Physical Sciences and Mathematics Commons^™

Slides: Best Management Practices For Oil And Gas Development And Comparative Water Quality Database Of Regulations Relating To Shale Oil And Gas, Matt Samelson, University Of Colorado Boulder. Getches-Wilkinson Center For Natural Resources, Energy, And The Environment. Intermountain Oil And Gas Bmp Project

Fracking, Water Quality and Public Health: Examining Current Laws and Regulations (March 20)

Presenter: Matt Samelson, J.D., Attorney, Consultant for Intermountain Oil and Gas Best Management Practices (BMP) Project, Getches-Wilkinson Center for Natural Resources, Energy and the Environment, University of Colorado Law School

34 slides

Cyclicity In The Nearshore Marine To Coastal, Lower Permian, Pebbley Beach Formation, Southern Sydney Basin, Australia: A Record Of Relative Sea-Level Fluctuations At The Close Of The Late Palaeozoic Gondwanan Ice Age, Brian G. Jones, Stuart C. Tye, James A. Maceachern, Kerrie L. Bann, Christopher R. Fielding

B. G. Jones

The Lower Permian (Artinskian to Sakmarian) Pebbley Beach Formation of the southernmost Sydney Basin in New South Wales, Australia, records sediment accumulation in shallow marine to coastal environments at the close of the Late Palaeozoic Gondwanan ice age. This paper presents a sequence stratigraphic re-evaluation of the upper half of the unit based on the integration of sedimentology and ichnology. Ten facies are recognized, separated into two facies associations. Facies Association A (7 facies) comprises variably bioturbated siltstones and sandstones with marine body fossils, interpreted to record sediment accumulation in open marine environments ranging from lower offshore to middle shoreface …

Aeolian-Fluvial Interaction: Evidence For Late Quaternary Channel Change And Wind-Rift Linear Dune Formation In The Northwestern Simpson Desert, Australia, Gerald C. Nanson, Brian G. Jones, David M. Price, Tim Pietsch, C Bristow, Cameron B. Hollands

B. G. Jones

In central Australia the most easterly extent of the MacDonnell Ranges borders the northwestern Simpson Desert where widely spaced strike ridges intercept the regional linear dunefield. Topographic basins have disrupted regional drainage lines and isolated dune sets from the main dunefield. In the western part of Camel Flat basin large, red coloured linear dunes of fine sand, ~ 74 ka and older, are oriented almost due north. Through gaps in the ranges the Todd River traversed the eastern part of the basin until ~25 ka when it apparently avulsed ~25 km eastwards to its present position. Subsequently, linear dunes, smaller, …

Macroglobulin And Haptoglobin Suppress Amyloid Formation By Interacting With Prefibrillar Protein Species, Justin J. Yerbury, Janet R. Kumita, Sarah Meehan, Christopher M. Dobson, Mark R. Wilson

Mark R Wilson

α2-Macroglobulin (α2M) and haptoglobin (Hp) are both abundant secreted glycoproteins that are best known for their protease trapping and hemoglobin binding activities, respectively. Like the small heat shock proteins, both these glycoproteins have in common the ability to protect a range of proteins from stress-induced amorphous aggregation and have been described as extracellular chaperones. Using an array of biophysical techniques, this study establishes that in vitro at substoichiometric levels and under physiological conditions α2M and Hp both inhibit the formation of amyloid fibrils from a range of proteins. We also provide evidence that both α2M and Hp interact with prefibrillar …

Potential Roles Of Abundant Extracellular Chaperones In The Control Of Amyloid Formation And Toxicity, Mark R. Wilson, Justin J. Yerbury, Stephen Poon

Mark R Wilson

The in vivo formation of fibrillar proteinaceous deposits called amyloid is associated with more than 40 serious human diseases, collectively referred to as protein deposition diseases. In many cases the amyloid deposits are extracellular and are found associated with newly identified abundant extracellular chaperones (ECs). Evidence is presented suggesting an important regulatory role for ECs in amyloid formation and disposal in the body. A model is presented which proposes that, under normal conditions, ECs stabilize extracellular misfolded proteins by binding to them, and then guide them to specific cell receptors for uptake and subsequent degradation. Thus ECs and their receptors …

The Two-Faced Nature Of Small Heat Shock Proteins: Amyloid Assembly And The Inhibition Of Fibril Formation. Relevance To Disease States, Heath W. Ecroyd, S Meehan, John A. Carver

