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Numerous studies have shown that cg05575921 methylation decreases in response to smoking. However, secondary to methodological issues, the magnitude and dose dependency of that response is as of yet unclear. This lack of certainty is a barrier to the use of DNA methylation clinically to assess and monitor smoking status. To better define this relationship, we conducted a joint analysis of methylation sensitive PCR digital (MSdPCR) assessments of cg05575921 methylation in whole blood and/or saliva DNA to smoking using samples from 421 smokers and 423 biochemically confirmed non-smokers from 4 previously published studies. We found that cg05575921 methylation manifested a curvilinear dose dependent decrease in response to increasing cigarette consumption. In whole blood DNA, the Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) of cg05575921 methylation for predicting daily smoking status was 0.98. In saliva DNA, the gross AUC was 0.91 with correction for cellular heterogeneity improving the AUC to 0.94. Methylation status was significantly associated with the Fagerstrom Test for Nicotine Dependence score, but with significant sampling heterogeneity. We conclude that MSdPCR assessments of cg05575921 methylation are a potentially powerful, clinically implementable tool for the assessment and management of smoking.

Multidrug resistant (MDR) tuberculosis (TB) is defined by the resistance of Mycobacterium tuberculosis, the causative organism, to the first-line antibiotics rifampicin and isoniazid. Mitigating or reversing resistance to these drugs offers a means of preserving and extending their use in TB treatment. R-loops are RNA/DNA hybrids that are formed in the genome during transcription, and can be lethal to the cell if not resolved. RNase HI is an enzyme that removes R-loops, and this activity is essential in M. tuberculosis: knockouts of rnhC, the gene encoding RNase HI, are non-viable. This essentiality supports it as a candidate target for the development of new antibiotics. In the model organism Mycolicibacterium smegmatis, RNase HI activity is provided by two RNase HI enzymes, RnhA and RnhC. We show that the partial depletion of RNase HI activity in M. smegmatis, by knocking out either of the genes encoding RnhA or RnhC, led to the accumulation of R-loops. The sensitivity of the knockout strains to the antibiotics moxifloxacin, streptomycin and rifampicin was increased, with sensitivity to the transcriptional inhibitor rifampicin strikingly increased by nearly 100-fold. We also show that R-loop accumulation accompanies partial transcriptional inhibition, suggesting a mechanistic basis for the synergy between RNase HI depletion and transcriptional inhibition. A model of how transcriptional inhibition can potentiate R-loop accumulation is presented. Finally, we identified four small molecules that inhibit recombinant RnhC activity and that also potentiated rifampicin activity in whole-cell assays against M. tuberculosis, supporting an on-target mode of action, and providing the first step in developing a new class of anti-mycobacterial drug.ImportanceThis study validates mycobacterial RNase HI as a druggable, vulnerable candidate for a new therapeutic treatment of M. tuberculosis with a novel mode of action. RNase HI depletion shows synergistic bacterial killing with some current first- and second-line antibiotics, suggesting that RNase HI inhibitors would combine well with these regimens, and could potentially accelerate the clearance of drug-sensitive strains. RNase HI inhibitors also have the potential to reduce the effective dose of rifampicin, with the comcommitant reduction in side effects. The potentiation of rifampicin efficacy conferred by RNase HI deficiency suggests that RNase HI inhibitors may be able to mitigate against development of rifampicin resistance. The synergy may also be able to reverse rifampicin resistance, rescuing this antibiotic for therapy. The surprising finding that low levels of transcriptional inhibition potentiate R-loop formation provides a key new insight into R-loop metabolism.

Nitrogen dioxide, NO2, is a free radical composed of the two most abundant elements in Earth's atmosphere, nitrogen and oxygen, and is relevant to atmospheric and combustion chemistry. The electronic structure of even its lowest-lying states is remarkably complex, with various conical intersections and Renner-Teller pairings, giving rise to complex and perturbed vibronic states. Here we report some analysis of the 18 molecular states of doublet spin-multiplicity formed by combining ground-state N(4Su) and O(3Pg) atoms. Three-dimensional potential energy surfaces were fit at the MRCI(Q)-F12/VTZ-F12 level, describing the lowest four (X, A, B, and C) electronic states. A properties-based diabatization procedure was applied to accommodate the intersections, producing energies in a quasidiabatic representation and yielding couplings that were also fit into surfaces. The low-lying vibrational levels on the ground X state were computed and compared with experimental measurements. Compared to experiment, the lowest 125 calculated vibrational levels (up to 8500 cm-1 above the zero-point energy) have a root-mean-squared error of 16.5 cm-1. In addition, dipole moments for each of the lowest four electronic states-and the transition dipoles between them-were also computed and fit. With the coupled energy and dipole surfaces, the electronic spectrum was calculated in absolute intensity and compared with experimental measurements. Detailed structure in the experimental spectrum was successfully reproduced, and the total integrated intensity matches experiment to an accuracy of ∼1.5% with no empirical adjustments.

Many experimental parameters determine the chemical and physical properties of interstellar ice analogues, each of which may influence the molecular synthesis that occurs in such ices. In part 1, James et al., RSC Adv., 2020, 10, 37517, we demonstrated the effects that the stoichiometric mixing ratio had on the chemical and physical properties of CO2 : NH3 mixtures and the impact on molecular synthesis induced by thermal processing. Here, in part 2, we extend this to include 1 keV electron irradiation at 20 K of several stoichiometric mixing ratios of CO2 : NH3 ices followed by thermal processing. We demonstrate that not all stoichiometric mixing ratios of CO2 : NH3 ice form the same products. Not only did the 4 : 1 ratio form a different residue after thermal processing, but O3 was observed after electron irradiation at 20 K, which was not observed in the other ratios. For the other ratios, the residue formed from a thermal reaction similar to the work shown in Part 1. However, conversion of ammonium carbamate to carbamic acid was hindered due to electron irradiation at 20 K. Our results demonstrate the need to systematically investigate stoichiometric mixing ratios to better characterise the chemical and physical properties of interstellar ice analogues to further our understanding of the routes of molecular synthesis under different astrochemical conditions.

