Elemental and isotopic geochemistry of kimberlites from the Lac de Gras field, northwest territories, Canada.

Detailed major/trace element and high-precision Hf-Nd-Sr isotope data has been acquired for 86 samples of kimberlites from the recently discovered Lac de Gras kimberlite field in the Northwest Territories, Canada, plus 23 samples from other Canadian kimberlite occurrences. This constitutes the most comprehensive geochemical database available for kimberlites at the present time, and allows detailed comparisons to be made with the well-documented kimberlites of the Kaapvaal craton, southern Africa. Major and trace element data shows that some Lac de Gras kimberlites have interacted extensively with continental crust, whereas others are minimally contaminated with crust but have physically incorporated large quantities (˃30%) of lithospheric mantle peridotite. Fresh, minimally-contaminated kimberlites from Lac de Gras have both elemental and isotopic characteristics that are transitional relative to those typical of southern African Group I and II kimberlites. The Hf-Nd isotope variations of these samples also define a linear array that strongly suggests mixing of two or more components/reservoirs within the mantle. Isotopic mixing models and mass balance considerations constrain the most likely candidate components/reservoirs to be depleted sub-continental lithospheric mantle and a component with an isotopically-enriched, negative ΔɛHf signature that is derived from beneath the lithosphere. Such a component has previously been identified in southern African kimberlites, indicating that it is globally extensive within the mantle. Its resfriction to magmas generated at great depths, and its unusual Hf isotope signature also suggest that it may reside in isolation at some mantle boundary layer. Ancient oceanic crust, generated by melting in the presence of garnet and subsequently subducted and stored below the lithosphere, could evolve to negative ΔɛHf compositions. Melts of this material, variably recombined with the depleted, garnet- rich melting residua that constitute the lithosphere, can then account for the Hf-Nd kimberiite isotopic array. Trace element characteristics, such as K and Sr anomalies, are consistent with those of OIB-like magmas derived from within the convecting mantle

Immune responses to BCG immunisation and Mycobacterium tuberculosis infection in non-human primates

The evaluation of new vaccines that are urgently needed against tuberculosis (TB) is hampered by the lack of an immune correlate of protection. One of the main measures of immune function utilised in TB vaccine studies is the assessment of interferon (IFN)-ɣ, as it is known that this cytokine is essential for immunity against infection. The studies conducted in this thesis uses the non-human primate model of TB to address whether two measurements of IFN-ɣ (the frequency of IFN-ɣ secreting cells and the concentration of IFN-ɣ secreted) can be related to survival and thus provide a correlate of protection. The Mycobacterium-specific IFN-ɣ profiles have been assessed in two primate species (rhesus macaques and cynomolgus macaques) following immunisation with BCG, or aerosol infection with Mycobacterium tuberculosis. Additionally, one of the most advanced novel TB vaccines (modified vaccinia virus Ankara expressing antigen 85A; MVA85A) has also been tested in this model. When human clinical trial data (provided by Oxford University) using BCG and BCG with an MVA85A boost were compared with results generated in similarly vaccinated macaques, it was observed that rhesus macaques have kinetically similar IFN-ɣ responses, but at different magnitudes. During a vaccine efficacy study, rhesus macaques were shown to be protected from M. tuberculosis infection by BCG vaccination. This allowed the opportunity for responses in animals protected against disease to be compared with those which were not protected. Although results showed that the capability to secrete larger concentrations of PPD-specific IFN-ɣ early after M. tuberculosis infection correlated with longer survival periods, this was not solely due to prior vaccination. Most of the IFN-ɣ responses during the vaccination periods did not relate to survival after challenge, except peak frequencies of IFN-ɣ secreting cells after BCG vaccination. Therefore, it was concluded that measuring IFN-ɣ alone does not provide the correlate of protection that is presently lacking in TB vaccine research

Activity of a Carbohydrate-Binding Module Therapy, Neumifil, against SARS-CoV-2 Disease in a Hamster Model of Infection.

