Optimised eucalypt domestication : an example using e. Cladocalyx, a species for low rainfall environments

Eucalyptus cladocalyx is endemic to South Australia and has been planted extensively on farmland throughout southern Australia and in dry, Mediterranean climates overseas. Its wood is hard, strong and naturally durable, making it suitable for fuelwood and solid-wood applications. Domestication in Australia commenced in 2001, when 11 provenance-progeny trials were established. The breeding objective is to maximise sawlog production per hectare per year. This thesis, presented as six chapters, examines genetic aspects of these trials that will influence the future direction of the species' domestication program. Chapter 1 argues that traditional methods and assumptions historically used to identify selections in the first-generation breeding programs of the main commercial tree species can be improved upon in the following ways: (1) Examination of wood properties (in addition to growth and form traits) during the first generation, taking advantage of modern labour-saving techniques, rather than delaying until later generations when unidentified adverse genetic correlations between traits may be problematic. (2) Employing molecular markers to determine population genetic parameters and reconstruct pedigree and inbreeding information from families that have unknown or uncertain ancestry. (3) Using recently-developed mixed-modelling techniques that allow integration of marker-based pedigree and inbreeding information to model genotype-by-environment (GxE) interactions using large datasets. Chapter 2 examines genetic parameters including heritability of growth and wood natural durability traits and additive genetic correlations among traits. The use of near infrared reflectance as a low-cost method of screening durability traits such as decay mass loss and wood extractive content is also investigated. Chapter 3 examines the use of marker-based data to modify traditional assumptions made in analysis of first generation breeding populations. Previously published growth-trait estimates, together with an earlier isozyme study, indicated that the traditional approach may give upwardly biased heritability estimates due to high and heterogeneous selfing. Models were implemented that compared the approach of treating families as half-sibs with analyses based on previously existing isozyme estimates of heterogeneous family outcrossing to modify pedigree assumptions. The results of genotyping mature trees from the majority of families in the breeding population using single-nucleotide polymorphism (SNP) markers are presented in Chapter 4. Population structure and diversity, family relatedness, inbreeding and inbreeding depression were investigated. Chapter 5 integrates the marker-based estimates of family-level relatedness and inbreeding of Chapter 4 into a quantitative genetic analysis across sites using an extension of the methodology developed in Chapter 3. Individual-tree mixed models based on (i) the traditional half-sib family assumption and (ii) a modified mixed model incorporating marker-based data were compared. Analysis of GxE was performed across the 11 sites using individual-tree, factor analytic mixed models. Chapter 6 concludes that the prospects for genetic improvement of E. cladocalyx are good, due to ample, heritable genetic variation and absence of adverse genetic correlations among traits. Analyses with integrated molecular marker data were significantly improved, as traditional models were unsuitable due to the breeding population's heterogeneous and unusually high levels of inbreeding. Integration of marker data into first-generation analyses of eucalypt breeding populations is likely to find wider application in future

Sorbent Structural Impacts Due to Humidity on Carbon Dioxide Removal Sorbents for Advanced Exploration Systems

The Life Support Systems Project (LSSP) under the Advanced Exploration Systems (AES) program builds upon the work performed under the AES Atmosphere Resource Recovery and Environmental Monitoring (ARREM) project focusing on the numerous technology development areas. The CO2 removal and associated air drying development efforts are focused on improving the current state-of-the-art system on the International Space Station (ISS) utilizing fixed beds of sorbent pellets by seeking more robust pelletized sorbents, evaluating structured sorbents, and examining alternate bed configurations to improve system efficiency and reliability. A component of the CO2 removal effort encompasses structural stability testing of existing and emerging sorbents. Testing will be performed on dry sorbents and sorbents that have been conditioned to three humidity levels. This paper describes the sorbent structural stability screening efforts in support of the LSS Project within the AES Program

Species-specificity of transcriptional regulation and the response to lipopolysaccharide in mammalian macrophages.

