bluuebunny/crossref_metadata_2025 huggingface dataset:
ORIGIN AND RESERVOIR ROCK CHARACTERISTICS OF DOLOSTONES IN THE EARLY TRIASSIC FEIXIANGUAN FORMATION, NE SICHUAN BASIN, CHINA: SIGNIFICANCE FOR FUTURE GAS EXPLORATION
Authors: Zhao Wenzhi , Luo Ping , Chen Gengsheng , Cao Hong , Zhang Baoming
Published: March 2006

Major discoveries of natural gas have recently been made in the oolitic dolostones of the Early Triassic Feixianguan Formation in NE Sichuan Province, Southern China. These dolostones were formed by three facies‐controlled dolomitization processes: (i) meteoric mixing zone dolomitization with dolomites having a relatively high degree of crystalline order (δ13C:−1.0 to 2.5%PDB; δ18O:−6.5 to −2.5%PDB); (ii) seepage‐reflux dolomitization associated with evaporative brines; the corresponding dolomite crystals are relatively ordered and were formed in tidal flat environments and platform‐margin oolitic shoals adjacent to lagoons; (iii) burial dolomitization (shallow to moderate burial depths, ca. 1,000 to 4,000m), whereby seawater‐derived brines were present in the host rock and the resultant water/rock reactions played a major role in dolomitization.

The three dolomitization processes were controlled by the arid climate prevailing during the Early Triassic, and also by fourth‐order relative sea‐level changes, especially with respect to the reflux dolomitization. Burial dolomitization, which is of second‐order of importance for porosity development, was strongly dependant on the presence of sufficient original porosity to facilitate water‐rock reactions within the carbonates. The best reservoir rocks formed as oolitic banks and bars in the vicinity of evaporative lagoonal‐tidal complexes which experienced optimal conditions for dolomitization. Dolostones with a dolomite content of 80% to 90% form good vuggy reservoir rocks at the present day, indicating that the intensity of dolomitization influences the quality of reservoir rocks.

According to our results, future gas exploration in the Feixianguan Formation dolostone reservoirs should focus on locating oolitic banks associated with evaporative lagoon and tidal flat complexes and delineating the best structural/lithological traps.
A METHOD FOR ANALYZING GEOTHERMAL GRADIENT HISTORIES USING THE STATISTICAL ASSESSMENT OF UNCERTAINTIES IN MATURITY MODELS
Authors: Huvaz O. , Thomsen R. O. , Noeth S.
Published: March 2006

A major factor contributing to uncertainty in basin modelling is the determination of the parameters necessary to reconstruct the basin's thermal history. Thermal maturity modelling is widely used in basin modelling for assessing the exploration risk. Of the available models, the chemical kinetic model Easy%Ro has gained wide acceptance.

In this study, the thermal gradient at five wells in the Danish North Sea is calibrated against vitrinite reflectance using the Easy%Ro model coupled with an inverse scheme in order to perform sensitivity analysis and to assess the uncertainty. The mean squared residual (MSR) is used as a quantitative measure of mismatch between the modelled and measured reflectance values. A 90% confidence interval is constructed for the determined mean of the squared residuals to assess the uncertainty for the given level of confidence. The sensitivity of the Easy%Ro model to variations in the thermal gradient is investigated using the uncertainty associated with scatter in the calibration data. The best thermal gradient (minimum MSR) is obtained from the MSR curve for each well. The aim is to show how the reconstruction of the thermal gradient is related to the control data and the applied model.

The applied method helps not only to determine the average thermal gradient history of a basin, but also helps to investigate the quality of the calibration data and provides a quick assessment of the uncertainty and sensitivity of any parameter in a forward deterministic model.
CHARACTERISATION OF EPEIRIC “LAYER‐CAKE” CARBONATE RESERVOIRS: UPPER MUSCHELKALK (MIDDLE TRIASSIC), THE NETHERLANDS
Authors: Borkhataria R. , Aigner T. , Pöppelreiter M. C. , Pipping J. C. P.
Published: March 2006

Upper Muschelkalk (Middle Triassic) carbonates produce natural gas at Coevorden field in the NE Netherlands. This is currently the only field which produces gas from this succession although several other prospects have been identified nearby. In order to help develop these hydrocarbons, this study proposes a facies and reservoir model of the Upper Muschelkalk in the NE Netherlands together with a regional framework intended to assist in further evaluation.