Heath Ecroyd

The ability of small heat-shock proteins (sHsps) such as alphaB-crystallin to inhibit the amorphous (disordered) aggregation of varied target proteins in a chaperone-like manner has been well described. The mechanistic details of this action are not understood. Amyloid fibril formation is an alternative off-folding pathway that leads to highly ordered beta-sheet-containing aggregates. Amyloid fibril formation is associated with a broad range of protein conformational diseases such as Alzhiemer's, Parkinson's and Huntington's and sHsp expression is elevated in the protein deposits that are characteristic of these disease states. The ability of sHsps to prevent fibril formation has been less well characterised. …

Carbanions: Formation, Structure And Thermochemistry, Stephen J. Blanksby, John H. Bowie

Stephen Blanksby

This chapter deals with even-electron carbanions: their formation, structure and thermochemical properties in the gas phase. There are a number of excellent reviews already available on the chemistry of carbanions: these discuss in the main, reactivity and anion molecule chemistry.1-4 In this chapter we focus primarily on the formation, structure and thermochemistry of simple hydrocarbon anions while other chapters in this encyclopaedia cover the broader aspects of carbanion chemistry (see Volume 1, “Strained Ring and Highly Basic Carbanions” and this volume, Reactions of Organic Molecules with Organic Ions: “Reactions of Anions with Carbonyl Centres: C–C Bond Forming Reactions”, and Unimolecular …

Carboxymethylated-K-Casein: A Convenient Tool For The Identification Of Polyphenolic Inhibitors Of Amyloid Fibril Formation, John A. Carver, Peter J. Duggan, Heath Ecroyd, Yanqin Liu, Adam G. Meyer, C E. Tranberg

Heath Ecroyd

Reduced and carboxymethylated-κ-casein (RCM-κ-CN) is a milk-derived amyloidogenic protein that readily undergoes nucleation-dependent aggregation and amyloid fibril formation via a similar pathway to disease-specific amyloidogenic peptides like amyloid beta (Aβ), which is associated with Alzheimer’s disease. In this study, a series of flavonoids, many known to be inhibitors of Aβ fibril formation, were screened for their ability to inhibit RCM-κ-CN fibrilisation, and the results were compared with literature data on Aβ inhibition. Flavonoids that had a high degree of hydroxylation and molecular planarity gave good inhibition of RCM-κ-CN fibril formation. IC50 values were between 10- and 200-fold higher with RCM-κ-CN …

The Dissociated Form Of Kappa-Casein Is The Precursor To Its Amyloid Fibril Formation, Heath Ecroyd, David Thorn, Yanqin Liu, John Carver

Heath Ecroyd

Bovine milk kappa-casein forms a self-associating oligomeric micelle-like species, in equilibrium with dissociated forms. In its native form, intra- and inter-molecular disulfide bonds lead to the formation of multimeric species ranging from monomers to decamers. When incubated under conditions of physiological pH and temperature, both reduced and non-reduced kappa-casein form highly structured beta-sheet amyloid fibrils. We investigated whether the precursor to kappa-casein fibril formation is a dissociated state of the protein or its oligomeric micelle-like form. We show that reduced kappa-casein is capable of forming fibrils well below its critical micelle concentration, i.e. at concentrations where only dissociated forms of …

Alphab-Crystallin Inhibits The Cell Toxicity Associated With Amyloid Fibril Formation By Kappa-Casein And The Amyloid-Beta Peptide, Francis C. Dehle, Heath Ecroyd, Ian F. Musgrave, John A. Carver

Heath Ecroyd

Amyloid fibril formation is associated with diseases such as Alzheimer’s, Parkinson’s, and prion diseases. Inhibition of amyloid fibril formation by molecular chaperone proteins, such as the small heat-shock protein αB-crystallin, may play a protective role in preventing the toxicity associated with this form of protein misfolding. Reduced and carboxymethylated κ-casein (RCMκ-CN), a protein derived from milk, readily and reproducibly forms fibrils at physiological temperature and pH. We investigated the toxicity of fibril formation by RCMκ-CN using neuronal model PC12 cells and determined whether the inhibition of fibril formation altered its cell toxicity. To resolve ambiguities in the literature, we also …

Communication: New Insight Into The Barrier Governing Co2 Formation From Oh + Co, Christopher J. Johnson, Berwyck L. Poad, Ben B. Shen, Robert E. Continetti

Faculty of Science - Papers (Archive)

