Search

A series of computational laboratory experiments aimed at teaching students principles of rational drug design are described and evaluated. These experiments range from an introduction to viewing protein-ligand complexes to optimizing geometries of potential drugs with quantum chemistry and automated docking. Student feedback indicates that such a course increased their appreciation for the roles of chemists in the drug discovery-development process.

A multi-institution collaborative team of Australian chemistry education researchers, teaching a total of over 3000 first year chemistry students annually, has explored a tool for diagnosing students' prior conceptions as they enter tertiary chemistry courses. Five core topics were selected and clusters of diagnostic items were assembled linking related concepts in each topic together. An ordered multiple choice assessment strategy was adopted to enable provision of formative feedback to students through combination of the specific distractors that they chose. Concept items were either sourced from existing research instruments or developed by the project team. The outcome is a diagnostic tool consisting of five topic clusters of five concept items that has been delivered in large introductory chemistry classes at five Australian institutions. Statistical analysis of data has enabled exploration of the composition and validity of the instrument including a comparison between delivery of the complete 25 item instrument with subsets of five items, clustered by topic. This analysis revealed that most items retained their validity when delivered in small clusters. Tensions between the assembly, validation and delivery of diagnostic instruments for the purposes of acquiring robust psychometric research data versus their pragmatic use are considered in this study.

This project utilizes visual and critical thinking approaches to develop a higher-education synergistic prelab training program for a large second-year undergraduate analytical chemistry class, directing more of the cognitive learning to the prelab phase. This enabled students to engage in more analytical thinking prior to engaging in the analytical action in the laboratory, motivating students to arrive at classes prepared to engage in the material rather than the mechanics (physical processes) of the practical exercises. This reduced the likelihood of cognitive overload at the beginning of the class. Video demonstrations were developed providing both visual demonstrations with audio explanations to reinforce each concept, and students were guided to these through compulsory prelab e-quizzes. The effectiveness of the program was evaluated by academic performance and an attitudinal survey. Attitudes toward the prelab program were very positive, particularly for the e-quizzes. There was no improvement on academic performance in laboratory reports; however, students reported that the prelab material had a positive effect on their learning, and that they were able to enter the laboratory with high levels of perceived preparedness. Given that student experiences in the laboratory are arguably as important as assessable outcomes, an attitudinal study such as this is extremely important.

Isothermal titration calorimetry was used to experimentally determine thermodynamic values for the ethylenediaminetetraacetic acid (EDTA)(aq) + M[superscript 2+](aq) reactions (M[superscript 2+] = Ca[superscript 2+] and Mg[superscript 2+]). Students showed that for reactions in a N-(2-hydroxyethyl)piperazine-N"-ethanesulfonic acid (HEPES) buffer (pH = 7.4), the Mg[superscript 2+] + EDTA reaction was endothermic, while Ca[superscript 2+] binding to EDTA was exothermic. EDTA is triply ionized at pH 7.4 and therefore must shed a proton to the buffer prior to chelating the M[superscript 2+] ion; thus the observed reaction enthalpies are strongly dependent on pH and buffer ionization enthalpy.

One of the most difficult challenges of incorporating literacy in the classroom--as called for by the "Common Core State Standards" (NGAC and CCSSO 2010)--is inspiring reluctant writers. Students are often unmotivated by essay assignments or having to write answers to open-ended questions. Some students may even view these as obstacles instead of learning opportunities, which means they aren't gaining experience in the scientific and engineering practice of obtaining, evaluating, and communicating information, as described in the "Next Generation Science Standards" (NGSS Lead States 2013). To address this shortcoming in the science classroom, the author implemented an ambitious project in which he substituted creating digital movies for traditional literacy assessments in his sophomore chemistry classes. His goal was to answer these research questions: (1) To what extent does creating a movie motivate sophomore chemistry students to read and write?; (2) To what extent does movie creation foster creative critical thinking and expression?; and (3) To what extent is the evaluation process of movies more engaging than traditional writing assignments? The author tested this activity with 153 of his sophomore chemistry students, using various reading levels. In his honors class, students were assigned to read a chapter on cellulose from Napoleon's Buttons (Le Couteur and Burreson 2003), a fascinating book that explains how 17 molecules affected human history, health, economics, and geopolitics. The chapter on cellulose details how glucose monomers link in different ways to produce the polymers known as cellulose. Students learn how slight differences in structure result in cellulose polymers having different functions and how cellulose affected the industrial revolution. The chapter draws upon "NGSS" core ideas from physical science and the crosscutting concepts of Patterns.