Distribution of facies and reservoir properties of the Upper Muschelkalk carbonates in the NE Netherlands indicate deposition on a storm‐dominated epeiric ramp with a very low gradient. The predominantly muddy and marly lithofacies types in proximal and distal parts of the ramp gradually interfinger with a shoreline‐detached “shoal”‐like ooidal grainstone complex. The best reservoir quality (permeability up to 60 mD) is recognised within dolomitised peloid ooid grainstones. These are interpreted as high‐energy backshoal deposits. Reservoir quality decreases in the limestone‐dominated “shoal” facies and the muddier foreshoal facies. A four‐fold hierarchy of depositional cycles describes the systematic and thus predictable vertical variation in reservoir quality (permeability) and quantity (net‐to‐gross). High‐resolution correlation suggests that medium‐scale cycles (5 to 15 metres thick) can be traced for hundreds of kilometres. Small‐scale cycles (1 to 3 metres thick) are persistent for several tens of kilometres and have sheet‐like geometries. Individual reservoir units (several decimetres thick) appear to be laterally continuous over a maximum of a few kilometres although internal flow barriers might be expected. Mapping of Upper Muschelkalk thickness and facies has clearly defined backshoal, ”shoal and foreshoal facies belts with distinctly different reservoir characteristics. Typically, reservoir quality and quantity decrease with increasing thickness of the Upper Muschelkalk and the underlying Middle Muschelkalk halite. The systematic variations in thickness are apparently controlled by a combination of palaeogeography and palaeotectonics. The best reservoir quality and highest quantity is found on a palaeohigh characterised by a relatively thin Upper Muschelkalk succession and the absence of underlying halite. These features can also be recognised in seismic data.

The results of this case study can also be applied in the integrated characterisation of similar epeiric carbonates constituting highly productive reservoirs in the Middle East, including the Khuff and Arab Formations.
HYDROCARBON SEEPAGE AND CARBONATE MOUND FORMATION: A BASIN MODELLING STUDY FROM THE PORCUPINE BASIN (OFFSHORE IRELAND)
Authors: Naeth J. , di Primio R. , Horsfield B. , Schaefer R. G. , Shannon P. M. , Bailey W. R. , Henriet J. P.
Published: March 2006

This study assesses whether the growth of deep water carbonate mounds on the continental slope of the north Atlantic may be associated with active hydrocarbon leakage. The carbonate mounds studied occur in two distinct areas of the Porcupine Basin, 200 km offshore Ireland, known as the Hovland‐Magellan and the Belgica areas.

To evaluate the possible link between hydrocarbon leakage and mound growth, we used two dimensional cross‐section and map‐based basin modelling. Geological information was derived from interpretation of five seismic lines across the province as well as the Connemara oilfield. Calibration data was available from the northern part of the study area and included vitrinite reflectance, temperature and apatite fission track data.

Modelling results indicate that the main Jurassic source rocks are mature to overmature for hydrocarbon generation throughout the basin. Hydrocarbon generation and migration started in the Late Cretaceous. Based on our stratigraphic and lithologic model definitions, hydrocarbon migration is modelled to be mainly vertical, with only Aptian and Tertiary deltaic strata directing hydrocarbon flow laterally out of the basin. Gas chimneys observed in the Connemara field were reproduced using flow modelling and are related to leakage at the apices of rotated Jurassic fault blocks. The model predicts significant focussing of gas migration towards the Belgica mounds, where Cretaceous and Tertiary carrier layers pinch out. In the Hovland‐Magellan area, no obvious focus of hydrocarbon flow was modelled from the 2D section, but drainage area analysis of Tertiary maps indicates a link between mound position and shallow Tertiary closures which may focus hydrocarbon flow towards the mounds.
DISTRIBUTION OF SOURCE ROCKS AND MATURITY MODELLING IN THE NORTHERN CENOZOIC SONG HONG BASIN (GULF OF TONKIN), VIETNAM
Authors: Andersen C. , Mathiesen A. , Nielsen L. H. , Tiem P. V. , Petersen H. I. , Dien P. T.
Published: March 2006