Mammalian macrophages differ in their basal gene expression profiles and response to the toll-like receptor 4 (TLR4) agonist, lipopolysaccharide (LPS). In human macrophages, LPS elicits a temporal cascade of transient gene expression including feed forward activators and feedback regulators that limit the response. Here we present a transcriptional network analysis of the response of sheep bone marrow-derived macrophages (BMDM) to LPS based upon RNA-seq at 0, 2, 4, 7, and 24 h post-stimulation. The analysis reveals a conserved transcription factor network with humans, and rapid induction of feedback regulators that constrain the response at every level. The gene expression profiles of sheep BMDM at 0 and 7 h post LPS addition were compared to similar data obtained from goat, cow, water buffalo, horse, pig, mouse and rat BMDM. This comparison was based upon identification of 8,200 genes annotated in all species and detected at >10TPM in at least one sample. Analysis of expression of transcription factors revealed a conserved transcriptional millieu associated with macrophage differentiation and LPS response. The largest co-expression clusters, including genes encoding cell surface receptors, endosome–lysosome components and secretory activity, were also expressed in all species and the combined dataset defines a macrophage functional transcriptome. All of the large animals differed from rodents in lacking inducible expression of genes involved in arginine metabolism and nitric oxide production. Instead, they expressed inducible transporters and enzymes of tryptophan and kynurenine metabolism. BMDM from all species expressed high levels of transcripts encoding transporters and enzymes involved in glutamine metabolism suggesting that glutamine is a major metabolic fuel. We identify and discuss transcripts that were uniquely expressed or regulated in rodents compared to large animals including ACOD1, CXC and CC chemokines, CD163, CLEC4E, CPM, CSF1, CSF2, CTSK, MARCO, MMP9, SLC2A3, SLC7A7, and SUCNR1. Conversely, the data confirm the conserved regulation of multiple transcripts for which there is limited functional data from mouse models and knockouts. The data provide a resource for functional annotation and interpretation of loci involved in susceptibility to infectious and inflammatory disease in humans and large animal species

Whitefish Wars: Pangasius, politics and consumer confusion in Europe

Rapid growth in production of the farmed Vietnamese whitefish pangasius and its trade with the European Union has provoked criticism of the fish’s environmental, social and safety credentials by actors including WWF and Members of the European Parliament and associated negative media coverage. This paper reviews the range of claims communicated about pangasius (identified as a form of mass mediated risk governance), in light of scientific evidence and analysis of data from the EU’s Rapid Alert System for Food and Feeds food safety notification system for imported seafood. This analysis shows pangasius is to be generally safe, environmentally benign, and beneficial for actors along the international value chains that characterise the trade. The case is made that increasingly politicised debates in Europe around risk and uncertainty are potentially counterproductive for EU seafood security and European aquaculture industry, and that the trade in pangasius can contribute to sustainable seafood consumption in a number of ways. Transparent evidence-based assessment and systems for communicating complex issues of risk for products such as pangasius are required in order to support continuance of fair and mutually beneficial trade

A blood-based biomarker panel indicates IL-10 and IL-12/23p40 are jointly associated as predictors of β-amyloid load in an AD cohort

Alzheimer’s Disease (AD) is the most common form of dementia, characterised by extracellular amyloid deposition as plaques and intracellular neurofibrillary tangles of tau protein. As no current clinical test can diagnose individuals at risk of developing AD, the aim of this project is to evaluate a blood-based biomarker panel to identify individuals who carry this risk. We analysed the levels of 22 biomarkers in clinically classified healthy controls (HC), mild cognitive impairment (MCI) and Alzheimer’s participants from the well characterised Australian Imaging, Biomarker and Lifestyle (AIBL) study of aging. High levels of IL-10 and IL-12/23p40 were significantly associated with amyloid deposition in HC, suggesting that these two biomarkers might be used to detect at risk individuals. Additionally, other biomarkers (Eotaxin-3, Leptin, PYY) exhibited altered levels in AD participants possessing the APOE ε4 allele. This suggests that the physiology of some potential biomarkers may be altered in AD due to the APOE ε4 allele, a major risk factor for AD. Taken together, these data highlight several potential biomarkers that can be used in a blood-based panel to allow earlier identification of individuals at risk of developing AD and/or early stage AD for which current therapies may be more beneficial

A blood-based biomarker panel indicates IL-10 and IL-12/23p40 are jointly associated as predictors of β-amyloid load in an AD cohort

Alzheimer’s Disease (AD) is the most common form of dementia, characterised by extracellular amyloid deposition as plaques and intracellular neurofibrillary tangles of tau protein. As no current clinical test can diagnose individuals at risk of developing AD, the aim of this project is to evaluate a blood-based biomarker panel to identify individuals who carry this risk. We analysed the levels of 22 biomarkers in clinically classified healthy controls (HC), mild cognitive impairment (MCI) and Alzheimer’s participants from the well characterised Australian Imaging, Biomarker and Lifestyle (AIBL) study of aging. High levels of IL-10 and IL-12/23p40 were significantly associated with amyloid deposition in HC, suggesting that these two biomarkers might be used to detect at risk individuals. Additionally, other biomarkers (Eotaxin-3, Leptin, PYY) exhibited altered levels in AD participants possessing the APOE ε4 allele. This suggests that the physiology of some potential biomarkers may be altered in AD due to the APOE ε4 allele, a major risk factor for AD. Taken together, these data highlight several potential biomarkers that can be used in a blood-based panel to allow earlier identification of individuals at risk of developing AD and/or early stage AD for which current therapies may be more beneficial

Caenorhabditis elegans Maintains Highly Compartmentalized Cellular Distribution of Metals and Steep Concentration Gradients of Manganese

