Temperature-induced DNA density transition in phage λ capsid revealed with contrast-matching SANS.

Structural details of a genome packaged in a viral capsid are essential for understanding how the structural arrangement of a viral genome in a capsid controls its release dynamics during infection, which critically affects viral replication. We previously found a temperature-induced, solid-like to fluid-like mechanical transition of packaged λ-genome that leads to rapid DNA ejection. However, an understanding of the structural origin of this transition was lacking. Here, we use small-angle neutron scattering (SANS) to reveal the scattering form factor of dsDNA packaged in phage λ capsid by contrast matching the scattering signal from the viral capsid with deuterated buffer. We used small-angle X-ray scattering and cryoelectron microscopy reconstructions to determine the initial structural input parameters for intracapsid DNA, which allows accurate modeling of our SANS data. As result, we show a temperature-dependent density transition of intracapsid DNA occurring between two coexisting phases-a hexagonally ordered high-density DNA phase in the capsid periphery and a low-density, less-ordered DNA phase in the core. As the temperature is increased from 20 °C to 40 °C, we found that the core-DNA phase undergoes a density and volume transition close to the physiological temperature of infection (~37 °C). The transition yields a lower energy state of DNA in the capsid core due to lower density and reduced packing defects. This increases DNA mobility, which is required to initiate rapid genome ejection from the virus capsid into a host cell, causing infection. These data reconcile our earlier findings of mechanical DNA transition in phage.

'SAXS-osmometer' method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state.

We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA-DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.

Correction: Concentration and temperature dependent interactions and state diagram of dispersions of copolymer microgels.

Correction for 'Concentration and temperature dependent interactions and state diagram of dispersions of copolymer microgels' by José Ruiz-Franco et al., Soft Matter, 2023, 19, 3614-3628, https://doi.org/10.1039/D3SM00120B.

Concentration and temperature dependent interactions and state diagram of dispersions of copolymer microgels.

We investigate by means of small angle neutron scattering experiments and numerical simulations the interactions and inter-particle arrangements of concentrated dispersions of copolymer poly(N-isopropylacrylamide)-poly(ethylene glycol methyl ether methacrylate) (PNIPAM-PEGMA) microgels across the volume phase transition (VPT). The scattering data of moderately concentrated dispersions are accurately modeled at all temperatures by using a star polymer form factor and static structure factors calculated from the effective potential obtained from simulations. Interestingly, for temperatures below the VPT temperature (VPTT), the radius of gyration and blob size of the particles significantly decrease with increasing the effective packing fraction in the non-overlapping regime. This is attributed to the presence of charges in the system associated with the use of an ionic initiator in the synthesis. Simulations using the experimentally corroborated interaction potential are used to explore the state diagram in a wide range of effective packing fractions. Below and slightly above the VPTT, the system undergoes an arrest transition mainly driven by the soft repulsion between the particles. Only well above the VPTT the system is found to phase separate before arresting. Our results highlight the versatility and potential of copolymer PNIPAM-PEGMA microgels to explore different kinds of arrested states balancing attraction and repulsion by changing temperature and packing fraction.

Scalable Quantum Logic Spectroscopy.

In quantum logic spectroscopy (QLS), one species of trapped ion is used as a sensor to detect the state of an otherwise inaccessible ion species. This extends precision measurements to a broader class of atomic and molecular systems for applications like atomic clocks and tests of fundamental physics. Here, we develop a new technique based on a Schrödinger cat interferometer to address the problem of scaling QLS to larger ion numbers. We demonstrate the basic features of this method using various combinations of ^{25}Mg^{+} logic ions and ^{27}Al^{+} spectroscopy ions. We observe higher detection efficiency by increasing the number of ^{25}Mg^{+} ions. Applied to multiple ^{27}Al^{+}, this method will improve the stability of high-accuracy optical clocks and could enable Heisenberg-limited QLS.

Active Compounds in Zingiber officinale as Possible Redox Inhibitors of 5-Lipoxygenase Using an In Silico Approach.