Uses a software package to prepare students for an organic synthesis using the Horner-Wittig reaction and investigates the role of the software in student learning. (Author/YDS)

We previously reported on the interaction of 10-chloro-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one (10-Cl-BBQ) with the Aryl hydrocarbon Receptor (AhR) and selective growth inhibition in breast cancer cell lines. We now report on a library of BBQ analogues with substituents on the phenyl and naphthyl rings for biological screening. Herein, we show that absence of the phenyl Cl of 10-Cl-BBQ to produce the simple BBQ molecule substantially enhanced the growth inhibitory effect with GI50 values of 0.001–2.1 μM in select breast cancer cell lines MCF-7, T47D, ZR-75-1, SKBR3, MDA-MB-468, BT20, BT474 cells, while having modest effects of 2.1–7 μM in other cell lines including HT29, U87, SJ-G2, A2780, DU145, BE2-C, MIA, MDA-MB-231 or normal breast cells, MCF10A (3.2 μM). The most potent growth inhibitory effect of BBQ was observed in the triple negative cell line, MDA-MB-468 with a GI50 value of 0.001 μM, presenting a 3,200-fold greater response than in the normal MCF10A breast cells. Additions of Cl, CH3, CN to the phenyl ring and ring expansion from benzoimidazole to dihydroquinazoline hindered the growth inhibitory potency of the BBQ analogues by blocking potential sites of CYP1 oxidative metabolism, while addition of Cl or NO2 to the naphthyl rings restored potency. In a cell-based reporter assay all analogues induced 1.2 to 10-fold AhR transcription activation. Gene expression analysis confirmed the induction of CYP1 oxygenases by BBQ. The CYP1 inhibitor α-naphthoflavone, and the SULT1A1 inhibitor quercetin significantly reduced the growth inhibitory effect of BBQ, confirming the importance of both phase I and II metabolic activation for growth inhibition. Conventional molecular modelling/docking revealed no significant differences between the binding poses of the most and least active analogues. More detailed DFT analysis at the DSD-PBEP86/Def-TZVPP level of theory could not identify significant geometric or electronic changes which would account for this varied AhR activation. Generation of Fukui functions at the same level of theory showed that CYP1 metabolism will primarily occur at the phenyl head group of the analogues, and substituents within this ring lead to lower cytotoxicity.

Presents research and related design features that distinguish a new generation of teacher enhancement efforts along with the design and results of evaluation approaches for a specific program. (KHR)

Children with cerebral palsy (CP) exhibit head instability during simple overground walking, which may comprise sensory input and reduce stepping accuracy. Investigations of head stability during more challenging tasks, where fall risk may be increased, are limited. This study explored differences in head stability between ambulatory children with hemiplegic CP (N = 9) and diplegia (N = 9) (GMFCS I and II) and typically developing (TD) children (N = 8) during a targeted stepping task. All children completed five trials stepping into two successive rectangular floor-based targets whilst walking along an 8 m walkway. Three-dimensional motion capture enabled calculation of head stability and foot placement within and before each target. A two-way mixed-design ANOVA compared differences between all groups and target approach. Children with diplegic CP showed greater sagittal, frontal, and resultant head-to-laboratory and head-to-trunk head instability compared to children with hemiplegic CP and TD children. Anteroposterior foot placement error was significantly greater in children with hemiplegic CP (8.5 ± 5.0 cm) compared to TD children (3.8 ± 1.5 cm). Group differences in head instability were not consistent with group differences in foot placement error. To better understand how head instability might affect fall risk in children with CP, more challenging environments should be tested in future.

Apart from its well-established role in the initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remain largely unexplored. Using GRO-seq analyses, we compared the terminator readthrough phenotype in the sua7-1 mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains. Approximately 74% of genes analyzed exhibited a 2-3-fold increase in readthrough of the poly(A)-termination signal in the TFIIBsua7-1 mutant compared to TFIIBWT cells. To understand the mechanistic basis of TFIIB’s role in termination, we performed the mass spectrometry of TFIIB—affinity purified from chromatin and soluble cellular fractions—from TFIIBsua7-1 and TFIIBWT cells. TFIIB purified from the chromatin fraction of TFIIBWT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with CF1A and Rat1 complexes in the TFIIBsua7-1 mutant. ChIP assays revealed about a 90% decline in the recruitment of termination factors in the TFIIBsua7-1 mutant compared to wild type cells. The overall conclusion of these results is that TFIIB affects the termination of transcription on a genome-wide scale, and the TFIIB–termination factor interaction plays a crucial role in the process.

Glaucoma, a leading cause of blindness, is a multifactorial condition that leads to progressive loss of retinal ganglion cells (RGCs) and vision. Therapeutic interventions based on reducing ocular hypertension are not always successful. Emerging features of glaucoma include mitochondrial dysfunction and oxidative stress. In the current study, NDI1-based gene therapy, which improves mitochondrial function and reduces reactive oxygen species, was delivered intraocularly via an adeno-associated viral vector (AAV). This AAV-NDI1 therapy protected RGCs from cell death in treated (1552.4 ± 994.0 RGCs/mm2) versus control eyes (1184.4 ± 978.4 RGCs/mm2, p < 0.05) in aged DBA/2J mice, a murine model of glaucoma. The photonegative responses (PhNRs) of RGCs were also improved in treated (6.4 ± 3.3 µV) versus control eyes (5.0 ± 3.1 µV, p < 0.05) in these mice. AAV-NDI1 also provided benefits in glaucomatous human lamina cribrosa (LC) cells by significantly increasing basal and maximal oxygen consumption rates and ATP production in these cells. Similarly, NDI1 therapy significantly protected H2O2-insulted primary porcine LC cells from oxidative stress. This study highlights the potential utility of NDI1 therapies and the benefits of improving mitochondrial function in the treatment of glaucoma.

