title: Solving the structure of the mycobacterial chromosome condensing protein Lsr2 in complex with DNA

authors: Summers, Emma Louise

abstract: Lsr2 is a DNA binding protein that is highly conserved in mycobacteria and related actinomycetes and it is thought to be essential in Mycobacterium tuberculosis. Previous studies have shown that Lsr2 is involved in down-regulating a range of genes involved in cell wall synthesis and metabolic functions and it is proposed that it does this by organisation of bacterial chromatin. We solved the structure of the N-terminal dimerisation domain of Lsr2 using crystallographic ab initio approaches1 whereas the C-terminal DNA binding domain structure was solved by others using NMR2. Electron microscopy shows that Lsr2 organises DNA into large helical structures involving several strands1. Whilst DNA binding by individual domains has been modelled based on the NMR structure, the exact mechanism of DNA binding and chromosome organisation by the entire protein is unknown. Lsr2 contains a long flexible loop between the two domains which may lead to the protein having a large range of movement, allowing it to bind DNA in a dynamic way. The Lsr2 dimer is also capable of forming linear oligomers through the interaction of overlapping N terminal residues and evidence of this has been shown in our crystal structure and using TEM1. We wish to solve the structure of Lsr2 bound to DNA. For the purposes of crystallisation of Lsr2 we have engineered the removal of important N-terminal residues involved in oligomersiation to prevent this process occurring in solution. The truncated form of Lsr2 provides a sub-population of purified Lsr2 that is DNA-free and we have utilised this population for binding specific dsDNA oligonucleotides for crystallisation. To date, we have determined the optimal length of DNA required and have refined the exact combination of nucleotides for ideal protein binding. We have progressed through the crystallisation of Lsr2 bound to a range of oligonucleotides. One oligonucleotide has yielded the most success to date with crystals that have diffracted to 2.7 Å resolution. Attempts to solve the structure using molecular replacement have thus far been unsuccessful. Our current focus is to reproduce crystals for improving resolution and for heavy atom soaking to assist with solving the structure.

text: Solving the structure of the mycobacterial chromosome condensing protein Lsr2 in complex with DNA Lsr2 is a DNA binding protein that is highly conserved in mycobacteria and related actinomycetes and it is thought to be essential in Mycobacterium tuberculosis. Previous studies have shown that Lsr2 is involved in down-regulating a range of genes involved in cell wall synthesis and metabolic functions and it is proposed that it does this by organisation of bacterial chromatin. We solved the structure of the N-terminal dimerisation domain of Lsr2 using crystallographic ab initio approaches1 whereas the C-terminal DNA binding domain structure was solved by others using NMR2. Electron microscopy shows that Lsr2 organises DNA into large helical structures involving several strands1. Whilst DNA binding by individual domains has been modelled based on the NMR structure, the exact mechanism of DNA binding and chromosome organisation by the entire protein is unknown. Lsr2 contains a long flexible loop between the two domains which may lead to the protein having a large range of movement, allowing it to bind DNA in a dynamic way. The Lsr2 dimer is also capable of forming linear oligomers through the interaction of overlapping N terminal residues and evidence of this has been shown in our crystal structure and using TEM1. We wish to solve the structure of Lsr2 bound to DNA. For the purposes of crystallisation of Lsr2 we have engineered the removal of important N-terminal residues involved in oligomersiation to prevent this process occurring in solution. The truncated form of Lsr2 provides a sub-population of purified Lsr2 that is DNA-free and we have utilised this population for binding specific dsDNA oligonucleotides for crystallisation. To date, we have determined the optimal length of DNA required and have refined the exact combination of nucleotides for ideal protein binding. We have progressed through the crystallisation of Lsr2 bound to a range of oligonucleotides. One oligonucleotide has yielded the most success to date with crystals that have diffracted to 2.7 Å resolution. Attempts to solve the structure using molecular replacement have thus far been unsuccessful. Our current focus is to reproduce crystals for improving resolution and for heavy atom soaking to assist with solving the structure.