The northern offshore part of the Cenozoic Song Hong Basin in the Gulf of Tonkin (East Vietnam Sea) is at an early stage of exploration with only a few wells drilled. Oil to source rock correlation indicates that coals are responsible for the sub‐commercial oil and gas accumulations in sandstones in two of the four wells which have been drilled on faulted anticlines and flower structures. The wells are located in a narrow, structurally inverted zone with a thick predominantly deltaic Miocene succession between the Song Chay and Vinh Ninh/Song Lo fault zones. These faults are splays belonging to the offshore extension of the Red River Fault Zone.

Access to a database of 3,500 km of 2D seismic data has allowed a detailed and consistent break‐down of the geological record of the northern part of the basin into chronostratigraphic events which were used as inputs to model the hydrocarbon generation history. In addition, seismic facies mapping, using the internal reflection characteristics of selected seismic sequences, has been applied to predict the lateral distribution of source rock intervals. The results based on Yükler ID basin modelling are presented as profiles and maturity maps. The robustness of the results are analysed by testing different heat flow scenarios and by transfer of the model concept to IES Petromod software to obtain a more acceptable temperature history reconstruction using the Easy%R0 algorithm.

Miocene coals in the wells located in the inverted zone between the fault splays are present in separate intervals. Seismic facies analysis suggests that the upper interval is of limited areal extent. The lower interval, of more widespread occurrence, is presently in the oil and condensate generating zones in deep synclines between inversion ridges. The Yükler modelling indicates, however, that the coaly source rock interval entered the main window prior to formation of traps as a result of Late Miocene inversion.

Lacustrine mudstones, similar to the highly oil‐prone Oligocene mudstones and coals which are exposed in the Dong Ho area at the northern margin of the Song Hong Basin and on Bach Long Vi Island in Gulf of Tonkin, are interpreted to be preserved in a system of undrilled NW–SE Paleogene half‐grabens NE of the Song Lo Fault Zone. This is based on the presence of intervals with distinct, continuous, high reflection seismic amplitudes. Considerable overlap exists between the shale‐prone seismic facies and the modelled extent of the present‐day oil and condensate generating zones, suggesting that active source kitchens also exist in this part of the basin. Recently reported oil in a well located onshore (BIO‐STB‐IX) at the margin of the basin, which is sourced mainly from “Dong Ho type” lacustrine mudstones supports the presence of an additional Paleogene sourced petroleum system.
GEOCHEMICAL CORRELATION OF OILS AND SOURCE ROCKS FROM CENTRAL AND NE SYRIA
Authors: Abboud M. , Philp R. P. , Allen J.
Published: March 2006

Eighteen crude oils and seven source rock samples from the Mesopotamian foredeep, NE Syria, and from the NE Palmyrides in the centre of the country have been characterized by geochemical techniques. The presence of two oil families (“A” and “B”) generated by different source rock types of different ages has been established on the basis of biomarker and carbon isotopic analyses. The data indicates that Groups A and B oils were generated by marine clastic and marine carbonate‐evaporitic source rocks, respectively. Group A oils, occurring in Middle Triassic, Middle Jurassic and Upper Cretaceous reservoir rocks in the NE Palmyride area, are geochemically similar to extracts from the Lower Triassic Amanus Shale Formation. Group B oils, which are present in Middle Triassic, Middle Jurassic and Upper Cretaceous reservoirs in the Mesopotamian foredeep, are geochemically similar to extracts of the Middle Triassic Kurra Chine Dolomite and Upper Cretaceous Shiranish Formations.
Time allocation between feeding and incubation in uniparental arctic‐breeding shorebirds: energy reserves provide leeway in a tight schedule
Authors: Tulp Ingrid , Schekkerman Hans
Published: March 2006