Despite their significant impact, comprehensive screenings and detailed analyses of per- and polyfluoroalkyl substance (PFAS) binding strengths at the orthosteric and allosteric sites of NRs are currently lacking. This study addresses this gap by focusing on the binding interaction analysis of both common and uncommon PFAS with the nuclear receptors (NRs) vitamin D receptor (VDR), peroxisome proliferator-activated receptor gamma (PPARγ), pregnane X receptor (PXR), and estrogen receptor alpha (ERα). Advanced docking simulations were used to screen 9507 PFAS chemicals at the orthosteric and allosteric sites of PPARγ, PXR, VDR, and ERα. All receptors exhibited strong binding interactions at the orthosteric and allosteric site with a significant number of PFAS. We verified the accuracy of the docking protocol through multiple docking controls and validations. A mixture modeling analysis indicates that PFAS can bind in various combinations with themselves and endogenous ligands simultaneously, to disrupt the endocrine system and cause carcinogenic responses. These findings reveal that PFAS can interfere with nuclear receptor activity by displacing endogenous or native ligands by binding to the orthosteric and allosteric sites. The purpose of this study is to explore the mechanisms through which PFAS exert their endocrine-disrupting effects, potentially leading to more targeted therapeutic strategies. Importantly, this study is the first to explore the binding of PFAS at allosteric sites and to model PFAS mixtures at nuclear receptors. Given the high concentration and persistence of PFAS in humans, this study further emphasizes the urgent need for further research into the carcinogenic mechanisms of PFAS and the development of therapeutic strategies that target nuclear receptors.

Immunosuppressive treatment in patients with rheumatic diseases can maintain disease remission but also increase risk of infection. Their response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is frequently blunted. In this study we evaluated the effect of immunosuppression exposure on humoral and T cell immune responses to SARS-CoV-2 infection and vaccination in two distinct cohorts of patients; one during acute SARS-CoV-2 infection and 3 months later during convalescence, and another prior to SARS-CoV-2 vaccination, with follow up sampling 6 weeks after vaccination. Results were compared between rituximab-exposed (in previous 6 months), immunosuppression-exposed (in previous 3 months), and non-immunosuppressed groups. The immune cell phenotype was defined by flow cytometry and ELISA. Antigen specific T cell responses were estimated using a whole blood stimulation interferon-γ release assay. A focused post-vaccine assessment of rituximab-treated patients using high dimensional spectral cytometry was conducted. Acute SARS-CoV-2 infection was characterised by T cell lymphopenia, and a reduction in NK cells and naïve CD4 and CD8 cells, without any significant differences between immunosuppressed and non-immunosuppressed patient groups. Conversely, activated CD4 and CD8 cell counts increased in non-immunosuppressed patients with acute SARS-CoV-2 infection but this response was blunted in the presence of immunosuppression. In rituximab-treated patients, antigen-specific T cell responses were preserved in SARS-CoV-2 vaccination, but patients were unable to mount an appropriate humoral response.

Understanding the relationships between porous transport layer (PTL) morphology and oxygen removal is essential to improve the polymer electrolyte water electrolyzer (PEWE) performance. Operando X-ray computed tomography and machine learning were performed on a model electrolyzer at different water flow rates and current densities to determine how these operating conditions alter oxygen transport in the PTLs. We report a direct observation of oxygen taking preferential pathways through the PTL, regardless of the water flow rate or current density (1-4 A/cm2). Oxygen distribution in the PTL had a periodic behavior with period of 400 μm. A computational fluid dynamics model was used to predict oxygen distribution in the PTL showing periodic oxygen front. Observed oxygen distribution is due to low in-plane PTL tortuosity and high porosity enabling merging of oxygen bubbles in the middle of the PTL and also due to aerophobicity of the layer.

Secondary organic aerosol (SOA) generated from the photooxidation of aromatic compounds in the presence of oxides of nitrogen (NOx) is known to efficiently absorb ultraviolet and visible radiation. With exposure to sunlight, the photodegradation of chromophoric compounds in the SOA causes this type of SOA to slowly photobleach. These photodegradation reactions may occur in cloud droplets, which are characterized by low concentrations of solutes, or in aerosol particles, which can have highly viscous organic phases and aqueous phases with high concentrations of inorganic salts. To investigate the effects of the surrounding matrix on the rates and mechanisms of photodegradation of SOA compounds, SOA was prepared in a smog chamber by photooxidation of toluene in the presence of NOx. The collected SOA was photolyzed for up to 24 h using near-UV radiation (300–400 nm) from a xenon arc lamp under different conditions: directly on the filter, dissolved in pure water, and dissolved in 1 M ammonium sulfate. The SOA mass absorption coefficient was measured as a function of irradiation time to determine photobleaching rates. Electrospray ionization high-resolution mass spectrometry coupled to liquid chromatography separation was used to observe changes in SOA composition resulting from the irradiation. The rate of decrease in SOA mass absorption coefficient due to photobleaching was the fastest in water, with the presence of 1 M ammonium sulfate modestly slowing down the photobleaching. By contrast, photobleaching directly on the filter was slower. The high-resolution mass spectrometry analysis revealed an efficient photodegradation of nitrophenol compounds on the filter but not in the aqueous phases, with relatively little change observed in the composition of the SOA irradiated in water or 1 M ammonium sulfate despite faster photobleaching than in the on-filter samples. This suggests that photodegradation of nitrophenols contributes much more significantly to photobleaching in the organic phase than in the aqueous phase. We conclude that the SOA absorption coefficient lifetime with respect to photobleaching and lifetimes of individual chromophores in SOA with respect to photodegradation will depend strongly on the sample matrix in which SOA compounds are exposed to sunlight.

