Addiction systems antagonize bacterial adaptive immunity.

This is the author accepted manuscript. The final version is available from Oxford University Press (OUP) via the DOI in this record. CRISPR-Cas systems provide adaptive immunity against mobile genetic elements, but employment of this resistance mechanism is often reported with a fitness cost for the host. Whether or not CRISPR-Cas systems are important barriers for the horizontal spread of conjugative plasmids, which play a crucial role in the spread of antibiotic resistance, will depend on the fitness costs of employing CRISPR-based defences and the benefits of resisting conjugative plasmids. To estimate these costs and benefits we measured bacterial fitness associated with plasmid immunity using Escherichia coli and the conjugative plasmid pOX38-Cm. We find that CRISPR-mediated immunity fails to confer a fitness benefit in the absence of antibiotics, despite the large fitness cost associated with carrying the plasmid in this context. Similar to many other conjugative plasmids, pOX38-Cm carries a CcdAB toxin-antitoxin (TA) addiction system. These addiction systems encode long-lived toxins and short-lived anti-toxins, resulting in toxic effects following the loss of the TA genes from the bacterial host. Our data suggest that the lack of a fitness benefit associated with CRISPR-mediated defence is due to expression of the TA system before plasmid detection and degradation. As most antibiotic resistance plasmids encode TA systems this could have important consequences for the role of CRISPR-Cas systems in limiting the spread of antibiotic resistance.European CommissionBiotechnology & Biological Sciences Research Council (BBSRC)Natural Environment Research CouncilRoyal Society of Biological SciencesNetherlands Organization of Scientific Research (NWO)Wellcome Trus

Protein Tyrosine Phosphatase-Induced Hyperactivity Is a Conserved Strategy of a Subset of BaculoViruses to Manipulate Lepidopteran Host Behavior

This is the final version. Available from PLoS via the DOI in this record.Many parasites manipulate host behavior to increase the probability of transmission. To date, direct evidence for parasitic genes underlying such behavioral manipulations is scarce. Here we show that the baculovirus Autographa californica nuclear polyhedrovirus (AcMNPV) induces hyperactive behavior in Spodoptera exigua larvae at three days after infection. Furthermore, we identify the viral protein tyrosine phosphatase (ptp) gene as a key player in the induction of hyperactivity in larvae, and show that mutating the catalytic site of the encoded phosphatase enzyme prevents this induced behavior. Phylogenetic inference points at a lepidopteran origin of the ptp gene and shows that this gene is well-conserved in a group of related baculoviruses. Our study suggests that ptp-induced behavioral manipulation is an evolutionarily conserved strategy of this group of baculoviruses to enhance virus transmission, and represents an example of the extended phenotype concept. Overall, these data provide a firm base for a deeper understanding of the mechanisms behind baculovirus-induced insect behavior. © 2012 van Houte et al.Program Strategic Alliances of the Royal Dutch Academy of SciencesMEERVOUD grant from the Netherlands Organization for Scientific ResearchC.T. de Wit Graduate School for Production Ecology and Resource Conservatio

CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: The datasets supporting this article have been uploaded as part of the electronic supplementary material, tables.CRISPR-Cas is an adaptive prokaryotic immune system that prevents phage infection. By incorporating phage-derived 'spacer' sequences into CRISPR loci on the host genome, future infections from the same phage genotype can be recognized and the phage genome cleaved. However, the phage can escape CRISPR degradation by mutating the sequence targeted by the spacer, allowing them to re-infect previously CRISPR-immune hosts, and theoretically leading to coevolution. Previous studies have shown that phage can persist over long periods in populations of Streptococcus thermophilus that can acquire CRISPR-Cas immunity, but it has remained less clear whether this coexistence was owing to coevolution, and if so, what type of coevolutionary dynamics were involved. In this study, we performed highly replicated serial transfer experiments over 30 days with S. thermophilus and a lytic phage. Using a combination of phenotypic and genotypic data, we show that CRISPR-mediated resistance and phage infectivity coevolved over time following an arms race dynamic, and that asymmetry between phage infectivity and host resistance within this system eventually causes phage extinction. This work provides further insight into the way CRISPR-Cas systems shape the population and coevolutionary dynamics of bacteria-phage interactions. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.European Union Horizon 202

A double stranded DNA fragment shows a significant decrease in double-helix stability after binding of monofunctional platinum amine compounds

Metals in Catalysis, Biomimetics & Inorganic Material

Cytokines and chemokines are detectable in swivel-derived exhaled breath condensate (SEBC): A pilot study in mechanically ventilated patients

