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Item Open Access When push comes to shove - RNA polymerase and DNA-bound protein roadblocks(Springer Science and Business Media LLC, 2023) Hao, N.; Donnelly, A.J.; Dodd, I.B.; Shearwin, K.E.In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.Item Open Access Combining ecology and technology to kick‐start oyster reef restoration(Wiley, 2023) Williams, B.R.; McAfee, D.; Connell, S.D.Techniques that enhance the recruitment of foundation species to restoration sites can inform the ecological development of the restored habitat. However, techniques are often considered in isolation, potentially overlooking synergies from combining them. Native oyster reefs have been lost worldwide, resulting in restoration efforts in systems that are often recruitment limited, or where recruiting oysters must spatially compete with opportunistic species. Here, we present a field-based study that combines ecological knowledge on positive species interactions with novel acoustic technology, both of which are demonstrated to boost oyster recruitment in isolation, to test whether their interaction synergistically enhances the early larval recruitment that drives oyster reef development. At three sites across a 20 ha oyster reef restoration in southern Australia, we used self-made speakers to broadcast healthy reef soundscapes that attract oysters and combine this with artificial kelp that facilitates oyster recruitment by suppressing competitive species (turfing algae). The combination of acoustic enrichment and artificial kelp increased oyster recruitment to the topside of substrate (326.98%increase), whereas only acoustic enrichment increased recruitment to the underside of substrate (126.95% increase). Our findings suggest that the combination ofmultiple techniques and their interactive effectsmight boost the early stages of reef development, providing proof-of-concept that these approaches can help oysters to build and bind reefs (i.e. recruit to the topside and underside, respectively). By combining ecology with technology during the first stages of a developing reef restoration, we show the potential value of these novel approaches to kick-start the recovery of lost oyster reefs.Item Open Access Optimal allocation of nature-based solutions to achieve climate mitigation and adaptation goals(Wiley, 2023) Villarreal-Rosas, J.; Rhodes, J.R.; Sonter, L.J.; Possingham, H.P.; Vogl, A.L.1. Nature-based solutions (NbS) can prevent further climate change and increase local communities' capacity to adapt to the current impacts of climate change. However, the benefits obtained from implementing NbS are not distributed equally across people. Thus, it is key to further understand how people are impacted when implementing NbS. 2. We developed a multi-objective prioritization approach to identify changes in (i) the biophysical provision of ecosystem services, (ii) optimal allocation of NbS and (iii) monetary benefits when targeting climate mitigation versus climate adaptation goals. We used the increase in metric tons of carbon storage as representative of climate mitigation and the decrease in on-site and downstream tons of sediment per year as representative of climate adaptation. 3. Planning strategies that target climate mitigation or climate adaptation goals separately represent a loss of between 30% and 60% of the maximum possible carbon sequestration or sediment retention benefits. Conversely, targeting climate mitigation and climate adaptation goals at the same time captured more than 90% of the maximum possible benefits for all objectives. 4. Priority NbS in the mitigation planning strategy included soil and water conservation and forest rehabilitation, while priority NbS in the adaptation planning strategy included grassland rehabilitation and hill terrace improvement. 5. Targeting mitigation and adaptation goals at the same time captures 35M USD (89% of the maximum attainable) in value of carbon restored and retained, and 2M USD (100% of the maximum attainable) of avoided maintenance costs to the KGA hydropower plant. Conversely, failing to incorporate adaptation goals when developing climate plans only captures 1M of avoided maintenance costs to the KGA hydropower plant. 