Glaucoma is the leading cause of irreversible blindness, and its pathophysiology includes neuroinflammatory changes. The present therapies for glaucoma target pressure-lowering mechanisms with limited success, making neuroinflammation a target for future interventions. This review summarizes the neuroinflammatory pathways seen in glaucoma and their interplay with stress. Glucocorticoids have been shown to activate proinflammatory glial cells, contributing to the neuroinflammation in glaucoma. Glucocorticoids have also been shown to increase the IOP directly. Stress-associated autonomic dysfunction can affect the vascular homeostasis in the retina and create oxidative stress. Diabetes, hyperglycemic-mediated endothelial damage, and vascular inflammation also play important roles in the neuroinflammation in glaucoma and diabetic retinopathy. Psychosocial stress has been implicated in an increased IOP and glaucoma outcomes. People who experience maladaptive chronic stress suffer from a condition known as allostatic load, which describes pathologic neuroendocrine dysregulation. The effects of allostatic load and chronic stress have been studied in patients affected by a lower socioeconomic status (SES) and marginalized racial identities. A lower SES is associated with higher rates of glaucoma and also affects the access to care and screening. Additionally, people of African ancestry are disproportionately affected by glaucoma for reasons that are multifactorial. In conclusion, this review explores neuroinflammation in glaucoma, highlighting opportunities for future investigation.

Cancer and ionizing radiation exposure are associated with inflammation. To identify a set of radiation-specific signatures of inflammation-associated genes in the blood of partially exposed radiotherapy patients, differential expression of 249 inflammatory genes was analyzed in blood samples from cancer patients and healthy individuals. The gene expression analysis on a cohort of 63 cancer patients (endometrial, head and neck, and prostate cancer) before and during radiotherapy (24 h, 48 h, ~1 week, ~4–8 weeks, and 1 month after the last fraction) identified 31 genes and 15 up- and 16 down-regulated genes. Transcription variability under normal conditions was determined using blood drawn on three separate occasions from four healthy donors. No difference in inflammatory expression between healthy donors and cancer patients could be detected prior to radiotherapy. Remarkably, repeated sampling of healthy donors revealed an individual endogenous inflammatory signature. Next, the potential confounding effect of concomitant inflammation was studied in the blood of seven healthy donors taken before and 24 h after a flu vaccine or ex vivo LPS (lipopolysaccharide) treatment; flu vaccination was not detected at the transcriptional level and LPS did not have any effect on the radiation-induced signature identified. Finally, we identified a radiation-specific signature of 31 genes in the blood of radiotherapy patients that were common for all cancers, regardless of the immune status of patients. Confirmation via MQRT-PCR was obtained for BCL6, MYD88, MYC, IL7, CCR4 and CCR7. This study offers the foundation for future research on biomarkers of radiation exposure, radiation sensitivity, and radiation toxicity for personalized radiotherapy treatment.

Up to 50% of patients with severe congenital heart disease (CHD) develop life-altering neurodevelopmental disability (NDD). It has been presumed that NDD arises in CHD cases because of hypoxia before, during, or after cardiac surgery. Recent studies detected an enrichment in de novo mutations in CHD and NDD, as well as significant overlap between CHD and NDD candidate genes. However, there is limited evidence demonstrating that genes causing CHD can produce NDD independent of hypoxia. A patient with hypoplastic left heart syndrome and gross motor delay presented with a de novo mutation in SMC5. Modeling mutation of smc5 in Xenopus tropicalis embryos resulted in reduced heart size, decreased brain length, and disrupted pax6 patterning. To evaluate the cardiac development, we induced the conditional knockout (cKO) of Smc5 in mouse cardiomyocytes, which led to the depletion of mature cardiomyocytes and abnormal contractility. To test a role for Smc5 specifically in the brain, we induced cKO in the mouse central nervous system, which resulted in decreased brain volume, and diminished connectivity between areas related to motor function but did not affect vascular or brain ventricular volume. We propose that genetic factors, rather than hypoxia alone, can contribute when NDD and CHD cases occur concurrently.

Assesses an evaluation model, employing an objectives rating system and a two-dimensional matrix to display the ratings, which was applied to 145 behavioral course objectives for a general chemistry course at Northern Virginia Community College to judge the appropriateness and adequacy of the course objectives. (AYC)

