title: Complete genome sequence of a New Zealand Mycobacterium tuberculosis strain responsible for ongoing transmission over the past 30 years.

authors: Mulholland, Claire V.

abstract: We report here the complete genome sequence of Mycobacterium tuberculosis strain Colonial S-type 1 (CS1), which has been responsible for ongoing outbreaks of tuberculosis in New Zealand over the past 30 years. CS1 appears to be highly transmissible, with greater rates of progression to active disease, compared to other circulating M. tuberculosis strains; therefore, comparison of its genomic content is of interest.

text: Complete genome sequence of a New Zealand Mycobacterium tuberculosis strain responsible for ongoing transmission over the past 30 years. We report here the complete genome sequence of Mycobacterium tuberculosis strain Colonial S-type 1 (CS1), which has been responsible for ongoing outbreaks of tuberculosis in New Zealand over the past 30 years. CS1 appears to be highly transmissible, with greater rates of progression to active disease, compared to other circulating M. tuberculosis strains; therefore, comparison of its genomic content is of interest.

year: 2022

title: Foaming Novatein Thermoplastic Protein

authors: Gavin, Chanelle Anne Rose

abstract: Most plastics are produced from non-renewable and/or non-biodegradable polymers. The negative environmental impact of these has been a strong driver for bioplastic development. Proteins are naturally occurring biopolymers which can be denatured and plasticised to produce thermoplastic materials. Novatein Thermoplastic Protein (NTP) is a patented blend of blood meal (a highly aggregated protein) and processing additives which: reduce hydrogen bonding, break cross links between cysteine residues, disrupt hydrophobic interactions, and facilitate protein unfolding. Water and triethylene glycol (TEG) are added as plasticisers to produce a powder which can be extruded, and subsequently injection moulded.
As Novatein is both bio-derived and biodegradable there is the opportunity for using it as an alternative loose fill packing material. This work aimed to develop an appropriate foaming method and the principles governing it. 
Foaming was initially investigated through extrusion which was unsuccessful due to the low speed and pressure drop. However, by using high speed and pressure, Novatein was successfully foamed in an injection moulder under free expansion. Foaming achieved densities between 0.2-0.5 g/cm3, at temperatures between 160-165°C. The mechanical properties varied with density but compressive strengths between 200 and 600 kPa and elastic moduli between 2.2 and 8 MPa were typical. Increasing temperature further did not improve expansion as the material degraded. The narrow processing window is characteristic of the material’s semi-crystalline nature which arises from residual protein secondary structure (α-helices and β-sheets). Although Novatein softens at high temperature, it does not form a typical melt.
Processing depends upon the interactions between protein, additives, and plasticisers. Highly plasticised Novatein phase separates into protein rich, protein-plasticiser, and plasticiser rich regions. This results in variable morphology characterised by: unfoamed regions, variable cell sizes and both open and closed cells. 

Varying water, urea and TEG impacted the foaming ability; adding urea lowered the extensional viscosity improving foaming while also acting as a blowing agent. Water and TEG reduced the shear viscosity and softening point respectively reducing expansion. Water was expected to improve expansion by acting as a blowing agent, however increasing water and TEG both increased cell size, but delayed stabilisation decreasing expansion.
Following nucleation a bubble grows by diffusion of gas molecules from the surrounding polymer. As these molecules leave, the viscosity increases, controlling bubble growth. Simultaneously, growth causes chain alignment within the surrounding polymer. Through FT-IR, bubbles were shown to appear in regions high in β-sheets. Two mechanisms were proposed; either a bubble nucleates near a β-sheet and grows until it encounters other β-sheet structures or that chain alignment enables hydrogen bonding between the chains, forming these structures. FT-IR also showed a high concentration of TEG at the bubble surface suggesting that nucleation occurred in regions high in water and TEG. The accumulation of TEG at a bubble surface occurs as water (steam) diffuses into the bubble causing expansion, pushing TEG into the surroundings.
Bubble stabilisation is achieved through either a loss plasticiser molecules or a decrease in temperature. In over plasticised blends, water keeps the viscosity in the surrounding polymer low, while increasing TEG reduced the softening point, both allowing more time for gases to diffuse out.
This work developed a suitable foaming method and an understanding of the role of protein secondary structure and rheology for Novatein, which can be foamed despite its high β-sheet content.

text: Foaming Novatein Thermoplastic Protein Most plastics are produced from non-renewable and/or non-biodegradable polymers. The negative environmental impact of these has been a strong driver for bioplastic development. Proteins are naturally occurring biopolymers which can be denatured and plasticised to produce thermoplastic materials. Novatein Thermoplastic Protein (NTP) is a patented blend of blood meal (a highly aggregated protein) and processing additives which: reduce hydrogen bonding, break cross links between cysteine residues, disrupt hydrophobic interactions, and facilitate protein unfolding. Water and triethylene glycol (TEG) are added as plasticisers to produce a powder which can be extruded, and subsequently injection moulded.
As Novatein is both bio-derived and biodegradable there is the opportunity for using it as an alternative loose fill packing material. This work aimed to develop an appropriate foaming method and the principles governing it. 
Foaming was initially investigated through extrusion which was unsuccessful due to the low speed and pressure drop. However, by using high speed and pressure, Novatein was successfully foamed in an injection moulder under free expansion. Foaming achieved densities between 0.2-0.5 g/cm3, at temperatures between 160-165°C. The mechanical properties varied with density but compressive strengths between 200 and 600 kPa and elastic moduli between 2.2 and 8 MPa were typical. Increasing temperature further did not improve expansion as the material degraded. The narrow processing window is characteristic of the material’s semi-crystalline nature which arises from residual protein secondary structure (α-helices and β-sheets). Although Novatein softens at high temperature, it does not form a typical melt.
Processing depends upon the interactions between protein, additives, and plasticisers. Highly plasticised Novatein phase separates into protein rich, protein-plasticiser, and plasticiser rich regions. This results in variable morphology characterised by: unfoamed regions, variable cell sizes and both open and closed cells. 