6. Our approach can be replicated in other locations to promote cost-effective investments in NbS able to secure both global and local benefits to people. This can improve the outcomes of international climate change financial schemes like the Green Climate Fund and the UN-REDD+ program.Item Metadata only Enhanced mitotic arrest and chromosome resolution for cytogenetic analysis in the eastern mosquitofish, Gambusia holbrooki(Elsevier BV, 2023) Mousavi, S.E.; Grützner, F.; Patil, J.G.Maximising the number of cells arrested at metaphase and their resolution is fundamentally important for molecular cytogenetic investigations, particularly in fish, which typically yield low mitotic index and have highly condensed chromosomes. To overcome these limitations, fish were injected with a mitotic stimulator (the yeast, Saccharomyces cerevisiae) to improve the mitotic index, and the intercalating agent ethidium bromide to produce elongated chromosomes. Specifically, adults were injected with activated yeast and then Colcemid (0.025 µg/µl solution, 10 µl per 1 g of body weight) at 24-96 h post yeast injections, followed by chromosome preparations from multiple tissues. Results showed that gill tissue had the highest number of dividing cells at 72 h post yeast exposure with no significant (p > 0.05) differences between the sexes. Nonetheless, sex-specific differences in the mitotic index were observed in spleen, kidney, and liver, which may be attributed to sex-specific differences in immune responses. For elongation of mitotic chromosomes, individuals (both sexes) were first injected with activated yeast and after 48 h with ethidium bromide (2 or 4 µg/ml) and Colcemid (0.05 µg/µl solution, 10 µl per 1 g of body weight). Following which, animals were sampled at three time points (1, 4 and 8 h) for chromosome preparations. The results show that the optimum elongation of metaphase chromosomes of males and females was achieved by using 2 µg/ml and 4 µg/ml, respectively, for 1 h. Interestingly, the average mitotic chromosome length (μm) of males and females post-ethidium bromide exposure was significantly different (p < 0.05) for both concentrations, except at 1 h exposure for 2 µg/ml EtBr. Such differences can be attributed to overall chromosomal condensation differences between sexes. Regardless, the increased mitotic index and chromosome resolution could benefit cytogenetic studies in other fish species.Item Open Access The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.(Proceedings of the National Academy of Sciences, 2023) Tobler, R.; Souilmi, Y.; Huber, C.D.; Bean, N.; Turney, C.S.M.; Grey, S.T.; Cooper, A.The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.Item Open Access Future shock: Ocean acidification and seasonal water temperatures alter the physiology of competing temperate and coral reef fishes(Elsevier BV, 2023) Mitchell, A.; Hayes, C.; Booth, D.J.; Nagelkerken, I.Climate change can directly (physiology) and indirectly (novel species interactions) modify species responses to novel environmental conditions during the initial stages of range shifts.Whilst the effects of climate warming on tropical species at their cold-water leading ranges are well-established, it remains unclear how future seasonal temperature changes, ocean acidification, and novel species interactions will alter the physiology of range-shifting tropical and competing temperate fish in recipient ecosystems. Here we used a laboratory experiment to examine how ocean acidification, future summer vs winter temperatures, and novel species interactions could affect the physiology of competing temperate and range-extending coral reef fish to determine potential range extension outcomes. In future winters (20 °C+elevated pCO₂) coral reef fish at their cold-water leading edges showed reduced physiological performance (lower body condition and cellular defence, and higher oxidative damage) compared to present-day summer (23 °C+control pCO₂) and future summer conditions (26 °C+elevated pCO₂). However, they showed a compensatory effect in future winters through increased long-term energy storage. Contrastingly, co-shoaling temperate fish showed higher oxidative damage, and reduced short-term energy storage and cellular defence in future summer than in future winter conditions at their warm-trailing edges. However, temperate fish benefitted from novel shoaling interactions and showed higher body condition and short-termenergy storage when shoaling with coral reef fish compared to same-species shoaling. We conclude that whilst during future summers, ocean warming will likely benefit coral reef fishes extending their ranges, future winter conditions may still