Aerosol–cloud–precipitation interactions (ACIs) provide the greatest source of uncertainties in predicting changes in Earth's energy budget due to poor representation of marine stratocumulus and the associated ACIs in climate models. Using in situ data from 329 cloud profiles across 24 research flights from the NASA ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES) field campaign in September 2016, August 2017, and October 2018, it is shown that contact between above-cloud biomass burning aerosols and marine stratocumulus over the Southeast Atlantic Ocean was associated with precipitation suppression and a decrease in the precipitation susceptibility (So) to aerosols. The 173 “contact” profiles with aerosol concentration (Na) greater than 500 cm−3 within 100 m above cloud tops had a 50 % lower precipitation rate (Rp) and a 20 % lower So, on average, compared to 156 “separated” profiles with Na less than 500 cm−3 up to at least 100 m above cloud tops. Contact and separated profiles had statistically significant differences in droplet concentration (Nc) and effective radius (Re) (95 % confidence intervals from a two-sample t test are reported). Contact profiles had 84 to 90 cm−3 higher Nc and 1.4 to 1.6 µm lower Re compared to separated profiles. In clean boundary layers (below-cloud Na less than 350 cm−3), contact profiles had 25 to 31 cm−3 higher Nc and 0.2 to 0.5 µm lower Re. In polluted boundary layers (below-cloud Na exceeding 350 cm−3), contact profiles had 98 to 108 cm−3 higher Nc and 1.6 to 1.8 µm lower Re. On the other hand, contact and separated profiles had statistically insignificant differences between the average liquid water path, cloud thickness, and meteorological parameters like surface temperature, lower tropospheric stability, and estimated inversion strength. These results suggest the changes in cloud microphysical properties were driven by ACIs rather than meteorological effects, and adjustments to existing relationships between Rp and Nc in model parameterizations should be considered to account for the role of ACIs.

This Classroom Activity Connections paper describes an extension to the "JCE" Classroom Activity #68 "Turning on the Light". A number of additional common items that display fluorescence under UV light are described, including fruits, vegetables, and seashells. Two classroom extensions on fluorescence are also described. From these activities, students should be able to: (i) understand how fluorescence works and (ii) develop an appreciation of the fact that many everyday items can exhibit fluorescence. (Contains 1 figure.)

Describes laboratory-oriented software programs that are short, time-saving, eliminate computational errors, and not found in public domain courseware. Program availability for IBM and Apple microcomputers is included. (RT)

We are exploring a simplified electrochemically mediated atom transfer radical polymerization method (se-ATRP), allowing us to create new carbon-grafted polymer assemblies with improved charge storage capabilities. These molecularly imprinted conjugations serve as an active component of a supercapacitor electrode that displayed a capacitance value 46.5% larger than that of pure polypyrrole and seemed to double the stability at select voltages. Furthermore, after more than 5000 charge/discharge cycles, 98.97% of the capacitance was retained. This capacitance enhancement is owned to the morphology the polymer represented by nano-ribbons and nanoparticles that are evenly wrapped around carbon nanotubes. This favours charge transfer associate with redox activity of the polymer during electrode’s charge–discharge life cycle. Moreover, carbon demonstrates dual functionality as a charge transport facilitator at first, and also as the stabilizing backbone for the polymer. The later results in improved lifetime of the electrode upon applied potential, which is always the most sought-after feature of polymer-based energy materials.

The southeastern Atlantic (SEA) and its associated cloud deck, off the west coast of central Africa, is an area where aerosol–cloud interactions can have a strong radiative impact. Seasonally, extensive biomass burning (BB) aerosol plumes from southern Africa reach this area. The NASA ObseRvations of Aerosols above CLouds and their intEractionS (ORACLES) study focused on quantitatively understanding these interactions and their importance. Here we present measurements of cloud condensation nuclei (CCN) concentration, aerosol size distribution, and characteristic vertical updraft velocity (w∗) in and around the marine boundary layer (MBL) collected by the NASA P-3B aircraft during the August 2017 ORACLES deployment. BB aerosol levels vary considerably but systematically with time; high aerosol concentrations were observed in the MBL (800–1000 cm−3) early on, decreasing midcampaign to concentrations between 500 and 800 cm−3. By late August and early September, relatively clean MBL conditions were sampled ( cm−3). These data then drive a state-of-the-art droplet formation parameterization from which the predicted cloud droplet number and its sensitivity to aerosol and dynamical parameters are derived. Droplet closure was achieved to within 20 %. Droplet formation sensitivity to aerosol concentration, w∗, and the hygroscopicity parameter, κ, vary and contribute to the total droplet response in the MBL clouds. When aerosol concentrations exceed ∼900 cm−3 and maximum supersaturation approaches 0.1 %, droplet formation in the MBL enters a velocity-limited droplet activation regime, where the cloud droplet number responds weakly to CCN concentration increases. Below ∼500 cm−3, in a clean MBL, droplet formation is much more sensitive to changes in aerosol concentration than to changes in vertical updraft. In the competitive regime, where the MBL has intermediate pollution (500–800 cm−3), droplet formation becomes much more sensitive to hygroscopicity (κ) variations than it does in clean and polluted conditions. Higher concentrations increase the sensitivity to vertical velocity by more than 10-fold. We also find that characteristic vertical velocity plays a very important role in driving droplet formation in a more polluted MBL regime, in which even a small shift in w∗ may make a significant difference in droplet concentrations. Identifying regimes where droplet number variability is driven primarily by updraft velocity and not by aerosol concentration is key for interpreting aerosol indirect effects, especially with remote sensing. The droplet number responds proportionally to changes in characteristic velocity, offering the possibility of remote sensing of w∗ under velocity-limited conditions.

