bluuebunny/crossref_metadata_2025_split huggingface dataset:
Replication Initiator Protein NS1 of the Parvovirus Minute Virus of Mice Binds to Modular Divergent Sites Distributed throughout Duplex Viral DNA
Authors: Cotmore Susan F. , Gottlieb Robert L. , Tattersall Peter 
Published: September 2007

ABSTRACT
To initiate DNA synthesis, the NS1 protein of minute virus of mice (MVM) first binds to a simple cognate recognition sequence in the viral origins, comprising two to three tandem copies of the tetranucleotide TGGT. However, this motif is also widely dispersed throughout the viral genome. Using an immunoselection procedure, we show that NS1 specifically binds to many internal sites, so that all viral fragments of more than ∼170 nucleotides effectively compete for NS1, often binding with higher affinity to these internal sites than to sites in the origins. We explore the diversity of the internal sites using competitive binding and DNase I protection assays and show that they vary between two extreme forms. Simple sites with three somewhat degenerate, tandem TGGT reiterations bind effectively but are minimally responsive to ATP, while complex sites, containing multiple variably spaced TGGT elements arranged as opposing clusters, bind NS1 with an affinity that can be enhanced ∼10-fold by ATP. Using immuno-selection procedures with randomized sequences embedded within specific regions of the genome, we explore possible binding configurations in these two types of site. We conclude that binding is modular, combinatorial, and highly flexible. NS1 recognizes two to six variably spaced, more-or-less degenerate forms of the 5′-TGGT-3′ motif, so that it binds efficiently to a wide variety of sequences. Thus, despite complex coding constraints, binding sites are configured at frequent intervals throughout duplex forms of viral DNA, suggesting that NS1 may serve as a form of chromatin to protect and tailor the environment of replicating genomes.
Identification of CD46 Binding Sites within the Adenovirus Serotype 35 Fiber Knob
Authors: Wang Hongjie , Liaw Yen-Chywan , Stone Daniel , Kalyuzhniy Oleksandr , Amiraslanov Imameddin , Tuve Sebastian , Verlinde Christophe L. M. J. , Shayakhmetov Dmitry , Stehle Thilo , Roffler Steve , Lieber André 
Published: September 2007

ABSTRACT

Species B human adenoviruses (Ads) are often associated with fatal illnesses in immunocompromised individuals. Recently, species B Ads, most of which use the ubiquitously expressed complement regulatory protein CD46 as a primary attachment receptor, have gained interest for use as gene therapy vectors. In this study, we focused on species B Ad serotype 35 (Ad35), whose trimeric fiber knob domain binds to three CD46 molecules with a

K
D

(equilibrium dissociation constant) of 15.5 nM. To study the Ad35 knob-CD46 interaction, we generated an expression library of Ad35 knobs with random mutations and screened it for CD46 binding. We identified four critical residues (Phe242, Arg279, Ser282, and Glu302) which, when mutated, ablated Ad35 knob binding to CD46 without affecting knob trimerization. The functional importance of the identified residues was validated in surface plasmon resonance and competition binding studies. To model the Ad35 knob-CD46 interaction, we resolved the Ad35 knob structure at 2-Å resolution by X-ray crystallography and overlaid it onto the existing structure for Ad11-CD46 interaction. According to our model, all identified Ad35 residues are in regions that interact with CD46, whereby one CD46 molecule binds between two knob monomers. This mode of interaction might have potential consequences for CD46 signaling and intracellular trafficking of Ad35. Our findings are also fundamental for better characterization of species B Ads and design of antiviral drugs, as well as for application of species B Ads as in vivo and in vitro gene transfer vectors.
Effects of chronic coffee consumption on glucose kinetics in the conscious rat
Authors: Shearer J. , Sellars E.A. , Farah A. , Graham T.E. , Wasserman D.H. 
Published: September 2007