Amyloid β oligomers (Aβo) are the main toxic species in Alzheimer's disease, which have been targeted for single drug treatment with very little success. In this work we report a new approach for identifying functional Aβo binding compounds. A tailored library of 971 fluorine containing compounds was selected by a computational method, developed to generate molecular diversity. These compounds were screened for Aβo binding by a combined 19F and STD NMR technique. Six hits were evaluated in three parallel biochemical and functional assays. Two compounds disrupted Aβo binding to its receptor PrPC in HEK293 cells. They reduced the pFyn levels triggered by Aβo treatment in neuroprogenitor cells derived from human induced pluripotent stem cells (hiPSC). Inhibitory effects on pTau production in cortical neurons derived from hiPSC were also observed. These drug-like compounds connect three of the pillars in Alzheimer's disease pathology, i.e. prion, Aβ and Tau, affecting three different pathways through specific binding to Aβo and are, indeed, promising candidates for further development.

Inverse opals, as ordered macroporous structures, are widely used due to their interesting optical response. The addition of metal oxide dopants increases their optical absorption. However, with heavy dopant concentrations, the doped inverse opal is affected by structural damage and higher solid volume fractions. In this work, the effect of dopant concentration on inverse opals was investigated by doping copper and nickel into TiO2. The inverse opal-like structure was prepared by infiltrating TiO2 sol–gel into polystyrene microsphere opal templates and then baking at 500 °C. The polystyrene opal templates were constructed by self-assembly convective deposition with vibration assistance. The fluorescence emission from Cu d-states and defect states in doped TiO2 structures were studied. The emission for copper-doped TiO2 was observed at a wavelength of 520 nm with excitation at 410 nm. Although the characteristic emission of the dopants was readily observed, the overall fluorescence intensity of the doped TiO2 layer was much lower than that of the undoped TiO2 structure. Chemical compositions investigated by x-ray photoluminescence showed that the dopants disturbed the TiO2 bonds and created defect states. The reflection of the fabricated film under visible wavelength was stronger at higher dopant concentrations. These results are explained because the inverse opal has a higher solid content and the higher reflectivity is likely to be due to the rutile phase of TiO2.

Cell behaviour and function is determined through the interactions of a multitude of molecules working in concert. To observe these molecular dynamics, biophysical studies have been developed that track single interactions. Fluorescence correlation spectroscopy (FCS) is an optical biophysical technique that non-invasively resolves single molecules through recording the signal intensity at the femtolitre scale. However, recording the behaviour of these biomolecules using in vitro-based assays often fails to recapitulate the full range of variables in vivo that directly confer dynamics. Therefore, there has been an increasing interest in observing the state of these biomolecules within living organisms such as the zebrafish Danio rerio. In this review, we explore the advancements of FCS within the zebrafish and compare and contrast these findings to those found in vitro.

The neural crest shows an astonishing multipotency, generating multiple neural derivatives, but also pigment cells, skeletogenic and other cell types. The question of how this process is controlled has been the subject of an ongoing debate for more than 35 years. Based upon new observations of zebrafish pigment cell development, we have recently proposed a novel, dynamic model that we believe goes some way to resolving the controversy. Here, we will firstly summarize the traditional models and the conflicts between them, before outlining our novel model. We will also examine our recent dynamic modelling studies, looking at how these reveal behaviors compatible with the biology proposed. We will then outline some of the implications of our model, looking at how it might modify our views of the processes of fate specification, differentiation, and commitment.

Mitochondrial energy production and function rely on optimal concentrations of the essential redox-active lipid, coenzyme Q (CoQ). CoQ deficiency results in mitochondrial dysfunction associated with increased mitochondrial oxidative stress and a range of pathologies. What drives CoQ deficiency in many of these pathologies is unknown, just as there currently is no effective therapeutic strategy to overcome CoQ deficiency in humans. To date, large-scale studies aimed at systematically interrogating endogenous systems that control CoQ biosynthesis and their potential utility to treat disease have not been carried out. Therefore, we developed a quantitative high-throughput method to determine CoQ concentrations in yeast cells. Applying this method to the Yeast Deletion Collection as a genome-wide screen, 30 genes not known previously to regulate cellular concentrations of CoQ were discovered. In combination with untargeted lipidomics and metabolomics, phosphatidylethanolamine N-methyltransferase (PEMT) deficiency was confirmed as a positive regulator of CoQ synthesis, the first identified to date. Mechanistically, PEMT deficiency alters mitochondrial concentrations of one-carbon metabolites, characterized by an increase in the S-adenosylmethionine to S-adenosylhomocysteine (SAM-to-SAH) ratio that reflects mitochondrial methylation capacity, drives CoQ synthesis, and is associated with a decrease in mitochondrial oxidative stress. The newly described regulatory pathway appears evolutionary conserved, as ablation of PEMT using antisense oligonucleotides increases mitochondrial CoQ in mouse-derived adipocytes that translates to improved glucose utilization by these cells, and protection of mice from high-fat diet-induced insulin resistance. Our studies reveal a previously unrecognized relationship between two spatially distinct lipid pathways with potential implications for the treatment of CoQ deficiencies, mitochondrial oxidative stress/dysfunction, and associated diseases., Graphical abstract Image 1, Highlights • Mitochondrial CoQ deficiency results in oxidative stress and a range of pathologies • The drivers of mitochondrial CoQ deficiency remain largely unknown • PEMT deficiency is the first identified positive regulator of mitochondrial CoQ • PEMT deficiency increases CoQ by increasing the mitochondrial SAM-to-SAH ratio • PEMT deficiency prevents insulin resistance by increasing mitochondrial CoQ

