David J.A. Evans

The interpretation and classification of subglacially-deformed materials

Abstract A general classification of subglacially-deformed materials is proposed, based on sediment properties and their relationship to styles of subglacial strain. Deformation till is defined as homogenized, usually diamictic material formed by glacially-induced shear of subsole materials. Three types are recognized: Type A , formed by pervasive, ductile deformation: Type B , formed by brittle shear; and comminution till , produced by the reduction of void space by in situ crushing and abrasion. The term glacitectonite is adopted for materials that have undergone subglacial shear but retain some of the structural characteristics of the parent material. Original structures may be truncated by glacitectonic fabric elements ( Type A ) or distorted but not truncated ( Type B ). The principles of strain and material response, particle orientation mechanisms, fabric development and drainage conditions are reviewed. Examples of deformation tills and glacitectonites from Breidamerkurjokull, Iceland; Slettmarkbreen, Norway; Loch Lomond, Scotland; and East Yorkshire, England, are used to illustrate the nature of subglacially-deformed materials and their relationship to former subglacial strain and drainage conditions. The geologic evidence suggests a continuum of bed strengths can be recognized in deforming substrata, ranging from high strength, low-strain Type B deformation till and comminution till to low strength, high strain Type A deformation till.

Identification of a cis-Acting Replication Element within the Poliovirus Coding Region

ABSTRACT The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel polioviruscis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560–11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

The active temperate glacial landsystem: a model based on Breiðamerkurjökull and Fjallsjökull, Iceland

Accurate interpretations of ancient glaciated terrains rely heavily on our knowledge of process–form relationships in contemporary glacierized basins. A landsystems model for temperate, actively receding glaciers is presented based upon Breiðamerkurjokull and Fjallsjokull, Iceland. Historical documentation, maps and/or aerial photography documenting recession since 1903 provide a unique series of “snapshots” of the evolving glacial geomorphology at these snouts. This documentation is employed in association with sedimentological investigations to assess the evolution of sediment–landform assemblages at active temperate glacier margins, using the wealth of geomorphological and sedimentological information produced during the recent recession of Breiðamerkurjokull and Fjallsjokull. Three depositional domains are recognized: (1) areas of extensive, low amplitude marginal dump, push and squeeze moraines derived largely from material on the glacier foreland and often recording annual recession of active ice; (2) incised and terraced glacifluvial forms, such as recessional ice-contact fans and hochsandur fans, and simple and complex, anabranched eskers and small areas of pitted outwash; (3) subglacial landform assemblages of flutes, drumlins and overridden push moraines located between ice-marginal glacifluvial depo-centres. The lack of supraglacial sediment in active temperate glaciers like Breiðamerkurjokull and Fjallsjokull generally precludes the widespread development of chaotic hummocky moraine. The hummocky terrain previously termed “kame and kettle topography” has mostly evolved by melt-out into a complex network of anabranched eskers over the period 1945–1998 or actually comprises pitted or kettled outwash (sandar). The tills across the foreland were emplaced by subglacial deformation and lodgement, and comprise materials derived from pre-existing stratified sediments in addition to localized abrasion of rock surfaces and patches of lake sediments. Till sequences thicker than 2 m have been constructed by the sequential plastering of till layers onto stratified sediments and bedrock. Because this stacking is a sub-marginal process, it is suggested that complex till sequences similar to those observed at Breiðamerkurjokull/Fjallsjokull may be employed in the reconstruction of ancient glacier margins. Additionally, the geomorphology of the active, temperate landsystem at east Breiðamerkurjokull may contain subtle surge signatures, verifying the historical record of small surges by this part of the glacier. This illustrates the danger of employing landform–sediment associations from restricted study areas (e.g. parts of landsystems) as representative process–form models for glaciated terrains.

Geomorphology and sedimentology of surging glaciers: a land-systems approach

The identification of surging glaciers and ice streams in glaciated landscapes is of major importance to the understanding of ice-sheet dynamics and for reconstructing ice sheets and climate. No single landform or diagnostic criterion has yet been found with which to identify surging glaciers. A surging-glacier land-system model is constructed using observations and measurements from contemporary surging-glacier snouts in Iceland, Svalbard, U.S.A. and Canada for differentiating ancient surging margins from other non-surging palaeoglaciers. This integrates the suite of landforms, sediments and stratigraphy produced at surging-glacier margins. Landforms produced during surging include thrust moraines, concertina eskers and subglacial crevasse-squeeze ridges. Sedimentary sequences are usually characterized by multiple stacked diamictons and stratified interbeds, which display severe glaciotectonic contortion and faulting. Hummocky moraine, comprising interbedded stratified sediments and mass-flow diamictons, has also been associated with surge margins where large quantities of supraglacial and englacial debris entrained during the surge event have melted out in situ. An example of the application of the land-system model is presented for east-central Alberta, Canada. A surging palaeo-ice stream is identified within this part of the southwestern Laurentide ice sheet, where thrust-block moraines, crevasse-squeeze ridges, flutings, hummocky moraine and glaciotectonized sediments are juxtaposed.

Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus

The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV.

MESANGIOCAPILLARY NEPHRITIS, PARTIAL LIPODYSTROPHY, AND HYPOCOMPLEMENTÆMIA

Abstract Three patients with partial lipodystrophy, C3 activation and hypocomplementaemia, and mesangiocapillary glomerulonephritis of the dense-deposit variety are described. It is proposed that the primary abnormality in these and other patients with this type of nephritis is C3 activation which results in prolonged hypocomplementaemia. This predisposes to the development of nephritis by a mechanism similar to that in patients known to have congenital deficiency of the complement system.

