First ROV exploration of the Perth Canyon: Canyon setting, faunal observations, and anthropogenic impacts.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Trotter, J. A., Pattiaratchi, C., Montagna, P., Taviani, M., Falter, J., Thresher, R., Hosie, A., Haig, D., Foglini, F., Hua, Q., & McCulloch, M. T. First ROV exploration of the Perth Canyon: Canyon setting, faunal observations, and anthropogenic impacts. Frontiers in Marine Science, 6, (2019):173, doi:10.3389/fmars.2019.00173.This study represents the first ROV-based exploration of the Perth Canyon, a prominent submarine valley system in the southeast Indian Ocean offshore Fremantle (Perth), Western Australia. This multi-disciplinary study characterizes the canyon topography, hydrography, anthropogenic impacts, and provides a general overview of the fauna and habitats encountered during the cruise. ROV surveys and sample collections, with a specific focus on deep-sea corals, were conducted at six sites extending from the head to the mouth of the canyon. Multi-beam maps of the canyon topography show near vertical cliff walls, scarps, and broad terraces. Biostratigraphic analyses of the canyon lithologies indicate Late Paleocene to Late Oligocene depositional ages within upper bathyal depths (200–700 m). The video footage has revealed a quiescent ‘fossil canyon’ system with sporadic, localized concentrations of mega- and macro-benthos (∼680–1,800 m), which include corals, sponges, molluscs, echinoderms, crustaceans, brachiopods, and worms, as well as plankton and nekton (fish species). Solitary (Desmophyllum dianthus, Caryophyllia sp., Vaughanella sp., and Polymyces sp.) and colonial (Solenosmilia variabilis) scleractinians were sporadically distributed along the walls and under overhangs within the canyon valleys and along its rim. Gorgonian, bamboo, and proteinaceous corals were present, with live Corallium often hosting a diverse community of organisms. Extensive coral graveyards, discovered at two disparate sites between ∼690–720 m and 1,560–1,790 m, comprise colonial (S. variabilis) and solitary (D. dianthus) scleractinians that flourished during the last ice age (∼18 ka to 33 ka BP). ROV sampling (674–1,815 m) spanned intermediate (Antarctic Intermediate Water) and deep waters (Upper Circumpolar Deep Water) with temperatures from ∼2.5 to 6°C. Seawater CTD profiles of these waters show consistent physical and chemical conditions at equivalent depths between dive sites. Their carbonate chemistry indicate supersaturation (Ωcalcite ∼ 1.3–2.2) with respect to calcite, but mild saturation to undersaturation (Ωaragonite ∼ 0.8–1.4) of aragonite; notably some scleractinians were found living below the aragonite saturation horizon (∼1,000 m). Seawater δ13C and nuclear bomb produced Δ14C compositions decrease in the upper canyon waters by up to ∼0.8‰ (<800 m) and 95‰ (<500 m), respectively, relative to measurements taken nearby in 1978, reflecting the ingress of anthropogenic carbon into upper intermediate waters.This work was supported by research funding from the Australian Research Council to MM (FL120100049) and JT (FT160100259), the Italian National Programme of Antarctic Research (PNRA16-00069 Graceful Project) to PM and MT, the Australian Institute of Nuclear Science and Engineering to MM, JT, JF, RT, MT, PM (AINSE Award 16/009). Supplementary oceanographic data are funded through Integrated Marine Observing System (IMOS) supported by the Australian Government

The use of phylogeny to interpret cross-cultural patterns in plant use and guide medicinal plant discovery: an example from Pterocarpus (Leguminosae)