Birds with uniparental incubation may face a time allocation problem between incubation and feeding. Eggs need regular warming to hatch successfully, but the parent must leave the nest to feed and safeguard its own survival. Time allocation during incubation is likely to depend on factors influencing egg cooling rates, parental energy requirements and feeding intake rate. How this allocation problem is resolved was subject of this study on arctic‐breeding shorebirds. We compared incubation rhythms between four uniparental shorebird species differing in size and expected to find both species differences and weather effects on the organisation of incubation.

Attentive behaviour and responses to variation in weather showed a remarkable consistency across species. All species alternated feeding bouts (recesses) with brooding bouts throughout the day. Recesses were concentrated in the warmer parts of the day, while recess duration showed little diurnal variation. Despite continuous daylight, a pronounced day‐night rhythmicity was apparent. The four species in this study spent a similar proportion (13–19%) of the time off their nest. After correction for weather effects, the number of recesses was largest in the smallest species, while recess duration was longest in the largest species. Total recess time per day increased on cold days through an increase of mean recess length, while the number of recesses decreased.

Comparing our observations to predictions derived from criteria that birds might use to organise their attentive behaviour, showed that the limits are set by parental requirements, while the energy stores of adults provide some leeway for short‐term adjustments to environmental variability.

If breeding birds trade off feeding time against incubation time, energy stores are expected to be influenced by weather. We expected uniparental species to be more likely to show weather effects on condition than biparentals, as in the latter ‘off duty’ time is much larger and independent of weather. This prediction was tested by comparing energy stores in two uniparental species and a biparental congener. While body mass of uniparental incubators decreased after a period with low temperatures, body mass of the biparental species did not.
Sex‐specific chick provisioning and diving behaviour in the wedge‐tailed shearwater Puffinus pacificus
Authors: Peck Darren R. , Congdon Bradley C.
Published: March 2006

Mechanisms that drive sex‐specific foraging behaviour in seabirds are not fully understood. In some cases, sexual‐size dimorphism has been implicated. However, recent empirical work indicates that foraging behaviour may also differ between sexes of monomorphic seabird taxa. We simultaneously examined sex‐specific differences in adult foraging behaviour, chick provisioning rates and maximum dive‐depths in a monomorphic seabird, the wedge‐tailed shearwater Puffinus pacificus. We found significant divergence between sexes. Mean foraging trip length was longer, provisioning rate lower and mean maximum dive‐depth shallower in females. We found no evidence of divergence in foraging behaviour due to condition‐dependant increases in self‐provisioning by females, or differences in the nest attendance patterns of each sex. In addition, chick body condition did not influence meal mass or trip length differently in one or other sex. Consistent with results obtained for dimorphic species we suggest that inter‐sexual competition at the foraging grounds provides the most parsimonious explanation for the sex‐specific differences observed in this monomorphic species. Based on our findings we believe this possibility warrants further critical investigation.
Evolution of the ovenbird‐woodcreeper assemblage (Aves: Furnariidae) ‐ major shifts in nest architecture and adaptive radiation
Authors: Irestedt Martin , Fjeldså Jon , Ericson Per G. P.
Published: March 2006