Epidemiological studies indicate that regular coffee consumption reduces the risk of developing type 2 diabetes. Despite these findings, the biological mechanisms by which coffee consumption exerts these effects are unknown. The aim of this study was twofold: to develop a rat model that would further delineate the effects of regular coffee consumption on glucose kinetics, and to determine whether coffee, with or without caffeine, alters the actions of insulin on glucose kinetics in vivo. Male Sprague–Dawley rats were fed a high-fat diet for 4 weeks in combination with one of the following: (i) drinking water as placebo (PL), (ii) decaffeinated coffee (2 g/100 mL) (DC), or (iii) alkaloid caffeine (20 mg/100 mL) added to decaffeinated coffee (2 g/100 mL) (CAF). Catheters were chronically implanted in a carotid artery and jugular vein for sampling and infusions, respectively. Recovered animals (5 days postoperative) were fasted for 5 h before hyperinsulinemic-euglycemic clamps (2 mU·kg–1·min–1). Glucose was clamped at 6 mmol/L and isotopes (2-deoxy-[14C]glucose and [3-3H]glucose) were administered to obtain indices of whole-body and tissue-specific glucose kinetics. Glucose infusion rates and measures of whole-body metabolic clearance were greater in DC than in PL or CAF, indicating increased whole-body insulin sensitivity. As the only difference between DC and CAF was the addition of alkaloid caffeine, it can be concluded that caffeine antagonizes the beneficial effects of DC. Given these findings, decaffeinated coffee may represent a nutritional means of combating insulin resistance.
Kappa opioids modulate the arterial baroreflex control of heart rate in conscious young sheep
Authors: Qi Wei , Smith Francine G. 
Published: September 2007

The present study tested the hypothesis that κ-opioids modulate the arterial baroreflex control of heart rate in conscious young sheep. Various parameters governing the arterial baroreflex control of heart rate were assessed before and after activation of κ-opiate receptors (KOR) by i.v. administration of the specific KOR agonist U-50488H (experiment 1) or vehicle (experiment 2) to conscious, chronically instrumented lambs aged 42 ± 2 days (n = 6). The 2 experiments were administered in random order at minimum intervals of 48 h. Thirty min after U-50488H treatment, there was an increase in diastolic and mean arterial pressure and in heart rate, returning to control levels by 90 min. A significant increase in the arterial pressure at the midpoint of the baroreflex range and in the minimum heart rate as well as a significant decrease in the heart rate range over which the arterial baroreflex operates were also seen at 30 min after U-50488H, gradually returning to control levels over 120 min. Vehicle had no effect on any of the parameters governing the arterial baroreflex control of heart rate. These data provide the first direct evidence that under physiological conditions in young lambs, the arterial baroreflex control of heart rate is altered after administration of the specific KOR agonist U-50488H, revealing a previously unidentified role for this opioid receptor.
Uranium–thorium–lead age-determinations with respect to the phanerozoic time-scale
Authors: Darnley A. G. 
Published: September 2007

Summary
Topics discussed in this short review are: the physical basis of the method, common lead ages, calculation of results, the significance of discordant results, and the selection of material for analysis. It is stressed that all aspects of the geology of an area, including its mineralogy and geochemistry, must be studied before age-determinations on material can be properly evaluated.
Potassium—argon methods with special reference to basic igneous rocks
Authors: Miller John Alfred , Fitch Frank John 
Published: September 2007

Summary
The theory, analytical method, and experimental errors of potassium–argon radiometric age-determination are briefly reviewed. The choice of suitable material for analysis and the application of the method to basic igneous and other rocks using whole-rock samples are described. ‘Discrepancy’ in potassium-argon age-determination is defined; geological factors that control the accuracy of potassium-argon ages, and must be taken into consideration in their interpretation, are discussed. It is asserted that, in favourable circumstances, potassium-argon age studies can provide a wide variety of alternative information of geological significance as well as, or instead of, indicating the initial age of consolidation of a rock: in particular, that it is possible to define the dates of subsequent cleavage, metasomatism, or metamorphism from a consideration of the discrepantly low ages obtained from older rocks.
The Tertiary period
Authors: Funnell Brian Michael 
Published: September 2007

Summary
A time-scale for the Tertiary period is suggested which is based on radiometric age-determinations published by March 1964. The principal boundaries are dated as follows:

Comparison with time-scales published previously (Holmes 1959; Evernden
et al.
1961; Kulp 1961) shows a number of differences in detail, but none of any magnitude. The date attributed to the Mio-Pliocene boundary is, however, rather younger than those given previously.
The Ordovician period
Authors: Whittington H. B. , Williams A. 
Published: September 2007

