title: Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola.

authors: Collins, Gemma Elyse

subjects: Collembola

abstract: Aim: To assess spatial patterns of genetic and species-level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences. Location: Namib Desert gravel plains. Taxon: Collembola (springtails). Methods: A total of 77 soil samples were collected along NE-SW (60 km) and E-W (160 km) transects from within a 4,000 km2 area of the Namib Desert gravel plains. We extracted 434 springtails from the 37 samples which contained Collembola and sequenced them at the COI gene locus. In the absence of specific taxonomic keys and previous genetic data for these taxa, we used Generalized Mixed Yule Coalescent (GMYC) analyses to provide putative species-level designations. Results: We obtained 341 successful COI sequences, 175 of which were unique haplotypes. GMYC analyses identified 30 putative species, with up to 28% sequence divergence (uncorrected p-distance). The distribution of genetic variants was disjunct, with 97% of haplotypes and 70% of "GMYC species" found only at single sites. Main conclusions: Dispersal events, although rare, may be facilitated by environmental events such as prevailing onshore winds or occasional flow of rainwater to the coast. We conclude that the high genetic diversity we observed is the result of ancient springtail lineages, patchy distribution of suitable habitats, and limited dispersal (gene flow) among habitable locations.

text: Ancient landscapes of the Namib Desert harbor high levels of genetic variability and deeply divergent lineages for Collembola. Aim: To assess spatial patterns of genetic and species-level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences. Location: Namib Desert gravel plains. Taxon: Collembola (springtails). Methods: A total of 77 soil samples were collected along NE-SW (60 km) and E-W (160 km) transects from within a 4,000 km2 area of the Namib Desert gravel plains. We extracted 434 springtails from the 37 samples which contained Collembola and sequenced them at the COI gene locus. In the absence of specific taxonomic keys and previous genetic data for these taxa, we used Generalized Mixed Yule Coalescent (GMYC) analyses to provide putative species-level designations. Results: We obtained 341 successful COI sequences, 175 of which were unique haplotypes. GMYC analyses identified 30 putative species, with up to 28% sequence divergence (uncorrected p-distance). The distribution of genetic variants was disjunct, with 97% of haplotypes and 70% of "GMYC species" found only at single sites. Main conclusions: Dispersal events, although rare, may be facilitated by environmental events such as prevailing onshore winds or occasional flow of rainwater to the coast. We conclude that the high genetic diversity we observed is the result of ancient springtail lineages, patchy distribution of suitable habitats, and limited dispersal (gene flow) among habitable locations.

year: 2019

title: Structural Changes and Chain Mobility During Processing of Bloodmeal-Based Thermoplastics

authors: Bier, James Michael

subjects: protein

abstract: The purpose of this study was to use concepts from classical polymer physics to develop a fundamental understanding of the interdependent relationship between structure, properties and processing in NovateinTM Thermoplastic Protein (NTP). NTP is produced from bloodmeal, a by-product of the meat industry which is 95% protein, by extruding with sodium sulphite, urea, sodium dodecyl sulphate, water and tri-ethylene glycol.  Dynamic mechanical thermal analysis (DMA) and differential scanning calorimetry (DSC) were used to investigate thermal transitions and chain relaxation, accompanied by synchrotron based Fourier transform infrared spectroscopy (FT-IR) to investigate chain architecture and structural changes. Extrusion, injection moulding and mechanical testing were used to investigate macroscopic properties, such as processability and mechanical properties.
Material pocket DMA enabled detection of glass transition temperatures not only for moulded NTP test pieces, but also for each processing step: bloodmeal,  NTP prior to extrusion, extruded NTP, and conditioned NTP. The pockets increased resolution for injection moulded and conditioned samples, revealing multiple transitions which indicated the presence of more than one phase. Spatially resolved FT-IR experiments were used to characterise the relative content and distribution of protein secondary structures in bloodmeal and NTP after each processing step. Increased chain mobility was observed due to the additives used, and also drastic structural rearrangement consistent with consolidation into a thermoplastic material after extrusion. Viscoelastic phenomena such as creep and stress relaxation further confirmed processed NTP was a consolidated thermoplastic, exhibiting time dependent behaviour characteristic of thermoplastic polymers.
The thermal properties of NTP suggested an underlying semi-crystalline structure, with protein secondary structures such as α-helices and β-sheets constraining motion in the amorphous phase, contributing to a broad glass transition region. These structures do not melt at typical temperatures encountered during extrusion processing, but are dispersed more evenly throughout an amorphous matrix.  Other than plasticisation, strong hydrogen bonding interactions stabilising secondary structures were the dominant influence on mechanical properties of the processed NTP. When TEG was included as a plasticiser, the degree of crystallinity decreased, and the fraction of randomly coiled protein chains was greater at all stages of processing compared to NTP without TEG. TEG competes with protein side groups for hydrogen bonding sites on the protein backbone, reducing secondary structure formation. β-sheets increased when NTP was heated in the absence of shear, displacing TEG and causing it to migrate out of the particles. The short residence time and presence of shear and mixing during extrusion and injection moulding prevented migration during processing, but an overall increase in β-sheet content was still observed after these processing steps.
The relationship between structure, properties and processing of NTP is therefore characterised by its semi crystalline nature, in which additives overcome protein-protein interactions in the amorphous phase enabling β-sheet dispersion throughout the material during processing. Future attempts at modifying properties should be informed by this understanding.