The Neotropical ovenbirds (Furnariidae) form an extraordinary morphologically and ecologically diverse passerine radiation, which includes many examples of species that are superficially similar to other passerine birds as a resulting from their adaptations to similar lifestyles. The ovenbirds further exhibits a truly remarkable variation in nest types, arguably approaching that found in the entire passerine clade. Herein we present a genus‐level phylogeny of ovenbirds based on both mitochondrial and nuclear DNA including a more complete taxon sampling than in previous molecular studies of the group. The phylogenetic results are in good agreement with earlier molecular studies of ovenbirds, and supports the suggestion that Geositta and Sclerurus form the sister clade to both core‐ovenbirds and woodcreepers. Within the core‐ovenbirds several relationships that are incongruent with traditional classifications are suggested. Among other things, the philydorine ovenbirds are found to be non‐monophyletic. The mapping of principal nesting strategies onto the molecular phylogeny suggests cavity nesting to be plesiomorphic within the ovenbird–woodcreeper radiation. It is also suggested that the shift from cavity nesting to building vegetative nests is likely to have happened at least three times during the evolution of the group. We suggest that the shifts in nest architecture within the furnariine and synallaxine ovenbirds have served as an ecological release that has facilitated diversification into new habitats and new morphological specializations.
Pentagastrin‐induced protein synthesis in the parotid gland of the anaesthetized rat, and its dependence on CCK‐A and ‐B receptors and nitric oxide generation
Authors: Aras Hülya Çevik , Ekström J.
Published: March 2006

In parotid glands of pentobarbitone‐anaesthetized rats, the incorporation of [3H]leucine into trichloroacetic acid‐insoluble materials, reflecting protein synthesis, increased by 17% (compared to saline‐treated rats) in response to infusion of pentagastrin (20 μg kg−1, i.v. for 1 h) under muscarinic and α‐ and β‐adrenoceptor blockade. Both the CCK‐A receptor antagonist lorglumide (48 mg kg−1, i.v.) and the CCK‐B receptor antagonist itriglumide (5.5 mg kg−1, i.v.), given separately, prevented the expected increase in pentagastrin and, in addition, reduced the glandular protein synthesis by 16 and 12%, respectively, below the level of saline‐treated rats. In rats treated with saline only, the glandular protein synthesis was reduced by 22% by the CCK‐A receptor antagonist and by 17% by the CCK‐B receptor antagonist; combined, the two antagonists caused no further reduction (20%). There was no increase in the glandular protein synthesis of pentagastrin‐treated rats compared to that of the saline‐treated rats when both groups of rats were exposed to a combination of the two types of CCK receptor antagonists. In pentagastrin‐treated rats, the protein synthesis in the parotid glands was 23% less in the presence of the non‐selective nitric oxide (NO) synthase inhibitor l‐NAME (30 mg kg−1, i.v.) than in its absence; the result was the same (23%) when the neuronal NO synthase inhibitor Nω‐propyl‐l‐arginine (N‐PLA; 30 mg kg−1, i.v.) replaced l‐NAME. The protein synthesis in rats treated with saline only was not reduced by l‐NAME; nor was the protein synthesis of saline‐treated rats different from that of pentagastrin‐ and l‐NAME‐treated rats. Thus, under ‘basal’ conditions, a portion of the glandular protein synthesis, as well as the whole increase in synthesis in response to administration of pentagastrin, engaged both types of CCK receptors. Furthermore, NO generation, owing to neuronal NO synthase activity, was required for the increase to occur in response to pentagastrin, whereas a non‐NO‐dependent pathway was responsible for the protein synthesis under ‘basal’ conditions.
Tests for presynaptic modulation of corticospinal terminals from peripheral afferents and pyramidal tract in the macaque
Authors: Jackson A. , Baker S. N. , Fetz E. E.
Published: March 2006

The efficacy of sensory input to the spinal cord can be modulated presynaptically during voluntary movement by mechanisms that depolarize afferent terminals and reduce transmitter release. It remains unclear whether similar influences are exerted on the terminals of descending fibres in the corticospinal pathway of Old World primates and man. We investigated two signatures of presynaptic inhibition of the macaque corticospinal pathway following stimulation of the peripheral nerves of the arm (median, radial and ulnar) and the pyramidal tract: (1) increased excitability of corticospinal axon terminals as revealed by changes in antidromically evoked cortical potentials, and (2) changes in the size of the corticospinal monosynaptic field potential in the spinal cord. Conditioning stimulation of the pyramidal tract increased both the terminal excitability and monosynaptic fields with similar time courses. Excitability was maximal between 7.5 and 10 ms following stimulation and returned to baseline within 40 ms. Conditioning stimulation of peripheral nerves produced no statistically significant effect in either measure. We conclude that peripheral afferents do not exert a presynaptic influence on the corticospinal pathway, and that descending volleys may produce autogenic terminal depolarization that is correlated with enhanced transmitter release. Presynaptic inhibition of afferent terminals by descending pathways and the absence of a reciprocal influence of peripheral input on corticospinal efficacy would help to preserve the fidelity of motor commands during centrally initiated movement.
Spatial distribution of inspiratory drive to the parasternal intercostal muscles in humans
Authors: Gandevia Simon C. , Hudson Anna L. , Gorman Robert B. , Butler Jane E. , De Troyer André
Published: March 2006