Ex vivo culture of mouse and human skin causes an inflammatory response characterized by production of multiple cytokines. We used ex vivo culture of mouse tail skin specimens to investigate mechanisms of this skin culture-induced inflammatory response. Multiplex assays revealed production of interleukin 1 alpha (IL‐1α), interleukin 1 beta (IL-1β), interleukin 6 (IL-6), chemokine C-X-C motif ligand 1 (CXCL1), granulocyte colony-stimulating factor (G-CSF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) during skin culture, and quantitative PCR revealed transcripts for these proteins were also increased. Ex vivo cultures of skin from myeloid differentiation primary response 88 deficient mice (Myd88(−/−)) demonstrated significantly reduced expression of transcripts for the aforementioned cytokines. The same result was observed with skin from interleukin 1 receptor type 1 deficient mice (Il1r1(−/−)). These data suggested the IL-1R1/MyD88 axis is required for the skin culture-induced inflammatory response and led us to investigate the role of IL-1α and IL-1β (the ligands for IL-1R1) in this process. Addition of IL-1α neutralizing antibody to skin cultures significantly reduced expression of Cxcl1, Il6 and Csf3. IL-1β neutralization did not reduce levels of these transcripts. These studies suggest that IL-1α promotes the skin the culture-induced inflammatory response.

The CF+ molecule is considered one of the key species for the study of fluorine chemistry in the interstellar medium (ISM). Its recent detection, as well as its potential use as a tracer for atomic...

We study the properties of solid-based random lasers by observing spectral emission shape, emission intensity, emission line width, and lasing threshold. Random lasers based on solid polymer film are prepared by combining titania nanoparticles with rhodamine 640 in poly(vinyl alcohol) (PVA) water solution. We compare samples with and without scatterers. Adding nanoparticles to the samples narrows the emission spectrum, and the lasing threshold can be observed. The amount of titanium dioxide (TiO2) or titania nanoparticles is varied and affects the properties of random lasers. The spectral emission line width becomes narrower, and the lasing threshold decreases when the amount of titania increases. Results obtained show that the properties of solid-based random lasers can be improved by increasing scattering, which enhances the feedback mechanism. The enhanced properties of random lasers are very useful for creating a reliable optical device for future applications in medical and biosensing fields.

An automated computational thermochemistry protocol based on explicitly correlated coupled-cluster theory was designed to produce highly accurate enthalpies of formation and atomization energies for small- to medium-sized molecular species (3-12 atoms). Each potential source of error was carefully examined, and the sizes of contributions to the total atomization enthalpies were used to generate uncertainty estimates. The protocol was first used to generate total atomization enthalpies for a family of four molecular species exhibiting a variety of charges, multiplicities, and electronic ground states. The new protocol was shown to be in good agreement with the Active Thermochemical Tables database for the four species: the methyl peroxy radical, methoxyoxoniumylidene (methyl peroxy cation), methyl peroxy anion, and methyl hydroperoxide. Updating the Active Thermochemical Tables to include those results yielded significantly improved accuracy for the formation enthalpies of those species. The derived protocol was then used to predict formation enthalpies for the larger ethyl peroxy family of species.

Alcohol and tobacco use are highly comorbid and exacerbate the associated morbidity and mortality of either substance alone. However, the relationship of alcohol consumption to the various forms of nicotine-containing products is not well understood. To improve this understanding, we examined the relationship of alcohol consumption to nicotine product use using self-report, cotinine, and two epigenetic biomarkers specific for smoking (cg05575921) and drinking (Alcohol T Scores (ATS)) in n = 424 subjects. Cigarette users had significantly higher ATS values than the other groups (p &lt, 2.2 × 10−16). Using the objective biomarkers, the intensity of nicotine and alcohol consumption was correlated in both the cigarette and smokeless users (R = −0.66, p = 3.1 × 10−14, R2 = 0.61, p = 1.97 × 10−4). Building upon this idea, we used the objective nicotine biomarkers and age to build and test a Balanced Random Forest classification model for heavy alcohol consumption (ATS &gt, 2.35). The model performed well with an AUC of 0.962, 89.3% sensitivity, and 85% specificity. We conclude that those who use non-combustible nicotine products drink significantly less than smokers, and cigarette and smokeless users drink more with heavier nicotine use. These findings further highlight the lack of informativeness of self-reported alcohol consumption and suggest given the public and private health burden of alcoholism, further research into whether using non-combustible nicotine products as a mode of treatment for dual users should be considered.

Experimental and simulation studies show that a hexagonal array of polystyrene particles on a gold substrate, capped with gold semi-shells, results in increased optical confinement of the resonance modes in comparison with those for arrays without metallic substrate or capping. Well-ordered arrays of polystyrene beads were fabricated by convective deposition, a solution-based self-assembly process. The polystyrene particles exhibited strong optical concentration, with photonic and plasmonic modes as detected in optical spectra and modelling. The resonance wavelengths of the plasmonic hexagonal array were modified by treating the hexagonal arrays with oxygen plasma at fixed power of 150 W for time periods of 0–10 min. The plasma treatment reduced the vertical height of the polystyrene particles, and the resonances were tuned and sharpened after plasma treatment. This increase is attributed to the improved uniformity of the gold semi-shell coating distributed over the polystyrene particles. Additionally, the plasma treatment increased the refractive index of the polystyrene particles due to cross-linking. Devices with these plasmonic hexagonal arrays enable enhanced light–matter interactions, with the flexibility to post-tune the resonance wavelengths.

