Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach

Objectives The development of daptomycin resistance in Staphylococcus aureus is associated with clinical treatment failures. The mechanism(s) of such resistance have not been clearly defined. Methods We studied an isogenic daptomycin-susceptible (DAPS) and daptomycin-resistant (DAPR) S. aureus strain pair (616; 701) from a patient with relapsing endocarditis during daptomycin treatment, using comparative transcriptomic and proteomic techniques. Results Minor differences in the genome content were found between strains by DNA hybridization. Transcriptomic analyses identified a number of genes differentially expressed in important functional categories: cell division; metabolism of bacterial envelopes; and global regulation. Of note, the DAPR isolate exhibited reduced expression of the major cell wall autolysis gene coincident with the up-regulation of genes involved in cell wall teichoic acid production. Using quantitative (q)RT-PCR on the gene cadre putatively involved in cationic peptide resistance, we formulated a putative regulatory network compatible with microarray data sets, mainly implicating bacterial envelopes. Of interest, qRT-PCR of this same gene cadre from two distinct isogenic DAPS/DAPR clinical strain pairs revealed evidence of other strain-dependent networks operative in the DAPR phenotype. Comparative proteomics of 616 versus 701 revealed a differential abundance of proteins in various functional categories, including cell wall-associated targets and biofilm formation proteins. Phenotypically, strains 616 and 701 showed major differences in their ability to develop bacterial biofilms in the presence of the antibacterial lipid, oleic acid. Conclusions Compatible with previous in vitro observations, in vivo-acquired DAPR in S. aureus is a complex, multistep phenomenon involving: (i) strain-dependent phenotypes; (ii) transcriptome adaptation; and (iii) modification of the lipid and protein contents of cellular envelope

Exploring glycopeptide-resistance in Staphylococcus aureus: a combined proteomics and transcriptomics approach for the identification of resistance-related markers

BACKGROUND: To unravel molecular targets involved in glycopeptide resistance, three isogenic strains of Staphylococcus aureus with different susceptibility levels to vancomycin or teicoplanin were subjected to whole-genome microarray-based transcription and quantitative proteomic profiling. Quantitative proteomics performed on membrane extracts showed exquisite inter-experimental reproducibility permitting the identification and relative quantification of >30% of the predicted S. aureus proteome. RESULTS: In the absence of antibiotic selection pressure, comparison of stable resistant and susceptible strains revealed 94 differentially expressed genes and 178 proteins. As expected, only partial correlation was obtained between transcriptomic and proteomic results during stationary-phase. Application of massively parallel methods identified one third of the complete proteome, a majority of which was only predicted based on genome sequencing, but never identified to date. Several over-expressed genes represent previously reported targets, while series of genes and proteins possibly involved in the glycopeptide resistance mechanism were discovered here, including regulators, global regulator attenuator, hyper-mutability factor or hypothetical proteins. Gene expression of these markers was confirmed in a collection of genetically unrelated strains showing altered susceptibility to glycopeptides. CONCLUSION: Our proteome and transcriptome analyses have been performed during stationary-phase of growth on isogenic strains showing susceptibility or intermediate level of resistance against glycopeptides. Altered susceptibility had emerged spontaneously after infection with a sensitive parental strain, thus not selected in vitro. This combined analysis allows the identification of hundreds of proteins considered, so far as hypothetical protein. In addition, this study provides not only a global picture of transcription and expression adaptations during a complex antibiotic resistance mechanism but also unravels potential drug targets or markers that are constitutively expressed by resistant strains regardless of their genetic background, amenable to be used as diagnostic targets

Dead-box proteins: a family affair—active and passive players in RNP-remodeling

DEAD-box proteins are characterized by nine conserved motifs. According to these criteria, several hundreds of these proteins can be identified in databases. Many different DEAD-box proteins can be found in eukaryotes, whereas prokaryotes have small numbers of different DEAD-box proteins. DEAD-box proteins play important roles in RNA metabolism, and they are very specific and cannot mutually be replaced. In vitro, many DEAD-box proteins have been shown to have RNA-dependent ATPase and ATP-dependent RNA helicase activities. From the genetic and biochemical data obtained mainly in yeast, it has become clear that these proteins play important roles in remodeling RNP complexes in a temporally controlled fashion. Here, I shall give a general overview of the DEAD-box protein family

Relationship-scale Conservation

Conservation can occur anywhere regardless of scale, political jurisdiction, or landownership. We present a framework to help managers at protected areas practice conservation at the scale of relationships. We focus on relationships between stakeholders and protected areas and between managers and other stakeholders. We provide a synthesis of key natural resources literature and present a case example to support our premise and recommendations. The purpose is 4-fold: 1) discuss challenges and threats to conservation and protected areas; 2) outline a relationship-scale approach to address conservation threats; 3) describe the tools and techniques that can be used to implement this approach; and 4) present a case example from rural Alaska, USA, to illustrate relationship-scale conservation. Our case example illustrates how aspects of this approach to conservation were applied to address a wildlife population decline. Tools needed to implement relationship-scale conservation include 1) collecting and documenting narratives of place; 2) measuring and monitoring trust and commitment; and 3) identifying and mitigating threats. We recommend that planners and managers, working with their research partners, redefine and refocus their goals and objectives to include these practices. Doing so will enable them to gain substantial applied knowledge about their stakeholders and foster and maintain place relationships as desired outcomes of conservation. The ultimate outcome is a better prognosis for long-term global survival of protected areas and biodiversity. Published 2014. This article is a U.S. Government work and is in the public domain in the USA

