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Full-Text Articles in Social and Behavioral Sciences

40 Years In Paradox: Post-Normalisation Sino-Japanese Relations, Yinan He Dec 2013

40 Years In Paradox: Post-Normalisation Sino-Japanese Relations, Yinan He

Yinan He

Post-normalisation Sino-Japanese relations have been fraught with contradictions. In particular, three paradoxes stand out over the past 40 years. First, despite many shared geopolitical and economic interests, China and Japan have never developed genuine strategic cooperation, and since the 2000s have even evinced a trend towards thinly-veiled or open rivalry. Second, time, rather than healing the wounds of past wars, has since the mid-1980s yielded only a more vivid and bitter recollection of history that has bedevilled both official and popular relations. Third, diplomatic and commercial ties as well as “thick” societal contacts developed since normalisation have failed to bridge ...


Alice In Oz - 'Please, Ma'am, Is This New Zealand? Or Australia?': The Lewis Carroll Alice In Wonderland Books In Australia, Michael K. Organ Oct 2013

Alice In Oz - 'Please, Ma'am, Is This New Zealand? Or Australia?': The Lewis Carroll Alice In Wonderland Books In Australia, Michael K. Organ

Michael Organ

There is no obvious connection between Australia and the very English Alice in Wonderland stories written by the Reverend Charles Dodgson (Lewis Carroll) in the latter half of the nineteenth century, apart from a few brief words uttered by Alice at the beginning of her adventures - 'Please, Ma'am, is this New Zealand? Or Australia?' - suggesting that, upon falling down a rabbit hole, she had been transported to the Antipodes ('Antipathies'), just as Lemuel Gulliver had found himself lost in Lilliput a century earlier. Yet the ongoing popularity and influence of these works in the former British colony is reflected ...


Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting Jul 2013

Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting

Professor Nick E Dixon

The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τC16), and domains shortened at the C-terminus by 11 and 18 residues ...


Effect Of Protein Stabilization On Charge State Distribution In Positive- And Negative Ion Electrospray Ionization Mass Spectra, Stephen J. Watt, Margaret Sheil, Jennifer L. Beck, Pavel Prosselkov, Gottfried Otting, Nicholas E. Dixon Jul 2013

Effect Of Protein Stabilization On Charge State Distribution In Positive- And Negative Ion Electrospray Ionization Mass Spectra, Stephen J. Watt, Margaret Sheil, Jennifer L. Beck, Pavel Prosselkov, Gottfried Otting, Nicholas E. Dixon

Professor Nick E Dixon

Changes in protein conformation are thought to alter charge state distributions observed in electrospray ionization mass spectra (ESI-MS) of proteins. In most cases, this has been demonstrated by unfolding proteins through acidification of the solution. This methodology changes the properties of the solvent so that changes in the ESI-MS charge envelopes from conformational changes are difficult to separate from the effects of changing solvent on the ionization process. A novel strategy is presented enabling comparison of ESI mass spectra of a folded and partially unfolded protein of the same amino acid sequence subjected to the same experimental protocols and conditions ...


Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck Jul 2013

Escherichia Coli Single-Stranded Dna-Binding Protein: Nanoesi-Ms Studies Of Salt-Modulated Subunit Exchange And Dna Binding Transactions, Claire E. Mason, Slobodan Jergic, Allen Lo, Yao Wang, Nicholas E. Dixon, Jennifer L. Beck

Professor Nick E Dixon

Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in ...


Architecture And Conservation Of The Bacterial Dna Replication Machinery, An Underexploited Drug Target, Andrew Robinson, Rebecca J. Causer, Nicholas E. Dixon Jul 2013

Architecture And Conservation Of The Bacterial Dna Replication Machinery, An Underexploited Drug Target, Andrew Robinson, Rebecca J. Causer, Nicholas E. Dixon

Professor Nick E Dixon

"New antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad-spectrum antibacterials. DNA replication is a conserved and essential process, and the large number of proteins that interact to replicate DNA in bacteria are ...