A Wnt microenvironment sustained by the hepatic central vein is essential for the segregation of liver functions into zones. Current liver culture systems lack localized Wnt cues and as a consequence fail to maintain the hepatocyte functional heterogeneity that is observed in the intact organ. In this study, organoid models and 2D-culture systems were used to identify cellular sources and Wnt presentation methods that could support the future development of zonated liverin vitrosystems. Using soluble ligands, we show that primary hepatocyte (PH)-derived organoids but not bile duct (BD)-derived organoids may be used to recapitulate the resting liver. We provide evidence that differentiation of PH-organoids in the presence of Wnt9b and Rspo3 induce pericentral maturation. Finally, we show that immobilization of Rspo3 onto beads in combination with soluble Wnt9b may be a valid strategy to recreate the central vein Wnt microenvironmentin vitro.

Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remain poorly understood., Cobalamin is an essential cofactor in all domains of life, yet its biosynthesis is restricted to some bacteria and archaea. Mycobacterium smegmatis, an environmental saprophyte frequently used as surrogate for the obligate human pathogen M. tuberculosis, carries approximately 30 genes predicted to be involved in de novo cobalamin biosynthesis. M. smegmatis also encodes multiple cobalamin-dependent enzymes, including MetH, a methionine synthase that catalyzes the final reaction in methionine biosynthesis. In addition to metH, M. smegmatis possesses a cobalamin-independent methionine synthase, metE, suggesting that enzyme use—MetH versus MetE—is regulated by cobalamin availability. Consistent with this notion, we previously described a cobalamin-sensing riboswitch controlling metE expression in M. tuberculosis. Here, we apply a targeted mass spectrometry-based approach to confirm de novo cobalamin biosynthesis in M. smegmatis during aerobic growth in vitro. We also demonstrate that M. smegmatis can transport and assimilate exogenous cyanocobalamin (CNCbl; also known as vitamin B12) and its precursor, dicyanocobinamide ([CN]2Cbi). However, the uptake of CNCbl and (CN)2Cbi in this organism is restricted and seems dependent on the conditional essentiality of the cobalamin-dependent methionine synthase. Using gene and protein expression analyses combined with single-cell growth kinetics and live-cell time-lapse microscopy, we show that transcription and translation of metE are strongly attenuated by endogenous cobalamin. These results support the inference that metH essentiality in M. smegmatis results from riboswitch-mediated repression of MetE expression. Moreover, differences observed in cobalamin-dependent metabolism between M. smegmatis and M. tuberculosis provide some insight into the selective pressures which might have shaped mycobacterial metabolism for pathogenicity. IMPORTANCE Alterations in cobalamin-dependent metabolism have marked the evolution of Mycobacterium tuberculosis into a human pathogen. However, the role(s) of cobalamin in mycobacterial physiology remains poorly understood. Using the nonpathogenic saprophyte M. smegmatis, we investigated the production of cobalamin, transport and assimilation of cobalamin precursors, and the role of cobalamin in regulating methionine biosynthesis. We confirm constitutive de novo cobalamin biosynthesis in M. smegmatis, in contrast with M. tuberculosis, which appears to lack de novo cobalamin biosynthetic capacity. We also show that uptake of cyanocobalamin (vitamin B12) and its precursors is restricted in M. smegmatis, apparently depending on the cofactor requirements of the cobalamin-dependent methionine synthase. These observations establish M. smegmatis as an informative foil to elucidate key metabolic adaptations enabling mycobacterial pathogenicity.

Osteoarthritis (OA), characterized by chondrocyte apoptosis and disturbance of the balance between catabolism and anabolism of the extracellular matrix (ECM), is the most common age-related degenerative joint disease worldwide. As sleep has been found to be beneficial for cartilage repair, and circular RNAs (circRNAs) have been demonstrated to be involved in the pathogenesis of OA, we performed RNA sequencing (RNA-seq), and found circRNA3503 was significantly increased after melatonin (MT)-induced cell sleep. Upregulation of circRNA3503 expression completely rescued the effects of interleukin-1β (IL-1β), which was used to simulate OA, on apoptosis, ECM degradation- and synthesis-related genes. Mechanistically, circRNA3503 acted as a sponge of hsa-miR-181c-3p and hsa-let-7b-3p. Moreover, as we previously showed that small extracellular vesicles (sEVs) derived from synovium mesenchymal stem cells (SMSCs) can not only successfully deliver nucleic acids to chondrocytes, but also effectively promote chondrocyte proliferation and migration, we assessed the feasibility of sEVs in combination with sleep-related circRNA3503 as an OA therapy. We successfully produced and isolated circRNA3503-loaded sEVs (circRNA3503-OE-sEVs) from SMSCs. Then, poly(D,l-lactide)-b-poly(ethylene glycol)-b-poly(D,l-lactide) (PDLLA-PEG-PDLLA, PLEL) triblock copolymer gels were used as carriers of sEVs. Through in vivo and in vitro experiments, PLEL@circRNA3503-OE-sEVs were shown to be a highly-effective therapeutic strategy to prevent OA progression. Through multiple pathways, circRNA3503-OE-sEVs alleviated inflammation-induced apoptosis and the imbalance between ECM synthesis and ECM degradation by acting as a sponge of hsa-miR-181c-3p and hsa-let-7b-3p. In addition, circRNA3503-OE-sEVs promoted chondrocyte renewal to alleviate the progressive loss of chondrocytes. Our results highlight the potential of PLEL@circRNA3503-OE-sEVs for preventing OA progression., Graphical abstract Image 1, Highlights • CircRNA3503 alleviated apoptosis and the imbalance between ECM synthesis and ECM degradation. • Wnt5a/b carried by sEVs promoted chondrocyte renewal to alleviate the progressive loss of chondrocytes. • PDLLA-PEG-PDLLA (PLEL) triblock copolymer gels showed good performance in slow release of sEVs. • PLEL@circRNA3503-OE-sEVs showed potential to prevent OA progression.

