction of the rare $B^0_s\rightarrow\phi\mu^+\mu^-$ decay is measured using data collected by the LHCb experiment at center-of-mass energies of 7, 8, and 13 TeV, corresponding to integrated luminosities of 1, 2, and 6 fb$^{-1}$, respectively. The branching fraction is reported in intervals of q$^2$, the square of the dimuon invariant mass. In the q$^2$ region between 1.1 and 6.0 GeV$^2$/c$^4$, the measurement is found to lie 3.6 standard deviations below a standard model prediction based on a combination of light cone sum rule and lattice QCD calculations. In addition, the first observation of the rare $B^0_s\rightarrow f_2^\prime(1525)\mu^+\mu^-$ decay is reported with a statistical significance of 9 standard deviations and its branching fraction is determined

Study of coherent J/ψJ/\psi production in lead-lead collisions at sNN \sqrt{{\mathrm{s}}_{\mathrm{NN}}} = 5 TeV

International audienceCoherent production of J/ψ mesons is studied in ultraperipheral lead-lead collisions at a nucleon-nucleon centre-of-mass energy of 5 TeV, using a data sample collected by the LHCb experiment corresponding to an integrated luminosity of about 10 μb$^{−1}$. The J/ψ mesons are reconstructed in the dimuon final state and are required to have transverse momentum below 1 GeV. The cross-section within the rapidity range of 2.0 < y < 4.5 is measured to be 4.45 ± 0.24 ± 0.18 ± 0.58 mb, where the first uncertainty is statistical, the second systematic and the third originates from the luminosity determination. The cross-section is also measured in J/ψ rapidity intervals. The results are compared to predictions from phenomenological models.[graphic not available: see fulltext

Measurement of χc1_{c1}(3872) production in proton-proton collisions at s \sqrt{s} = 8 and 13 TeV

International audienceThe production cross-section of the χ$_{c1}$(3872) state relative to the ψ(2S) meson is measured using proton-proton collision data collected with the LHCb experiment at centre-of-mass energies of $\sqrt{s}$ = 8 and 13 TeV, corresponding to integrated luminosities of 2.0 and 5.4 fb$^{−1}$, respectively. The two mesons are reconstructed in the J/ψπ$^{+}$π$^{−}$ final state. The ratios of the prompt and nonprompt χ$_{c1}$(3872) to ψ(2S) production cross-sections are measured as a function of transverse momentum, p$_{T}$, and rapidity, y, of the χ$_{c1}$(3872) and ψ(2S) states, in the kinematic range 4 < p$_{T}$< 20 GeV/c and 2.0 < y < 4.5. The prompt ratio is found to increase with p$_{T}$, independently of y. For the prompt component, the double ratio of the χ$_{c1}$(3872) and ψ(2S) production cross-sections between 13 and 8 TeV is observed to be consistent with unity, independent of p$_{T}$ and centre-of-mass energy.[graphic not available: see fulltext