Upper Hunter Valley particle characterization study: final report

This study provides an analysis of the composition of PM2.5 (particulate matter with a diameter of less than 2.5 micrometres) in the two main population centres in the Upper Hunter, namely Muswellbrook and Singleton, during 012.The finer PM2.5 particles have been studied because they are of greatest concern owing to their impact on health. Samples were collected for 24 hours every third day and analysed for the components of PM2.5, specifically twenty elements, fourteen soluble ions, two anhydrous sugars (levoglucosan and mannosan) that are found in woodsmoke, organic carbon (OC), and black carbon (BC), as well as gravimetric mass. The chemical composition of all the samples from each site was analysed using a mathematical technique called Positive Matrix Factorisation (PMF), which is widely used in air pollution source apportionment studies. This identified eight factors (also called ‘fingerprints’) which represent the mix of components that tend to vary together in time. Further analysis, using information about known sources and knowledge of atmospheric chemistry as well as wind sector and seasonal analysis, was undertaken to identify the most likely source of emissions for each factor and hence the contribution that each source makes to the measured PM2.5 concentrations. © 2013 CSIROSummary (factsheet) also attached

Composition of Clean Marine Air and Biogenic Influences on VOCs during the MUMBA Campaign

Volatile organic compounds (VOCs) are important precursors to the formation of ozone and fine particulate matter, the two pollutants of most concern in Sydney, Australia. Despite this importance, there are very few published measurements of ambient VOC concentrations in Australia. In this paper, we present mole fractions of several important VOCs measured during the campaign known as MUMBA (Measurements of Urban, Marine and Biogenic Air) in the Australian city of Wollongong (34°S). We particularly focus on measurements made during periods when clean marine air impacted the measurement site and on VOCs of biogenic origin. Typical unpolluted marine air mole fractions during austral summer 2012-2013 at latitude 34°S were established for CO2 (391.0 ± 0.6 ppm), CH4 (1760.1 ± 0.4 ppb), N2O (325.04 ± 0.08 ppb), CO (52.4 ± 1.7 ppb), O3 (20.5 ± 1.1 ppb), acetaldehyde (190 ± 40 ppt), acetone (260 ± 30 ppt), dimethyl sulphide (50 ± 10 ppt), benzene (20 ± 10 ppt), toluene (30 ± 20 ppt), C8H10 aromatics (23 ± 6 ppt) and C9H12 aromatics (36 ± 7 ppt). The MUMBA site was frequently influenced by VOCs of biogenic origin from a nearby strip of forested parkland to the east due to the dominant north-easterly afternoon sea breeze. VOCs from the more distant densely forested escarpment to the west also impacted the site, especially during two days of extreme heat and strong westerly winds. The relative amounts of different biogenic VOCs observed for these two biomes differed, with much larger increases of isoprene than of monoterpenes or methanol during the hot westerly winds from the escarpment than with cooler winds from the east. However, whether this was due to different vegetation types or was solely the result of the extreme temperatures is not entirely clear. We conclude that the clean marine air and biogenic signatures measured during the MUMBA campaign provide useful information about the typical abundance of several key VOCs and can be used to constrain chemical transport model simulations of the atmosphere in this poorly sampled region of the world. © 2019 The Author

The MUMBA campaign: measurements of urban, marine and biogenic air

The Measurements of Urban, Marine and Biogenic Air (MUMBA) campaign took place in Wollongong, New South Wales (a small coastal city approximately 80 km south of Sydney, Australia) from 21 December 2012 to 15 February 2013. Like many Australian cities, Wollongong is surrounded by dense eucalyptus forest, so the urban airshed is heavily influenced by biogenic emissions. Instruments were deployed during MUMBA to measure the gaseous and aerosol composition of the atmosphere with the aim of providing a detailed characterisation of the complex environment of the ocean–forest–urban interface that could be used to test the skill of atmospheric models. The gases measured included ozone, oxides of nitrogen, carbon monoxide, carbon dioxide, methane and many of the most abundant volatile organic compounds. The aerosol characterisation included total particle counts above 3 nm, total cloud condensation nuclei counts, mass concentration, number concentration size distribution, aerosol chemical analyses and elemental analysis. The campaign captured varied meteorological conditions, including two extreme heat events, providing a potentially valuable test for models of future air quality in a warmer climate. There was also an episode when the site sampled clean marine air for many hours, providing a useful additional measure of the background concentrations of these trace gases within this poorly sampled region of the globe. In this paper we describe the campaign, the meteorology and the resulting observations of atmospheric composition in general terms in order to equip the reader with a sufficient understanding of the Wollongong regional influences to use the MUMBA datasets as a case study for testing a chemical transport model. © Author(s) 2017.The data are available from PANGAEA (http://doi.pangaea.de/10.1594/PANGAEA.871982)

Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

Evolutionary consequences of host shifts represent a challenge to identify the mechanisms involved in the emergence of influenza A (IA) viruses. In this study we focused on the evolutionary history of H7 IA virus in wild and domestic birds, with a particular emphasis on host shifts consequences on the molecular evolution of the hemagglutinin (HA) gene. Based on a dataset of 414 HA nucleotide sequences, we performed an extensive phylogeographic analysis in order to identify the overall genetic structure of H7 IA viruses. We then identified host shift events and investigated viral population dynamics in wild and domestic birds, independently. Finally, we estimated changes in nucleotide substitution rates and tested for positive selection in the HA gene. A strong association between the geographic origin and the genetic structure was observed, with four main clades including viruses isolated in North America, South America, Australia and Eurasia-Africa. We identified ten potential events of virus introduction from wild to domestic birds, but little evidence for spillover of viruses from poultry to wild waterbirds. Several sites involved in host specificity (addition of a glycosylation site in the receptor binding domain) and virulence (insertion of amino acids in the cleavage site) were found to be positively selected in HA nucleotide sequences, in genetically unrelated lineages, suggesting parallel evolution for the HA gene of IA viruses in domestic birds. These results highlight that evolutionary consequences of bird host shifts would need to be further studied to understand the ecological and molecular mechanisms involved in the emergence of domestic bird-adapted viruses

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

An outbreak of highly pathogenic avian influenza in Australia in 1997 caused by an H7N4 virus

In November of 1997 an outbreak of highly pathogenic-avian influenza occurred near the town of Tamworth, in northern New South Wales, Australia. The viruses isolated from chickens on two commercial chicken farms were identified as H7N4 viruses, with hemagglutinin cleavage site amino acid sequences of RKRKRG and intravenous pathogenicity indices of 2.52 and 2.90, respectively. A virus with an identical nucleotide sequence, but with an intravenous pathogenicity index of 1.30, was also isolated from cloacal swabs collected from asymptomatic emus kept on a third property

Lower Hunter particle characterisation study appendices to the final report to the NSW Environment Protection Authority

The Lower Hunter Particle Characterisation Study was commissioned by the NSW Environment Protection Authority in 2013 to investigate the composition and major sources of particle pollution in the Lower Hunter. The study was conducted by scientists from the former Office of Environment and Heritage (OEH), CSIRO and the Australian Nuclear Science and Technology Organisation (ANSTO), with oversight from the NSW Ministry of Health, and completed in 2016. Focusing on very small particles, invisible to the human eye, which can be inhaled and can pass through the throat and nose and into the lungs, the study aimed to determine the composition and major sources of fine particles (PM2.5) and coarse particles (PM2.5-10). Fine particles were monitored at four sites, including two sites representative of regional population exposures (Newcastle, Beresfield) and two sites near the Port of Newcastle (Mayfield and Stockton). Coarse particles were monitored at Mayfield and Stockton, the two sites near the Port of Newcastle

Lower Hunter particle characterisation study Final Report to the NSW Environment Protection Authority

The Lower Hunter Particle Characterisation Study (LHPCS) provides details about the composition and major sources of PM2.5 (fine airborne particles)and PM2.5-10(coarse airborne particles). Measurements were made for one year from March 2014 to February 2015 at two air quality monitoring stations representative of regional population exposures (Newcastle and Beresfield) and two stations near the Port of Newcastle (Mayfield and Stockton). Annual average PM2.5 concentrations were very similar at Newcastle, Mayfield and Beresfield (6.4–6.7 μg m-3) but about 40% higher at Stockton (9.1 μg m-3). The higher levels at Stockton were mainly due to both more sea salt and to the primary ammonium nitrate, which was only detected at Stockton. The ammonium nitrate, which contributed on average 19% of the PM2.5 mass (and ~40% in winter), was identified as very likely to be due to primary emissions from Orica’s ammonium nitrate manufacturing facility on Kooragang Island. Other than the ammonium nitrate, PM2.5 composition and sources were found to be fairly similar across the four sites. Key results on the sources and their contributions are: fresh sea salt particles: 24% at Newcastle, decreasing to 13% at Beresfield; pollutant-aged sea salt: ~23% at all sites; this is sea salt reacted with industrial, commercial, road and non-road transport emissions from local and regional sources; wood smoke: 15% at Beresfield, decreasing to 6% at Stockton; secondary ammonium sulfate: ~10% at all sites; soil dust: ~10% at all sites; vehicles: ~10% at three sites, but only 5% at Stockton; industry factors: ~12% at three sites but 24% at Stockton; mixed shipping/industry: ~3% at all sites; nitrate: 19% ammonium nitrate at Stockton and secondary nitrate at other sites (6-11%). On an annual average basis, there is an approximately 50:50 split between primary and secondary particles at three sites (Newcastle, Beresfield and Mayfield) and a 65:35 split at Stockton because of the significant contribution from the primary ammonium nitrate. PM2.5-10 composition and sources were only determined at the stations near the Port of Newcastle. The 2½ times higher annual average PM2.5-10 concentration at Stockton (21.5 μg m-3) than at Mayfield (8.3 μg m-3) was found to be mainly due to a much higher contribution by fresh sea salt particles at Stockton. The PM2.5-10 factors and their contributions were identified as:  fresh sea salt: 13.6 μg m-3 at Stockton, 3.3 μg m-3 at Mayfield  industry plus pollutant-aged sea salt: 2.4 μg m-3 at both sites  light-absorbing carbon: 2.2 μg m-3 at Stockton, 0.9 μg m-3 at Mayfield  soil: 2.3 μg m-3 at Stockton, 1.2 μg m-3 at Mayfield  bioaerosol: 1.1 μg m-3 at Stockton, 0.5 μg m-3 at Mayfield. Most PM2.5-10 particles are primary particles or physical combinations of primary emissions, but there is evidence of chemical reactions in the pollutant-aged sea salt factor. Coal particles could contribute up to 10% of PM2.5-10 particles. Further investigations are needed to clarify the contribution of coal