5-Lipoxygenase (5-LOX) converts arachidonic acid to lipidic inflammatory mediators such as leukotrienes (LTs). In diseases such as asthma, LTs contribute to a physiopathology that could be reverted by blocking 5-LOX. Natural products with anti-inflammatory potential such as ginger have been used as nutraceuticals since ancient times. 6-Gingerol and 6-shogaol are the most abundant compounds in the ginger rhizome; they possess anti-inflammatory, antioxidant, and chemopreventive properties. In the present study, 6-gingerol and 6-shogaol structures were analyzed and compared with two commercial 5-LOX inhibitors (zileuton and atreleuton) and with other inhibitor candidates (3f, NDGA, CP 209, caffeic acid, and caffeic acid phenethyl ester (CAPE)). The pharmacokinetics and toxicological properties of 6-gingerol, 6-shogaol, and the other compounds were evaluated. Targeted molecular coupling was performed to identify the optimal catalytic pocket for 5-LOX inhibition. The results showed that 6-gingerol and 6-shogaol follow all of the recommended pharmacokinetic parameters. These compounds could be inhibitors of 5-LOX because they present specific interactions with the residues involved in molecular inhibition. The current study demonstrated the potential of 6-gingerol and 6-shogaol as anti-inflammatory agents that inhibit 5-LOX, as they present a high level of performance in the toxicological analysis and could be catabolized by the cytochrome p450 enzymatic complex; however, 6-gingerol was superior in safety compared to 6-shogaol.

Metabolomic Profiling, Antioxidant and Enzyme Inhibition Properties and Molecular Docking Analysis of Antarctic Lichens.

The lichen species Lecania brialmontii, Pseudephebe pubescens, and Sphaerophorus globosus are part of the prominent lichenoflora of the Antarctic territory. In this work, we report the metabolomic identification of ethanolic extracts of these species, their antioxidant and cholinesterase enzyme inhibitory activity, and conduct a molecular docking analysis with typical compounds. Eighteen compounds were identified by UHPLC-ESI-QTOF-MS in L. brialmontii, 18 compounds in P. pubescens, and 14 compounds in S. globosus. The content of phenolic compounds was variable among the species, ranging from 0.279 to 2.821 mg AG/g, and all three species showed high inhibition potential on the cholinesterase enzymes. Molecular docking showed important interactions between AChE and BChE with the selected compounds. This study evidences the chemical fingerprint of three species of the order Lecanorales that support the continuation of the study of other biological activities and their potential for medical research.

Concentration and size effects on the size-selective particle purification method using the critical Casimir force.

Critical Casimir force (CCF) is a solvent fluctuation introduced interaction between particles dispersed in a binary solvent. Recently, it has been demonstrated that the CCF induced attraction between particles can trigger particle size-sensitive aggregation, and has thus been used as an efficient way to purify nanoparticles by size. Here, combining small angle neutron scattering and dynamic light scattering, we investigate the effects of size and concentration on this particle size separation method. Increasing the particle concentration does not significantly affect the purification method, but the solvent composition needs to be adjusted for an optimized efficiency. This purification method is further demonstrated to work also very efficiently for systems with particle size ranging from 15 nm to about 50 nm with a very large size polydispersity. These results indicate that for both short-ranged and long-ranged attraction relative to the particle diameter, the CCF introduced particle aggregation is always size sensitive. This implies that particle aggregation is strongly affected by size polydispersity for many colloidal systems. We further propose a method to use light scattering to help identify the temperature range within which this particle purification method can work efficiently instead of using neutron scattering.

Lifetime-Limited Interrogation of Two Independent

Laser decoherence limits the stability of optical clocks by broadening the observable resonance linewidths and adding noise during the dead time between clock probes. Correlation spectroscopy avoids these limitations by measuring correlated atomic transitions between two ensembles, which provides a frequency difference measurement independent of laser noise. Here, we apply this technique to perform stability measurements between two independent clocks based on the ^{1}S_{0}↔^{3}P_{0} transition in ^{27}Al^{+}. By stabilizing the dominant sources of differential phase noise between the two clocks, we observe coherence between them during synchronous Ramsey interrogations as long as 8 s at a frequency of 1.12×10^{15} Hz. The observed contrast in the correlation spectroscopy signal is consistent with the 20.6 s ^{3}P_{0} state lifetime and represents a measurement instability of (1.8±0.5)×10^{-16}/sqrt[τ/s] for averaging periods longer than the probe duration when dead time is negligible.

Perkinsus mediterraneus infection induces oxidative stress in the mollusc Mimachlamys varia.

Perkinsus mediterraneus is a protozoan parasite that can cause marine mollusc diseases known as perkinsosis being a serious threat for clam cultures worldwide. The aim of the present study was first to determine the Perkinsus species infecting the variegated scallop Mimachlamys varia and then to evaluate the existence of oxidative stress in gills of M. varia according to different degrees of infection. DNA sequencing confirmed that P. mediterraneus was the species infecting M. varia. ROS production was progressively increasing with the degree of infection although the differences were only significant in the high-infected group. Low degree of infection significantly increased superoxide dismutase (SOD) and glutathione S-transferase (GST) activities and nitrite levels with respect to the control group. In the high-infected group, a significant increase was evidenced in all analysed enzymes, catalase, SOD, glutathione reductase and GST. Non-significant differences in MDA levels were observed between the control and low-infected groups; however, a significant increase in MDA levels was observed in the high-infected group. In conclusion, the infection by Perkinsus mediterraneus in M. varia induces oxidative stress and an antioxidant response directly related to the infection degree that can contribute to the pathogenicity of the infection.

