Bionomics of the pied stilt (Himantopus leucocephalus) in New Zealand : with special reference to breeding behaviour: a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Zoology at Massey University

Aims of the Study. Although the Pied Stilt, Himantopus h.leucocephalus, Gould,1837*Nomenclature for New Zealand birds follows that laid down in the Annotated Checklist of the Birds of New Zealand (Kinsky,1970). Other bird species are as prescribed in the Handbook of British Birds (Witherby et al, 1943) or in the specific reference works quoted. is one of New Zealand's most common wading birds there has been very little published work on it. The purpose of this study therefore was to gain knowledge of the general biology of the Pied Stilt with special reference to breeding behaviour. It has been suggested (L.Gurr, pers.comm.) that the large numbers of Pied Stilt may be responsible for genetic swamping, through interbreeding, of the Black Stilt Himantopus novaezealandiae Gould, 1841 which is now quite rare and its breeding range restricted to a very small area of New Zealand - the Waitaki River system. The intention was that this study should provide information as a background to further investigation of the problem. This study is based on field observations made between February 1969 and December 1970 in the Manawatu district around Palmerston North, where Pied Stilts are found in large enough numbers to permit relatively easy observation, except during the winter months when their numbers drop considerably

A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations.

BackgroundEukaryotic cell proliferation involves DNA replication, a tightly regulated process mediated by a multitude of protein factors. In budding yeast, the initiation of replication is facilitated by the heterohexameric origin recognition complex (ORC). ORC binds to specific origins of replication and then serves as a scaffold for the recruitment of other factors such as Cdt1, Cdc6, the Mcm2-7 complex, Cdc45 and the Dbf4-Cdc7 kinase complex. While many of the mechanisms controlling these associations are well documented, mathematical models are needed to explore the network's dynamic behaviour. We have developed an ordinary differential equation-based model of the protein-protein interaction network describing replication initiation.ResultsThe model was validated against quantified levels of protein factors over a range of cell cycle timepoints. Using chromatin extracts from synchronized Saccharomyces cerevisiae cell cultures, we were able to monitor the in vivo fluctuations of several of the aforementioned proteins, with additional data obtained from the literature. The model behaviour conforms to perturbation trials previously reported in the literature, and accurately predicts the results of our own knockdown experiments. Furthermore, we successfully incorporated our replication initiation model into an established model of the entire yeast cell cycle, thus providing a comprehensive description of these processes.ConclusionsThis study establishes a robust model of the processes driving DNA replication initiation. The model was validated against observed cell concentrations of the driving factors, and characterizes the interactions between factors implicated in eukaryotic DNA replication. Finally, this model can serve as a guide in efforts to generate a comprehensive model of the mammalian cell cycle in order to explore cancer-related phenotypes

The evolution of the class A scavenger receptors

<p>Abstract</p> <p>Background</p> <p>The class A scavenger receptors are a subclass of a diverse family of proteins defined based on their ability to bind modified lipoproteins. The 5 members of this family are strikingly variable in their protein structure and function, raising the question as to whether it is appropriate to group them as a family based on their ligand binding abilities.</p> <p>Results</p> <p>To investigate these relationships, we defined the domain architecture of each of the 5 members followed by collecting and annotating class A scavenger receptor mRNA and amino acid sequences from publicly available databases. Phylogenetic analyses, sequence alignments, and permutation tests revealed a common evolutionary ancestry of these proteins, indicating that they form a protein family. We postulate that 4 distinct gene duplication events and subsequent domain fusions, internal repeats, and deletions are responsible for the diverse protein structures and functions of this family. Despite variation in domain structure, there are highly conserved regions across all 5 members, indicating the possibility that these regions may represent key conserved functional motifs.</p> <p>Conclusions</p> <p>We have shown with significant evidence that the 5 members of the class A scavenger receptors form a protein family. We have indicated that these receptors have a common origin which may provide insight into future functional work with these proteins.</p

Differential chromatin proteomics of the MMS-induced DNA damage response in yeast

<p>Abstract</p> <p>Background</p> <p>Protein enrichment by sub-cellular fractionation was combined with differential-in-gel-electrophoresis (DIGE) to address the detection of the low abundance chromatin proteins in the budding yeast proteome. Comparisons of whole-cell extracts and chromatin fractions were used to provide a measure of the degree of chromatin association for individual proteins, which could be compared across sample treatments. The method was applied to analyze the effect of the DNA damaging agent methyl methanesulfonate (MMS) on levels of chromatin-associated proteins.</p> <p>Results</p> <p>Up-regulation of several previously characterized DNA damage checkpoint-regulated proteins, such as Rnr4, Rpa1 and Rpa2, was observed. In addition, several novel DNA damage responsive proteins were identified and assessed for genotoxic sensitivity using either DAmP (decreased abundance by mRNA perturbation) or knockout strains, including Acf2, Arp3, Bmh1, Hsp31, Lsp1, Pst2, Rnr4, Rpa1, Rpa2, Ste4, Ycp4 and Yrb1. A strain in which the expression of the Ran-GTPase binding protein Yrb1 was reduced was found to be hypersensitive to genotoxic stress.</p> <p>Conclusion</p> <p>The described method was effective at unveiling chromatin-associated proteins that are less likely to be detected in the absence of fractionation. Several novel proteins with altered chromatin abundance were identified including Yrb1, pointing to a role for this nuclear import associated protein in DNA damage response.</p

