Dehydration stress and Mayaro virus vector competence in Aedes aegypti.

IMPORTANCE: Relative humidity (RH) is an environmental variable that affects mosquito physiology and can impact pathogen transmission. Low RH can induce dehydration in mosquitoes, leading to alterations in physiological and behavioral responses such as blood-feeding and host-seeking behavior. We evaluated the effects of a temporal drop in RH (RH shock) on mortality and Mayaro virus vector competence in Ae. aegypti. While dehydration induced by humidity shock did not impact virus infection, we detected a significant effect of dehydration on mosquito mortality and blood-feeding frequency, which could significantly impact transmission dynamics.

A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test.

OBJECTIVES: Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies. METHODS: The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein. RESULTS: SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002). CONCLUSIONS: Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.

Rapid cloud removal of dimethyl sulfide oxidation products limits SO2 and cloud condensation nuclei production in the marine atmosphere.

Oceans emit large quantities of dimethyl sulfide (DMS) to the marine atmosphere. The oxidation of DMS leads to the formation and growth of cloud condensation nuclei (CCN) with consequent effects on Earth's radiation balance and climate. The quantitative assessment of the impact of DMS emissions on CCN concentrations necessitates a detailed description of the oxidation of DMS in the presence of existing aerosol particles and clouds. In the unpolluted marine atmosphere, DMS is efficiently oxidized to hydroperoxymethyl thioformate (HPMTF), a stable intermediate in the chemical trajectory toward sulfur dioxide (SO2) and ultimately sulfate aerosol. Using direct airborne flux measurements, we demonstrate that the irreversible loss of HPMTF to clouds in the marine boundary layer determines the HPMTF lifetime (τHPMTF < 2 h) and terminates DMS oxidation to SO2 When accounting for HPMTF cloud loss in a global chemical transport model, we show that SO2 production from DMS is reduced by 35% globally and near-surface (0 to 3 km) SO2 concentrations over the ocean are lowered by 24%. This large, previously unconsidered loss process for volatile sulfur accelerates the timescale for the conversion of DMS to sulfate while limiting new particle formation in the marine atmosphere and changing the dynamics of aerosol growth. This loss process potentially reduces the spatial scale over which DMS emissions contribute to aerosol production and growth and weakens the link between DMS emission and marine CCN production with subsequent implications for cloud formation, radiative forcing, and climate.

Impact of Biomass Burning Organic Aerosol Volatility on Smoke Concentrations Downwind of Fires.

Biomass burning particulate matter (BBPM) affects regional air quality and global climate, with impacts expected to continue to grow over the coming years. We show that studies of North American fires have a systematic altitude dependence in measured BBPM normalized excess mixing ratio (NEMR; ΔPM/ΔCO), with airborne and high-altitude studies showing a factor of 2 higher NEMR than ground-based measurements. We report direct airborne measurements of BBPM volatility that partially explain the difference in the BBPM NEMR observed across platforms. We find that when heated to 40-45 °C in an airborne thermal denuder, 19% of lofted smoke PM1 evaporates. Thermal denuder measurements are consistent with evaporation observed when a single smoke plume was sampled across a range of temperatures as the plume descended from 4 to 2 km altitude. We also demonstrate that chemical aging of smoke and differences in PM emission factors can not fully explain the platform-dependent differences. When the measured PM volatility is applied to output from the High Resolution Rapid Refresh Smoke regional model, we predict a lower PM NEMR at the surface compared to the lofted smoke measured by aircraft. These results emphasize the significant role that gas-particle partitioning plays in determining the air quality impacts of wildfire smoke.

Prospective Surveillance of Respiratory Infections in British Antarctic Survey Bases During the COVID-19 Pandemic.