Are Strategies Favoring Pattern Matching a Viable Way to Improve Complexity Estimation Based on Sample Entropy?

It has been suggested that a viable strategy to improve complexity estimation based on the assessment of pattern similarity is to increase the pattern matching rate without enlarging the series length. We tested this hypothesis over short simulations of nonlinear deterministic and linear stochastic dynamics affected by various noise amounts. Several transformations featuring a different ability to increase the pattern matching rate were tested and compared to the usual strategy adopted in sample entropy (SampEn) computation. The approaches were applied to evaluate the complexity of short-term cardiac and vascular controls from the beat-to-beat variability of heart period (HP) and systolic arterial pressure (SAP) in 12 Parkinson disease patients and 12 age- and gender-matched healthy subjects at supine resting and during head-up tilt. Over simulations, the strategies estimated a larger complexity over nonlinear deterministic signals and a greater regularity over linear stochastic series or deterministic dynamics importantly contaminated by noise. Over short HP and SAP series the techniques did not produce any practical advantage, with an unvaried ability to discriminate groups and experimental conditions compared to the traditional SampEn. Procedures designed to artificially increase the number of matches are of no methodological and practical value when applied to assess complexity indexes.

Destination Joint Spacers, Reinfection, and Antimicrobial Suppression.

In this cohort of 51 patients managed with retained "destination spacers" after the resection of infected joint prostheses, the presence of preoperative sinus drainage was significantly associated with reinfection. Chronic antimicrobial suppression after destination-spacer retention did not significantly prevent reinfections.

Viral encephalopathy and retinopathy (VER) disease in Epinephelus marginatus from the Balearic Islands marine protected areas.

This is the first description of a betanodavirus infection in the dusky grouper Epinephelus marginatus within the marine protected areas (MPAs) of the Balearic Islands. Histopathology techniques were employed to describe neurological lesions in infected fish. Abnormal swimming, mortality, and neurological lesions were detected in all analysed grouper individuals. Virus particles were observed by means of transmission electron microscopy. Reverse transcription of RNA1 and RNA2 followed by cDNA amplification and sequencing allowed viral classification. Phylogenetic analysis showed the isolates from wild E. marginatus of the Balearic Islands MPAs to be closely related to Dicentrarchus labrax and Mullus barbatus strains from Cyprus and Italy. Although vertical transmission from infected spawners has been described as the major route for nodavirus infection, we point out in this work that horizontal transmission among sub-clinical fishes after migration or commercial import for aquaculture production could play a major role in the spreading of the disease in MPAs.

Refined Multiscale Entropy Using Fuzzy Metrics: Validation and Application to Nociception Assessment.

The refined multiscale entropy (RMSE) approach is commonly applied to assess complexity as a function of the time scale. RMSE is normally based on the computation of sample entropy (SampEn) estimating complexity as conditional entropy. However, SampEn is dependent on the length and standard deviation of the data. Recently, fuzzy entropy (FuzEn) has been proposed, including several refinements, as an alternative to counteract these limitations. In this work, FuzEn, translated FuzEn (TFuzEn), translated-reflected FuzEn (TRFuzEn), inherent FuzEn (IFuzEn), and inherent translated FuzEn (ITFuzEn) were exploited as entropy-based measures in the computation of RMSE and their performance was compared to that of SampEn. FuzEn metrics were applied to synthetic time series of different lengths to evaluate the consistency of the different approaches. In addition, electroencephalograms of patients under sedation-analgesia procedure were analyzed based on the patient's response after the application of painful stimulation, such as nail bed compression or endoscopy tube insertion. Significant differences in FuzEn metrics were observed over simulations and real data as a function of the data length and the pain responses. Findings indicated that FuzEn, when exploited in RMSE applications, showed similar behavior to SampEn in long series, but its consistency was better than that of SampEn in short series both over simulations and real data. Conversely, its variants should be utilized with more caution, especially whether processes exhibit an important deterministic component and/or in nociception prediction at long scales.

Haplosporidium pinnae sp. nov., a haplosporidan parasite associated with mass mortalities of the fan mussel, Pinna nobilis, in the Western Mediterranean Sea.