Introduction. Exhaled breath condensate (EBC) is a noninvasive method to collect samples from the respiratory tract. Usually, a thermoelectric cooling module is required to collect sufficient EBC volume for analyses. In here, we assessed the feasibility of cytokine and chemokine detection in EBC collected directly from the ventilator circuit without the use of a cooling module: swivel-derived exhaled breath condensate (SEBC). Methods. SEBC was prospectively collected from the swivel adapter and stored at -80°C. The objective of this study was to detect cytokines and chemokines in SEBC with a multiplex immunoassay. Secondary outcomes were to assess the correlation between cytokine and chemokine concentrations in SEBC and mechanical ventilation parameters, systemic inflammation parameters, and hemodynamic parameters. Results. Twenty-nine SEBC samples were obtained from 13 ICU patients. IL-1β, IL-4, IL-8, and IL-17 were detected in more than 90% of SEBC samples, and significant correlations between multiple cytokines and chemokines were found. Several significant correlations were found between cytokines and chemokines in SEBC and mechanical ventilation parameters and serum lactate concentrations. Conclusion. This pilot study showed that it is feasible to detect cytokines and chemokines in SEBC samples obtained without a cooling module. Despite small sample size, correlations were found between cytokines and chemokines in SEBC and mechanical ventilation parameters, as well as serum lactate concentrations. This simple SEBC collection method provides the opportunity to collect EBC samples in large prospective ICU cohorts

Microbial community succession on developing lesions on human enamel

Dental caries is one of the most common diseases in the world. However, our understanding of how the microbial community composition changes in vivo as caries develops is lacking.An in vivo model was used in a longitudinal cohort study to investigate shifts in the microbial community composition associated with the development of enamel caries.White spot lesions were generated in vivo on human teeth predetermined to be extracted for orthodontic reasons. The bacterial microbiota on sound enamel and on developing carious lesions were identified using the Human Oral Microbe Identification Microarray (HOMIM), which permits the detection of about 300 of the approximate 600 predominant bacterial species in the oral cavity.After only seven weeks, 75% of targeted teeth developed white spot lesions (8 individuals, 16 teeth). The microbial community composition of the plaque over white spot lesions differed significantly as compared to sound enamel. Twenty-five bacterial taxa, including Streptococcus mutans, Atopobium parvulum, Dialister invisus, and species of Prevotella and Scardovia, were significantly associated with initial enamel lesions. In contrast, 14 bacterial taxa, including species of Fusobacterium, Campylobacter, Kingella, and Capnocytophaga, were significantly associated with sound enamel.The bacterial community composition associated with the progression of enamel lesions is specific and much more complex than previously believed. This investigation represents one of the first longitudinally-derived studies for caries progression and supports microbial data from previous cross-sectional studies on the development of the disease. Thus, the in vivo experiments of generating lesions on teeth destined for extraction in conjunction with HOMIM analyses represent a valid model to study succession of supragingival microbial communities associated with caries development and to study efficacy of prophylactic and restorative treatments

Biplanar versus conventional two-dimensional ultrasound guidance for radial artery catheterisation

Background: Ultrasound guidance increases first-pass success rates and decreases the number of cannulation attempts and complications during radial artery catheterisation but it is debatable whether short-, long-, or oblique-axis imaging is superior for obtaining access. Three-dimensional (3D) biplanar ultrasound combines both short- and long-axis views with their respective benefits. This study aimed to determine whether biplanar imaging would improve the accuracy of radial artery catheterisation compared with conventional 2D imaging. Methods: This before-and-after trial included adult patients who required radial artery catheterisation for elective cardiothoracic surgery. The participating anaesthesiologists were experienced in 2D and biplanar ultrasound-guided vascular access. The primary endpoint was successful catheterisation in one skin break without withdrawals. Secondary endpoints were the numbers of punctures and withdrawals, scanning and procedure times, needle visibility, perceived mental effort of the operator, and posterior wall puncture or other mechanical complications. Results: From November 2021 until April 2022, 158 patients were included and analysed (2D=75, biplanar=83), with two failures to catheterise in each group. First-pass success without needle redirections was 58.7% in the 2D group and 60.2% in the biplanar group (difference=1.6%; 95% confidence interval [CI], –14.0%–17.1%; P=0.84), and first-pass success within one skin break was 77.3% in the 2D group vs 81.9% in the biplanar group (difference=4.6%; 95% CI, 8.1%–17.3%; P=0.473). None of the secondary endpoints differed significantly. Conclusions: Biplanar ultrasound guidance did not improve success rates nor other performance measures of radial artery catheterisation. The additional visual information acquired with biplanar imaging did not offer any benefit. Clinical trial registration: N9687 (Dutch Trial Register).</p