Development of Crop.LCA, an adaptable screening life cycle assessment tool for agricultural systems: a Canadian scenario assessment

There is an increasing demand for sustainable agricultural production as part of the transition towards a globally sustainable economy. To quantify impacts of agricultural systems on the environment, life cycle assessment (LCA) is ideal because of its holistic approach. Many tools have been developed to conduct LCAs in agriculture, but they are not publicly available, not open-source, and have a limited scope. Here, a new adaptable open-source tool (Crop.LCA) for carrying out LCA of cropping systems is presented and tested in an evaluation study with a scenario assessment of 4 cropping systems using an agroecosystem model (DNDC) to predict soil GHG emissions. The functional units used are hectares (ha) of land and gigajoules (GJ) of harvested energy output, and 4 impact categories were evaluated: cumulative energy demand (CED), 100-year global warming potential (GWP), eutrophication and acidification potential. DNDC was used to simulate 28 years of cropping system dynamics, and the results were used as input in Crop.LCA. Data were aggregated for each 4-year rotation and statistically analyzed. Introduction of legumes into the cropping system reduced CED by 6%, GWP by 23%, and acidification by 19% per ha. These results highlight the ability of Crop.LCA to capture cropping system characteristics in LCA, and the tool constitutes a step forward in increasing the accuracy of LCA of cropping systems as required for bio-economy system assessments. Furthermore, the tool is open-source, highly transparent and has the necessary flexibility to assess agricultural systems

Development of Crop.LCA, an adaptable screening life cycle assessment tool for agricultural systems: a Canadian scenario assessment

There is an increasing demand for sustainable agricultural production as part of the transition towards a globally sustainable economy. To quantify impacts of agricultural systems on the environment, life cycle assessment (LCA) is ideal because of its holistic approach. Many tools have been developed to conduct LCAs in agriculture, but they are not publicly available, not open-source, and have a limited scope. Here, a new adaptable open-source tool (Crop.LCA) for carrying out LCA of cropping systems is presented and tested in an evaluation study with a scenario assessment of 4 cropping systems using an agroecosystem model (DNDC) to predict soil GHG emissions. The functional units used are hectares (ha) of land and gigajoules (GJ) of harvested energy output, and 4 impact categories were evaluated: cumulative energy demand (CED), 100-year global warming potential (GWP), eutrophication and acidification potential. DNDC was used to simulate 28 years of cropping system dynamics, and the results were used as input in Crop.LCA. Data were aggregated for each 4-year rotation and statistically analyzed. Introduction of legumes into the cropping system reduced CED by 6%, GWP by 23%, and acidification by 19% per ha. These results highlight the ability of Crop.LCA to capture cropping system characteristics in LCA, and the tool constitutes a step forward in increasing the accuracy of LCA of cropping systems as required for bio-economy system assessments. Furthermore, the tool is open-source, highly transparent and has the necessary flexibility to assess agricultural systems

Climate and Soil Characteristics Determine Where No-Till Management Can Store Carbon in Soils and Mitigate Greenhouse Gas Emissions

Article number: 11665 (2019)201

Climate and soil characteristics determine where no-till management can store carbon in soils and mitigate greenhouse gas emissions

Adoption of no-till management on croplands has become a controversial approach for storing carbon in soil due to conflicting findings. Yet, no-till is still promoted as a management practice to stabilize the global climate system from additional change due to anthropogenic greenhouse gas emissions, including the 4 per mille initiative promoted through the UN Framework Convention on Climate Change. We evaluated the body of literature surrounding this practice, and found that SOC storage can be higher under no-till management in some soil types and climatic conditions even with redistribution of SOC, and contribute to reducing net greenhouse gas emissions. However, uncertainties tend to be large, which may make this approach less attractive as a contributor to stabilize the climate system compared to other options. Consequently, no-till may be better viewed as a method for reducing soil erosion, adapting to climate change, and ensuring food security, while any increase in SOC storage is a co-benefit for society in terms of reducing greenhouse gas emissions.Facultad de Ciencias Agrarias y Forestale