BACKGROUND: The British Antarctic bases offer a semiclosed environment for assessing the transmission and persistence of seasonal respiratory viruses. METHODS: Weekly swabbing was performed for respiratory pathogen surveillance (including SARS-CoV-2), at 2 British Antarctic Survey bases, during 2020: King Edward Point (KEP, 30 June to 29 September, 9 participants, 124 swabs) and Rothera (9 May to 6 June, 27 participants, 127 swabs). Symptom questionnaires were collected for any newly symptomatic cases that presented during this weekly swabbing period. RESULTS: At KEP, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (2), adenovirus (1), parainfluenza 3 (1), and respiratory syncytial virus B (1). At Rothera, swabs tested positive for non-SARS-CoV-2 seasonal coronavirus (3), adenovirus (2), parainfluenza 4 (1), and human metapneumovirus (1). All bacterial agents identified were considered to be colonizers and not pathogenic. CONCLUSIONS: At KEP, the timeline indicated that the parainfluenza 3 and adenovirus infections could have been linked to some of the symptomatic cases that presented. For the other viruses, the only other possible sources were the visiting ship crew members. At Rothera, the single symptomatic case presented too early for this to be linked to the subsequent viral detections, and the only other possible source could have been a single nonparticipating staff member.

Airborne Emission Rate Measurements Validate Remote Sensing Observations and Emission Inventories of Western U.S. Wildfires.

Carbonaceous emissions from wildfires are a dynamic mixture of gases and particles that have important impacts on air quality and climate. Emissions that feed atmospheric models are estimated using burned area and fire radiative power (FRP) methods that rely on satellite products. These approaches show wide variability and have large uncertainties, and their accuracy is challenging to evaluate due to limited aircraft and ground measurements. Here, we present a novel method to estimate fire plume-integrated total carbon and speciated emission rates using a unique combination of lidar remote sensing aerosol extinction profiles and in situ measured carbon constituents. We show strong agreement between these aircraft-derived emission rates of total carbon and a detailed burned area-based inventory that distributes carbon emissions in time using Geostationary Operational Environmental Satellite FRP observations (Fuel2Fire inventory, slope = 1.33 ± 0.04, r2 = 0.93, and RMSE = 0.27). Other more commonly used inventories strongly correlate with aircraft-derived emissions but have wide-ranging over- and under-predictions. A strong correlation is found between carbon monoxide emissions estimated in situ with those derived from the TROPOspheric Monitoring Instrument (TROPOMI) for five wildfires with coincident sampling windows (slope = 0.99 ± 0.18; bias = 28.5%). Smoke emission coefficients (g MJ-1) enable direct estimations of primary gas and aerosol emissions from satellite FRP observations, and we derive these values for many compounds emitted by temperate forest fuels, including several previously unreported species.

Understanding the Evolution of Smoke Mass Extinction Efficiency Using Field Campaign Measurements.

Aerosol mass extinction efficiency (MEE) is a key aerosol property used to connect aerosol optical properties with aerosol mass concentrations. Using measurements of smoke obtained during the Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ) campaign we find that mid-visible smoke MEE can change by a factor of 2-3 between fresh smoke (<2 hr old) and one-day-old smoke. While increases in aerosol size partially explain this trend, changes in the real part of the aerosol refractive index (real(n)) are necessary to provide closure assuming Mie theory. Real(n) estimates derived from multiple days of FIREX-AQ measurements increase with age (from 1.40 - 1.45 to 1.5-1.54 from fresh to one-day-old) and are found to be positively correlated with organic aerosol oxidation state and aerosol size, and negatively correlated with smoke volatility. Future laboratory, field, and modeling studies should focus on better understanding and parameterizing these relationships to fully represent smoke aging.

How to design and implement a university-based COVID-19 testing programme? An evaluation of a novel RT-LAMP COVID-19 testing programme in a UK university.

BACKGROUND: Little is known about how asymptomatic testing as a method to control transmission of COVID-19 can be implemented, and the prevalence of asymptomatic infection within university populations. The objective of this study was to investigate how to effectively set-up and implement a COVID-19 testing programme using novel reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) technology and to quantify the scale of asymptomatic infection on a university campus. METHODS: An observational study to describe the set-up and implementation of a novel COVID-19 testing programme on a UK university campus between September and December 2020. RT-LAMP testing was used to identify asymptomatic cases. RESULTS: A total of 1,673 tests were performed using RT-LAMP during the study period, of which 9 were positive for COVID-19, giving an overall positivity rate of 0.54%, equivalent to a rate in the tested population of 538 cases per 100,000 over the duration of testing. All positive tests were found to be positive on RT-PCR testing, giving a false positive rate of 0%. CONCLUSIONS: This study shows that it is possible to rapidly setup a universal university testing programme for COVID-19 in collaboration with local healthcare providers using RT-LAMP testing. Positive results were comparable to those in the local population, though with a different peak of infection. Further research to inform the design of the testing programme includes focus groups of those who underwent testing and further interrogation of the demographics of those opting to be tested to identify potential access problems or inequalities.

