Physical Sciences and Mathematics Commons^™

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 …

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 the …

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

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.

Sediment Mixing At Nonda Rock: Investigations Of Stratigraphic Integrity At An Early Archaeological Site In Northern Australia And Implications For The Human Colonisation Of The Continent, Richard Roberts, C White, L K Fifield, Christian Turney, M Bird, John Tibby, Bruno David, John Magee, Jerome Mialanes

Richard G Roberts

No abstract provided.

Afromontane Foragers Of The Late Pleistocene: Site Formation, Chronology And Occupational Pulsing At Melikane Rockshelter, Lesotho, Brian Stewart, Genevieve Dewar, Mike Morley, Robyn Inglis, Mark Wheeler, Zenobia Jacobs, Richard Roberts

Richard G Roberts

This paper provides a preliminary chronostratigraphic and palaeoenvironmental framework for the Late Pleistocene archaeological sequence at Melikane Rockshelter in mountainous eastern Lesotho. Renewed excavations at Melikane form part of a larger project investigating marginal landscape use by Late Pleistocene foragers in southern Africa. Geoarchaeological work undertaken at the site supports in-field observations that Melikane experienced regular, often intensive, input of groundwater via fissures in the shelter’s rear wall. This strong hydrogeological connection resulted in episodic disturbances of the sedimentary sequence, exacerbated by other processes such as bioturbation. Despite this taphonomic complexity, a robust chronology for Melikane has been developed, based …

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

Faculty of Science - Papers (Archive)

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 tRNA_CUA 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.

Slides: The Promise And Peril Of Oil Shale: Federal Law And Policy, David Bernhardt

The Promise and Peril of Oil Shale Development (February 5)

Presenter: David Bernhardt, Brownstein Hyatt Farber Schreck, Denver, CO

13 slides

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

Faculty of Science - Papers (Archive)

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.

Data Report: Clast Counts And Petrography Of Gravels From Site C0007, Iodp Expedition 316, Nankai Trough, Christopher L. Fergusson

Faculty of Science - Papers (Archive)

Gravel beds drilled during Integrated Ocean Drilling Program Expedition 316 at Site C0007 in the eastern Nankai Trough, ~100km offshore from the Kii Peninsula of Honshu, southwest Japan, have been investigated using 26 samples from two horizons (Cores 316-C0007C/C-17H and 316-C0007D-12R). The gravel from Core 316-C0007c-17H is from a 1.7m thick layer, whereas the gravel from Core 316-C0007D-12R is from a layer 4.55m thick. The upper parts of both layers are normally graded. The gravel is clast-supported, polymictic, of granule to pebble size, moderately to poorly sorted, and with subrounded to angular fragments. Clast types are similar from both cores …

A Re-Examination Of A Human Femur Found At The Blind River Site, East London, South Africa: Its Age, Morphology, And Breakage Pattern, Zenobia Jacobs, Qian Wang, David L. Roberts, P V. Tobias

Faculty of Science - Papers (Archive)

ABSTRACT Modern human femoral features might have appeared in the early Middle Stone Age (156 ka to 20 ka) in South Africa, as demonstrated by the recent re-examination of a human femur fossil found at the Blind River Site, East London in the 1930s, if new dating results hold. Two optically stimulated luminescence dates from the relocated original Blind River shallow marine/estuarine deposits that contained the femur gave almost identical ages of ~120 ka, corresponding to the early part of the Last Interglacial (Oxygen Isotope Stage 5). Overall, the slender headless femur is of modern human form. The distal epiphysis …

An Alternative Approach To Coal Mine Site Water Management: A Case Study On West Cliff Colliery, Antony Volcich, Stephen A. Short, Adrian C. Hutton, Robert John Morrison

Faculty of Science - Papers (Archive)

The provision of water supply, its usage and discharge, are major concerns for all mines, often accounting for a significant portion of the daily running costs. To reduce these costs, mines will collect as much site runoff as possible, and recycle the water whenever economically feasible. The constant recycling of on-site waters can mean that, over time, the levels of salinity, acidity or alkalinity, or other contaminants may build up within the internal water management system to a point which may lead to problems with licensed discharge requirements. This project investigated the water quality at West Cliff Colliery, in order …

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

Faculty of Science - Papers (Archive)

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τ_C16. We show that the extreme C-terminal region of τ_C16 constitutes the site of interaction with α. The τ_C16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τ_C16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (K_D) of the α−τ_C16 complex to be ∼260 pM. Competition with immobilized τ_C16 by …

Identification Of The Rest Regulon Reveals Extensive Transposable Element-Mediated Binding Site Duplication, Rory Johnson, Richard J. Gamblin, Lezanne Ooi, Alexander W. Bruce, Ian J. Donaldson, David R. Westhead, Ian Wood, Richard M. Jackson, Noel J. Buckley

Faculty of Science - Papers (Archive)

The genome-wide mapping of gene-regulatory motifs remains a major goal that will facilitate the modelling of gene-regulatory networks and their evolution. The repressor element 1 is a long, conserved transcription factor-binding site which recruits the transcriptional repressor REST to numerous neuron-specific target genes. REST plays important roles in multiple biological processes and disease states. To map RE1 sites and target genes, we created a position specific scoring matrix representing the RE1 and used it to search the human and mouse genomes. We identified 1301 and 997 RE1s inhuman and mouse genomes, respectively, of which >40% are novel. By employing an …

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

Faculty of Science - Papers (Archive)

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 …

The Role Of Trust In The North Blackforest: An Evaluation Of A Citizen Panel Project, Ragnar E. Löfstedt

RISK: Health, Safety & Environment (1990-2002)

Dr. Löfstedt explores the effectiveness of a public participation project conducted in Germany, designed to involve citizens in the siting of municipal waste disposal plants.

Evaluation Of Siting Strategies: The Case Of Two Uk Waste Tire Incinerators, Ragnar E. Lofstedt

RISK: Health, Safety & Environment (1990-2002)

Examines the circumstances that may have contributed to differing outcomes with respect to siting similar facilities in the UK.

Review Of: Peter K. Lagoy, Risk Assessment: Principles And Applications For Hazardous Waste And Related Sites (Noyes Publications 1994), Adam K. Sacharoff

RISK: Health, Safety & Environment (1990-2002)

Review of the book: Peter K. LaGoy, Risk Assessment: Principles and Applications for Hazardous Waste and Related Sites (Noyes Publications 1994). Appendices, figures, index, notes, preface, references, tables. LC 94-2510; ISBN 0-8155-1349-6. [260 pp. Cloth $48.00. 120 Mill Road, Park Ridge NJ 07656.]

Risk Perception And Trust: Challenges For Facility Siting, Howard Kunreuther, Paul Slovic, Donald Macgregor

RISK: Health, Safety & Environment (1990-2002)

The authors maintain that, by granting legitimacy to different notions of fairness and building on common values such as responsibility, it is possible to design siting procedures that promote social cohesion, trust and a sense of fair play.

Economic Impacts Of Noxious Facilities: Incorporating The Effects Of Risk Aversion, Leslie A. Nieves

RISK: Health, Safety & Environment (1990-2002)

The author suggests an integrative approach for projecting economic impacts of facilities that elicit public Risk aversion. She incorporates both economic stimulus effects and perception-based effects of facilities on the host area economy. Empirical findings are compared and an impact estimation framework is suggested for integrating psychometric and econometric techniques.