Despite its relative simplicity, the role of tunneling in the reaction OH + CO → H + CO(2) has eluded the quantitative predictive powers of theoretical reaction dynamics. In this study a one-dimensional effective barrier to the formation of H + CO(2) from the HOCO intermediate is directly extracted from dissociative photodetachment experiments on HOCO and DOCO. Comparison of this barrier to a computed minimum-energy barrier shows that tunneling deviates significantly from the calculated minimum-energy pathway, predicting product internal energy distributions that match those found in the experiment and tunneling lifetimes short enough to contribute significantly to the overall reaction. …

Alunite Formation Within Silica Stalactites From The Sydney Region, South-Eastern Australia, Robert A. Wray

Faculty of Science - Papers (Archive)

"This paper presents X-ray diffraction and SEM evidence for the formation of alunite, and possibly small quantities of natroalunite, within opal-A stalactites formed on quartz sandstone near Sydney in south-eastern, Australia. Alunite has been reported as a speleogenetic mineral from sediments within a number of caves around the world, but this is believed to be the first report of speleothemic alunite in opaline silica speleothems. Individual alunite crystals have not been visually identified, but SEM X-ray element mapping suggests the alunite has formed amongst kaolinite clay. Sedimentary alunite and natroalunite formation is usually associated with the reaction of sulphuric acid …

The Two-Faced Nature Of Small Heat Shock Proteins: Amyloid Assembly And The Inhibition Of Fibril Formation. Relevance To Disease States, Heath W. Ecroyd, S Meehan, John A. Carver

Faculty of Science - Papers (Archive)

The ability of small heat-shock proteins (sHsps) such as alphaB-crystallin to inhibit the amorphous (disordered) aggregation of varied target proteins in a chaperone-like manner has been well described. The mechanistic details of this action are not understood. Amyloid fibril formation is an alternative off-folding pathway that leads to highly ordered beta-sheet-containing aggregates. Amyloid fibril formation is associated with a broad range of protein conformational diseases such as Alzhiemer's, Parkinson's and Huntington's and sHsp expression is elevated in the protein deposits that are characteristic of these disease states. The ability of sHsps to prevent fibril formation has been less well characterised. …

Carboxymethylated-K-Casein: A Convenient Tool For The Identification Of Polyphenolic Inhibitors Of Amyloid Fibril Formation, John A. Carver, Peter J. Duggan, Heath Ecroyd, Yanqin Liu, Adam G. Meyer, C E. Tranberg

Faculty of Science - Papers (Archive)

Reduced and carboxymethylated-κ-casein (RCM-κ-CN) is a milk-derived amyloidogenic protein that readily undergoes nucleation-dependent aggregation and amyloid fibril formation via a similar pathway to disease-specific amyloidogenic peptides like amyloid beta (Aβ), which is associated with Alzheimer’s disease. In this study, a series of flavonoids, many known to be inhibitors of Aβ fibril formation, were screened for their ability to inhibit RCM-κ-CN fibrilisation, and the results were compared with literature data on Aβ inhibition. Flavonoids that had a high degree of hydroxylation and molecular planarity gave good inhibition of RCM-κ-CN fibril formation. IC50 values were between 10- and 200-fold higher with RCM-κ-CN …

Alphab-Crystallin Inhibits The Cell Toxicity Associated With Amyloid Fibril Formation By Kappa-Casein And The Amyloid-Beta Peptide, Francis C. Dehle, Heath Ecroyd, Ian F. Musgrave, John A. Carver

Faculty of Science - Papers (Archive)

Amyloid fibril formation is associated with diseases such as Alzheimer’s, Parkinson’s, and prion diseases. Inhibition of amyloid fibril formation by molecular chaperone proteins, such as the small heat-shock protein αB-crystallin, may play a protective role in preventing the toxicity associated with this form of protein misfolding. Reduced and carboxymethylated κ-casein (RCMκ-CN), a protein derived from milk, readily and reproducibly forms fibrils at physiological temperature and pH. We investigated the toxicity of fibril formation by RCMκ-CN using neuronal model PC12 cells and determined whether the inhibition of fibril formation altered its cell toxicity. To resolve ambiguities in the literature, we also …

Protein Chemistry Of Amyloid Fibrils And Chaperones: Implications For Amyloid Formation And Disease, Justin J. Yerbury, Janet R. Kumita

Faculty of Science - Papers (Archive)