The rapid global spread of severe acute respiratory coronavirus 2 (SARS-CoV-2) has resulted in an urgent effort to find efficacious therapeutics. Broad-spectrum therapies which could be used for other respiratory pathogens confer advantages, as do those based on targeting host cells that are not prone to the development of resistance by the pathogen. We tested an intranasally delivered carbohydrate-binding module (CBM) therapy, termed Neumifil, which is based on a CBM that has previously been shown to offer protection against the influenza virus through the binding of sialic acid receptors. Using the recognised hamster model of SARS-CoV-2 infection, we demonstrate that Neumifil significantly reduces clinical disease severity and pathological changes in the nasal cavity. Furthermore, we demonstrate Neumifil binding to the human angiotensin-converting enzyme 2 (ACE2) receptor and spike protein of SARS-CoV-2. This is the first report describing the testing of this type of broad-spectrum antiviral therapy in vivo and provides evidence for the advancement of Neumifil in further preclinical and clinical studies

Development of a cost-effective ovine antibody-based therapy against SARS-CoV-2 infection and contribution of antibodies specific to the spike subunit proteins.

Antibodies against SARS-CoV-2 are important to generate protective immunity, with convalescent plasma one of the first therapies approved. An alternative source of polyclonal antibodies suitable for upscaling would be more amendable to regulatory approval and widespread use. In this study, sheep were immunised with SARS-CoV-2 whole spike protein or one of the subunit proteins: S1 and S2. Once substantial antibody titres were generated, plasma was collected and samples pooled for each antigen. Non-specific antibodies were removed via affinity-purification to yield candidate products for testing in a hamster model of SARS-CoV-2 infection. Affinity-purified polyclonal antibodies to whole spike, S1 and S2 proteins were evaluated for in vitro for neutralising activity against SARS-CoV-2 Wuhan-like virus (Australia/VIC01/2020) and a recent variant of concern, B.1.1.529 BA.1 (Omicron), antibody-binding, complement fixation and phagocytosis assays were also performed. All antibody preparations demonstrated an effect against SARS-CoV-2 disease in the hamster model of challenge, with those raised against the S2 subunit providing the most promise. A rapid, cost-effective therapy for COVID-19 was developed which provides a source of highly active immunoglobulin specific to SARS-CoV-2 with multi-functional activity

Elucidation of the ebola virus VP24 cellular interactome and disruption of virus biology through targeted inhibition of host-cell protein function

Viral pathogenesis in the infected cell is a balance between antiviral responses and subversion of host-cell processes. Many viral proteins specifically interact with host-cell proteins to promote virus biology. Understanding these interactions can lead to knowledge gains about infection and provide potential targets for antiviral therapy. One such virus is Ebola, which has profound consequences for human health and causes viral hemorrhagic fever where case fatality rates can approach 90%. The Ebola virus VP24 protein plays a critical role in the evasion of the host immune response and is likely to interact with multiple cellular proteins. To map these interactions and better understand the potential functions of VP24, label-free quantitative proteomics was used to identify cellular proteins that had a high probability of forming the VP24 cellular interactome. Several known interactions were confirmed, thus placing confidence in the technique, but new interactions were also discovered including one with ATP1A1, which is involved in osmoregulation and cell signaling. Disrupting the activity of ATP1A1 in Ebola-virus-infected cells with a small molecule inhibitor resulted in a decrease in progeny virus, thus illustrating how quantitative proteomics can be used to identify potential therapeutic targets

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity

Background Ebolaviruses cause a severe and often fatal haemorrhagic fever in humans, with some species such as Ebola virus having case fatality rates approaching 90%. Currently, the worst Ebola virus outbreak since the disease was discovered is occurring in West Africa. Although thought to be a zoonotic infection, a concern is that with increasing numbers of humans being infected, Ebola virus variants could be selected which are better adapted for human-to-human transmission. Results To investigate whether genetic changes in Ebola virus become established in response to adaptation in a different host, a guinea pig model of infection was used. In this experimental system, guinea pigs were infected with Ebola virus (EBOV), which initially did not cause disease. To simulate transmission to uninfected individuals, the virus was serially passaged five times in naïve animals. As the virus was passaged, virulence increased and clinical effects were observed in the guinea pig. An RNAseq and consensus mapping approach was then used to evaluate potential nucleotide changes in the Ebola virus genome at each passage. Conclusions Upon passage in the guinea pig model, EBOV become more virulent, RNA editing and also coding changes in key proteins become established. The data suggest that the initial evolutionary trajectory of EBOV in a new host can lead to a gain in virulence. Given the circumstances of the sustained transmission of EBOV in the current outbreak in West Africa, increases in virulence may be associated with prolonged and uncontrolled epidemics of EBOV