Background: Increasing use of non-combusted forms of nicotine such as e-cigarettes poses important public health questions regarding their specific risks relative to combusted tobacco products such as cigarettes. To fully delineate these risks, improved biomarkers that can distinguish between these forms of nicotine use are needed. Prior work has suggested that methylation status at cg05575921 may serve as a specific biomarker of combusted tobacco smoke exposure. We hypothesized combining this epigenetic biomarker with conventional metabolite assays could classify the type of nicotine product consumption. Therefore, we determined DNA methylation and serum cotinine values in samples from 112 smokers, 35 e-cigarette users, 19 smokeless tobacco users and 269 controls, and performed mass spectroscopy analyses of urine samples from all nicotine users and 22 verified controls to determine urinary levels of putatively nicotine product specific substances; propylene glycol, 2-cyanoethylmercapturic acid (CEMA) and anabasine. Results: 1) Cigarette smoking was associated with a dose dependent demethylation of cg05575921 and increased urinary CEMA and anabasine levels, 2) e-cigarette use did not demethylate cg05575921, 3) smokeless tobacco use also did not demethylate cg05575921 but was positively associated with anabasine levels 4) CEMA and cg05575921 levels were highly correlated and 5) propylene glycol levels did not reliably distinguish use groups. Conclusions: Cg05575921 assessments distinguish exposure to tobacco smoke from smokeless sources of nicotine including e-cigarettes and smokeless tobacco, neither of which are associated with cg05575921 demethylation. A combination of methylomic and metabolite profiling may allow for accurate classification use status of a variety of nicotine containing products.

Actin is an intracellular protein that constitutes a primary component of the cellular cytoskeleton and is accordingly crucial for various cell functions. Actin assembles into semi-flexible filaments that cross-link to form higher order structures within the cytoskeleton. In turn, the actin cytoskeleton regulates cell shape, and participates in cell migration and division. A variety of theoretical models have been proposed to investigate actin dynamics across distinct scales, from the stochastic nature of protein and molecular motor dynamics to the deterministic macroscopic behavior of the cytoskeleton. Yet, the relationship between molecular-level actin processes and cellular-level actin network behavior remains understudied, where prior models do not holistically bridge the two scales together.

The Paris climate agreement requires all nations to reduce greenhouse gas (GHG) emissions. Accordingly, countries have made ambitious targets to be achieved by 2030. Road transport as a maj...

Smoking is the largest preventable cause of mortality and the largest environmental driver of epigenetic aging. Contingency management-based strategies can be used to treat smoking but require objective methods of verifying quitting status. Prior studies have suggested that cg05575921 methylation reverts as a function of smoking cessation, but that it can be used to verify the success of smoking cessation has not been unequivocally demonstrated. To test whether methylation can be used to verify cessation, we determined monthly cg05575921 levels in a group of 67 self-reported smokers undergoing biochemically monitored contingency management-based smoking cessation therapy, as part of a lung imaging protocol. A total of 20 subjects in this protocol completed three months of cotinine verified smoking cessation. In these 20 quitters, the reversion of cg05575921 methylation was dependent on their initial smoking intensity, with methylation levels in the heaviest smokers reverting to an average of 0.12% per day over the 3-month treatment period. In addition, we found suggestive evidence that some individuals may have embellished their smoking history to gain entry to the study. Given the prominent effect of smoking on longevity, we conclude that DNA methylation may be a useful tool for guiding and incentivizing contingency management-based approaches for smoking cessation.

Objectives Routine exercise is thought to be among the only disease-modifying treatments for Parkinson's disease; however, patients' progressive loss of physical ability limits its application. Therefore, we sought to investigate whether a ketone ester drink, which has previously been shown to enhance endurance exercise performance in elite athletes, could also improve performance in persons with Parkinson's disease. Participants 14 patients, aged 40-80 years, with Hoehn and Yahr stage 1-2 Parkinson's disease. Intervention A randomized, placebo-controlled, crossover study in which each participant was administered a ketone ester drink or an isocaloric carbohydrate-based control drink on separate occasions prior to engaging in a steady state cycling test at 80 rpm to assess endurance exercise performance. Outcomes measures The primary outcome variable was length of time participants could sustain a therapeutic 80 rpm cadence. Secondary, metabolic outcomes measures included cardiorespiratory parameters as well as serum β-hydroxybutyrate, glucose, and lactate. Results The ketone ester increased the time that participants were able to sustain an 80 rpm cycling cadence by 24 ± 9% (p = 0.027). Correspondingly, the ketone ester increased β-hydroxybutyrate levels to >3 mmol/L and decreased respiratory exchange ratio, consistent with a shift away from carbohydrate-dependent metabolism. Conclusion Ketone ester supplementation improved endurance exercise performance in persons with Parkinson's disease and may, therefore, be useful as an adjunctive therapy to enhance the effectiveness of exercise treatment for Parkinson's disease.

Anodic passivation for copper exposed to aqueous NaCl (model seawater) is rate limited by diffusion of a poorly soluble Cu(I) chloro species. As a result, a protective layer of CuCl forms on copper metal (with approx. 1 μm thickness) that is then put under strain at more positive applied potentials with explosive events causing current spikes and particulate product expulsion. In this report, the mechanism for this explosive film rupture and particle expulsion process is shown to occur (i) in the absence of underlying anodic gas evolution, and (ii) linked to the presence/nature of gaseous solutes. The film rupture event is proposed to be fundamentally dependent on gas bubble nucleation (triggered by the release of interfacial stress) with surface tension effects by dissolved gases affecting the current spike pattern. Oxygen O2, hydrogen H2, and helium He suppress current spikes and behave differently to argon Ar, nitrogen N2, and carbon dioxide CO2, which considerably enhance current spikes. Vacuum-degassing the electrolyte solution results in behaviour very similar to that observed in the presence of helium. The overall corrosion rate for copper microelectrodes is compared and parameters linked to passivation and corrosion processes are discussed.