Antimicrobial peptides (AMPs) are found in nearly all living organisms, show broad spectrum antibacterial activity, and can modulate the immune system. Furthermore, they have a very low level of resistance induction in bacteria, which makes them an ideal target for drug development and for targeting multi-drug resistant bacteria ‘Superbugs’. Despite this promise, AMP therapeutic use is hampered as typically they are toxic to mammalian cells, less active under physiological conditions and are susceptible to proteolytic degradation. Research has focused on addressing these limitations by modifying natural AMP sequences by including e.g., d-amino acids and N-terminal and amino acid side chain modifications to alter structure, hydrophobicity, amphipathicity, and charge of the AMP to improve antimicrobial activity and specificity and at the same time reduce mammalian cell toxicity. Recently, multimerisation (dimers, oligomer conjugates, dendrimers, polymers and self-assembly) of natural and modified AMPs has further been used to address these limitations and has created compounds that have improved activity and biocompatibility compared to their linear counterparts. This review investigates how modifying and multimerising AMPs impacts their activity against bacteria in planktonic and biofilm states of growth.

Trace amine-associated receptor 5 (TAAR5) is a G protein-coupled receptor that belongs to the TAARs family (TAAR1-TAAR9). TAAR5 is expressed in the olfactory epithelium and is responsible for sensing 3-methylamine (TMA). However, recent studies showed that TAAR5 is also expressed in the limbic brain regions and is involved in the regulation of emotional behaviour and adult neurogenesis, suggesting that TAAR5 antagonism may represent a novel therapeutic strategy for anxiety and depression. We used the AtomNet® model, the first deep learning neural network for structure-based drug discovery, to identify putative TAAR5 ligands and tested them in an in vitro BRET assay. We found two mTAAR5 antagonists with low to submicromolar activity that are able to inhibit the cAMP production induced by TMA. Moreover, these two compounds also inhibited the mTAAR5 downstream signalling, such as the phosphorylation of CREB and ERK. These two hits exhibit drug-like properties and could be used to further develop more potent TAAR5 ligands with putative anxiolytic and antidepressant activity.

Dementia is a global medical and societal challenge; it has devastating personal, social and economic costs, which will increase rapidly as the world’s population ages. Despite this, there are no disease-modifying treatments for dementia; current therapy modestly improves symptoms but does not change the outcome. Therefore, new treatments are urgently needed—particularly any that can slow down the disease’s progression. Many of the neurodegenerative diseases that lead to dementia are characterised by common pathological responses to abnormal protein production and misfolding in brain cells, raising the possibility of the broad application of therapeutics that target these common processes. The unfolded protein response (UPR) is one such mechanism. The UPR is a highly conserved cellular stress response to abnormal protein folding and is widely dysregulated in neurodegenerative diseases. In this review, we describe the basic machinery of the UPR, as well as the evidence for its overactivation and pathogenicity in dementia, and for the marked neuroprotective effects of its therapeutic manipulation in murine models of these disorders. We discuss drugs identified as potential UPR-modifying therapeutic agents—in particular the licensed antidepressant trazodone—and we review epidemiological and trial data from their use in human populations. Finally, we explore future directions for investigating the potential benefit of using trazodone or similar UPR-modulating compounds for disease modification in patients with dementia.

Alpha-1 antitrypsin (AAT) is the canonical serine protease inhibitor of neutrophil-derived proteases and can modulate innate immune mechanisms through its anti-inflammatory activities mediated by a broad spectrum of protein, cytokine, and cell surface interactions. AAT contains a reactive methionine residue that is critical for its protease-specific binding capacity, whereby AAT entraps the protease on cleavage of its reactive centre loop, neutralises its activity by key changes in its tertiary structure, and permits removal of the AAT-protease complex from the circulation. Recently, however, the immunomodulatory role of AAT has come increasingly to the fore with several prominent studies focused on lipid or protein-protein interactions that are predominantly mediated through electrostatic, glycan, or hydrophobic potential binding sites. The aim of this review was to investigate the spectrum of AAT molecular interactions, with newer studies supporting a potential therapeutic paradigm for AAT augmentation therapy in disorders in which a chronic immune response is strongly linked.

Non-viral gene delivery has become a popular approach in tissue engineering, as it permits the transient delivery of a therapeutic gene, in order to stimulate tissue repair. However, the efficacy of non-viral delivery vectors remains an issue. Our lab has created gene-activated scaffolds by incorporating various non-viral delivery vectors, including the glycosaminoglycan-binding enhanced transduction (GET) peptide into collagen-based scaffolds with proven osteogenic potential. A modification to the GET peptide (FLR) by substitution of arginine residues with histidine (FLH) has been designed to enhance plasmid DNA (pDNA) delivery. In this study, we complexed pDNA with combinations of FLR and FLH peptides, termed GET* nanoparticles. We sought to enhance our gene-activated scaffold platform by incorporating GET* nanoparticles into collagen–nanohydroxyapatite scaffolds with proven osteogenic capacity. GET* N/P 8 was shown to be the most effective formulation for delivery to MSCs in 2D. Furthermore, GET* N/P 8 nanoparticles incorporated into collagen–nanohydroxyapatite (coll–nHA) scaffolds at a 1:1 ratio of collagen:nanohydroxyapatite was shown to be the optimal gene-activated scaffold. pDNA encoding stromal-derived factor 1α (pSDF-1α), an angiogenic chemokine which plays a role in BMP mediated differentiation of MSCs, was then delivered to MSCs using our optimised gene-activated scaffold platform, with the aim of significantly increasing angiogenesis as an important precursor to bone repair. The GET* N/P 8 coll–nHA scaffolds successfully delivered pSDF-1α to MSCs, resulting in a significant, sustained increase in SDF-1α protein production and an enhanced angiogenic effect, a key precursor in the early stages of bone repair.