reduce coral reef fish physiological functioning, and may therefore slow their establishment at higher latitudes. In contrast, temperate fish species benefit from co-shoaling with smaller-sized tropical fishes, but this benefit may dissipate due to their reduced physiological functioning under future summer temperatures and increasing body sizes of co-shoaling tropical species.Item Open Access Dynamic axial control over optically levitating particles in air with an electrically-tunable variable-focus lens(Optical Society of America, 2016) Zhu, W.; Eckerskorn, N.; Upadhya, A.; Li, L.; Rode, A.V.; Lee, W.M.Efficient delivery of viruses, proteins and biological macromelecules into a micrometer-sized focal spot of an XFEL beam for coherent diffraction imaging inspired new development in touch-free particle injection methods in gaseous and vacuum environments. This paper lays out our ongoing effort in constructing an all-optical particle delivery approach that uses piconewton photophoretic and femtonewton light-pressure forces to control particle delivery into the XFEL beam. We combine a spatial light modulator (SLM) and an electrically tunable lens (ETL) to construct a variable-divergence vortex beam providing dynamic and stable positioning of levitated micrometer-size particles, under normal atmospheric pressure. A sensorless wavefront correction approach is used to reduce optical aberrations to generate a high quality vortex beam for particle manipulation. As a proof of concept, stable manipulation of optically-controlled axial motion of trapped particles is demonstrated with a response time of 100ms. In addition, modulation of trapping intensity provides a measure of the mass of a single, isolated particle. The driving signal of this oscillatory motion can potentially be phase-locked to an external timing signal enabling synchronization of particle delivery into the x-ray focus with XFEL pulse train.Item Open Access Holo-UNet: hologram-to-hologram neural network restoration for high fidelity low light quantitative phase imaging of live cells(Optica Publishing Group, 2020) Zhang, Z.; Zheng, Y.; Xu, T.; Upadhya, A.; Lim, Y.J.; Mathews, A.; Xie, L.; Lee, W.M.Intensity shot noise in digital holograms distorts the quality of the phase images after phase retrieval, limiting the usefulness of quantitative phase microscopy (QPM) systems in long term live cell imaging. In this paper, we devise a hologram-to-hologram neural network, Holo-UNet, that restores high quality digital holograms under high shot noise conditions (submW/cm2 intensities) at high acquisition rates (sub-milliseconds). In comparison to current phase recovery methods, Holo-UNet denoises the recorded hologram, and so prevents shot noise from propagating through the phase retrieval step that in turn adversely affects phase and intensity images. Holo-UNet was tested on 2 independent QPM systems without any adjustment to the hardware setting. In both cases, Holo-UNet outperformed existing phase recovery and block-matching techniques by ∼ 1.8 folds in phase fidelity as measured by SSIM. Holo-UNet is immediately applicable to a wide range of other high-speed interferometric phase imaging techniques. The network paves the way towards the expansion of high-speed low light QPM biological imaging with minimal dependence on hardware constraints.Item Open Access Structured Back Focal Plane Interferometry (SBFPI)(Nature Publishing Group, 2019) Upadhya, A.; Zheng, Y.; Li, L.; Lee, W.M.Back focal plane interferometry (BFPI) is one of the most straightforward and powerful methods for achieving sub-nanometer particle tracking precision at high speed (MHz). BFPI faces technical challenges that prohibit tunable expansion of linear detection range with minimal loss to sensitivity, while maintaining robustness against optical aberrations. In this paper, we devise a tunable BFPI combining a structured beam (conical wavefront) and structured detection (annular quadrant photodiode). This technique, which we termed Structured Back Focal Plane Interferometry (SBFPI), possesses three key novelties namely: extended tracking range, low loss in sensitivity, and resilience to spatial aberrations. Most importantly, the conical wavefront beam preserves the axial Gouy phase shift and lateral beam waist that can then be harnessed in a conventional BFPI system. Through a series of experimental results, we were able to tune detection sensitivity and detection range over the SBFPI parameter