text: Structural Changes and Chain Mobility During Processing of Bloodmeal-Based Thermoplastics The purpose of this study was to use concepts from classical polymer physics to develop a fundamental understanding of the interdependent relationship between structure, properties and processing in NovateinTM Thermoplastic Protein (NTP). NTP is produced from bloodmeal, a by-product of the meat industry which is 95% protein, by extruding with sodium sulphite, urea, sodium dodecyl sulphate, water and tri-ethylene glycol.  Dynamic mechanical thermal analysis (DMA) and differential scanning calorimetry (DSC) were used to investigate thermal transitions and chain relaxation, accompanied by synchrotron based Fourier transform infrared spectroscopy (FT-IR) to investigate chain architecture and structural changes. Extrusion, injection moulding and mechanical testing were used to investigate macroscopic properties, such as processability and mechanical properties.
Material pocket DMA enabled detection of glass transition temperatures not only for moulded NTP test pieces, but also for each processing step: bloodmeal,  NTP prior to extrusion, extruded NTP, and conditioned NTP. The pockets increased resolution for injection moulded and conditioned samples, revealing multiple transitions which indicated the presence of more than one phase. Spatially resolved FT-IR experiments were used to characterise the relative content and distribution of protein secondary structures in bloodmeal and NTP after each processing step. Increased chain mobility was observed due to the additives used, and also drastic structural rearrangement consistent with consolidation into a thermoplastic material after extrusion. Viscoelastic phenomena such as creep and stress relaxation further confirmed processed NTP was a consolidated thermoplastic, exhibiting time dependent behaviour characteristic of thermoplastic polymers.
The thermal properties of NTP suggested an underlying semi-crystalline structure, with protein secondary structures such as α-helices and β-sheets constraining motion in the amorphous phase, contributing to a broad glass transition region. These structures do not melt at typical temperatures encountered during extrusion processing, but are dispersed more evenly throughout an amorphous matrix.  Other than plasticisation, strong hydrogen bonding interactions stabilising secondary structures were the dominant influence on mechanical properties of the processed NTP. When TEG was included as a plasticiser, the degree of crystallinity decreased, and the fraction of randomly coiled protein chains was greater at all stages of processing compared to NTP without TEG. TEG competes with protein side groups for hydrogen bonding sites on the protein backbone, reducing secondary structure formation. β-sheets increased when NTP was heated in the absence of shear, displacing TEG and causing it to migrate out of the particles. The short residence time and presence of shear and mixing during extrusion and injection moulding prevented migration during processing, but an overall increase in β-sheet content was still observed after these processing steps.
The relationship between structure, properties and processing of NTP is therefore characterised by its semi crystalline nature, in which additives overcome protein-protein interactions in the amorphous phase enabling β-sheet dispersion throughout the material during processing. Future attempts at modifying properties should be informed by this understanding.

year: 2013

title: Incentivising change in the Lake Rotorua catchment

authors: Grayling, Anna

abstract: Anna Grayling is the Rotorua Lakes Business Manager for Bay of Plenty Regional Council. After completing a Bachelor of Law and a Bachelor of Sciences at the University of Waikato, Anna’s career began as an ecological consultant. Following this role, Anna spent five years in planning and policy for both the district and regional councils. For the last five years Anna has been dedicated to the Rotorua Te Arawa Lakes Programme. She is now the project lead for the Incentive Fund Development for land-use change in the Lake Rotorua catchment.
Alastair MacCormick has worked as a Lakes Restoration Officer with the Bay of Plenty Regional Council since 2007. His primary function has been the implementation of nutrient discharge limits under Rule 11. An experienced user of the Overseer nutrient budgeting software, and with broad knowledge of farming systems in the catchment, he also provides information and advice on the issues and complications associated with nutrient accounting.

text: Incentivising change in the Lake Rotorua catchment Anna Grayling is the Rotorua Lakes Business Manager for Bay of Plenty Regional Council. After completing a Bachelor of Law and a Bachelor of Sciences at the University of Waikato, Anna’s career began as an ecological consultant. Following this role, Anna spent five years in planning and policy for both the district and regional councils. For the last five years Anna has been dedicated to the Rotorua Te Arawa Lakes Programme. She is now the project lead for the Incentive Fund Development for land-use change in the Lake Rotorua catchment.
Alastair MacCormick has worked as a Lakes Restoration Officer with the Bay of Plenty Regional Council since 2007. His primary function has been the implementation of nutrient discharge limits under Rule 11. An experienced user of the Overseer nutrient budgeting software, and with broad knowledge of farming systems in the catchment, he also provides information and advice on the issues and complications associated with nutrient accounting.

year: 2013