year: 2018

title: Locked into legitimacy: a study of the place of values in politics & society

authors: Bedggood, David

abstract: The object of this thesis is the analysis of the nature, extent and origins of political beliefs and their particular role in legitimising state authority in New Zealand. In the first part two general approaches to the problem of legitimacy are considered. The first, associated with Western ‘social science’, assumes that democracy is representative of all interest groups, and is characterised by shared norms and procedures termed the ‘civic culture’. The author examines the evidence and shows that there are no valid empirical grounds in support of this assumption. The second approach, associated with Marxism, makes the reverse assumption, that the working-class in liberal democracies continues to be exploited, and that allegiance to the state in the working-class is less the consequence of ‘free choice’ than of system constraint.

In the second part the author attempts to develop a model of the causal influences which shaped the political beliefs of the working-class in New Zealand history. An assessment of the historical and contemporary evidence shows that the ‘loyalty’ of the majority of the working-class to the state was as much the product of physical, legal and symbolic constraints, as that of social mobility, rising, living standards, and welfare provisions. The author concludes that the forces which shape political consciousness in New Zealand society have been centralised and consolidated by the state as a hegemonic culture pre-empting freedom of political choice.

text: Locked into legitimacy: a study of the place of values in politics & society The object of this thesis is the analysis of the nature, extent and origins of political beliefs and their particular role in legitimising state authority in New Zealand. In the first part two general approaches to the problem of legitimacy are considered. The first, associated with Western ‘social science’, assumes that democracy is representative of all interest groups, and is characterised by shared norms and procedures termed the ‘civic culture’. The author examines the evidence and shows that there are no valid empirical grounds in support of this assumption. The second approach, associated with Marxism, makes the reverse assumption, that the working-class in liberal democracies continues to be exploited, and that allegiance to the state in the working-class is less the consequence of ‘free choice’ than of system constraint.

In the second part the author attempts to develop a model of the causal influences which shaped the political beliefs of the working-class in New Zealand history. An assessment of the historical and contemporary evidence shows that the ‘loyalty’ of the majority of the working-class to the state was as much the product of physical, legal and symbolic constraints, as that of social mobility, rising, living standards, and welfare provisions. The author concludes that the forces which shape political consciousness in New Zealand society have been centralised and consolidated by the state as a hegemonic culture pre-empting freedom of political choice.

year: 1974

title: Artefacts, biology and bias in museum collection research

authors: Wehi, Priscilla M.

subjects: experimenta design

abstract: Museum collections are increasingly subjected to scientific scrutiny, including molecular, isotopic and trace-element analyses. Recent advances have extended analyses from natural history specimens to historical artefacts. We highlight three areas of concern that can influence interpretation of data derived from museum collections: sampling issues associated with museum collection use, methods of analysis, and the value of cross-referencing data with historical documents and data sets. We use a case study that focuses on kiwi (Apteryx spp.) feather samples from valuable 19th century Māori cloaks in New Zealand to show how sampling and analysis challenges need to be minimized by careful design. We argue that aligning historical records with scientific data generated from museum collections significantly improves data interpretation.

text: Artefacts, biology and bias in museum collection research Museum collections are increasingly subjected to scientific scrutiny, including molecular, isotopic and trace-element analyses. Recent advances have extended analyses from natural history specimens to historical artefacts. We highlight three areas of concern that can influence interpretation of data derived from museum collections: sampling issues associated with museum collection use, methods of analysis, and the value of cross-referencing data with historical documents and data sets. We use a case study that focuses on kiwi (Apteryx spp.) feather samples from valuable 19th century Māori cloaks in New Zealand to show how sampling and analysis challenges need to be minimized by careful design. We argue that aligning historical records with scientific data generated from museum collections significantly improves data interpretation.

year: 2012-07