Mathematical formulation of quantum circuit design problems in networks of quantum computers

In quantum circuit design, the question arises how to distribute qubits, used in algorithms, over the various quantum computers, and how to order them within a quantum computer. In order to evaluate these problems, we define the global and local reordering problems for distributed quantum computing. We formalise the mathematical problems and model them as integer linear programming problems, to minimise the number of SWAP gates or the number of interactions between different quantum computers. For global reordering, we analyse the problem for various geometries of networks: completely connected networks, general networks, linear arrays and grid-structured networks. For local reordering, in networks of quantum computers, we also define the mathematical optimisation problem

Evaluation of the image quality and validity of handheld echocardiography for stroke volume and left ventricular ejection fraction quantification:a method comparison study

Bedside quantification of stroke volume (SV) and left ventricular ejection fraction (LVEF) is valuable in hemodynamically compromised patients. Miniaturized handheld ultrasound (HAND) devices are now available for clinical use. However, the performance level of HAND devices for quantified cardiac assessment is yet unknown. The aim of this study was to compare the validity of HAND measurements with standard echocardiography (SE) and three-dimensional echocardiography (3DE). Thirty-six patients were scanned with HAND, SE and 3DE. LVEF and SV quantification was done with automated software for the HAND, SE and 3DE dataset. The image quality of HAND and SE was evaluated by scoring segmental endocardial border delineation (2 = good, 1 = poor, 0 = invisible). LVEF and SV of HAND was evaluated against SE and 3DE using correlation and Bland-Altman analysis. The correlation, bias, and limits of agreement (LOA) between HAND and SE were 0.68 [0.46:0.83], 1.60% [- 2.18:5.38], and 8.84% [- 9.79:12.99] for LVEF, and 0.91 [0.84:0.96], 1.32 ml [- 0.36:4.01], 15.54 ml [- 18.70:21.35] for SV, respectively. Correlation, bias, and LOA between HAND and 3DE were 0.55 [0.6:0.74], - 0.56% [- 2.27:1.1], and 9.88% [- 13.29:12.17] for LVEF, and 0.79 [0.62:0.89], 6.78 ml [2.34:11.21], 12.14 ml [- 26.32:39.87] for SV, respectively. The image quality scores were 9.42 ± 2.0 for the apical four chamber views of the HAND dataset and 10.49 ± 1.7 for the SE dataset and (P &lt; 0.001). Clinically acceptable accuracy, precision, and image quality was demonstrated for HAND measurements compared to SE. In comparison to 3DE, HAND showed a clinically acceptable accuracy and precision for LVEF quantification.</p

Evaluation of the image quality and validity of handheld echocardiography for stroke volume and left ventricular ejection fraction quantification:a method comparison study

Bedside quantification of stroke volume (SV) and left ventricular ejection fraction (LVEF) is valuable in hemodynamically compromised patients. Miniaturized handheld ultrasound (HAND) devices are now available for clinical use. However, the performance level of HAND devices for quantified cardiac assessment is yet unknown. The aim of this study was to compare the validity of HAND measurements with standard echocardiography (SE) and three-dimensional echocardiography (3DE). Thirty-six patients were scanned with HAND, SE and 3DE. LVEF and SV quantification was done with automated software for the HAND, SE and 3DE dataset. The image quality of HAND and SE was evaluated by scoring segmental endocardial border delineation (2 = good, 1 = poor, 0 = invisible). LVEF and SV of HAND was evaluated against SE and 3DE using correlation and Bland-Altman analysis. The correlation, bias, and limits of agreement (LOA) between HAND and SE were 0.68 [0.46:0.83], 1.60% [- 2.18:5.38], and 8.84% [- 9.79:12.99] for LVEF, and 0.91 [0.84:0.96], 1.32 ml [- 0.36:4.01], 15.54 ml [- 18.70:21.35] for SV, respectively. Correlation, bias, and LOA between HAND and 3DE were 0.55 [0.6:0.74], - 0.56% [- 2.27:1.1], and 9.88% [- 13.29:12.17] for LVEF, and 0.79 [0.62:0.89], 6.78 ml [2.34:11.21], 12.14 ml [- 26.32:39.87] for SV, respectively. The image quality scores were 9.42 ± 2.0 for the apical four chamber views of the HAND dataset and 10.49 ± 1.7 for the SE dataset and (P &lt; 0.001). Clinically acceptable accuracy, precision, and image quality was demonstrated for HAND measurements compared to SE. In comparison to 3DE, HAND showed a clinically acceptable accuracy and precision for LVEF quantification.</p