Many cells rearrange proteins and other components into spatially distinct domains in a process called polarization. This asymmetric patterning is required for a number of biological processes including asymmetric division, cell migration, and embryonic development. Proteins involved in polarization are highly conserved and include members of the Par and Rho protein families. Despite the importance of these proteins in polarization, it is not yet known how they interact and regulate each other to produce the protein localization patterns associated with polarization. In this study, we develop and analyse a biologically based mathematical model of polarization that incorporates interactions between Par and Rho proteins that are consistent with experimental observations of CDC-42. Using minimal network and eFAST sensitivity analyses, we demonstrate that CDC-42 is predicted to reinforce maintenance of anterior PAR protein polarity which in turn feedbacks to maintain CDC-42 polarization, as well as supporting posterior PAR protein polarization maintenance. The mechanisms for polarity maintenance identified by these methods are not sufficient for the generation of polarization in the absence of cortical flow. Additional inhibitory interactions mediated by the posterior Par proteins are predicted to play a role in the generation of Par protein polarity. More generally, these results provide new insights into the role of CDC-42 in polarization and the mutual regulation of key polarity determinants, in addition to providing a foundation for further investigations.

The origin of the even–odd rotational state population alternation in the (16)O(2)(a(1)Δ(g)) fragments resulting from the ultraviolet (UV) photodissociation of (16)O(3), a phenomenon first observed over 30 years ago, has been elucidated using full quantum theory. The calculated (16)O(2)(a(1)Δ(g)) rotational state distribution following the 266-nm photolysis of 60 K ozone shows a strong even–odd propensity, in excellent agreement with the new experimental rotational state distribution measured under the same conditions. Theory indicates that the even rotational states are significantly more populated than the adjacent odd rotational states because of a preference for the formation of the A′ Λ-doublet, which can only occupy even rotational states due to the exchange symmetry of the two bosonic (16)O nuclei, and thus not as a result of parity-selective curve crossing as previously proposed. For nonrotating ozone, its dissociation on the excited B(1)A′ state dictates that only A′ Λ-doublets are populated, due to symmetry conservation. This selection rule is relaxed for rotating parent molecules, but a preference still persists for A′ Λ-doublets. The A′′/A′ ratio increases with increasing ozone rotational quantum number, and thus with increasing temperature, explaining the previously observed temperature dependence of the even–odd population alternation. In light of these results, it is concluded that the previously proposed parity-selective curve-crossing mechanism cannot be a source of heavy isotopic enrichment in the atmosphere.

Among all the molecular species found in the interstellar medium, molecules with threefold symmetry axes play a special role, as their rotational spectroscopy allows them to act as practical gas thermometers. Methyl-cyanide (CH3CN) is the second most abundant of those (after ammonia). We compute in this paper the collisional dynamics of methyl-cyanide in collision with helium, for both the A- and the E-symmetries of CH3CN. The potential energy surface is determined using the CCSD(T)-F12b formalism and fit with convenient analytic functions. We compute the rotationally inelastic cross sections for all levels up to 510 cm−1 of collision energy, employing at low energy exact Coupled Channels methods, and at higher energies, approximate Coupled States methods. For temperatures from 7 K up to 300 K, rates of quenching are computed and most are found to differ from those reported earlier (up to a factor of a thousand), calling for a possible reexamination of the temperatures assigned to low density gasses.

Low-loss photonic waveguides in lithium niobate offer versatile functionality as nonlinear frequency converters, switches, and modulators for integrated optics. Combining the flexibility of laser processing with liquid phase epitaxy we have fabricated and characterized lithium niobate channel waveguides on lithium niobate and lithium tantalate. We used liquid phase epitaxy with K2O flux on laser-machined lithium niobate and lithium tantalate substrates. The laser-driven rapid-prototyping technique can be programmed to give machined features of various sizes, and liquid phase epitaxy produces high quality single-crystal, lithium niobate channels. The surface roughness of the lithium niobate channels on a lithium tantalate substrate was measured to be 90 nm. The lithium niobate channel waveguides exhibit propagation losses of 0.26 &plusmn, 0.04 dB/mm at a wavelength of 633 nm. Second harmonic generation at 980 nm was demonstrated using the channel waveguides, indicating that these waveguides retain their nonlinear optical properties.

A polydimethylsiloxane film patterned by a self-assembled array has been demonstrated as a strain sensor. A monolayer of 580 nm polystyrene spheres prepared by convective deposition was the template to transfer a periodic pattern to a polydimethylsiloxane (PDMS) film. Optical diffraction through the stretched PDMS film, enabled strain sensing perpendicular and parallel to the stretching direction, with sensitivities of 1.7 nm/% strain and 4.0 nm/% strain, respectively. The PDMS film was used as a vibration sensor at 50 Hz.

The initiation of adolescent smoking is difficult to detect using carbon monoxide or cotinine assays. Previously, we and others have shown that the methylation of cg05575921 is an accurate predictor of adult smoking status. But the dose and time dependency of the demethylation response to smoking initiation in adolescents is not yet well understood. To this end, we conducted three consecutive annual in-person interviews and biological samplings of 448 high school students (wave 1 (W1)-wave 3 (W3)). At W1 (n = 448), 62 subjects reported using tobacco and 72 subjects reported using cannabis at least once in their life-time with 38 and 20 subjects having a positive cotinine and cannabinoid levels, respectively, at W1 intake. At W3 (n = 383), 67 subjects reported using tobacco and 60 subjects reported using cannabis at least once with 75 and 60 subjects having positive cotinine and cannabinoid levels, respectively, at W3. Subjects with undetectable cotinine levels at all three-time waves had stable levels of cg05575921 methylation throughout the study (88.7% at W1 and 88.8% at W3, n = 149), while subjects with positive cotinine levels at all 3 time points manifested a steady decrease in cg05575921 methylation (81.8% at W1 and 71.3% at the W3, n = 12). In those subjects with an affirmative smoking self-report at W3 (n = 17), the amount of demethylation at cg05575921 was correlated with time and intensity of smoking. We conclude that cg05575921 methylation is a sensitive, dose-dependent indicator of early stages of smoking, and may help to identify smokers in the early stages of smoking.