Heterogeneity in biological assemblages and exposure in chemical risk assessment: Exploring capabilities and challenges in methodology with two landscape-scale case studies.

Chemical exposure concentrations and the composition of ecological receptors (e.g., species) vary in space and time, resulting in landscape-scale (e.g. catchment) heterogeneity. Current regulatory, prospective chemical risk assessment frameworks do not directly address this heterogeneity because they assume that reasonably worst-case chemical exposure concentrations co-occur (spatially and temporally) with biological species that are the most sensitive to the chemical's toxicity. Whilst current approaches may parameterise fate models with site-specific data and aim to be protective, a more precise understanding of when and where chemical exposure and species sensitivity co-occur enables risk assessments to be better tailored and applied mitigation more efficient. We use two aquatic case studies covering different spatial and temporal resolution to explore how geo-referenced data and spatial tools might be used to account for landscape heterogeneity of chemical exposure and ecological assemblages in prospective risk assessment. Each case study followed a stepwise approach: i) estimate and establish spatial chemical exposure distributions using local environmental information and environmental fate models; ii) derive toxicity thresholds for different taxonomic groups and determine geo-referenced distributions of exposure-toxicity ratios (i.e., potential risk); iii) overlay risk data with the ecological status of biomonitoring sites to determine if relationships exist. We focus on demonstrating whether the integration of relevant data and potential approaches is feasible rather than making comprehensive and refined risk assessments of specific chemicals. The case studies indicate that geo-referenced predicted environmental concentration estimations can be achieved with available data, models and tools but establishing the distribution of species assemblages is reliant on the availability of a few sources of biomonitoring data and tools. Linking large sets of geo-referenced exposure and biomonitoring data is feasible but assessment of risk will often be limited by the availability of ecotoxicity data. The studies highlight the important influence that choices for aggregating data and for the selection of statistical metrics have on assessing and interpreting risk at different spatial scales and patterns of distribution within the landscape. Finally, we discuss approaches and development needs that could help to address environmental heterogeneity in chemical risk assessment.

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

BACKGROUND: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. RESULTS: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. CONCLUSIONS: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Towards an In Vitro 3D Model for Photosynthetic Cancer Treatment: A Study of Microalgae and Tumor Cell Interactions.

As hypoxic tumors show resistance to several clinical treatments, photosynthetic microorganisms have been recently suggested as a promising safe alternative for oxygenating the tumor microenvironment. The relationship between organisms and the effect microalgae have on tumors is still largely unknown, evidencing the need for a simple yet representative model for studying photosynthetic tumor oxygenation in a reproducible manner. Here, we present a 3D photosynthetic tumor model composed of human melanoma cells and the microalgae Chlamydomonas reinhardtii, both seeded into a collagen scaffold, which allows for the simultaneous study of both cell types. This work focuses on the biocompatibility and cellular interactions of the two cell types, as well as the study of photosynthetic oxygenation of the tumor cells. It is shown that both cell types are biocompatible with one another at cell culture conditions and that a 10:1 ratio of microalgae to cells meets the metabolic requirement of the tumor cells, producing over twice the required amount of oxygen. This 3D tumor model provides an easy-to-use in vitro resource for analyzing the effects of photosynthetically produced oxygen on a tumor microenvironment, thus opening various potential research avenues.

Variability and Time of Day Dependence of Ozone Photochemistry in Western Wildfire Plumes.