Summary

Stratigraphical and palaeontological evidence for the location of the boundaries of the Ordovician System is examined and considered to be less important than historical priority, so that the Tremadoc is excluded from the system. Reasons are also given for reverting to the twofold subsystemic division advocated by Lapworth in which the base of the
Nema-graptus gracilis
Zone (or its correlatives) is taken as the lower limit of the Upper Ordovician. The only reliable radiometric age-determination is that of 445 m.y. for the early Upper Ordovician; an estimate of 500 m.y. for the base of the Ordovician appears reasonable.
Analytic Procedure and Results of an Isotope Geochemical Surface Survey in an Area of the British North Sea
Authors: Faber E. , Stahl W. 
Published: September 2007

Summary
A sample preparation system for the determination of stable carbon isotope ratios in hydrocarbons, which are adsorbed in sediment samples, has been developed. The system consists of: (1) a degassing line, (2) a hydrocarbon separation and oxidation unit, and (3) an isotope mass spectrometer.

As little as 25 µl CH
4
desorbed from a sediment sample is sufficient to achieve an accuracy of ± 1 parts/10
18
for δ
13
C determinations. Typical methane yields are 20 µl CH
4
200 g
−1
sediment in the investigated area. Approximately 200 g sample material are routinely introduced into the degassing procedure. Natural degassing during or after sampling decreases the yields (i.e. the amount of hydrocarbons) at the samples. Laboratory experiments indicate that these effects can be minimized if the samples are rapidly degassed in a laboratory at the sampling site or quickly brought to low temperatures (≤ −80°C) immediately after sampling.

As an example of the application of the method, the results of a geochemical reconnaissance surface survey covering the area of the Forties Field in the North Sea are discussed. Some 24 sediment cores have been taken from an area of about 5500 km
2
. Sediment samples from the lowermost part of the cores (≤2 m long) have been degassed and the amounts of methane, the molecular composition of the hydrocarbons, and the
13
C/
12
C-isotope ratios of the methane have been determined. The geochemical data of the sediment gases, especially the δ
12
C
1
and the C
1
-yield data, favour that area for petroleum prospection, in which the large oil field is situated. The results indicate that methane migrates from deep source rocks to the surface and can be used as a guide to generating hydrocarbon source rocks and reservoirs.
Applications of Geochemistry to Sandstone Reservoir Studies
Authors: Irwin Hilary , Hurst Andrew 
Published: September 2007

Summary
The mineralogy and chemical composition of reservoir sandstones can be easily and quickly determined. Our knowledge of the chemical and physical properties of each mineral (both detrital and authigenic) allows us to define environmental limits within which each mineral is stable. This information is useful in establishing the burial history of the reservoir sediments and in the anticipation of production problems.
Examples are discussed to illustrate how a detailed sequence of diagenetic events can be established from petrographic analysis of only a wide selection of core samples. The evolution of pore fluid with time and the source of pore fluid can be deduced using the geochemistry of the mineral assemblage. Carbonate cements can preserve evidence of diagenetic events which is obscured or removed from more porous and permeable parts of a sandstone sequence.
Stable isotope geochemistry can be used to establish the source of carbonate cement which is characterized by the carbon isotopes. In addition, the stable isotope composition of oxygen from carbonate and silicate cements details changes in pore fluid with time and can indicate the depth at which cement precipitation occurred. This information is invaluable in reconstructuring the burial history of a sandstone sequence.
Geochemistry, integrated with sedimentology should be applied to understanding cementation controls. This will allow models of the distribution of cement to be constructed and enable more accurate modelling of fluid movement in the reservoir. This should be especially useful in achieving better reservoir simulation and better prediction of the effects of stimulation and enhancement techniques.
Organofacies and Early Maturation Effects in Upper Jurassic Sediments From the Inner Moray Firth Basin, North Sea
Authors: Pearson M. J. , Watkins D. 
Published: September 2007

Summary
A study of oil source rock characteristics and the degree of organic maturity has been carried out on a thick succession of Upper Jurassic sediments from the inner part of the Moray Firth Basin. The sequence, which attains a thickness of up to 1000 m, consists of organic-rich mudstones and silty shales with periodic intercalations of turbidite sands. Samples representative of finer grained lithologies covering a range of present burial depths from 800 to 2400 m were selected from four exploration wells, one each in Blocks 12/21 to 12/24, immediately northeast of the Beatrice Oil Field.

