Phenome-wide identification of therapeutic genetic targets, leveraging knowledge graphs, graph neural networks, and UK Biobank data.

The ongoing expansion of human genomic datasets propels therapeutic target identification; however, extracting gene-disease associations from gene annotations remains challenging. Here, we introduce Mantis-ML 2.0, a framework integrating AstraZeneca's Biological Insights Knowledge Graph and numerous tabular datasets, to assess gene-disease probabilities throughout the phenome. We use graph neural networks, capturing the graph's holistic structure, and train them on hundreds of balanced datasets via a robust semi-supervised learning framework to provide gene-disease probabilities across the human exome. Mantis-ML 2.0 incorporates natural language processing to automate disease-relevant feature selection for thousands of diseases. The enhanced models demonstrate a 6.9% average classification power boost, achieving a median receiver operating characteristic (ROC) area under curve (AUC) score of 0.90 across 5220 diseases from Human Phenotype Ontology, OpenTargets, and Genomics England. Notably, Mantis-ML 2.0 prioritizes associations from an independent UK Biobank phenome-wide association study (PheWAS), providing a stronger form of triaging and mitigating against underpowered PheWAS associations. Results are exposed through an interactive web resource.

Bending the Curve of Global Freshwater Biodiversity Loss: An Emergency Recovery Plan.

Despite their limited spatial extent, freshwater ecosystems host remarkable biodiversity, including one-third of all vertebrate species. This biodiversity is declining dramatically: Globally, wetlands are vanishing three times faster than forests, and freshwater vertebrate populations have fallen more than twice as steeply as terrestrial or marine populations. Threats to freshwater biodiversity are well documented but coordinated action to reverse the decline is lacking. We present an Emergency Recovery Plan to bend the curve of freshwater biodiversity loss. Priority actions include accelerating implementation of environmental flows; improving water quality; protecting and restoring critical habitats; managing the exploitation of freshwater ecosystem resources, especially species and riverine aggregates; preventing and controlling nonnative species invasions; and safeguarding and restoring river connectivity. We recommend adjustments to targets and indicators for the Convention on Biological Diversity and the Sustainable Development Goals and roles for national and international state and nonstate actors.

The effects of ionic liquids on azide-alkyne cycloaddition reactions.

The effect of a series of ionic liquids on the regioselectivity of the azide-alkyne cycloaddition process was investigated, demonstrating an increased selectivity for the least hindered triazole. The effects of an ionic liquid on the activation parameters for the process were determined and found to be intermediate between coordinating and non-coordinating salts. The importance of knowing the water content of the system is demonstrated by marked changes in the activation parameters in the presence of small concentrations of water.

The role of Nrf2 in ultraviolet A mediated heme oxygenase 1 induction in human skin fibroblasts.

Ultraviolet-A (UVA, 320-380 nm) radiation is an oxidative stress that strongly induces heme oxygenase 1 (HO-1) expression in cultured human primary skin fibroblasts (FEK4). In this study, we show that NF-E2-related factor 2 (Nrf2) protein accumulates and HO-1 is strongly induced following UVA irradiation of FEK4 cells. Down-regulation of Nrf2 with specific short interfering RNA (siRNA) against Nrf2 (siNrf2) largely abolished the induction of HO-1 following either UVA irradiation or hemin treatment, suggesting that Nrf2 activation mediated modulation of HO-1 by both these agents. Furthermore, a reduction of free heme levels led to a strong decrease in UVA-induced Nrf2 and HO-1 protein levels confirming a clear role for heme in the UV-mediated stress response. Knock-down of Nrf2 protein enhanced membrane damage induced by UVA irradiation, indicating that Nrf2 has a crucial protective role in these cells.

A role for Bach1 and HO-2 in suppression of basal and UVA-induced HO-1 expression in human keratinocytes.

Ultraviolet A (UVA) radiation is an oxidizing agent that strongly induces the heme oxygenase 1 (HO-1) gene and expression of the protein in cultured human skin fibroblasts but weakly induces it in skin keratinocytes. Lower basal levels of HO-1 and much higher basal levels of HO-2 protein are observed in keratinocytes compared with fibroblasts. Using both overexpression and knockdown approaches, we demonstrate that HO-2 modulates basal and UVA-induced HO-1 protein levels, whereas HO-1 levels do not affect HO-2 levels in skin fibroblasts and keratinocytes. Silencing of Bach1 strongly increases HO-1 levels in transformed HaCaT keratinocytes and these HO-1 levels are not further increased by either UVA irradiation or silencing of HO-2. This is consistent with the conclusion that high constitutive levels of HO-2 expression in keratinocytes are responsible for the resistance of these cells to HO-1 induction by UVA radiation and that Bach1 plays a predominant role in influencing the lack of HO-1 expression in keratinocytes. Bach1 inhibition leading to HO-1 induction reduced UVA-irradiation-induced damage as monitored both by the extent of LDH release and by nuclear condensation, so that Bach1 inhibition seems to protect against UVA-irradiation-induced damage in keratinocytes.