Characterization Of Cleavage Events In The Multifunctional Cilium Adhesin Mhp684 (P146) Reveals A Mechanism By Which Mycoplasma Hyopneumoniae Regulates Surface Topography, Daniel Bogema, Ania T. Deutscher, Lauren K. Woolley, Lisa M. Seymour, Benjamin B. A Raymond, Jessica L. Tacchi, Matthew P. Padula, Nicholas E. Dixon, F Chris Minion, Cheryl Jenkins, Mark J. Walker, Steven P. Djordjevic Jul 2013

Characterization Of Cleavage Events In The Multifunctional Cilium Adhesin Mhp684 (P146) Reveals A Mechanism By Which Mycoplasma Hyopneumoniae Regulates Surface Topography, Daniel Bogema, Ania T. Deutscher, Lauren K. Woolley, Lisa M. Seymour, Benjamin B. A Raymond, Jessica L. Tacchi, Matthew P. Padula, Nicholas E. Dixon, F Chris Minion, Cheryl Jenkins, Mark J. Walker, Steven P. Djordjevic

Professor Nick E Dixon

Mycoplasma hyopneumoniae causes enormous economic losses to swine production worldwide by colonizing the ciliated epithelium in the porcine respiratory tract, resulting in widespread damage to the mucociliary escalator, prolonged inflammation, reduced weight gain, and secondary infections. Protein Mhp684 (P146) comprises 1,317 amino acids, and while the N-terminal 400 residues display significant sequence identity to the archetype cilium adhesin P97, the remainder of the molecule is novel and displays unusual motifs. Proteome analysis shows that P146 preprotein is endogenously cleaved into three major fragments identified here as P50P146, P40P146, and P85P146 that reside on the cell surface. Liquid chromatography with ...


Defining The Structural Basis Of Human Plasminogen Binding By Streptococcal Surface Enolase, Amanda J. Cork, Slobodan Jergic, Sven Hammerschmidt, Bostjan Kobe, Vijay Pancholi, Justin L.P. Benesch, Carol V, Robinson, Nicholas E. Dixon, J Andrew Aquilina, Mark J. Walker Jul 2013

Defining The Structural Basis Of Human Plasminogen Binding By Streptococcal Surface Enolase, Amanda J. Cork, Slobodan Jergic, Sven Hammerschmidt, Bostjan Kobe, Vijay Pancholi, Justin L.P. Benesch, Carol V, Robinson, Nicholas E. Dixon, J Andrew Aquilina, Mark J. Walker

Professor Nick E Dixon

The flesh-eating bacterium group A Streptococcus (GAS) binds and activates human plasminogen, promoting invasive disease. Streptococcal surface enolase (SEN), a glycolytic pathway enzyme, is an identified plasminogen receptor of GAS. Here we used mass spectrometry (MS) to confirm that GAS SEN is octameric, thereby validating in silico modeling based on the crystal structure of S. pneumoniae -enolase. Site-directed mutagenesis of surface-located lysine residues (SENK252+255A, SENK304A, SENK334A, SENK344E, SENK435L and SEN434-435) was used to examine their roles in maintaining structural integrity, enzymatic function and plasminogen binding. Structural integrity of the GAS SEN octamer was retained for all mutants except ...


Essential Biological Processes Of An Emerging Pathogen: Dna Replication, Transcription, And Cell Division In Acinetobacter Spp., Andrew Robinson, Anthony J. Brzoska, Kylie M. Turner, Ryan Withers, Elizabeth J. Harry, Peter J. Lewis, Nicholas E. Dixon Jul 2013

Essential Biological Processes Of An Emerging Pathogen: Dna Replication, Transcription, And Cell Division In Acinetobacter Spp., Andrew Robinson, Anthony J. Brzoska, Kylie M. Turner, Ryan Withers, Elizabeth J. Harry, Peter J. Lewis, Nicholas E. Dixon

Professor Nick E Dixon

Species of the bacterial genus Acinetobacter are becoming increasingly important as a source of hospital-acquired infections (31, 185, 204). Acinetobacter spp. are ubiquitous nonmotile gammaproteobacteria, typified by metabolic versatility and a capacity for natural transformation (172, 204). The species of most clinical relevance is A. baumannii; however, pathogenic strains of A. lwoffi and A. baylyi have also been described (38, 185, 215).