The human parasternal intercostal muscles are obligatory inspiratory muscles with a diminishing mechanical advantage from cranial to caudal interspaces. This study determined whether inspiratory neural drive to these muscles is graded, and whether this distribution matches regional differences in inspiratory mechanical advantage. To determine the neural drive, intramuscular EMG was recorded from the first to the fifth parasternal intercostals during resting breathing in six subjects. All interspaces showed phasic inspiratory activity but the onset of activity relative to inspiratory flow in the fourth and fifth spaces was delayed compared with that in cranial interspaces. Activity in the first, second and third interspaces commenced, on average, within the first 10% of inspiratory time, and sometimes preceded inspiratory airflow. In contrast, activity in the fourth and fifth interspaces began after an average 33% of inspiratory time. The peak inspiratory discharge frequency of motor units in the first interspace averaged 13.4 ± 1.0 Hz (mean ±s.e.m.) and was significantly greater than in all other interspaces, in particular in the fifth space (8.0 ± 1.0 Hz). Phasic inspiratory activity was sometimes superimposed on tonic activity. In the first interspace, only 3% of units had tonic firing, but this proportion increased to 34% in the fifth space. In five subjects, recordings were also made from the medial and lateral extent of the second parasternal intercostal. Both portions showed phasic inspiratory activity which began within the first 6% of inspiratory time. Motor units from the lateral and medial portions fired at the same peak discharge rate (10.4 ± 0.7 versus 10.7 ± 0.6 Hz). These observations indicate that the distribution of neural drive to the parasternal intercostals in humans has a rostrocaudal gradient, but that the drive is uniform along the mediolateral extent of the second interspace. The distribution of inspiratory neural drive to the parasternal intercostals parallels the spatial distribution of inspiratory mechanical advantage, while tonic activity was higher where mechanical advantage was lower.
Effect of ADP on slow‐twitch muscle fibres of the rat: implications for muscle fatigue
Authors: Macdonald W. A. , Stephenson D. G.
Published: March 2006

Slow‐twitch mechanically skinned fibres from rat soleus muscle were bathed in solutions mimicking the myoplasmic environment but containing different [ADP] (0.1 μm to 1.0 mm). The effect of ADP on sarcoplasmic reticulum (SR) Ca2+‐content was determined from the magnitude of caffeine‐induced force responses, while temporal changes in SR Ca2+‐content allowed determination of the effective rates of the SR Ca2+‐pump and of the SR Ca2+‐leak. The SR Ca2+‐pump rate, estimated at pCa (−log10[Ca2+]) 7.8, was reduced by 20% as the [ADP] was increased from 0.1 to 40 μm, with no further alteration when the [ADP] was increased to 1.0 mm. The SR Ca2+‐leak rate constant was not altered by increasing [ADP] from 0.1 to 40 μm, but was increased by 26% when the [ADP] was elevated to 1.0 mm. This ADP‐induced SR Ca2+‐leak was insensitive to ruthenium red but was abolished by 2,5‐di(tert‐butyl)‐1,4‐hydroquinone (TBQ), indicating that the leak pathway is via the SR Ca2+‐pump and not the SR Ca2+‐release channel. The decrease in SR Ca2+‐pump rate and SR Ca2+‐leak rate when [ADP] was increased led to a 40% decrease in SR Ca2+‐loading capacity. Elevation of [ADP] had only minor direct effects on the contractile apparatus of slow‐twitch fibres. These results suggest that ADP has only limited depressing effects on the contractility of slow‐twitch muscle fibres. This is in contrast to the marked effects of ADP on force responses in fast‐twitch muscle fibres and may contribute to the fatigue‐resistant nature of slow‐twitch muscle fibres.
Epithelial carbonic anhydrases facilitate PCO2 and pH regulation in rat duodenal mucosa
Authors: Mizumori Misa , Meyerowitz Justin , Takeuchi Tetsu , Lim Shu , Lee Paul , Supuran Claudiu T. , Guth Paul H. , Engel Eli , Kaunitz Jonathan D. , Akiba Yasutada
Published: March 2006