Understanding the mechanisms by which amyloid fibrils are formed, both in vivo and in vitro, is vital for developing methods to treat and prevent debilitating deposition diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes and systemic amyloidoses. In recent years, computer modelling and biophysical studies have broadened our understanding of the biochemical mechanisms underpinning protein aggregation. As a result, it is now believed that the ability to form fibrils is an intrinsic property of polypeptide chains and not isolated to disease-related proteins or peptides. Molecular chaperones are a diverse group of functionally related proteins well known for their …

The Dissociated Form Of Kappa-Casein Is The Precursor To Its Amyloid Fibril Formation, Heath Ecroyd, David Thorn, Yanqin Liu, John Carver

Faculty of Science - Papers (Archive)

Bovine milk kappa-casein forms a self-associating oligomeric micelle-like species, in equilibrium with dissociated forms. In its native form, intra- and inter-molecular disulfide bonds lead to the formation of multimeric species ranging from monomers to decamers. When incubated under conditions of physiological pH and temperature, both reduced and non-reduced kappa-casein form highly structured beta-sheet amyloid fibrils. We investigated whether the precursor to kappa-casein fibril formation is a dissociated state of the protein or its oligomeric micelle-like form. We show that reduced kappa-casein is capable of forming fibrils well below its critical micelle concentration, i.e. at concentrations where only dissociated forms of …

A Bio-Inspired Molecular Catalyst That Selectively Catalyzes Water Oxidation In Seawater, Without Significant Chlorine Formation, Robin Brimblecombe, G. Charles Dismukes, Gerhard F. Swiegers, Leone Spiccia

Faculty of Science - Papers (Archive)

Most transport fuels are derived from fossil fuels, generate greenhouse gases, and consume significant amounts of water in the extraction, purification, and/or burning processes. The generation of hydrogen using solar energy to split water, ideally from sea water or other non-potable sources, could potentially provide an unlimited, clean fuel for the future. Solar, electrochemical water splitting typically combines a photoanode at which water oxidation occurs, with a cathode for proton reduction to hydrogen. In recent work we have found that a bioinspired tetra-manganese cluster catalyzes water oxidation at relatively low overpotentials (0.38 V) when doped into a Nafion proton conduction …

Macroglobulin And Haptoglobin Suppress Amyloid Formation By Interacting With Prefibrillar Protein Species, Justin J. Yerbury, Janet R. Kumita, Sarah Meehan, Christopher M. Dobson, Mark R. Wilson

Faculty of Science - Papers (Archive)

α₂-Macroglobulin (α₂M) and haptoglobin (Hp) are both abundant secreted glycoproteins that are best known for their protease trapping and hemoglobin binding activities, respectively. Like the small heat shock proteins, both these glycoproteins have in common the ability to protect a range of proteins from stress-induced amorphous aggregation and have been described as extracellular chaperones. Using an array of biophysical techniques, this study establishes that in vitro at substoichiometric levels and under physiological conditions α₂M and Hp both inhibit the formation of amyloid fibrils from a range of proteins. We also provide evidence that both …

Dissociation From The Oligomeric State Is The Rate-Limiting Step In Fibril Formation By Kappa-Casein, Heath Ecroyd, Tomas Koudelka, David Thorn, Danielle M. Williams, Glyn Devlin, Peter Hoffmann, John A. Carver

Faculty of Science - Papers (Archive)

Amyloid fibrils are aggregated and precipitated forms of protein in which the protein exists in highly ordered, long, unbranching threadlike formations that are stable and resistant to degradation by proteases. Fibril formation is an ordered process that typically involves the unfolding of a protein to partially folded states that subsequently interact and aggregate through a nucleation-dependent mechanism. Here we report on studies investigating the molecular basis of the inherent propensity of the milk protein, kappa-casein, to form amyloid fibrils. Using reduced and carboxymethylated kappa-casein ( RCM kappa-CN), we show that fibril formation is accompanied by a characteristic increase in thioflavin …

Strategic Roles Of Axial Histidines In Structure Formation And Redox Regulation Of Tetraheme Cytochrome C3, Y Takayama, N D Werbeck, H Komori, K Morita, Kiyoshi Ozawa, Y Higuchi, H Akutsu

Faculty of Science - Papers (Archive)

Tetraheme cytochrome c3 (cyt c3) exhibits extremely low reduction potentials and unique properties. Since axial ligands should be the most important factors for this protein, every axial histidine of Desulfovibrio vulgaris Miyazaki F cyt c3 was replaced with methionine, one by one. On mutation at the fifth ligand, the relevant heme could not be linked to the polypeptide, revealing the essential role of the fifth histidine in heme linking. The fifth histidine is the key residue in the structure formation and redox regulation of a c-type cytochrome. A crystal structure has been obtained for only H25M cyt c3. The overall …