Some reactions produce extremely hot nascent products which nevertheless can form sufficiently long-lived van der Waals (vdW) complexes-with atoms or molecules from a bath gas-as to be observed via microwave spectroscopy. Theoretical calculations of such unbound resonance states can be much more challenging than ordinary bound-state calculations depending on the approach employed. One encounters not just the floppy, and perhaps multiwelled potential energy surface (PES) characteristic of vdWs complexes, but in addition, one must contend with excitation of the intramolecular modes and its corresponding influence on the PES. Straightforward computation of the (resonance) rovibrational levels of interest, involves the added complication of the unbound nature of the wave function, often treated with techniques such as introducing a complex absorbing potential. Here, we have demonstrated that a simplified approach of making a series of vibrationally effective PESs for the intermolecular coordinates-one for each reaction product vibrational quantum number of interest-can produce vdW levels for the complex with spectroscopic accuracy. This requires constructing a series of appropriately weighted lower-dimensional PESs for which we use our freely available PES-fitting code AUTOSURF. The applications of this study are the Ar-CS and Ar-SiS complexes, which are isovalent to Ar-CO and Ar-SiO, the latter of which we considered in a previously reported study. Using a series of vibrationally effective PESs, rovibrational levels and predicted microwave transition frequencies for both complexes were computed variationally. A series of shifting rotational transition frequencies were also computed as a function of the diatom vibrational quantum number. The predicted transitions were used to guide and inform an experimental effort to make complementary observations. Comparisons are given for the transitions that are within the range of the spectrometer and were successfully recorded. Calculations of the rovibrational level pattern agree to within 0.2% with experimental measurements.

Random lasing properties were investigated with and without hexagonal boron nitride using rhodamine 6G doped film as the gain medium. Aluminum nitride nanocolumns as scatterers were introduced on top of the hBN layer. A lower threshold of 1.38 mJ/cm2 was achieved in samples containing hBN. Significantly higher threshold was observed when no hBN was present. Results suggest the potential of utilising hBN as an ultrathin flexible substrate for random lasing applications.

This study demonstrated the value of coagulation approaches to the control of species in coal seam gas (CSG) associated water which can result in scaling of downstream membranes and equipment. The hypothesis was that coagulation can be effective at removing turbidity causing species, alkaline earth ions and dissolved silicates from a CSG associated water compositions. Both simulated and real CSG associated water were treated using a jar tester and addition of either aluminium chlorohydrate (ACH), aluminium sulphate (alum) or ferric chloride. All coagulants reduced the turbidity (> 95 %) and also removed alkaline earth ions and dissolved silicates (ca. 29 % for calcium; 0 % for magnesium; 60 % for barium; 21 % for strontium; 33 % for silica). Formation of a muscovite-like material was predicted using AqMB process simulation software to be responsible for silicate removal and barium sulphate precipitated when alum was used. Increasing turbidity and salinity did not appear to exhibit a significant impact upon coagulant performance. Notably, the co-presence of solution turbidity and organic matter in real CSG associated water samples promoted coagulant performance (ca. 75 % for calcium; 30 % for magnesium; 75 % for barium; 50 % for strontium; 48 % for silica). This observation was ascribed to the promotion of polymeric Alb and colloidal Alc species which were more effective materials for water clarification (compared to monomeric Ala species). Coagulation strategies appear prospective for the pre-treatment of CSG associated water samples to minimize fouling of downstream equipment and membranes employed for desalination.

Photoinitiated reactions in van der Waals complexes provide a means to examine reactive pathways from well-defined initial geometries. In recent work, we re-examined reactive pathways following resonant two-photon ionization (R2PI) of the chlorobenzene-ammonia (PhCl⋯NH3) dimer. The dimer cation radical reacts primarily via Cl atom loss, and additional channels corresponding to HCl and H atom loss were identified. The structure of the reactive complex was confirmed as an in-plane σ-type, and computational studies of the dimer cation radical potential energy landscape revealed two nearly isoenergetic arenium ion intermediates (or Wheland intermediates). The intermediate produced from ipso addition was not stable with respect to either Cl or HCl loss, and the relative branching observed in experiment was well reproduced by microcanonical transition state theory (TST) calculations. Here, we report experimental and computational studies of the related PhBr⋯NH3 dimer, examined for the first time. We present evidence that the dimer structure is also an in-plane σ-type. However, in contrast to the PhCl⋯NH3 system, calculations predict that the structure of the reactive intermediate corresponds to a distonic ion-radical complex, where the radical density is largely localized on the bromine atom. The calculated barrier to HBr loss is sufficiently high to render this channel nearly insignificant (less than 1% branching) in TST calculations, yet experiment shows a sizable (37%) branching into this channel. We rationalize these results in terms of a roaming Br radical mechanism for HBr formation.