space. We also identified a figure of merit based on the experimental optimum that allows us to identify optimal SBPFI configurations that balance both range and sensitivity. In addition, we also studied the resilience of SBFPI against asymmetric spatial aberrations (astigmatism of up to 0.8 λ) along the lateral directions. The simplicity and elegance of SBFPI will accelerate its dissemination to many associated fields in optical detection, interferometry and force spectroscopy.Item Metadata only Cymredoxin, a [2Fe–2S] ferredoxin, supports catalytic activity of the p-cymene oxidising P450 enzyme CYP108N12(Elsevier BV, 2023) Giang, P.D.; Churchman, L.R.; Stok, J.E.; Bell, S.G.; De Voss, J.J.Rhodococcus globerulus is a metabolically active organism that has been shown to utilise eucalypt oil as its sole source of carbon and energy. This oil includes 1,8-cineole, p-cymene and limonene. Two identified and characterised cytochromes P450 (P450s) from this organism initiate the biodegradation of the monoterpenes 1,8- cineole (CYP176A1) and p-cymene (CYP108N12). Extensive characterisation has been completed for CYP176A1 and it has been successfully reconstituted with its immediate redox partner, cindoxin, and E. coli flavodoxin reductase. Two putative redox partner genes are encoded in the same operon as CYP108N12 and here the isolation, expression, purification, and characterisation of its specific [2Fe–2S] ferredoxin redox partner, cymredoxin is presented. Reconstitution of CYP108N12 with cymredoxin in place of putidaredoxin, a [2Fe–2S] redox partner of another P450, improves both the rate of electron transfer (from 13 ± 2 to 70 ± 1 μM NADH/ min/μM CYP108N12) and the efficiency of NADH utilisation (the so-called coupling efficiency increases from 13% to 90%). Cymredoxin improves the catalytic ability of CYP108N12 in vitro. Aldehyde oxidation products of the previously identified substrates p-cymene (4-isopropylbenzaldehyde) and limonene (perillaldehyde) were observed in addition to major hydroxylation products 4-isopropylbenzyl alcohol and perillyl alcohol respectively. These further oxidation products had not previously been seen with putidaredoxin supported oxidation. Furthermore, when supported by cymredoxin CYP108N12 is able to oxidise a wider range of substrates than previously reported. These include o-xylene, α-terpineol, (− )-carveol and thymol yielding o-tolylmethanol, 7- hydroxyterpineol, (4R)-7-hydroxycarveol and 5-hydroxymethyl-2-isopropylphenol, respectively. Cymredoxin is also capable of supporting CYP108A1 (P450terp) and CYP176A1 activity, allowing them to catalyse the hydroxylation of their native substrates α-terpineol to 7-hydroxyterpineol and 1,8-cineole to 6β-hydroxycineole respectively. These results indicate that cymredoxin not only improves the catalytic capability of CYP108N12 but can also support the activity of other P450s and prove useful for their characterisation.Item Open Access Time capsules of biodiversity: Future research directions for groundwater-dependent ecosystems of the Great Artesian Basin(FRONTIERS MEDIA SA, 2023) Beasley-Hall, P.G.; Murphy, N.P.; King, R.A.; White, N.E.; Hedges, B.A.; Cooper, S.J.B.; Austin, A.D.; Guzik, M.T.The Great Artesian Basin of Australia represents one of the largest and deepest basins of freshwater on Earth. Thousands of springs fed by the Basin are scattered across Australia’s arid zone, often representing the sole sources of freshwater for thousands of kilometers. As “islands” in the desert, the springs support endemic fauna and flora that have undergone millions of years of evolution in almost total isolation. Here, we review the current body of knowledge surrounding Great Artesian Basin springs and their significance from ecological, evolutionary, and cultural perspectives using South Australian spring wetlands as a case study. We begin by identifying the status of these springs as critical sources of groundwater, the unique biodiversity they support, and their cultural significance to the Arabana people as Traditional Custodians of the land. We then summarize known threats to the springs and their biota, both exogenous and endogenous, and the potential impacts of such processes. Finally, considering the status of these at-risk habitats as time capsules of biodiversity, we discuss lessons that can be learnt from current conservation and management practices in South Australia. We propose key recommendations for improved biodiversity assessment and