Kerogen preparations from all samples are dominated by amorphous algal sapropel, but contain appreciable coarsely particulate terrigenous material originating from vascular plants and probably introduced into the restricted marine basin of deposition by distal turbidity currents. This organofacies is highly rated as a potential oil source, but maturation levels are consistently low within the drilled wells. Independent maturation-specific parameters, including vitrinite reflectance, sporomorph colour, solvent extract and extractable hydrocarbon:organic carbon ratios and the carbon preference index of nC
21
-nC
33
alkanes indicate immature organic matter at depths above 2000 m. A pronounced increase in extract ratios below 2000 m indicates approach to the oil generation threshold at the base of the deepest section. Initially high CPI values in the uppermost samples (except where migrated oil is present in Block 12/23-1) decrease steadily with burial.

Significant amounts of steranes and triterpanes are present in the sediment extracts and have been identified by combined gas chromatography-mass spectrometry (GC/MS). A C
28
pentacyclic triterpane (17αH,18αH,21βH-28,30-bisnorhopane) was identified in unusual abundance. Isomerization occurs at one or more chiral centres in the steranes, rearranged steranes and hopane type pentacyclic triterpanes in response to increased burial and temperature (Mackenzie
et al.
1980). These changes have been assessed in terms of relative abundances of certain specific isomers and compared with abundances in other basinal sequences with known maturational trends. A consideration of all parameters places the onset of intense oil generation somewhat below the base of the deepest section (Block 12/24-1) and sets limits on the maximum relative uplift experienced by the other sections.
Oil Potential of Coals: A Geochemical Approach
Authors: Durand B. , Paratte M. 
Published: September 2007

Summary

Rock-Eval and pyrolysis GC data show that coals from various origins generate on thermal cracking up to 30% weight in form of hydrocarbons. Most of them consist of oil-type components (C
6
+ hydrocarbons) up to about 1.5% vitrinite reflectance maturity. Therefore fair quantities of oil should be generated during maturation of such samples. Paradoxically, coal-rich sediments contain only minute amounts of oil, whatever their maturity rank. This is interpreted by an easy expulsion of hydrocarbons from coals during burial. Moreover, trapping of oil in the ‘microporosity’ of coals, or due to their ‘plastic’ behaviour is unlikely.

Therefore coals should have a fair potential for oil generation and expulsion and the observed poor association between coal measures and oil pools is due to geological reasons rather than to geochemical ones.
Distributions and yields of the generated hydrocarbons may be quite different from one sample to another. For instance, North Sea coals do not resemble coals from Tertiary deltas.
Use of Porphyrins as a Maturity Parameter for Oils and Sediments
Authors: Barwise A. J. G. 
Published: September 2007

Summary
There is considerable interest at present in the use of biological markers, both as maturity parameters for oils and sediments, and oil-oil and oil-source rock correlations. Earlier work on biomarkers concentrated on the distribution of steranes and triterpanes; but with new analytical techniques becoming available other biomarker classes are under investigation, such as aromatics, sulphur compounds and porphyrins.
Porphyrins in oils and sediments are probably derived from chlorophylls in algae or photosynthetic bacteria. Until recently, little was known about the structure of geological porphyrins, but now several compounds have been isolated, purified and characterized. Two main types of porphyrins are present, DPEP and ETIO, and it has been shown that with increasing thermal maturity the relative concentration of ETIO-porphyrins increases with respect to DPEP-porphyrins.
Thus a measure of ratio (1) in sediments and oils should reveal the thermal maturity of these samples. A suite of oils and related source rocks have been examined, and their porphyrin distributions recorded. Porphyrins show large changes in ratio (1), ranging from 0.8, in the least mature oils, to zero in the most mature oils. Changes in molecular distribution were similar in the sediment extracts, and porphyrins seem to be useful maturation parameters in the range %Ro 0.3 to 0.8; after which they are thermally destroyed.
The Compilation of an Earth Science Bibliography for the North Sea and Adjacent Areas
Authors: McKay D. J. 
Published: September 2007