Varying water, urea and TEG impacted the foaming ability; adding urea lowered the extensional viscosity improving foaming while also acting as a blowing agent. Water and TEG reduced the shear viscosity and softening point respectively reducing expansion. Water was expected to improve expansion by acting as a blowing agent, however increasing water and TEG both increased cell size, but delayed stabilisation decreasing expansion.
Following nucleation a bubble grows by diffusion of gas molecules from the surrounding polymer. As these molecules leave, the viscosity increases, controlling bubble growth. Simultaneously, growth causes chain alignment within the surrounding polymer. Through FT-IR, bubbles were shown to appear in regions high in β-sheets. Two mechanisms were proposed; either a bubble nucleates near a β-sheet and grows until it encounters other β-sheet structures or that chain alignment enables hydrogen bonding between the chains, forming these structures. FT-IR also showed a high concentration of TEG at the bubble surface suggesting that nucleation occurred in regions high in water and TEG. The accumulation of TEG at a bubble surface occurs as water (steam) diffuses into the bubble causing expansion, pushing TEG into the surroundings.
Bubble stabilisation is achieved through either a loss plasticiser molecules or a decrease in temperature. In over plasticised blends, water keeps the viscosity in the surrounding polymer low, while increasing TEG reduced the softening point, both allowing more time for gases to diffuse out.
This work developed a suitable foaming method and an understanding of the role of protein secondary structure and rheology for Novatein, which can be foamed despite its high β-sheet content.

year: 2019

title: Tephras and New Zealand archaeology

authors: Lowe, David J.

subjects: tephrochronology

abstract: Establishing an accurate date for earliest Polynesian settlement in New Zealand is essential for understanding patterns of settlement and associated environmental impacts, and the processes and rates of cultural change in Eastern Polynesia. Tephra deposits from five volcanic centres, together with exotic sea-rafted pumice, provide isochronous constraints on the timing of earliest settlement and human impacts in northern New Zealand. A local basaltic tephra from Rangitoto Island (Auckland) and locally distributed andesitic tephras from Egmont volcano directly date human occupation to c. AD 1400–1450. Distal andesitic tephras (Tufa Trig Formation) from Mt Ruapehu, Tongariro volcanic centre, help constrain the timing of earliest anthropogenic deforestation signals in Hawke's Bay. Sea-rafted Loisels Pumice(s), although of uncertain stratigraphic reliability in places, overlies cultural remains that can be no younger than c. AD 1350 along the east coast, North Island. The regionally extensive rhyolitic Kaharoa Tephra, which erupted from Okataina volcano between c. AD  1300–1390, is the critical “settlement layer” datum for dating prehistory in the North Island: no human artefacts are recorded beneath it and the earliest inferred environmental impacts by humans are dated to c. AD  1280, just prior to its deposition. This maximum date matches the earliest radiocarbon dates derived for both settlement and human impacts from archaeological and natural sites (c. AD 1250), and implies that the onset of deforestation was essentially contemporaneous with initial settlement.
The widespread rhyolitic Taupo Tephra, which erupted from Taupo volcano c. AD 200, provides an isochronous benchmark well before earliest settlement. The tephra may coincide approximately with a putative earlier transient contact in New Zealand based on Pacific rat-bone (Rattus exulans) dates. More precise calendrical dates on the tephras—via dendrochronology or ice-core records or other dating methods—would help refine assessment of the timing of earliest settlement, while extending the distributional range of critical tephra layers, through application of crypto-tephra analysis, could lead to a greater understanding of settlement patterns.

text: Tephras and New Zealand archaeology Establishing an accurate date for earliest Polynesian settlement in New Zealand is essential for understanding patterns of settlement and associated environmental impacts, and the processes and rates of cultural change in Eastern Polynesia. Tephra deposits from five volcanic centres, together with exotic sea-rafted pumice, provide isochronous constraints on the timing of earliest settlement and human impacts in northern New Zealand. A local basaltic tephra from Rangitoto Island (Auckland) and locally distributed andesitic tephras from Egmont volcano directly date human occupation to c. AD 1400–1450. Distal andesitic tephras (Tufa Trig Formation) from Mt Ruapehu, Tongariro volcanic centre, help constrain the timing of earliest anthropogenic deforestation signals in Hawke's Bay. Sea-rafted Loisels Pumice(s), although of uncertain stratigraphic reliability in places, overlies cultural remains that can be no younger than c. AD 1350 along the east coast, North Island. The regionally extensive rhyolitic Kaharoa Tephra, which erupted from Okataina volcano between c. AD  1300–1390, is the critical “settlement layer” datum for dating prehistory in the North Island: no human artefacts are recorded beneath it and the earliest inferred environmental impacts by humans are dated to c. AD  1280, just prior to its deposition. This maximum date matches the earliest radiocarbon dates derived for both settlement and human impacts from archaeological and natural sites (c. AD 1250), and implies that the onset of deforestation was essentially contemporaneous with initial settlement.
The widespread rhyolitic Taupo Tephra, which erupted from Taupo volcano c. AD 200, provides an isochronous benchmark well before earliest settlement. The tephra may coincide approximately with a putative earlier transient contact in New Zealand based on Pacific rat-bone (Rattus exulans) dates. More precise calendrical dates on the tephras—via dendrochronology or ice-core records or other dating methods—would help refine assessment of the timing of earliest settlement, while extending the distributional range of critical tephra layers, through application of crypto-tephra analysis, could lead to a greater understanding of settlement patterns.

year: 2000