monitoring of Great Artesian Basin springs nationwide, including 1) enhanced legal protections for spring biota; 2) increased taxonomic funding and capacity; 3) improved biodiversity monitoring methods, and 4) opportunities for reciprocal knowledge-sharing with Aboriginal peoples when conducting biodiversity research.Item Open Access An ancient, Antarctic-specific species complex: large divergences between multiple Antarctic lineages of the tardigrade genus Mesobiotus(Elsevier BV, 2022) Short, K.A.; Sands, C.J.; McInnes, S.J.; Pisani, D.; Stevens, M.I.; Convey, P.Antarctica has been isolated and progressively glaciated for over 30 million years, with only approximately 0.3 % of its area currently ice-free and capable of supporting terrestrial ecosystems. As a result, invertebrate populations have become isolated and fragmented, in some cases leading to speciation. Terrestrial invertebrate species currently found in Antarctica often show multi-million year, and even Gondwanan, heritage, with little evidence of recent colonisation. Mesobiotus is a globally distributed tardigrade genus. It has commonly been divided into two "groups", referred to as harmsworthi and furciger, with both groups currently considered cosmopolitan, with global reports including from both the Arctic and the Antarctic. However, some authors considered that Meb. furciger, as originally described, may represent an Antarctic-specific lineage. Using collections of tardigrades from across the Antarctic continent and publicly available sequences obtained from online databases, we use mitochondrial and nuclear ribosomal sequence data to clarify the relationships of Antarctic Mesobiotus species. Our analyses show that all Antarctic members belong to a single lineage, evolving separately from non-Antarctic representatives. Within this Antarctic lineage there are further deep divisions among geographic regions of the continent, consistent with the presence of a species complex. Based on our data confirming the deep divisions between this Antarctic lineage, which includes representatives of both groups, we recommend that the use of furciger and harmsworthi group terminology is now abandoned, as it leads to systematic and biogeographical confusion.Item Metadata only Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming(Elsevier BV, 2021) Mitchell, K.J.; Bover, P.; Salis, A.T.; Mudge, C.; Heiniger, H.; Thompson, M.; Hockett, B.; Weyrich, L.S.; Cooper, A.; Meachen, J.A.Natural Trap Cave (Bighorn Mountains, Wyoming) preserves an abundance of fossil remains from extinct Late Pleistocene fauna and is situated near a past migration route that likely connected populations in Eastern Beringia and the contiguous US—the ice-free corridor between the Cordilleran and Laurentide icesheets. Some palaeontological evidence supports a correspondingly high affinity between fauna recorded in Natural Trap Cave and Eastern Beringia versus elsewhere in the contiguous US, but this hypothesis has not yet been extensively tested using genetic data. In the present study, we analysed 16 horse specimens and one camel specimen from Natural Trap Cave. Of the horse specimens we analysed, we obtained 10 unique and previously unreported mitochondrial haplotypes belonging to two distinct (extinct) genetic clades—two haplotypes corresponded to a caballine horse (Equus sp.) and eight corresponded to the stilt-legged horse (Haringtonhippus francisci). With only one exception, it appears these newly sequenced individuals all shared a common ancestor more recently with Eastern Beringian individuals than with others from the contiguous US. In addition, mitochondrial data from a specimen assigned to Camelops sp. revealed that it shares a closer affinity with specimens from the Yukon Territory than those from Idaho or Nevada, though all appear to belong to a single species (“yesterday’s camel”; Camelops cf. hesternus). Together, these results are consistent with a high level of genetic connectivity between horse and camel populations in the Bighorn Mountains and Eastern Beringia during the Pleistocene.Item Open Access Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem(Springer Science and Business Media LLC, 2021) Saccò, M.; Blyth, A.J.; Humphreys, W.F.; Cooper, S.J.B.; White, N.E.; Campbell, M.; Mousavi-Derazmahalleh, M.; Hua, Q.; Mazumder, D.; Smith, C.; Griebler, C.; Grice, K.Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR—low rainfall and HR—high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.Item Metadata only Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation.(Elsevier BV, 2022) Tudini, E.; Andrews, J.; Lawrence, D.M.; King-Smith, S.L.; Baker, N.; Baxter, L.; Beilby, J.; Bennetts, B.; Beshay, V.; Black, M.; Boughtwood, T.F.; Brion, K.; Cheong, P.L.; Christie, M.; Christodoulou, J.; Chong, B.; Cox, K.; Davis, M.R.; Dejong, L.; Dinger, M.E.; et al.Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.Item Open Access Targeting malaria parasites with novel derivatives of azithromycin(Frontiers Media SA, 2022) Burns, A.L.; Sleebs, B.E.; Gancheva, M.; McLean, K.T.; Siddiqui, G.; Venter, H.; Beeson, J.G.; O’Handley, R.; Creek, D.J.; Ma, S.; Frölich, S.; Goodman, C.D.; McFadden, G.I.; Wilson, D.W.Introduction: The spread of artemisinin resistant Plasmodium falciparum parasites is of global concern and highlights the need to identify new antimalarials for future treatments. Azithromycin, a macrolide antibiotic used clinically against malaria, kills parasites via two mechanisms: ‘delayed death’ by inhibiting the bacterium-like ribosomes of the apicoplast, and ‘quick-killing’ that kills rapidly across the entire blood stage development. Methods: Here, 22 azithromycin analogues were explored for delayed death and quick-killing activities against P. falciparum (the most virulent human malaria) and P. knowlesi (a monkey parasite that frequently infects humans). Results: Seventeen analogues showed improved quick-killing against both Plasmodium species, with up to 38 to 20-fold higher potency over azithromycin after less than 48 or 28 hours of treatment for P. falciparum and P. knowlesi, respectively. Quick-killing analogues maintained activity throughout the blood stage lifecycle, including ring stages of P. falciparum parasites (<12 hrs treatment) and were >5-fold more selective against P. falciparum than human cells. Isopentenyl pyrophosphate supplemented parasites that lacked an apicoplast were equally sensitive to quick-killing analogues, confirming that the quick killing activity of these drugs was not directed at the apicoplast. Further, activity against the related apicoplast containing parasite Toxoplasma gondii and the gram-positive bacterium Streptococcus pneumoniae did not show improvement over azithromycin, highlighting the specific improvement in antimalarial quick-killing activity. Metabolomic profiling of parasites subjected to the most potent compound showed a build-up of non-haemoglobin derived peptides that was similar to chloroquine, while also exhibiting accumulation of haemoglobin-derived peptides that was absent for chloroquine treatment. Discussion: The azithromycin analogues characterised in this study expand the structural diversity over previously reported quick-killing compounds and provide new starting points to develop azithromycin analogues with quickkilling antimalarial activity.Item Open Access The APOE E4 allele is associated with faster rates of neuroretinal thinning in a prospective cohort study of suspect and early glaucoma(Elsevier BV, 2022) Mullany, S.; Marshall, H.; Diaz-Torres, S.; Berry, E.C.; Schmidt, J.M.; Thomson, D.; Qassim, A.; To, M.-S.; Dimasi, D.; Kuot, A.; Knight, L.S.W.; Hollitt, G.; Kolovos, A.; Schulz, A.; Lake, S.; Mills, R.A.; Agar, A.; Galanopoulos, A.; Landers, J.; Mitchell, P.; et al.Purpose: To investigate the association between the apolipoprotein E (APOE) E4 dementia-risk allele and prospective longitudinal retinal thinning in a cohort study of suspect and early manifest glaucoma. Design: Retrospective analysis of prospective cohort data. Participants: This study included all available eyes from participants recruited to the Progression Risk of Glaucoma: Relevant SNPs [single nucleotide polymorphisms] with Significant Association (PROGRESSA) study with genotyping data from which APOE genotypes could be determined. Methods: Apolipoprotein E alleles and genotypes were determined in PROGRESSA, and their distributions were compared with an age-matched and ancestrally matched normative cohort, the Blue Mountains Eye Study. Structural parameters of neuroretinal atrophy measured using spectral-domain OCT were compared within the PROGRESSA cohort on the basis of APOE E4 allele status. Main Outcome Measures: Longitudinal rates of thinning in the macular ganglion celleinner plexiform layer (mGCIPL) complex and the peripapillary retinal nerve fiber layer (pRNFL). Results: Rates of mGCIPL complex thinning were faster in participants