Recent studies indicate an important role for the transcriptional co-activator Yes-associated protein (YAP), and its regulatory pathway Hippo, in controlling cell growth and fate during lens development; however, the exogenous factors that promote this pathway are yet to be identified. Given that fibroblast growth factor (FGF)-signaling is an established regulator of lens cell behavior, the current study investigates the relationship between this pathway and Hippo/YAP-signaling during lens cell proliferation and fibre differentiation. Rat lens epithelial explants were cultured with FGF2 to induce epithelial cell proliferation or fibre differentiation. Immunolabeling methods were used to detect the expression of Hippo-signaling components, Total and Phosphorylated YAP, as well as fibre cell markers, Prox-1 and β-crystallin. FGF-induced lens cell proliferation was associated with a strong nuclear localisation of Total-YAP and low-level immuno-staining for phosphorylated-YAP. FGF-induced lens fibre differentiation was associated with a significant increase in cytoplasmic phosphorylated YAP (inactive state) and enhanced expression of core Hippo-signaling components. Inhibition of YAP with Verteporfin suppressed FGF-induced lens cell proliferation and ablated cell elongation during lens fibre differentiation. Inhibition of either FGFR- or MEK/ERK-signaling suppressed FGF-promoted YAP nuclear translocation. Here we propose that FGF promotes Hippo/YAP-signaling during lens cell proliferation and differentiation, with FGF-induced nuclear-YAP expression playing an essential role in promoting the proliferation of lens epithelial cells. An FGF-induced switch from proliferation to differentiation, hence regulation of lens growth, may play a key role in mediating Hippo suppression of YAP transcriptional activity.

The usage of Photosystem II (PS II)–inhibiting herbicides, identified as a risk to ecosystem health and resilience, has been reduced in agricultural activities adjacent to the Great Barrier Reef, Australia over the past 10 years. Two PS II herbicides (diuron and hexazinone) and three metabolites (desethyl atrazine, hydroxyatrazine and DCPMU) were recently detected at low concentrations in the regional aquifer of the South Johnstone River sub-basin, in the Wet Tropics, Australia. This study presents results from monitoring 12 PS II herbicides in soil profile, porewater sampled through the vadose zone monitoring system, and groundwater from bores. Among the 12 PS II herbicides, only hexazinone and metribuzin were applied relatively recently, in November 2014. Hexazinone exhibited substantial transport through the vadose zone, with decreasing concentration with depth, and eventually disappeared over-time. Metribuzin was not detected in the groundwater, in soil profile or through the vadose zone. Diuron was detected in the soil profile, through the vadose zone and in bores at the site. Its two metabolites—1-(3,4-dichlorophenyl)-3-methylurea (DCPMU) and 3,4-dichloroaniline—were detected in the deepest port at 4 m, indicating the transformation of diuron into these metabolites and potential leaching. The other nine PS II herbicides were not detected in the soil profile, through the vadose zone or in bores at the site. Some of the PS II herbicides were detected in the soil profile and beyond the root zone, depending on their application record and persistence in the environment. Therefore, the data shows that the herbicides are long lived at low concentrations. However, herbicide concentrations in subsoil, vadose zone and groundwater are low (less than environmental guideline values) and are detected at much lower concentrations than in surface runoff.

Electrochemical studies have been conducted at copper microelectrodes (125, 50, and 25 μm in diameter) immersed in aqueous 0.5 M NaCl. Cyclic and linear sweep voltammetry were used to explore the corrosion of copper in chloride media. Cyclic voltammetry revealed the reversible Cu(I)/Cu(0) potential at approximately −0.11 V vs. SCE associated with the formation of a dense CuCl blocking layer (confirmed by in situ Raman and fluorescence measurements). Although continuous dissolution of Cu(I) occurs, only an increase in the driving potential into the region of the Cu(II)/Cu(I) potential at approximately +0.14 V vs. SCE started more rapid and stochastic dissolution/corrosion processes. The corrosion process is demonstrated to be linked to two distinct mechanisms based on (A) slow molecular dissolution and (B) fast colloidal dissolution. A polymer of intrinsic microporosity (PIM-EA-TB) is employed to suppress colloidal processes to reveal the underlying molecular processes.

The groundwater in the dry climatic, agricultural regions of Sri Lanka has been a focus of research for more than two decades as a likely contributor to the epidemic chronic kidney disease that does not have an identified causality (CKDu). The intense agriculture that heavily depends on irrigation and excessive use of agrochemicals, as well as the increasing population that prompt over-extraction and sewage discharge presents increasing threats to these groundwaters. Particulate organic matter (POM), stable environmental isotopes (13C, 15N, 18O and 2H) together with hydrochemistry were used to determine the natural and anthropogenic sources of solutes, and their dynamics in these waters. Twenty nine domestic drinking water wells and spring were sampled from CKDu endemic Medawachchiya area during the dry season of 2018. POM of most waters were found to have aquatic origin resulted from biological processes that assimilate nutrients in groundwater. The isotopic compositions (18O and 15N) of nitrate provided evidence for anthropogenic nitrate inputs in some wells and denitrification of potentially anthropogenic nitrates in others. These waters were recharged locally and subjected to varying degrees of evaporation. The water–rock interactions, evaporation, and anthropogenic inputs significantly influence shallow drinking water quality in wells (

OBJECTIVES: Saliva contains biomarkers for systemic as well as oral diseases. This study was undertaken to assess the variability in the sources of such biomarkers (plasma, cells), and attempted to identify saliva deterioration markers in order to improve saliva diagnostic outcomes. MATERIALS AND METHODS: Inter- and intra-subject variation in salivary gingival crevicular fluid levels were determined by measuring salivary albumin and transferrin levels. The purity of collected glandular secretions was determined by bacterial culture, and the variability in epithelial cell numbers by cell counting and optical density measurement. Saliva sample deterioration markers were identified by RP-HPLC and LC-ESI-MS/MS. RESULTS: Ten-fold variations were observed in plasma-derived albumin and transferrin levels, emphasizing the need for biomarker normalization with respect to plasma contributions to saliva. Epithelial cell levels varied 50-fold in samples collected before and after a meal. Salivary fungal levels varied within subjects, and among subjects from 0 to >1,000 colony-forming units per milliliter. In saliva samples incubated for various time intervals at 37°C, five peptides were identified that steadily increased in intensity over time and which could be explored as “deterioration markers”. CONCLUSION: Taking saliva characteristics appropriately into account will help realize the promise that this body fluid is suitable to be exploited for reliable health care monitoring and surveillance.