Australian advances in vegetation classification and the need for a national, science-based approach

This editorial introduces the Australian Journal of Botany special issue ‘Vegetation science for decision-making’. Vegetation science and classification are crucial to understanding Australian landscapes. From the mulga shrublands of the arid interior to the monsoon rain forests of northern Australia, we have culturally and scientifically built upon the delineation of vegetation into recognisable and repeatable patterns. As remote sensing and database capacities increase, this improved capability to measure vegetation and share data also prompts collaboration and synthesis of complex, specialised datasets. Although the task faces significant challenges, the growing body of literature demonstrates a strong discipline. In Australia, purpose-driven products describe vegetation at broad scales (e.g. the National Vegetation Information System, the Terrestrial Ecosystem Research Network). At fine scales however (i.e. that of the vegetation community), no uniform framework or agreed protocols exist. Climate and landform dictate vegetation patterns at broad scales, but microtopography, microclimate and biotic processes act as filters at finer scales. This is the scale where climate-change impacts are most likely to be detected and effected; this is the scale at which a deeper understanding of evolutionary ecology will be achieved, and it is the scale at which species need to be protected. A common language and system for understanding Australian communities and impetus for collecting data at this scale is needed. In the face of ongoing climate and development pressures and an increasingly complex set of tools to manage these threats (e.g. offset policies, cumulative impact assessments), a nationally collaborative approach is needed. It is our hope that this special issue will help to achieve this

A plot-based analysis of the vegetation of the Northern Territory, Australia: a first assessment within the International Vegetation Classification framework

Aims: To develop an interim classification of the vegetation of the Northern Territory at the International Vegetation Classification (IVC) division (level 4) and macrogroup (level 5) levels. These types are produced to assist in the development of an integrated nationwide plot and floristically based classification of Australia allowing integration within a global perspective. Study Area: The Northern Territory of Australia covers an area of 1.42 million square kilometres, almost 20% of Australia’s land mass. It comprises three distinct climatic zones including tropical, subtropical and arid vegetation types. Methods: We used collated vegetation data held by two organisations: the Northern Territory Government, Department of Environment, Parks and Water Security and the Terrestrial Ecosystem Research Network (a total of 45,710 plots used). We applied semi-supervised quantitative classification methods to define vegetation types at the IVC division and macrogroup levels. Analyses used kR-CLUSTER methods on presence/absence data. Macrogroups were characterised by taxa with the highest frequency of occurrence across plots. Additional analyses were conducted (cluster) to elucidate interrelationships between macrogroups and to assist in the assessment of division level typology. Results: We propose 21 macrogroups and place these within higher thematic levels of the IVC. Conclusions: We found that the IVC hierarchy and associated standard procedures and protocols provide a useful classification tool for Australian ecosystems. The divisions and macrogroups provide a valid framework for subsequent analysis of Northern Territory vegetation types at the detailed levels of the IVC. A consistent typology for the Northern Territory (and hopefully in future, for all of Australia) has numerous benefits, in that they can be used for various applications using a well-structured, systematic and authoritative description and classification that is placed in a continental and global context, readily enabling the one system to be used in studies from the local to global level. Taxonomic reference: Northern Territory Herbarium (2022). Abbreviations: DVT = Definitive Vegetation Type; IVC = International Vegetation Classification; nMDS = non-metric multidimensional scaling; NT = Northern Territory; NTVSD = Northern Territory Vegetation Site Database; NVIS = National Vegetation Information System; WA = Western Australia

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials

Toxic metal(loid) speciation during weathering of iron sulfide mine tailings under semi-arid climate

Toxic metalliferous mine-tailings pose a significant health risk to ecosystems and neighboring communities from wind and water dispersion of particulates containing high concentrations of toxic metal(loid)s (e.g., Pb, As, Zn). Tailings are particularly vulnerable to erosion before vegetative cover can be reestablished, i.e., decades or longer in semi-arid environments without intervention. Metal(loid) speciation, linked directly to bioaccessibility and lability, is controlled by mineral weathering and is a key consideration when assessing human and environmental health risks associated with mine sites. At the semi-arid Iron King Mine and Humboldt Smelter Superfund site in central Arizona, the mineral assemblage of the top 2 m of tailings has been previously characterized. A distinct redox gradient was observed in the top 0.5 m of the tailings and the mineral assemblage indicates progressive transformation of ferrous iron sulfides to ferrihydrite and gypsum, which, in turn weather to form schwertmannite and then jarosite accompanied by a progressive decrease in pH (7.3 to 2.3). Within the geochemical context of this reaction front, we examined enriched toxic metal(loid)s As, Pb, and Zn with surficial concentrations 41.1, 10.7, 39.3 mM kg-1 (3080, 2200, and 2570 mg kg-1), respectively. The highest bulk concentrations of As and Zn occur at the redox boundary representing a 1.7 and 4.2 fold enrichment relative to surficial concentrations, respectively, indicating the translocation of toxic elements from the gossan zone to either the underlying redox boundary or the surface crust. Metal speciation was also examined as a function of depth using X-ray absorption spectroscopy (XAS). The deepest sample (180 cm) contains sulfides (e.g., pyrite, arsenopyrite, galena, and sphalerite). Samples from the redox transition zone (25-54 cm) contain a mixture of sulfides, carbonates (siderite, ankerite, cerrusite, and smithsonite) and metal(loid)s sorbed to neoformed secondary Fe phases, principally ferrihydrite. In surface samples (0-35 cm), metal(loid)s are found as sorbed species or incorporated into secondary Fe hydroxysulfate phases, such as schwertmannite and jarosites. Metal-bearing efflorescent salts (e.g., ZnSO4·nH2O) were detected in the surficial sample. Taken together, these data suggest the bioaccessibility and lability of metal(loid)s are altered by mineral weathering, which results in both the downward migration of metal(loid)s to the redox boundary, as well as the precipitation of metal salts at the surface.24 month embargo; published online: 7 February 2015This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.We acknowledge support from Cancer Research UK (C5047/A22530, C309/A11566, C368/A6743, A368/A7990, C14303/A17197) and the Dallaglio Foundation. We also acknowledge support from the National Institute of Health Research (NIHR) (The Biomedical Research Centre at The Institute of Cancer Research & The Royal Marsden NHS Foundation Trust and the project "Prostate Cancer: Mechanisms of Progression and Treatment (PROMPT)" [G0500966/75466]). We thank the Wellcome Trust, Bob Champion Cancer Trust, The Orchid Cancer appeal, The RoseTrees Trust, The North West Cancer Research Fund, Big C, The King family, and The Masonic Charitable Foundation for funding. This research is supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001202), the UK Medical Research Council (FC001202), and the Wellcome Trust (FC001202). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Mutational signatures of ionizing radiation in second malignancies