harboring ≥1 copies of the APOE E4 allele (b ¼ e0.13 mm/year; P ≤0.001). This finding was strongest in eyes affected by normal-tension glaucoma (NTG; b ¼ e0.20 mm/year; P ¼ 0.003). Apolipoprotein E E4 allele carriers were also more likely to be lost to followup (P ¼ 0.01) and to demonstrate a thinner average mGCIPL complex (70.9 mm vs. 71.9 mm; P ¼ 0.011) and pRNFL (77.6 mm vs. 79.2 mm; P ¼ 0.045) after a minimum of 3 years of monitoring. Conclusions: The APOE E4 allele was associated with faster rates of mCGIPL complex thinning, particularly in eyes with NTG. These results suggest that the APOE E4 allele may be a risk factor for retinal ganglion cell degeneration in glaucoma.Item Metadata only Termite sensitivity to temperature affects global wood decay rates.(American Association for the Advancement of Science (AAAS), 2022) Zanne, A.E.; Flores-Moreno, H.; Powell, J.R.; Cornwell, W.K.; Dalling, J.W.; Austin, A.T.; Classen, A.T.; Eggleton, P.; Okada, K.-I.; Parr, C.L.; Adair, E.C.; Adu-Bredu, S.; Alam, M.A.; Alvarez-Garzón, C.; Apgaua, D.; Aragón, R.; Ardon, M.; Arndt, S.K.; Ashton, L.A.; Barber, N.A.; et al.Deadwood is a large global carbon store with its store size partially determined by biotic decay. Microbial wood decay rates are known to respond to changing temperature and precipitation. Termites are also important decomposers in the tropics but are less well studied. An understanding of their climate sensitivities is needed to estimate climate change effects on wood carbon pools. Using data from 133 sites spanning six continents, we found that termite wood discovery and consumption were highly sensitive to temperature (with decay increasing >6.8 times per 10°C increase in temperature)-even more so than microbes. Termite decay effects were greatest in tropical seasonal forests, tropical savannas, and subtropical deserts. With tropicalization (i.e., warming shifts to tropical climates), termite wood decay will likely increase as termites access more of Earth's surface.Item Metadata only Exploring lipid affinities of persistent organic pollutants and MeO-PBDEs in blubber of marine mammals(Elsevier Ltd, 2022) Weijs, L.; Covaci, A.; Carroll, A.; Kemper, C.; Melvin, S.Although lipophilic compounds have been the focus of numerous studies in marine mammals, their association with lipids is widely accepted, but rarely scrutinized. This pilot study aimed to investigate potential relationships between individual lipids from different lipid classes identified through a non-targeted Nuclear Magnetic Resonance (NMR) based lipidomics approach and legacy POPs in the blubber of long-finned pilot whales, sperm whales, common bottlenose dolphins, and Indo-Pacific bottlenose dolphins. Concentrations of selected POPs such as HCB and HCHs in sperm whales from Tasmania were found to differ from those in long-finned pilot whales and common bottlenose dolphins from the same location. Profiles of NMR spectra measured in blubber of sperm whales were also distinctly different compared to the pilot whales and common bottlenose dolphins. Two groups of Indo-Pacific bottlenose dolphins from South Australia that were 20 years apart showed highly comparable profiles of NMR signals despite having higher concentrations of several POP classes in the more recent group. More specific correlations were investigated between selected POPs (n = 12) and all detected NMR signals (n = 63) in all species. Outcomes were species-specific, but difficult to interpret due to the lack of available literature for marine mammals and the small sample sizes per species. Because of the key role of lipids in the bioaccumulation of POPs and in the incidence of diseases, more attention should be given to the identification and characterization of lipid species in future toxicological studies. However, future studies should focus on one marine mammal species to increase sample sizes and limit the number of confounding factors, such as diet, that can influence POP and lipid levels and profiles.Item Open Access All-optica sub-Kelvin sympathetic cooling of a levitated microsphere in vacuum(Optical Society of America, 2022) Arita, Y.; Bruce, G.D.; Wright, E.M.; Simpson, S.H.; Zemanek, P.; Dholakia, K.We demonstrate all-optical sympathetic cooling of a laser-trapped microsphere to sub-Kelvin temperatures, mediated by optical binding to a feedback-cooled adjacent particle. Our study opens prospects for multi-particle quantum entanglement and sensing in levitated optomechanics.