This study provides morphological and molecular characterization of a new species, Haplosporidium pinnae), very likely responsible for mass mortality of fan mussels, Pinna nobilis, in the Western Mediterranean Sea. The parasite was found in dead or moribund P. nobilis but did not occur in healthy fan mussels from locations that were not affected by abnormal mortality. Histological examination of infected fan mussels showed uninucleate cells of a haplosporidan parasite throughout the connective tissue and hemolymph sinuses of the visceral mass and binucleate cells and, rarely, multinucleate plasmodia were also detected in the connective tissue. Additionally, stages of sporulation occurred in the epithelium of the host digestive gland tubules. Spores were slightly ellipsoidal with a hinged operculum in one pole. Typical haplosporosomes were not found with TEM but vesicles with two concentric membranes resembling haplosporosomes were abundant in the cytoplasm of the multinucleate plasmodia occurring in host digestive gland tubules. SEM analysis showed multiple structures on the spore surface; some spores had two or four long tape-like filaments attached to the spore wall. Phylogenetic analysis based on the SSU rDNA sequence placed this parasite within a large clade including species of the order Haplosporida, not in the Bonamia/Minchinia subclade or the subclade containing most Haplosporidium species, but within a subclade of Haplosporidium sp. from Penaeus vannamei. Our results suggested that H. pinnae and the parasite of P. vannamei may represent a distinct new genus within the order Haplosporida.

Ultrasound-Guided Percutaneous Dilatational Tracheostomies in 2 Difficult Airways.

Ultrasound has become a rapid, safe, and easy-to-use tool for anesthesiologists. It reduces complications, morbidity, and mortality, especially in patients with anatomic abnormalities in whom a traditional approach may be both difficult and risky. We report 2 cases of symptomatic patients with a difficult airway due to displacement of the trachea by a neck mass. Real-time ultrasound imaging was performed for percutaneous dilatational tracheostomies, identifying important structures, without any complications.

Modeling Respiratory Depression Induced by Remifentanil and Propofol during Sedation and Analgesia Using a Continuous Noninvasive Measurement of pCO2.

Respiratory depression is a common adverse effect of propofol and remifentanil. We aimed to develop a model for respiratory depressant effects of propofol with remifentanil in patients undergoing endoscopy with sedation. Data were available for 136 patients undergoing endoscopy with sedation. Participants randomly received infusions of propofol and remifentanil. Predicted plasma concentrations, outputted by infusion pumps, were available. Transcutaneous arterial pressure of carbon dioxide (pCO2) was measured. Data were analyzed using nonlinear mixed-effects modeling methods. Covariate relationships were investigated for age, noxious stimuli (endoscopy tube insertion), and A118G genotype for the µ-opioid receptor (OPRM1). Participants had a median (range) age of 64.0 (25.0-88.0) years, weight of 70.0 (35.0-98.0) kg, and height of 164.0 (147.0-190.0) cm. Seven percent were recessive homozygous for OPRM1 polymorphism. An indirect-effect model with a "modulator" compartment best described pCO2 data (P < 0.001) over a direct-effect model. Remifentanil inhibited pCO2 removal with an IC50 of 1.13 ng/ml and first-order rate constant (ke 0) of 0.28 minute(-1). Propofol affected the modulator compartment with an IC50 of 4.97 µg/ml (no effect-site compartment). Propofol IC50 and remifentanil ke 0 were reduced with increasing age. Noxious stimuli and genotype were not significant covariates. An indirect-effect model with a rebound mechanism can describe remifentanil- and propofol-induced changes in pCO2 in patients undergoing noxious procedures. The model may be useful for identifying optimal dosing schedules for these drugs in a combination that provides adequate sedation but avoids respiratory depression.

Multiscale entropy analysis of heart rate variability in heart failure, hypertensive, and sinoaortic-denervated rats: classical and refined approaches.

The analysis of heart rate variability (HRV) by nonlinear methods has been gaining increasing interest due to their ability to quantify the complexity of cardiovascular regulation. In this study, multiscale entropy (MSE) and refined MSE (RMSE) were applied to track the complexity of HRV as a function of time scale in three pathological conscious animal models: rats with heart failure (HF), spontaneously hypertensive rats (SHR), and rats with sinoaortic denervation (SAD). Results showed that HF did not change HRV complexity, although there was a tendency to decrease the entropy in HF animals. On the other hand, SHR group was characterized by reduced complexity at long time scales, whereas SAD animals exhibited a smaller short- and long-term irregularity. We propose that short time scales (1 to 4), accounting for fast oscillations, are more related to vagal and respiratory control, whereas long time scales (5 to 20), accounting for slow oscillations, are more related to sympathetic control. The increased sympathetic modulation is probably the main reason for the lower entropy observed at high scales for both SHR and SAD groups, acting as a negative factor for the cardiovascular complexity. This study highlights the contribution of the multiscale complexity analysis of HRV for understanding the physiological mechanisms involved in cardiovascular regulation.