Iron (Fe) homeostasis in plants is governed by a complex network of regulatory elements and transcription factors (TFs), as both Fe toxicity and deficiency negatively impact plant growth and physiology. The Fe homeostasis network is well characterized in Arabidopsis thaliana and remains poorly understood in monocotyledon species such as rice (Oryza sativa L.). Recent investigation of the rice Fe homeostasis network revealed OsIRO3, a basic Helix–Loop–Helix (bHLH) TF as a putative negative regulator of genes involved in Fe uptake, transport, and storage. We employed CRISPR-Cas9 gene editing to target the OsIRO3 coding sequence and generate two independent T-DNA-free, loss-of-function iro3 mutants in rice cv. Nipponbare. The iro3 mutant plants had similar phenotype under nutrient-sufficient conditions and had stunted growth under Fe-deficient conditions, relative to a T-DNA free, wild-type control (WT). Under Fe deficiency, iro3 mutant shoots had reduced expression of Fe chelator biosynthetic genes (OsNAS1, OsNAS2, and OsNAAT1) and upregulated expression of an Fe transporter gene (OsYSL15), relative to WT shoots. We place our results in the context of the existing literature and generate a model describing the role of OsIRO3 in rice Fe homeostasis and reinforce the essential function of OsIRO3 in the rice Fe deficiency response.

Aircraft-based measurements of methane (CH4) and other air pollutants in the Athabasca Oil Sands Region (AOSR) were made during a summer intensive field campaign between 13 August and 7 September 2013 in support of the Joint Canada–Alberta Implementation Plan for Oil Sands Monitoring. Chemical signatures were used to identify CH4 sources from tailings ponds (BTEX VOCs), open pit surface mines (NOy and rBC) and elevated plumes from bitumen upgrading facilities (SO2 and NOy). Emission rates of CH4 were determined for the five primary surface mining facilities in the region using two mass-balance methods. Emission rates from source categories within each facility were estimated when plumes from the sources were spatially separable. Tailings ponds accounted for 45 % of total CH4 emissions measured from the major surface mining facilities in the region, while emissions from operations in the open pit mines accounted for ∼ 50 %. The average open pit surface mining emission rates ranged from 1.2 to 2.8 t of CH4 h−1 for different facilities in the AOSR. Amongst the 19 tailings ponds, Mildred Lake Settling Basin, the oldest pond in the region, was found to be responsible for the majority of tailings ponds emissions of CH4 ( > 70 %). The sum of measured emission rates of CH4 from the five major facilities, 19.2 ± 1.1 t CH4 h−1, was similar to a single mass-balance determination of CH4 from all major sources in the AOSR determined from a single flight downwind of the facilities, 23.7 ± 3.7 t CH4 h−1. The measured hourly CH4 emission rate from all facilities in the AOSR is 48 ± 8 % higher than that extracted for 2013 from the Canadian Greenhouse Gas Reporting Program, a legislated facility-reported emissions inventory, converted to hourly units. The measured emissions correspond to an emissions rate of 0.17 ± 0.01 Tg CH4 yr−1 if the emissions are assumed as temporally constant, which is an uncertain assumption. The emission rates reported here are relevant for the summer season. In the future, effort should be devoted to measurements in different seasons to further our understanding of the seasonal parameters impacting fugitive emissions of CH4 and to allow for better estimates of annual emissions and year-to-year variability.

TiS2 oxidation: moisture is the critical element preventing environmental stability The degradation dynamics of TiS2 reveal that the flakes oxidise in water and atmosphere, pointing towards moisture as the key driving force. A team led by Valeria Nicolosi at Trinity College Dublin used advanced electron microscopy techniques to investigate the influence of different environments on the deterioration pathways of TiS2, a promising candidate for future energy storage applications. By comparing the effect of ex-situ oxidation by water and oxygen at room temperature, and in-situ oxidation at high temperatures, water was proven to effectively oxidise the TiS2 flakes from the edges thereby forming an amorphous oxide phase. Conversely, the degradation was found to proceed more slowly in atmosphere or vacuum conditions. These results suggest that TiS2 oxidation could be avoided in a desiccated environment that would prevent water molecules from dissociating in reactive ionic species.