The study of traditional knowledge of medicinal plants has led to discoveries that have helped combat diseases and improve healthcare. However, the development of quantitative measures that can assist our quest for new medicinal plants has not greatly advanced in recent years. Phylogenetic tools have entered many scientific fields in the last two decades to provide explanatory power, but have been overlooked in ethnomedicinal studies. Several studies show that medicinal properties are not randomly distributed in plant phylogenies, suggesting that phylogeny shapes ethnobotanical use. Nevertheless, empirical studies that explicitly combine ethnobotanical and phylogenetic information are scarce.In this study, we borrowed tools from community ecology phylogenetics to quantify significance of phylogenetic signal in medicinal properties in plants and identify nodes on phylogenies with high bioscreening potential. To do this, we produced an ethnomedicinal review from extensive literature research and a multi-locus phylogenetic hypothesis for the pantropical genus Pterocarpus (Leguminosae: Papilionoideae). We demonstrate that species used to treat a certain conditions, such as malaria, are significantly phylogenetically clumped and we highlight nodes in the phylogeny that are significantly overabundant in species used to treat certain conditions. These cross-cultural patterns in ethnomedicinal usage in Pterocarpus are interpreted in the light of phylogenetic relationships.This study provides techniques that enable the application of phylogenies in bioscreening, but also sheds light on the processes that shape cross-cultural ethnomedicinal patterns. This community phylogenetic approach demonstrates that similar ethnobotanical uses can arise in parallel in different areas where related plants are available. With a vast amount of ethnomedicinal and phylogenetic information available, we predict that this field, after further refinement of the techniques, will expand into similar research areas, such as pest management or the search for bioactive plant-based compounds

First ROV Exploration of the Perth Canyon: Canyon Setting, Faunal Observations, and Anthropogenic Impacts

This study represents the first ROV-based exploration of the Perth Canyon, a prominent submarine valley system in the southeast Indian Ocean offshore Fremantle (Perth), Western Australia. This multi-disciplinary study characterizes the canyon topography, hydrography, anthropogenic impacts, and provides a general overview of the fauna and habitats encountered during the cruise. ROV surveys and sample collections, with a specific focus on deep-sea corals, were conducted at six sites extending from the head to the mouth of the canyon. Multi-beam maps of the canyon topography show near vertical cliff walls, scarps, and broad terraces. Biostratigraphic analyses of the canyon lithologies indicate Late Paleocene to Late Oligocene depositional ages within upper bathyal depths (200–700 m). The video footage has revealed a quiescent ‘fossil canyon’ system with sporadic, localized concentrations of mega- and macro-benthos (∼680–1,800 m), which include corals, sponges, molluscs, echinoderms, crustaceans, brachiopods, and worms, as well as plankton and nekton (fish species). Solitary (Desmophyllum dianthus, Caryophyllia sp., Vaughanella sp., and Polymyces sp.) and colonial (Solenosmilia variabilis) scleractinians were sporadically distributed along the walls and under overhangs within the canyon valleys and along its rim. Gorgonian, bamboo, and proteinaceous corals were present, with live Corallium often hosting a diverse community of organisms. Extensive coral graveyards, discovered at two disparate sites between ∼690–720 m and 1,560–1,790 m, comprise colonial (S. variabilis) and solitary (D. dianthus) scleractinians that flourished during the last ice age (∼18 ka to 33 ka BP). ROV sampling (674–1,815 m) spanned intermediate (Antarctic Intermediate Water) and deep waters (Upper Circumpolar Deep Water) with temperatures from ∼2.5 to 6°C. Seawater CTD profiles of these waters show consistent physical and chemical conditions at equivalent depths between dive sites. Their carbonate chemistry indicate supersaturation (Ωcalcite ∼ 1.3–2.2) with respect to calcite, but mild saturation to undersaturation (Ωaragonite ∼ 0.8–1.4) of aragonite; notably some scleractinians were found living below the aragonite saturation horizon (∼1,000 m). Seawater δ13C and nuclear bomb produced Δ14C compositions decrease in the upper canyon waters by up to ∼0.8‰ (&lt;800 m) and 95‰ (&lt;500 m), respectively, relative to measurements taken nearby in 1978, reflecting the ingress of anthropogenic carbon into upper intermediate waters

Loss-of-function mutations in the X-linked biglycan gene cause a severe syndromic form of thoracic aortic aneurysms and dissections.