Summary
This paper acts as an introduction to the bibliography of the North Sea and adjacent areas that is being compiled by the Exploration Division Library of Britoil. The paper gives an overview of Earth Science literature. Considerable attention is paid to the use of on-line information retrieval, which was the primary method of data collection for the bibliography. The bibliography itself will be available separately, and it is emphasised that it contains references only to publications that are publicly available.
Evaluation of exhumation mechanisms for coherent blueschists in western Baja California, Mexico
Authors: Sedlock Richard L. 
Published: September 2007

Abstract

Structural data and field observations from Franciscan-type coherent blueschists in western Baja California, Mexico, are used to test proposed mechanisms for exhumation of these high-pressure, low-temperature (high
P/T
) metamorphic rocks. Analysis of specific observations that are predicted by, consistent with, or inconsistent with specific mechanisms supports extension and normal faulting as the dominant mechanism in Baja. Erosion and strike-slip faulting may have been active, but their contributions cannot be documented and are inferred to be minor. Buoyancy forces and ductile flow probably played a negligible role. Extension and exhumation probably occurred in Late Cretaceous and Paleogene time, while subduction continued at the convergent margin west of North America. Blueschists probably were exhumed to shallow crustal levels by 30 Ma, and possibly before a decrease in convergence rate at about 40 Ma. Coherent blueschists lie in the footwalls of major normal fault zones that contain serpentinite-matrix mélange with exotic blocks of greenschist, amphibolite, eclogite, and blueschist. Mélange probably formed before normal slip on the fault zones. Most mélange components are consistent with tectonic thinning of the mantle wedge and adjacent parts of the accretionary prism that once lay structurally higher than the lower-plate blueschists. Many of these findings may be applicable to similar rocks in California, including Franciscan blueschists.
Ductile deformation and mass loss in the Franciscan Subduction Complex: implications for exhumation processes in accretionary wedges
Authors: Ring Uwe , Brandon Mark T. 
Published: September 2007

AbstractDeformation measurements from 64 sandstone samples collected in three study areas from the Eastern Belt of the Franciscan Complex are used to evaluate how the high-pressure metamorphic interior of the Franciscan wedge was exhumed. Pressure estimates indicate 25–30 km of exhumation in this part of the Franciscan Complex. Much of the Eastern Belt has a semi-penetrative cleavage that formed by solution mass transfer (SMT) while the rocks were moving through the wedge. Individual samples have absolute principal stretches ofSX= 1.00–1.52,SY= 0.60–1.21, andSZ= 0.33–0.81. Strain magnitudes and directions are quite variable at the local scale. The deformation at the regional scale is estimated by calculating tensor averages for groups of measurements. The three study areas, which are spaced over a distance ofc.500 km along the Franciscan margin, give remarkably similar averages, which indicates that the deformation of the Eastern Belt is consistent at the regional scale. The tensor average for all data indicates a nearly verticalZdirection withSX= 0.96,SY= 0.92, andSZ= 0.70.SXandSYare near one because at the local scale, theXandYdirections vary considerably in orientation, which means that their stretch contributions are averaged out at the regional scale. This unusual strain type, consisting of both plane strain and uniaxial shortening, results from the fact that shortening inZwas balanced by a pervasive mass-loss volume strain, averaging about 38%. The geometry of directed fibre overgrowths was used to measure internal rotations. These data indicate that in sandstones, SMT deformation was nearly coaxial (mean kinematic vorticity number is 0.05 at the regional scale and generally <0.4 for individual samples). A simple one-dimensional steady-state model indicates that ductile thinning accounted for onlyc.10% of the overall exhumation. Ductile shortening across the Franciscan wedge was very slow, at rates <8 × 10−17s−1(<0.3% Ma−1). Assuming that this strain was active in an across-strike zone <200 km wide, we estimate that horizontal ductile flow would have accounted for <0.25% of the total convergence across the Franciscan margin. We conclude that the SMT mechanism operated slowly as a background deformation process, and that the dislocation glide mechanism was completely inactive down to depths of 25–30 km. Thus, the stability of the Franciscan wedge was probably better defined by the Coulomb wedge criterion than by a viscous wedge criterion. No definitive normal faults have been found in or adjacent to the Eastern Belt. Therefore, we infer that wedge taper was mainly controlled by deep accretion and erosion of an emergent forearc high.