Understanding the efficiency and variability of photochemical ozone (O3) production from western wildfire plumes is important to accurately estimate their influence on North American air quality. A set of photochemical measurements were made from the NOAA Twin Otter research aircraft as a part of the Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ) experiment. We use a zero-dimensional (0-D) box model to investigate the chemistry driving O3 production in modeled plumes. Modeled afternoon plumes reached a maximum O3 mixing ratio of 140 ± 50 ppbv (average ± standard deviation) within 20 ± 10 min of emission compared to 76 ± 12 ppbv in 60 ± 30 min in evening plumes. Afternoon and evening maximum O3 isopleths indicate that plumes were near their peak in NOx efficiency. A radical budget describes the NOx volatile - organic compound (VOC) sensitivities of these plumes. Afternoon plumes displayed a rapid transition from VOC-sensitive to NOx-sensitive chemistry, driven by HOx (=OH + HO2) production from photolysis of nitrous acid (HONO) (48 ± 20% of primary HOx) and formaldehyde (HCHO) (26 ± 9%) emitted directly from the fire. Evening plumes exhibit a slower transition from peak NOx efficiency to VOC-sensitive O3 production caused by a reduction in photolysis rates and fire emissions. HOx production in evening plumes is controlled by HONO photolysis (53 ± 7%), HCHO photolysis (18 ± 9%), and alkene ozonolysis (17 ± 9%).

Novel Analysis to Quantify Plume Crosswind Heterogeneity Applied to Biomass Burning Smoke.

We present a novel method, the Gaussian observational model for edge to center heterogeneity (GOMECH), to quantify the horizontal chemical structure of plumes. GOMECH fits observations of short-lived emissions or products against a long-lived tracer (e.g., CO) to provide relative metrics for the plume width (wi/wCO) and center (bi/wCO). To validate GOMECH, we investigate OH and NO3 oxidation processes in smoke plumes sampled during FIREX-AQ (Fire Influence on Regional to Global Environments and Air Quality, a 2019 wildfire smoke study). An analysis of 430 crosswind transects demonstrates that nitrous acid (HONO), a primary source of OH, is narrower than CO (wHONO/wCO = 0.73-0.84 ± 0.01) and maleic anhydride (an OH oxidation product) is enhanced on plume edges (wmaleicanhydride/wCO = 1.06-1.12 ± 0.01). By contrast, NO3 production [P(NO3)] occurs mainly at the plume center (wP(NO3)/wCO = 0.91-1.00 ± 0.01). Phenolic emissions, highly reactive to OH and NO3, are narrower than CO (wphenol/wCO = 0.96 ± 0.03, wcatechol/wCO = 0.91 ± 0.01, and wmethylcatechol/wCO = 0.84 ± 0.01), suggesting that plume edge phenolic losses are the greatest. Yet, nitrophenolic aerosol, their oxidation product, is the greatest at the plume center (wnitrophenolicaerosol/wCO = 0.95 ± 0.02). In a large plume case study, GOMECH suggests that nitrocatechol aerosol is most associated with P(NO3). Last, we corroborate GOMECH with a large eddy simulation model which suggests most (55%) of nitrocatechol is produced through NO3 in our case study.

Correction to: Genome-enabled insights into the biology of thrips as crop pests.

An amendment to this paper has been published and can be accessed via the original article.

Genome-enabled insights into the biology of thrips as crop pests.

BACKGROUND: The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS: We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS: Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest.

BACKGROUND: Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species' feeding and habitat traits, defining potential targets for pest management strategies. RESULTS: Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys' capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. CONCLUSIONS: Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

213 nm laser written waveguides in Ge-doped planar silica without hydrogen loading.

In this paper we present the first example of waveguides fabricated by UV writing in non-hydrogen loaded Ge-doped planar silica with 213 nm light. Single mode waveguides were fabricated and the numerical apertures and mode field diameters were measured for a range of writing fluences. A peak index change of 5.3 x 10-3 was inferred for the waveguide written with 70 kJ cm-2. The refractive index change is sufficient to match the index structure of standard optical fiber. Uniformity of the written structures was measured and a propagation loss of 0.39 ± 0.03 dB cm-1 was determined through cutback measurements.

Individual inscription of spectrally multiplexed Bragg gratings in optical multicore fibers using small spot direct UV writing.

We have demonstrated the inscription of Bragg gratings into five individual cores of a seven core fiber using small spot direct UV writing. With this technique, we defined spectrally multiplexed Bragg gratings consecutively in separate cores as well as spectrally multiplexed gratings at the same longitudinal location in different cores. The effect of bending on the optical spectrum was evaluated to allow the differentiation between cross-exposure and cross-talk, and an alignment process to reduce cross-exposure by 13 dB was found.