Development of an automated cylindrical ion trap mass spectrometer for the determination of atmospheric volatile organic compounds.

Volatile organic compounds released from the biosphere are known to have a large impact on atmospheric chemistry. Field instruments for the detection of these trace gases are often limited by the lack of instrument portability and the inability to distinguish compounds of interest from background or other interfering compounds. We have developed an automated sampling and preconcentration system, coupled to a lightweight, low-power cylindrical ion trap mass spectrometer. The instrument was evaluated by measuring isoprene concentrations during a field campaign at the University of Michigan Biological Station PROPHET lab. Isoprene was preconcentrated by sampling directly into a short capillary column precooled without the aid of cryogens. The capillary column was then rapidly heated by moving the column to a preheated region to obtain fast separation of isoprene from other components, followed by detection with a cylindrical ion trap. This combination yielded a detection limit of approximately 80 ppt (parts per trillion) for isoprene with a measurement frequency of one sample every 11 min. The data obtained by the automated sampling and preconcentration system during the PROPHET 2005 campaign were compared to those of other field instruments measuring isoprene at this site in an intercomparison exercise. The intercomparisons suggest the new inlet system, when coupled with this ion trap detector, provides a viable field instrument for the fast, precise, and quantitative determination of isoprene and other trace gases over a variety of atmospheric conditions.

Airborne measurements of peroxy radicals using the PERCA technique.

The Peroxy Radical Chemical Amplifier (PERCA) technique is a proven method for measurement of ambient levels of peroxy radicals at ground level, but there are no published instances of the technique being used on an aerial platform. Here we describe deployment of a PERCA on the former UK Meteorological Office C-130 Hercules research aircraft. The instrument uses the established method of chemical amplification and conversion of peroxy radicals to nitrogen dioxide (NO2) by doping the sample air-flow matrix with CO and NO, subsequently measuring the NO2 yield with an improved 'Luminox' LMA-3 NO2 detector. NO2 from the amplification chemistry is distinguished from other sources of NO2 reaching the detector by periodically injecting CO approximately 1 s downstream of the NO injection point (termination mode). Chain lengths (CL's) for the amplification chemistry were typically approximately 260 (ground level) to approximately 200 (7,000 m). This variation with altitude is less than the variation associated with the 'age' of the PFA inlet material where the amplification chemistry occurs; CL's of approximately 200 with old tubing to approximately 300 with new clean tubing were typical (ground level values). The CL determinations were made in-flight using an onboard calibration unit based on the 254 nm photolysis of 7.5 to 10 parts per billion (by volume, ppbv) of CH3I in air, producing CH3O2 in a quantitative manner. The noise-equivalent detection limit for peroxy radicals (HO2 + RO2) is 2 parts per trillion (by volume, pptv) at 3,650 m when the background ambient ozone levels are stable, based on a 5 min average of five 30 s amplification cycles and five 30 s termination cycles. This detection limit is a function of several factors but is most seriously degraded when there is large variability in the ambient ozone concentration. This paper describes the instrument design, considers its performance and proposes design improvements. It concludes that the performance of an airborne PERCA in the free troposphere can be superior to that of ground-based instruments when similar sampling frequencies are compared.

Chemical ionization mass spectrometer instrument for the measurement of tropospheric HO2 and RO2.

Laboratory characterizations of the peroxy radical chemical ionization mass spectrometer (PerCIMS) instrument have been performed. The instrument functions by drawing ambient air through a 50-microm-diameter orifice into an inlet held at low pressure. Peroxy radicals (HO2 and RO2) within this air are detected by amplified chemical conversion into a unique ion (HSO4-) via the chemistry initiated by the addition of NO and SO2 to the inlet. HSO4- ions are then quantified by a quadrupole filter mass spectrometer. PerCIMS provides measurements of the sum of peroxy radicals, HO2 + RO2 (HOxROx mode), or the HO2 component only (HO2 mode), achieved through the control of concentration of NO and SO2 added to the instrument. The characterization and response of this instrument have been evaluated through modeling of inlet chemistry and laboratory experiments and have also been demonstrated through successful deployment during field campaigns. The performance of PerCIMS with respect to calibration pressure and relative humidity is reported, as are the sensitivities of the instrument to organic peroxy radicals with different hydrocarbon groups. These data show PerCIMS to be a practical field instrument for the fast and accurate evaluation of the concentration of peroxy radicals over a variety of atmospheric conditions. The estimated accuracy of the derived [HOxROx] concentrations is +/- 35% (at the 95% confidence interval), while [HO2] measurements have accuracies of +/- 41% (at the 95% confidence interval). Typical precision of measurements well above the detection limit is 10%, and typical detection limits are 1 x 10(7) radicals cm(-3) for 15-s averaging times.