Evaluation of the efficacy and safety of dual antiplatelet therapy with or without warfarin in patients with a clinical indication for DAPT and chronic anticoagulation: A meta-analysis of observational studies.

OBJECTIVE: To compare the efficacy and safety of dual antiplatelet therapy (DAPT) and triple therapy (TT, dual antiplatelet plus warfarin) in patients with myocardial infarction (MI) or PCI with stenting (PCI-S) who also require chronic oral anticoagulation. BACKGROUND: Recommendations for the optimal antiplatelet/anticoagulant treatment regimen for patients undergoing PCI-S or MI who also require oral anticoagulation are largely based on evidence from observational studies and expert opinions. METHODS: A systematic search was performed for studies comparing TT vs. DAPT in patients post PCI-S or MI and requiring chronic anticoagulation. Primary outcome was all-cause mortality. Secondary outcomes were ischemic stroke, major bleeding, MI, and stent thrombosis. Pooled relative risks (RR) were calculated using random effects model. RESULTS: A total of 17 studies were included, with 14,921 patients [TT: 5,819(39%) and DAPT: 9,102(61%)] and a mean follow-up of 1.6 years. The majority of patients required oral anticoagulation for atrial fibrillation. Compared to DAPT, patients treated with TT had no significant difference in all-cause mortality [RR: 0.81, 95% confidence interval (CI): 0.61-1.08, P = 0.15], MI [RR 0.74, 95% CI: 0.51-1.06, P = 0.10], and stent thrombosis [RR 0.67, 95% CI: 0.35-1.30, P = 0.24]. Patients treated with TT had significantly increased risk of major bleeding [RR 1.20, 95% CI: 1.03-1.39, P = 0.02], whereas the risk for ischemic stroke was significantly lower [RR 0.59, 95% CI: 0.38-0.92, P = 0.02]. CONCLUSIONS: All-cause mortality appears similar in patients treated with TT or DAPT although TT was associated with higher rates of major bleeding and a lower risk for ischemic stroke. © 2015 Wiley Periodicals, Inc.

Sedation-analgesia with propofol and remifentanil: concentrations required to avoid gag reflex in upper gastrointestinal endoscopy.

BACKGROUND: The purpose of this study was to identify optimal target propofol and remifentanil concentrations to avoid a gag reflex in response to insertion of an upper gastrointestinal endoscope. METHODS: Patients presenting for endoscopy received target-controlled infusions (TCI) of both propofol and remifentanil for sedation-analgesia. Patients were randomized to 4 groups of fixed target effect-site concentrations: remifentanil 1 ng•mL (REMI 1) or 2 ng•mL (REMI 2) and propofol 2 µg•mL (PROP 2) or 3 µg•mL (PROP 3). For each group, the other drug (propofol for the REMI groups and vice versa) was increased or decreased using the "up-down" method based on the presence or absence of a gag response in the previous patient. A modified isotonic regression method was used to estimate the median effective Ce,50 from the up-down method in each group. A concentration-effect (sigmoid Emax) model was built to estimate the corresponding Ce,90 for each group. These data were used to estimate propofol bolus doses and remifentanil infusion rates that would achieve effect-site concentrations between Ce,50 and Ce,90 when a TCI system is not available for use. RESULTS: One hundred twenty-four patients were analyzed. To achieve between a 50% and 90% probability of no gag response, propofol TCIs were between 2.40 and 4.23 µg•mL (that could be achieved with a bolus of 1 mg•kg) when remifentanil TCI was fixed at 1 ng•mL, and target propofol TCIs were between 2.15 and 2.88 µg•mL (that could be achieved with a bolus of 0.75 mg•kg) when remifentanil TCI was fixed at 2 ng•mL. Remifentanil ranges were 1.00 to 4.79 ng•mL and 0.72 to 3.19 ng•mL when propofol was fixed at 2 and 3 µg•mL, respectively. CONCLUSIONS: We identified a set of propofol and remifentanil TCIs that blocked the gag response to endoscope insertion in patients undergoing endoscopy. Propofol bolus doses and remifentanil infusion rates designed to achieve similar effect-site concentrations can be used to prevent gag response when TCI is not available.