Molecular Analysis of the Epidermal Growth Factor-like Short Consensus Repeat Domain-mediated Protein-Protein Interactions DISSECTION OF THE CD97-CD55 COMPLEX

Epidermal growth factor-like (EGF) and short consensus repeat (SCR) domains are commonly found in cell surface and soluble proteins that mediate specific protein-protein recognition events. Unlike the immunoglobulin (Ig) superfamily, very little is known about the general properties of intermolecular interactions encoded by these common modules, and in particular, how specificity of binding is achieved. We have dissected the binding of CD97 (a member of the EGF-TM7 family) to the complement regulator CD55, two cell surface modular proteins that contain EGF and SCR domains, respectively. We demonstrate that the interaction is mediated solely by these domains and is characterized by a low affinity (86 μm) and rapid off-rate (at least 0.6 s−1). The interaction is Ca2+ -dependent but is unaffected by glycosylation of the EGF domains. Using biotinylated multimerized peptides in cell binding assays and surface plasmon resonance, we show that a CD97-related EGF-TM7 molecule (termed EMR2), differing by only three amino acids within the EGF domains, binds CD55 with aK D at least an order of magnitude weaker than that of CD97. These results suggest that low affinity cell-cell interactions may be a general feature of highly expressed cell surface proteins and that specificity of SCR-EGF binding can be finely tuned by a small number of amino acid changes on the EGF module surface.

A Hepatitis C Virus cis-Acting Replication Element Forms a Long-Range RNA-RNA Interaction with Upstream RNA Sequences in NS5B

ABSTRACT The genome of hepatitis C virus (HCV) contains cis-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5′ and 3′ noncoding regions (5′ and 3′ NCRs) and in the NS5B coding sequence. Through the application of several algorithmically independent bioinformatic methods to detect phylogenetically conserved, thermodynamically favored RNA secondary structures, we demonstrate a long-range interaction between sequences in the previously described CRE (5BSL3.2, now SL9266) with a previously predicted unpaired sequence located 3′ to SL9033, approximately 200 nucleotides upstream. Extensive reverse genetic analysis both supports this prediction and demonstrates a functional requirement in genome replication. By mutagenesis of the Con-1 replicon, we show that disruption of this alternative pairing inhibited replication, a phenotype that could be restored to wild-type levels through the introduction of compensating mutations in the upstream region. Substitution of the CRE with the analogous region of different genotypes of HCV produced replicons with phenotypes consistent with the hypothesis that both local and long-range interactions are critical for a fundamental aspect of genome replication. This report further extends the known interactions of the SL9266 CRE, which has also been shown to form a “kissing loop” interaction with the 3′ NCR (P. Friebe, J. Boudet, J. P. Simorre, and R. Bartenschlager, J. Virol. 79:380-392, 2005), and suggests that cooperative long-range binding with both 5′ and 3′ sequences stabilizes the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.

Large-scale reorganization and sedimentation of terrestrial ice streams during late Wisconsinan Laurentide Ice Sheet deglaciation.

Glacial geomorphological mapping of Shuttle Radar Topography Mission (SRTM) data from the western Canadian Prairies demonstrates that during the last (late Wisconsinan) deglaciation of the Laurentide Ice Sheet terrestrial ice streams underwent a major reorganization of their flow configuration. This reorganization involved a 90° shift in flow direction and was accompanied by a corresponding increase in the influence of topography on streaming flow. Ice streams included both topographically confined and “pure” ice streams that flowed independent of topography. Streaming flow is recorded by suites of highly elongate (>60 km long) subglacial bedforms, bounded sharply at their lateral margins by prominent moraines. Initial streaming flow was unconfined by topography but was replaced progressively, and crosscut, by younger topographically confined flows. Flow reorganization is inferred to have been caused by temporal and spatial variations in the interaction between frozen and thawed bed conditions, with thinning and shutdown of one ice stream ultimately triggering initiation of others. This highlights the role of internal glaciodynamically driven reorganization in triggering streaming flow within large ice sheets and shows that large-scale flow reorganization can occur over the time scale of a single deglaciation in terrestrial ice streams.

Polyphase deformation at an oscillating ice margin following the Loch Lomond Readvance, central Scotland, UK

The sequence of glacitectonic disturbance of an ice-contact delta during the initial stages of deglaciation following the Loch Lomond Readvance is examined. An ice-marginal, Gilbert-type deltaic sequence exposed in Drumbeg quarry, Drymen (Scotland) displays a polyphase deformation history that is punctuated by periods of erosion and deposition. Progradation of the delta into ice-dammed Lake Blane led to a temporary stabilisation of the Loch Lomond glacier during recession from its Loch Lomond Readvance maximum position. This was followed by a NE-directed readvance into the ice-contact slope of the delta, resulting in proglacial deformation (D1) and the formation of a thrust-block ridge. In the middle to outer parts of the delta complex, sedimentation continued uninterrupted. Subsequent retreat of the ice was accompanied by erosion and deposition as the ice-contact slope was re-established. A second phase of readvance resulted in subglacial, ductile shearing (D2) and deposition of a diamicton during NE-directed over-riding of the delta sediments by the ice. The direction of ice flow subsequently changed towards the SE. This was followed by a further retreat of the ice and re-establishment of the fan-delta complex. The complexity of the glacitectonic sequence at Drumbeg records the impact of an oscillating ice margin responding to either relative deepening of the lake waters in contact with the receding snout, or climatic controls. It provides further evidence that many of the Scottish Highland glaciers were subject to active recession rather than stagnation at the end of the Loch Lomond Readvance.