Incorporation Of Chlorinated Analogues Of Aliphatic Amino Acids During Cell-Free Protein Synthesis, Dannon J. Stigers, Zachary I. Watts, James E. Hennessy, Hye-Kyung Kim, Romeo Martini, Matthew C. Taylor, Kiyoshi Ozawa, Jeffrey W. Keillor, Nicholas E. Dixon, Christopher J. Easton Jul 2013

Incorporation Of Chlorinated Analogues Of Aliphatic Amino Acids During Cell-Free Protein Synthesis, Dannon J. Stigers, Zachary I. Watts, James E. Hennessy, Hye-Kyung Kim, Romeo Martini, Matthew C. Taylor, Kiyoshi Ozawa, Jeffrey W. Keillor, Nicholas E. Dixon, Christopher J. Easton

Professor Nick E Dixon

3-Chloro-Abu and 4-chloro-Nva are biosynthetically incorporated into E. coli peptidyl-Pro cis-trans isomerase B, as substitutes for Val and Leu, respectively. The extent of incorporation is up to 90%, and substituted protein is catalytically active. By contrast, 4-chloro-Val is not an effective replacement for Ile.


Nanometer-Scale Distance Measurements In Proteins Using Gd3+ Spin Labeling, Alexey Potapov, Hiromasa Yagi, Thomas Huber, Slobodan Jergic, Nicholas E. Dixon, Gottfried Otting, Daniella Goldfarb Jul 2013

Nanometer-Scale Distance Measurements In Proteins Using Gd3+ Spin Labeling, Alexey Potapov, Hiromasa Yagi, Thomas Huber, Slobodan Jergic, Nicholas E. Dixon, Gottfried Otting, Daniella Goldfarb

Professor Nick E Dixon

Methods for measuring nanometer-scale distances between specific sites in proteins are essential for analysis of their structure and function. In this work we introduce Gd3+ spin labeling for nanometer-range distance measurements in proteins by high-field pulse electron paramagnetic resonance (EPR). To evaluate the performance of such measurements, we carried out four-pulse double-electron electron resonance (DEER) measurements on two proteins, p75ICD and τC14, labeled at strategically selected sites with either two nitroxides or two Gd3+ spin labels. In analogy to conventional site-directed spin labeling using nitroxides, Gd3+ tags that are derivatives of dipicolinic acid were covalently attached to cysteine thiol groups ...


Proteomic Dissection Of Dna Polymerization, Jennifer L. Beck, Thitima Urathamakul, Stephen James Watt, Margaret Sheil, Patrick M. Schaeffer, Nicholas E. Dixon Jul 2013

Proteomic Dissection Of Dna Polymerization, Jennifer L. Beck, Thitima Urathamakul, Stephen James Watt, Margaret Sheil, Patrick M. Schaeffer, Nicholas E. Dixon

Professor Nick E Dixon

DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is called the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerisation and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions is a current research topic. Mass spectrometry is a technique that can be used to identify the sites of these ...


Helicase-Binding To Dnai Exposes A Cryptic Dna-Binding Site During Helicase Loading In Bacillus Subtilis, Charikleia Ioannou, Patrick M. Schaeffer, Nicholas E. Dixon, Panos Soultanas Jul 2013

Helicase-Binding To Dnai Exposes A Cryptic Dna-Binding Site During Helicase Loading In Bacillus Subtilis, Charikleia Ioannou, Patrick M. Schaeffer, Nicholas E. Dixon, Panos Soultanas

Professor Nick E Dixon

The Bacillus subtilis DnaI, DnaB and DnaD proteins load the replicative ring helicase DnaC onto DNA during priming of DNA replication. Here we show that DnaI consists of a C-terminal domain (Cd) with ATPase and DNA-binding activities and an N-terminal domain (Nd) that interacts with the replicative ring helicase. A Zn21-binding module mediates the interaction with the helicase and C67, C70 and H84 are involved in the coordination of the Zn21. DnaI binds ATP and exhibits ATPase activity that is not stimulated by ssDNA, because the DNAbinding site on Cd is masked by Nd. The ATPase activity resides on the ...


Ultrasensitive Detection Of Antibodies Using A New Tus-Ter-Lock Immunopcr System, Isabelle Morin, Nicholas E. Dixon, Patrick M. Schaeffer Jul 2013

Ultrasensitive Detection Of Antibodies Using A New Tus-Ter-Lock Immunopcr System, Isabelle Morin, Nicholas E. Dixon, Patrick M. Schaeffer

Professor Nick E Dixon

A system consisting of a protein LG coated surface for the capture of mammalian antibodies (target), and an antigen fused to Tus and stoichiometrically linked to a DNA template via the Tus-Ter-lock sequence allowed the ultrasensitive detection of 5.5 attomol of target by real-time immunoPCR in complex media. © The Royal Society of Chemistry 2010.