Study of charmonium and charmonium-like contributions in B+ → J/ψηK+ decays

A study of B+→ J/ψηK+ decays, followed by J/ψ → μ+μ− and η → γγ, is performed using a dataset collected with the LHCb detector in proton-proton collisions at centre-of-mass energies of 7, 8 and 13 TeV, corresponding to an integrated luminosity of 9 fb−1. The J/ψη mass spectrum is investigated for contributions from charmonia and charmonium-like states. Evidence is found for the B+→ (ψ2(3823) → J/ψη)K+ and B+→ (ψ(4040) → J/ψη)K+ decays with significance of 3.4 and 4.7 standard deviations, respectively. This constitutes the first evidence for the ψ2(3823) → J/ψη decay

Observation of the doubly charmed baryon decay Ξcc++→Ξc′+π+

The Ξcc++→Ξc′+π+ decay is observed using proton-proton collisions collected by the LHCb experiment at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 5.4 fb−1. The Ξcc++→Ξc′+π+ decay is reconstructed partially, where the photon from the Ξc′+→Ξc+γ decay is not reconstructed and the pK−π+ final state of the Ξc+ baryon is employed. The Ξcc++→Ξc′+π+branching fraction relative to that of the Ξcc++→Ξc+π+ decay is measured to be 1.41 ± 0.17 ± 0.10, where the first uncertainty is statistical and the second systematic. [Figure not available: see fulltext.

Measurement of the photon polarization in Λb→Λγ\Lambda_b \to \Lambda \gamma decays

The photon polarization in $b \to s \gamma$ transitions is measured for the first time in radiative b-baryon decays exploiting the unique spin structure of $\Lambda_b \to \Lambda \gamma$ decays. A data sample corresponding to an integrated luminosity of $6\;fb^{-1}$ collected by the LHCb experiment in $pp$ collisions at a center-of-mass energy of $13\;TeV$ is used. The photon polarization is measured to be $\alpha_{\gamma}= 0.82^{\,+\,0.17\,+\,0.04}_{\,-\,0.26\,-\,0.13}$, where the first uncertainty is statistical and the second systematic. This result is in agreement with the Standard Model prediction and previous measurements in b-meson decays. Charge-parity breaking effects are studied for the first time in this observable and found to be consistent with $CP$ symmetry.Comment: All figures and tables, along with machine-readable versions and any supplementary material and additional information, are available at https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2021-030.html (LHCb public pages

Observation of Two New Excited Ξb0 States Decaying to Λb0 K-π+

Two narrow resonant states are observed in the Λb0K-π+ mass spectrum using a data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the LHCb experiment and corresponding to an integrated luminosity of 6 fb-1. The minimal quark content of the Λb0K-π+ system indicates that these are excited Ξb0 baryons. The masses of the Ξb(6327)0 and Ξb(6333)0 states are m[Ξb(6327)0]=6327.28-0.21+0.23±0.12±0.24 and m[Ξb(6333)0]=6332.69-0.18+0.17±0.03±0.22 MeV, respectively, with a mass splitting of Δm=5.41-0.27+0.26±0.12 MeV, where the uncertainties are statistical, systematic, and due to the Λb0 mass measurement. The measured natural widths of these states are consistent with zero, with upper limits of Γ[Ξb(6327)0]<2.20(2.56) and Γ[Ξb(6333)0]<1.60(1.92) MeV at a 90% (95%) credibility level. The significance of the two-peak hypothesis is larger than nine (five) Gaussian standard deviations compared to the no-peak (one-peak) hypothesis. The masses, widths, and resonant structure of the new states are in good agreement with the expectations for a doublet of 1D Ξb0 resonances

Observation of Cabibbo-suppressed two-body hadronic decays and precision mass measurement of the Ωc0\Omega_{c}^{0} baryon

The first observation of the singly Cabibbo-suppressed $\Omega_{c}^{0}\to\Omega^{-}K^{+}$ and $\Omega_{c}^{0}\to\Xi^{-}\pi^{+}$ decays is reported, using proton-proton collision data at a centre-of-mass energy of $13\,{\rm TeV}$, corresponding to an integrated luminosity of $5.4\,{\rm fb}^{-1}$, collected with the LHCb detector between 2016 and 2018. The branching fraction ratios are measured to be $\frac{\mathcal{B}(\Omega_{c}^{0}\to\Omega^{-}K^{+})}{\mathcal{B}(\Omega_{c}^{0}\to\Omega^{-}\pi^{+})}=0.0608\pm0.0051({\rm stat})\pm 0.0040({\rm syst})$, $\frac{\mathcal{B}(\Omega_{c}^{0}\to\Xi^{-}\pi^{+})}{\mathcal{B}(\Omega_{c}^{0}\to\Omega^{-}\pi^{+})}=0.1581\pm0.0087({\rm stat})\pm0.0043({\rm syst})\pm0.0016({\rm ext})$. In addition, using the $\Omega_{c}^{0}\to\Omega^{-}\pi^{+}$ decay channel, the $\Omega_{c}^{0}$ baryon mass is measured to be $M(\Omega_{c}^{0})=2695.28\pm0.07({\rm stat})\pm0.27({\rm syst})\pm0.30({\rm ext})\,{\rm MeV}/c^{2}$, improving the precision of the previous world average by a factor of four.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-011.html (LHCb public pages