Ionizing radiation is a potent carcinogen, inducing cancer through DNA damage. The signatures of mutations arising in human tissues following in vivo exposure to ionizing radiation have not been documented. Here, we searched for signatures of ionizing radiation in 12 radiation-associated second malignancies of different tumour types. Two signatures of somatic mutation characterize ionizing radiation exposure irrespective of tumour type. Compared with 319 radiation-naive tumours, radiation-associated tumours carry a median extra 201 deletions genome-wide, sized 1-100 base pairs often with microhomology at the junction. Unlike deletions of radiation-naive tumours, these show no variation in density across the genome or correlation with sequence context, replication timing or chromatin structure. Furthermore, we observe a significant increase in balanced inversions in radiation-associated tumours. Both small deletions and inversions generate driver mutations. Thus, ionizing radiation generates distinctive mutational signatures that explain its carcinogenic potential.This work was supported by funding from the Wellcome Trust (grant reference 077012/Z/05/Z), Skeletal Cancer Action Trust, Rosetrees Trust UK, Bone Cancer Research Trust, the RNOH NHS Trust, the National Institute for Health Research Health Protection Research Unit in Chemical and Radiation Hazards and Threats at Newcastle University in partnership with Public Health England. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England. Tissue was obtained from the RNOH Musculoskeletal Research Programme and Biobank, co-ordinated by Mrs Deidre Brooking and Mrs Ru Grinnell, Biobank staff, RNOH. Support was provided to AMF by the National Institute for Health Research, UCLH Biomedical Research Centre, and the CRUK UCL Experimental Cancer Centre. S.N.Z. and S.B. are personally funded through Wellcome Trust Intermediate Clinical Research Fellowships, P.J.C. through a Wellcome Trust Senior Clinical Research Fellowship

What is the economic evidence for mHealth? A systematic review of economic evaluations of mHealth solutions

Background Mobile health (mHealth) is often reputed to be cost-effective or cost-saving. Despite optimism, the strength of the evidence supporting this assertion has been limited. In this systematic review the body of evidence related to economic evaluations of mHealth interventions is assessed and summarized. Methods Seven electronic bibliographic databases, grey literature, and relevant references were searched. Eligibility criteria included original articles, comparison of costs and consequences of interventions (one categorized as a primary mHealth intervention or mHealth intervention as a component of other interventions), health and economic outcomes and published in English. Full economic evaluations were appraised using the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist and The PRISMA guidelines were followed. Results Searches identified 5902 results, of which 318 were examined at full text, and 39 were included in this review. The 39 studies spanned 19 countries, most of which were conducted in upper and upper-middle income countries (34, 87.2%). Primary mHealth interventions (35, 89.7%), behavior change communication type interventions (e.g., improve attendance rates, medication adherence) (27, 69.2%), and short messaging system (SMS) as the mHealth function (e.g., used to send reminders, information, provide support, conduct surveys or collect data) (22, 56.4%) were most frequent; the most frequent disease or condition focuses were outpatient clinic attendance, cardiovascular disease, and diabetes. The average percent of CHEERS checklist items reported was 79.6% (range 47.62–100, STD 14.18) and the top quartile reported 91.3–100%. In 29 studies (74.3%), researchers reported that the mHealth intervention was cost-effective, economically beneficial, or cost saving at base case. Conclusions Findings highlight a growing body of economic evidence for mHealth interventions. Although all studies included a comparison of intervention effectiveness of a health-related outcome and reported economic data, many did not report all recommended economic outcome items and were lacking in comprehensive analysis. The identified economic evaluations varied by disease or condition focus, economic outcome measurements, perspectives, and were distributed unevenly geographically, limiting formal meta-analysis. Further research is needed in low and low-middle income countries and to understand the impact of different mHealth types. Following established economic reporting guidelines will improve this body of research