Direct Imaging Of Lipid-Ion Network Formation Under Physiological Conditions By Frequency Modulation Atomic Force Microscopy, Michael J. Higgins, Suzi P. Jarvis, Takeshi Fukuma

Faculty of Science - Papers (Archive)

Various metal cations in physiological solutions interact with lipid headgroups in biological membranes, having an impact on their structure and stability, yet little is known about the molecular-scale dynamics of the lipid-ion interactions. Here we directly investigate the extensive lipid-ion interaction networks and their transient formation between headgroups in a dipalmitoylphosphatidylcholine bilayer under physiological conditions. The spatial distribution of ion occupancy is imaged in real space by frequency modulation atomic force microscopy with sub-Angstrom resolution.

Potential Roles Of Abundant Extracellular Chaperones In The Control Of Amyloid Formation And Toxicity, Mark R. Wilson, Justin J. Yerbury, Stephen Poon

Faculty of Science - Papers (Archive)

The in vivo formation of fibrillar proteinaceous deposits called amyloid is associated with more than 40 serious human diseases, collectively referred to as protein deposition diseases. In many cases the amyloid deposits are extracellular and are found associated with newly identified abundant extracellular chaperones (ECs). Evidence is presented suggesting an important regulatory role for ECs in amyloid formation and disposal in the body. A model is presented which proposes that, under normal conditions, ECs stabilize extracellular misfolded proteins by binding to them, and then guide them to specific cell receptors for uptake and subsequent degradation. Thus ECs and their receptors …

Cyclicity In The Nearshore Marine To Coastal, Lower Permian, Pebbley Beach Formation, Southern Sydney Basin, Australia: A Record Of Relative Sea-Level Fluctuations At The Close Of The Late Palaeozoic Gondwanan Ice Age, Brian G. Jones, Stuart C. Tye, James A. Maceachern, Kerrie L. Bann, Christopher R. Fielding

Faculty of Science - Papers (Archive)

The Lower Permian (Artinskian to Sakmarian) Pebbley Beach Formation of the southernmost Sydney Basin in New South Wales, Australia, records sediment accumulation in shallow marine to coastal environments at the close of the Late Palaeozoic Gondwanan ice age. This paper presents a sequence stratigraphic re-evaluation of the upper half of the unit based on the integration of sedimentology and ichnology. Ten facies are recognized, separated into two facies associations. Facies Association A (7 facies) comprises variably bioturbated siltstones and sandstones with marine body fossils, interpreted to record sediment accumulation in open marine environments ranging from lower offshore to middle shoreface …

Aeolian-Fluvial Interaction: Evidence For Late Quaternary Channel Change And Wind-Rift Linear Dune Formation In The Northwestern Simpson Desert, Australia, Gerald C. Nanson, Brian G. Jones, David M. Price, Tim Pietsch, C Bristow, Cameron B. Hollands

Faculty of Science - Papers (Archive)

In central Australia the most easterly extent of the MacDonnell Ranges borders the northwestern Simpson Desert where widely spaced strike ridges intercept the regional linear dunefield. Topographic basins have disrupted regional drainage lines and isolated dune sets from the main dunefield. In the western part of Camel Flat basin large, red coloured linear dunes of fine sand, ~ 74 ka and older, are oriented almost due north. Through gaps in the ranges the Todd River traversed the eastern part of the basin until ~25 ka when it apparently avulsed ~25 km eastwards to its present position. Subsequently, linear dunes, smaller, …

Carbanions: Formation, Structure And Thermochemistry, Stephen J. Blanksby, John H. Bowie

Faculty of Science - Papers (Archive)

This chapter deals with even-electron carbanions: their formation, structure and thermochemical properties in the gas phase. There are a number of excellent reviews already available on the chemistry of carbanions: these discuss in the main, reactivity and anion molecule chemistry.1-4 In this chapter we focus primarily on the formation, structure and thermochemistry of simple hydrocarbon anions while other chapters in this encyclopaedia cover the broader aspects of carbanion chemistry (see Volume 1, “Strained Ring and Highly Basic Carbanions” and this volume, Reactions of Organic Molecules with Organic Ions: “Reactions of Anions with Carbonyl Centres: C–C Bond Forming Reactions”, and Unimolecular …