The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon Jul 2013

The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon

Professor Nick E Dixon

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τC16 derivatives for binding to α gave values of KD of 7 μM for ...


High-Yield Cell-Free Protein Synthesis For Site-Specific Incorporation Of Unnatural Amino Acids At Two Sites, Kiyoshi Ozawa, Karin V. Loscha, Kekini V. Kuppan, Choy Theng Loh, Nicholas E. Dixon, Gottfried Otting Jul 2013

High-Yield Cell-Free Protein Synthesis For Site-Specific Incorporation Of Unnatural Amino Acids At Two Sites, Kiyoshi Ozawa, Karin V. Loscha, Kekini V. Kuppan, Choy Theng Loh, Nicholas E. Dixon, Gottfried Otting

Professor Nick E Dixon

Using aminoacyl-tRNA synthetase/suppressor tRNA pairs derived from Methanocaldococcus jannaschii, an Escherichia coli cell-free protein production system affords proteins with site-specifically incorporated unnatural amino acids (UAAs) in high yields through the use of optimized amber suppressor tRNACUA opt and optimization of reagent concentrations. The efficiency of the cell-free system allows the incorporation of trifluoromethyl-phenylalanine using a polyspecific synthetase evolved previously for p-cyanophenylalanine, and the incorporation of UAAs at two different sites of the same protein without any re-engineering of the E. coli cells used to make the cell-free extract.


Site-Specific Covalent Attachment Of Dna To Proteins Using A Photoactivatable Tus-Ter Complex, Dahdah B. Dahdah, Isabelle Morin, Morgane Moreau, Nicholas E. Dixon, Patrick M. Schaeffer Jul 2013

Site-Specific Covalent Attachment Of Dna To Proteins Using A Photoactivatable Tus-Ter Complex, Dahdah B. Dahdah, Isabelle Morin, Morgane Moreau, Nicholas E. Dixon, Patrick M. Schaeffer

Professor Nick E Dixon

Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.


Synthesis And Applications Of Covalent Protein-Dna Conjugates, Patrick M. Schaeffer, Nicholas E. Dixon Jul 2013

Synthesis And Applications Of Covalent Protein-Dna Conjugates, Patrick M. Schaeffer, Nicholas E. Dixon

Professor Nick E Dixon

Synthetic protein-DNA conjugates are valuable tools with applications in fields including nanobiotechnology, bioanalytical chemistry, and molecular diagnostics, and various synthetic methods for their production have been developed during the past three decades. The present article reviews current methodologies for the synthesis of covalent protein-DNA conjugates with particular focus on the regiospecificity and stoichiometry of these reactions.


Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon Jul 2013

Structure Of The Theta Subunit Of Escherichia Coli Dna Polymerase Iii In Complex With The Epsilon Subunit, Max A Keniry, Ah-Young Park, Elisabeth A. Owen, Samir M. Hamdan, Guido Pintacuda, Gottfried Otting, Nicholas E. Dixon

Professor Nick E Dixon

The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the α, ε, and θ subunits. The θ subunit is the smallest and least understood subunit. The three-dimensional structure of θ in a complex with the unlabeled N-terminal domain of the ε subunit, ε186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of ε186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of θ in a methanol-water ...


The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting Jul 2013

The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting

Professor Nick E Dixon

Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the α-subunit. The ε-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to α via a segment of 57 additional C-terminal residues, and also to θ, whose function is less well defined. The present study shows that θ greatly enhances the solubility of ε during cell-free synthesis. In addition, synthesis of ε in the presence of θ and α resulted in a soluble ternary complex that could readily be purified and analyzed by NMR spectroscopy ...


Replication Termination In Escherichia Coli: Structure And Anti-Helicase Activity Of The Tus-Ter Complex, Cameron Neylon, Andrew V. Kralicek, Thomas M. Hill, Nicholas E. Dixon Jul 2013

Replication Termination In Escherichia Coli: Structure And Anti-Helicase Activity Of The Tus-Ter Complex, Cameron Neylon, Andrew V. Kralicek, Thomas M. Hill, Nicholas E. Dixon

Professor Nick E Dixon

The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the ...


Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon Jul 2013

Proofreading Exonuclease On A Tether: The Complex Between The E. Coli Dna Polymerase Iii Subunits Α, Ε, Θ And Β Reveals A Highly Flexible Arrangement Of The Proofreading Domain, Kiyoshi Ozawa, Nicholas P. Horan, Andrew Robinson, Hiromasa Yagi, Flynn R. Hill, Slobodan Jergic, Zhi-Qiang Xu, Karin V. Loscha, Nan Li, Moeava Tehei, Aaron J. Oakley, Gottfried Otting, Thomas Huber, Nicholas E. Dixon

Professor Nick E Dixon

A complex of the three (αεθ) core subunits and the β2 sliding clamp is responsible for DNA synthesis by Pol III, the Escherichia coli chromosomal DNA replicase. The 1.7 Å crystal structure of a complex between the PHP domain of α (polymerase) and the C-terminal segment of ε (proofreading exonuclease) subunits shows that ε is attached to α at a site far from the polymerase active site. Both α and ε contain clamp-binding motifs (CBMs) that interact simultaneously with β2 in the polymerization mode of DNA replication by Pol III. Strengthening of both CBMs enables isolation of stable αεθ ...


A Novel Zinc-Binding Fold In The Helicase Interaction Domain Of The Bacillus Subtilis Dnal Helicase Loader, Karin V. Loscha, Kristaps Jaudzems, Charikleia Ioannou, Xun-Cheng Su, Flynn R. Hill, Gottfried Otting, Nicholas E. Dixon, Edvards Liepinsh Jul 2013

A Novel Zinc-Binding Fold In The Helicase Interaction Domain Of The Bacillus Subtilis Dnal Helicase Loader, Karin V. Loscha, Kristaps Jaudzems, Charikleia Ioannou, Xun-Cheng Su, Flynn R. Hill, Gottfried Otting, Nicholas E. Dixon, Edvards Liepinsh

Professor Nick E Dixon

The helicase loader protein DnaI (the Bacillus subtilis homologue of Escherichia coli DnaC) is required to load the hexameric helicase DnaC (the B. subtilis homologue of E. coli DnaB) onto DNA at the start of replication. While the C-terminal domain of DnaI belongs to the structurally well-characterized AAA+ family of ATPases, the structure of the N-terminal domain, DnaI-N, has no homology to a known structure. Three-dimensional structure determination by nuclear magnetic resonance (NMR) spectroscopy shows that DnaI presents a novel fold containing a structurally important zinc ion. Surface plasmon resonance experiments indicate that DnaI-N is largely responsible for binding of ...


Flexibility Revealed By The 1.85 Å Crystal Structure Of The Β Sliding-Clamp Subunit Of Escherichia Coli Dna Polymerase Iii, Aaron J. Oakley, Pavel Prosselkov, Gene Wijffels, Jennifer L. Beck, Matthew Cj Wilce, Nicholas E. Dixon Jul 2013

Flexibility Revealed By The 1.85 Å Crystal Structure Of The Β Sliding-Clamp Subunit Of Escherichia Coli Dna Polymerase Iii, Aaron J. Oakley, Pavel Prosselkov, Gene Wijffels, Jennifer L. Beck, Matthew Cj Wilce, Nicholas E. Dixon

Professor Nick E Dixon

The subunit of the Escherichia coli replicative DNA polymerase III holoenzyme is the sliding clamp that interacts with the (polymerase) subunit to maintain the high processivity of the enzyme. The protein is a ring-shaped dimer of 40.6 kDa subunits whose structure has previously been determined at a resolution of 2.5 Å [Kong et al. (1992), Cell, 69, 425-437]. Here, the construction of a new plasmid that directs overproduction of to very high levels and a simple procedure for large-scale purification of the protein are described. Crystals grown under slightly modified conditions diffracted to beyond 1.9 Å at ...