Organic acids are known to be emitted from combustion processes and are key photochemical products of biogenic and anthropogenic precursors. Despite their multiple environmental impacts, such as on acid deposition and human–ecosystem health, little is known regarding their emission magnitudes or detailed chemical formation mechanisms. In the current work, airborne measurements of 18 gas-phase low-molecular-weight organic acids were made in the summer of 2013 over the oil sands region of Alberta, Canada, an area of intense unconventional oil extraction. The data from these measurements were used in conjunction with emission retrieval algorithms to derive the total and speciated primary organic acid emission rates, as well as secondary formation rates downwind of oil sands operations. The results of the analysis indicate that approximately 12 t day−1 of low-molecular-weight organic acids, dominated by C1–C5 acids, were emitted directly from off-road diesel vehicles within open pit mines. Although there are no specific reporting requirements for primary organic acids, the measured emissions were similar in magnitude to primary oxygenated hydrocarbon emissions, for which there are reporting thresholds, measured previously ( ≈ 20 t day−1). Conversely, photochemical production of gaseous organic acids significantly exceeded the primary sources, with formation rates of up to ≈ 184 t day−1 downwind of the oil sands facilities. The formation and evolution of organic acids from a Lagrangian flight were modelled with a box model, incorporating a detailed hydrocarbon reaction mechanism extracted from the Master Chemical Mechanism (v3.3). Despite evidence of significant secondary organic acid formation, the explicit chemical box model largely underestimated their formation in the oil sands plumes, accounting for 39, 46, 26, and 23 % of the measured formic, acetic, acrylic, and propionic acids respectively and with little contributions from biogenic VOC precursors. The model results, together with an examination of the carbon mass balance between the organic acids formed and the primary VOCs emitted from oil sands operations, suggest the existence of significant missing secondary sources and precursor emissions related to oil sands and/or an incomplete mechanistic and quantitative understanding of how they are processed in the atmosphere.

The occurrence of nonliquid and liquid physical states of submicron atmospheric particulate matter (PM) downwind of an urban region in central Amazonia was investigated. Measurements were conducted during two intensive operating periods (IOP1 and IOP2) that took place during the wet and dry seasons of the GoAmazon2014/5 campaign. Air masses representing variable influences of background conditions, urban pollution, and regional- and continental-scale biomass burning passed over the research site. As the air masses varied, particle rebound fraction, an indicator of physical state, was measured in real time at ground level using an impactor apparatus. Micrographs collected by transmission electron microscopy confirmed that liquid particles adhered, while nonliquid particles rebounded. Relative humidity (RH) was scanned to collect rebound curves. When the apparatus RH matched ambient RH, 95 % of the particles adhered as a campaign average. Secondary organic material, produced for the most part by the oxidation of volatile organic compounds emitted from the forest, produces liquid PM over this tropical forest. During periods of anthropogenic influence, by comparison, the rebound fraction dropped to as low as 60 % at 95 % RH. Analyses of the mass spectra of the atmospheric PM by positive-matrix factorization (PMF) and of concentrations of carbon monoxide, total particle number, and oxides of nitrogen were used to identify time periods affected by anthropogenic influences, including both urban pollution and biomass burning. The occurrence of nonliquid PM at high RH correlated with these indicators of anthropogenic influence. A linear model having as output the rebound fraction and as input the PMF factor loadings explained up to 70 % of the variance in the observed rebound fractions. Anthropogenic influences can contribute to the presence of nonliquid PM in the atmospheric particle population through the combined effects of molecular species that increase viscosity when internally mixed with background PM and increased concentrations of nonliquid anthropogenic particles in external mixtures of anthropogenic and biogenic PM.

The field of silicon photonics has experienced widespread adoption in the datacoms industry over the past decade, with a plethora of other applications emerging more recently such as light detection and ranging (LIDAR), sensing, quantum photonics, programmable photonics and artificial intelligence. As a result of this, many commercial complementary metal oxide semiconductor (CMOS) foundries have developed open access silicon photonics process lines, enabling the mass production of silicon photonics systems. On the other side of the spectrum, several research labs, typically within universities, have opened up their facilities for small scale prototyping, commonly exploiting e-beam lithography for wafer patterning. Within this ecosystem, there remains a challenge for early stage researchers to progress their novel and innovate designs from the research lab to the commercial foundries because of the lack of compatibility of the processing technologies (e-beam lithography is not an industry tool). The CORNERSTONE rapid-prototyping capability bridges this gap between research and industry by providing a rapid prototyping fabrication line based on deep-UV lithography to enable seamless scaling up of production volumes, whilst also retaining the ability for device level innovation, crucial for researchers, by offering flexibility in its process flows. This review article presents a summary of the current CORNERSTONE capabilities and an outlook for the future.

Liver disease and disorders associated with aberrant hepatocyte metabolism can be initiated via drug and environmental toxicant exposures. In this study, we tested the hypothesis that gene and metabolic profiling can reveal commonalities in liver response to different toxicants and provide the capability to identify early signatures of acute liver toxicity. We used Sprague Dawley rats and three classical hepatotoxicants: acetaminophen (2 g/kg), bromobenzene (0.4 g/kg), and carbon tetrachloride (0.3 g/kg), to identify early perturbations in liver metabolism after a single acute exposure dose. We measured changes in liver genes and plasma metabolites at two time points (5 and 10 h) and used genome-scale metabolic models to identify commonalities in liver responses across the three toxicants. We found strong correlations for gene and metabolic profiles between the toxicants, indicative of similarities in the liver response to toxicity. We identified several injury-specific pathways in lipid and amino acid metabolism that changed similarly across the three toxicants. Our findings suggest that several plasma metabolites in lipid and amino acid metabolism are strongly associated with the progression of liver toxicity, and as such, could be targeted and clinically assessed for their potential as early predictors of acute liver toxicity.

Preparation of cis and trans isomers of the kinetically labile bis glycinato copper (II) has a number of advantages including its facility, economy, ready theoretical interpretation, and biological relevance. Background information, laboratory procedures, results/discussion are provided for this experiment which can be completed in a single, three- to four-hour laboratory session. (Author/JN)