Thoracic aortic aneurysm and dissection (TAAD) is typically inherited in an autosomal dominant manner, but rare X-linked families have been described. So far, the only known X-linked gene is FLNA, which is associated with the periventricular nodular heterotopia type of Ehlers-Danlos syndrome. However, mutations in this gene explain only a small number of X-linked TAAD families. We performed targeted resequencing of 368 candidate genes in a cohort of 11 molecularly unexplained Marfan probands. Subsequently, Sanger sequencing of BGN in 360 male and 155 female molecularly unexplained TAAD probands was performed. We found five individuals with loss-of-function mutations in BGN encoding the small leucine-rich proteoglycan biglycan. The clinical phenotype is characterized by early-onset aortic aneurysm and dissection. Other recurrent findings include hypertelorism, pectus deformity, joint hypermobility, contractures, and mild skeletal dysplasia. Fluorescent staining revealed an increase in TGF-β signaling, evidenced by an increase in nuclear pSMAD2 in the aortic wall. Our results are in line with those of prior reports demonstrating that Bgn-deficient male BALB/cA mice die from aortic rupture. In conclusion, BGN gene defects in humans cause an X-linked syndromic form of severe TAAD that is associated with preservation of elastic fibers and increased TGF-β signaling.Genet Med 19 4, 386-395

Southeastern Association of Law Libraries Annual Meeting

The 2009 SEAALL Annual Meeting was held in Athens Georgia, April 16-18, 2009

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Early Devonian (mid-Lochkovian) brachiopod, coral and conodont faunas from Manildra, New South Wales, Australia

Silicified faunas, dominated by brachiopods (55 species: an increase of 64% over previous reports), from low in the Early Devonian (mid-Lochkovian) Garra limestone at Manildra, east-central New South Wales, are documented, complemented by documentation of associated tabulate and rugose corals (12 and 4 specif;s respectively), and conodonts (14 species and subspecies from 57 samples), pivotal in assessing the age of these faunas. Other, surprisingly rare, elements (principally molluscs) are reported but not documented, Also documented are the tabulate and rugose corals from the immediately underlying uppermost Maradana Shale - 4 and 2 spp respectively, all occurring as well, though less well-preserved, among the silicified faunas of the Garra Limestone - and conodonts from carbonate intervals in the overlying Mandagery Park Formation. The conodont faunas indicate maximum ages of delta Zone for the Garra Limestone at Manildra and pesavis Zone to early Pragian for carbonates in the overlying Mandagery Park Formation. The silicified brachiopod assemblage from the lower beds of the Garra limestone has Old-World Realm biogeographic affinities with noteworthy connections with various brachiopod assemblages from western North America and Arctic Canada. Closest affinities are with the early Quadrithyris Zone or transitional Gypzdula pelagica-Quadrithyris Zone of Nevada. Contrary to recent assumptions that the provincial sensitivity of brachiopods makes them of very limited value in making long-range stratigraphic alignments, the consistent ages resulting from conodont data and comparison of the brachiopod faunas with Early Devonian faunas from western and Arctic North America is evidence that compelling stratigraphic alignments may be obtained intercontinentally using brachiopods - providing, as in the present case, the faunas are diverse and are from the same biogeographic realm. New data are provided for assessing the sedimentary context, palaeoecology and biogeographic affinities of the brachiopod, coral and conodont faunas from Manildra. The deeper-water Maradana Shale shallows upwards into the shallow marine, brachiopod-dominated Garra Limestone The latter is characterised by angular, poorly sorted allochemical constituents, high mud contents, and encrusting algal mats of Girvanella, all implying low-energy conditions with limited post-mortem transport. This is supported by the relatively low degree of valve disarticulation of the silicified brachiopod assemblages. The sedimentological data accord with a shallow (photic zone), open marine environment, with moderate to low-energy conditions of a protected zone within a carbonate platform or shelf-margin. The Garra Limestone is terminated by an influx of clastics and volcaniclastics, the Mandagery Park Formation (redefined). The 55 species of brachiopods from the Garra Limestone at Manildra are referred to 36 genera including two new rhynchonellid genera, Protodorsisinus and Discamella, with type species P. similis sp nov. and D troparvis sp, nov. respectively. A new species of the cemented strophomenid, Colleto.stracia, is described but not named. None of the coral and conodont taxa documented appear to be new.54 page(s