Rotation Patterns And Trend Estimation For Repeated Surveys Using Rotation Group Estimates, Craig Mclaren, David Steel Jun 2013

Rotation Patterns And Trend Estimation For Repeated Surveys Using Rotation Group Estimates, Craig Mclaren, David Steel

Professor David Steel

A general approach for constructing filters to produce trend estimates from a repeated survey is described. This approach accounts for the correlation structure induced by the rotation pattern used in the survey. Different filters are developed depending on whether the trend analysis is based on elementary estimates available for each rotation group or overall estimates obtained by combining the rotation group estimates. The properties of trend estimates obtained directly from the elementary estimates, those obtained from the simple average of the rotation group estimates and trend estimates obtained from the best linear unbiased estimates of the population characteristics of interest ...


Ignoring A Level In A Multilevel Model: Evidence From Uk Census Data, Mark Tramner, David Steel Jun 2013

Ignoring A Level In A Multilevel Model: Evidence From Uk Census Data, Mark Tramner, David Steel

Professor David Steel

Because of the inherent multilevel nature of census data, it is often appropriate to use multilevel models to investigate relationships between census variables. For a local population, the data available from the census allow a three-level nested model to be assumed, with an individual level (level 1), an enumeration district (ED) level (level 2), and a ward level (level 3). The consequences of ignoring one of the three levels in this model are assessed here theoretically. Empirical results, based on 1991 UK Census data, are also provided, comparing the variance components estimated from the three-level model with analyses based on ...


The Impact Of Different Rotation Patterns On The Sampling Variance Of Seasonally Adjusted And Trend Estimates, Craig Mclaren, David Steel Jun 2013

The Impact Of Different Rotation Patterns On The Sampling Variance Of Seasonally Adjusted And Trend Estimates, Craig Mclaren, David Steel

Professor David Steel

Many economic and social time series are based on sample surveys which have complex sample designs. The sample design affects the properties of the time series. In particular, the overlap of the sample from period to period affects the variability of the time series of survey estimates, and the seasonally adjusted and trend estimates produced from them. The Census X11 and X11ARIMA packages are commonly used to produce seasonally adjusted estimates and can also be used to produce estimates of trend. This paper considers the implications of different overlap patterns on the sampling variance of seasonally adjusted and trend estimates ...


An Evaluation Of A Large-Scale Cati Household Survey Using Random Digit Dialling, Don Bennett, David Steel Jun 2013

An Evaluation Of A Large-Scale Cati Household Survey Using Random Digit Dialling, Don Bennett, David Steel

Professor David Steel

omputer-assisted telephone interviewing and random digit dialling are increasingly being used to conduct household surveys in Australia. However, there is little published information concerning Australian experience with such surveys. In 1995 the Government Statistician's Office in Queensland conducted a household survey to study population migration using these techniques. The survey involved a sample of 110 000 telephone numbers resulting in 38 000 responding households. This article describes a computerized survey management system that was developed and which provided information concerning important operational and quality aspects of the survey.


Optimum Allocation Of Sample To Strata And Stages With Simple Additional Constraints, Robert Clark, David Steel Jun 2013

Optimum Allocation Of Sample To Strata And Stages With Simple Additional Constraints, Robert Clark, David Steel

Professor David Steel

The optimum allocation of a sample to strata and stages in a stratified two-stage design for a simple cost function is well known. In practice there may be reasons to impose simple additional constraints. It is shown how the theory for optimum allocation can be generalized to account for such constraints. A simple way of assessing the effect that each constraint has on the efficiency of the sample design is developed. This general approach allows several additional constraints that are used in practice to be applied. Data from the 1996 redesign of the Australian Monthly Labour Force Survey are used ...


Statistical Indicators For Local Government Areas: A Case Study Of The Shoalhaven Lga, 1997, Nell Stetner-Houweling, David Steel, Greg Pullen Jun 2013

Statistical Indicators For Local Government Areas: A Case Study Of The Shoalhaven Lga, 1997, Nell Stetner-Houweling, David Steel, Greg Pullen

Professor David Steel

Decision makers and planers need to have relevant and reliable information to give a picture of how different areas are developing economically and socially. However, there is a perceived lack of timely and easily accessible data at the Local Government Area (LGA) level. This study produced a statistical profile of the Shoalhaven (LGA) by developing a conceptual framework, which represents the key economic, social, and population characteristics of the LGA. The statistical data available from the Australian Bureau of Statistics (ABS) at the level of the LGA, was investigated and summarised. Other sources of information available to create a statistical ...