Bioinorganic chemistry is critical to cellular function. Homeostasis of manganese (Mn), for example, is essential for life. A lack of methods for direct in situ visualization of Mn and other biological metals within intact multicellular eukaryotes limits our understanding of management of these metals. We provide the first quantitative subcellular visualization of endogenous Mn concentrations (spanning two orders of magnitude) associated with individual cells of the nematode, Caenorhabditis elegans

Decreased Serum Zinc Is An Effect Of Ageing And Not Alzheimer\u27s Disease

We examined the distribution of zinc in the periphery (erythrocytes and serum) in a large, well-characterised cohort, the Australian Imaging, Biomarkers and Lifestyle (AIBL) study, in order to determine if there is systemic perturbation in zinc homeostasis in Alzheimer’s disease (AD). We observed an age dependent decrease in serum zinc of approximately 0.4% per year. When correcting for the age dependent decline in serum zinc no significant difference between healthy controls (HC), mildly cognitively impaired (MCI) or AD subjects was observed

PATH-38. ROSETTE-FORMING GLIONEURONAL TUMOR IS DEFINED BY FGFR1 ACTIVATING ALTERATIONS WITH FREQUENT ACCOMPANYING PI3K AND MAPK PATHWAY MUTATIONS

Abstract BACKGROUND Rosette-forming glioneuronal tumor (RGNT) is an uncommon CNS tumor originally described in the fourth ventricle characterized by a low-grade glial neoplasm admixed with a rosette-forming neurocytic component. METHODS We reviewed clinicopathologic features of 42 patients with RGNT. Targeted next-generation sequencing was performed, and genome-wide methylation profiling is underway. RESULTS The 20 male and 22 female patients had a mean age of 25 years (range 3–47) at time of diagnosis. Tumors were located within or adjacent to the lateral ventricle (n=16), fourth ventricle (15), third ventricle (9), and spinal cord (2). All 31 tumors assessed to date contained FGFR1 activating alterations, either in-frame gene fusion, kinase domain tandem duplication, or hotspot missense mutation in the kinase domain (p.N546 or p.K656). While 7 of these 31 tumors harbored FGFR1 alterations as the solitary pathogenic event, 24 contained additional pathogenic alterations within PI3-kinase or MAP kinase pathway genes: 5 with additional PIK3CA and NF1 mutations, 4 with PIK3CA mutation, 3 with PIK3R1 mutation (one of which also contained focal RAF1 amplification), 5 with PTPN11 mutation (one with additional PIK3R1 mutation), and 2 with NF1 deletion. The other 5 cases demonstrated anaplastic features including hypercellularity and increased mitotic activity. Among these anaplastic cases, 3 harbored inactivating ATRX mutations and two harbored CDKN2A homozygous deletion, in addition to the FGFR1 alterations plus other PI3-kinase and MAP kinase gene mutations seen in those RGNT without anaplasia. CONCLUSION Independent of ventricular location, RGNT is defined by FGFR1 activating mutations or rearrangements, which are frequently accompanied by mutations involving PIK3CA, PIK3R1, PTPN11, NF1, and KRAS. Whereas pilocytic astrocytoma and ganglioglioma are characterized by solitary activating MAP kinase pathway alterations (e.g. BRAF fusion or mutation), RGNT are genetically more complex with dual PI3K-Akt-mTOR and Ras-Raf-MAPK pathway activation. Rare anaplastic examples may show additional ATRX and/or CDKN2A inactivation

A blood-based predictor for neocortical Aβ burden in Alzheimer\u27s disease: results from the AIBL study

Dementia is a global epidemic with Alzheimer’s disease (AD) being the leading cause. Early identification of patients at risk of developing AD is now becoming an international priority. Neocortical Aβ (extracellular β-amyloid) burden (NAB), as assessed by positron emission tomography (PET), represents one such marker for early identification. These scans are expensive and are not widely available, thus, there is a need for cheaper and more widely accessible alternatives. Addressing this need, a blood biomarker-based signature having efficacy for the prediction of NAB and which can be easily adapted for population screening is described. Blood data (176 analytes measured in plasma) and Pittsburgh Compound B (PiB)-PET measurements from 273 participants from the Australian Imaging, Biomarkers and Lifestyle (AIBL) study were utilised. Univariate analysis was conducted to assess the difference of plasma measures between high and low NAB groups, and cross-validated machine-learning models were generated for predicting NAB. These models were applied to 817 non-imaged AIBL subjects and 82 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) for validation. Five analytes showed significant difference between subjects with high compared to low NAB. A machine-learning model (based on nine markers) achieved sensitivity and specificity of 80 and 82%, respectively, for predicting NAB. Validation using the ADNI cohort yielded similar results (sensitivity 79% and specificity 76%). These results show that a panel of blood-based biomarkers is able to accurately predict NAB, supporting the hypothesis for a relationship between a blood-based signature and Aβ accumulation, therefore, providing a platform for developing a population-based scree