The duodenum is the site of mixing of massive amounts of gastric H+ with secreted HCO3−, generating CO2 and H2O accompanied by the neutralization of H+. We examined the role of membrane‐bound and soluble carbonic anhydrases (CA) by which H+ is neutralized, CO2 is absorbed, and HCO3− is secreted. Rat duodena were perfused with solutions of different pH and P with or without a cell‐permeant CA inhibitor methazolamide (MTZ) or impermeant CA inhibitors. Flow‐through pH and P electrodes simultaneously measured perfusate and effluent pH and P. High CO2 (34.7 kPa) perfusion increased net CO2 loss from the perfusate compared with controls (pH 6.4 saline, P≈ 0) accompanied by portal venous (PV) acidification and P increase. Impermeant CA inhibitors abolished net perfusate CO2 loss and increased net HCO3− gain, whereas all CA inhibitors inhibited PV acidification and P increase. The changes in luminal and PV pH and [CO2] were also inhibited by the Na+–H+ exchanger‐1 (NHE1) inhibitor dimethylamiloride, but not by the NHE3 inhibitor S3226. Luminal acid decreased total CO2 output and increased H+ loss with PV acidification and P increase, all inhibited by all CA inhibitors. During perfusion of a 30% CO2 buffer, loss of CO2 from the lumen was CA dependent as was transepithelial transport of perfused 13CO2. H+ and CO2 loss from the perfusate were accompanied by increases of PV H+ and tracer CO2, but unchanged PV total CO2, consistent with CA‐dependent transmucosal H+ and CO2 movement. Inhibition of membrane‐bound CAs augments the apparent rate of net basal HCO3− secretion. Luminal H+ traverses the apical membrane as CO2, is converted back to cytosolic H+, which is extruded via NHE1. Membrane‐bound and cytosolic CAs cooperatively facilitate secretion of HCO3− into the lumen and CO2 diffusion into duodenal mucosa, serving as important acid–base regulators.
Uncoupling Insulin
Authors: Leslie Mitch
Published: March 2006

Like a good actor, the Sir2 proteins don't stick to the same role. That's the message of a new study confirming that the proteins exert opposite effects on the glucose-regulating hormone insulin depending on whether they are in worms or mammals. The work fills in details of how the mammalian protein governs insulin.
Biomarkers of Aging: Combinatorial or Systems Model?
Authors: Kriete Andres
Published: March 2006

Systemwide functional and structural changes caused by the aging process encourage the implementation of new bioinformatics search strategies for markers of aging. Combinatorial biomarkers should be particularly favored, as they can quantify processes on multiple levels of biological organization and overcome an otherwise limited ability to access heterogeneities in populations. An even more challenging but rational approach is the development of systems biology models to describe molecular pathways and key networks mechanistically as they relate to age. Such reverse engineered models not only indicate critical and diagnostic components (that is, potential biomarkers) but also should be able to predict the progression of aging through computer simulation.
Chain of Command
Authors: Leslie Mitch
Published: March 2006

When prosecutors are trying to break up a Mafia conspiracy, they usually start with the lowly perpetrators and work up to the bosses. Researchers probing how one biochemical pathway controls worm aging are following the opposite course. They know that the protein DAF-16 extends survival, but they are still rounding up the genes that do its bidding. A new study catches more than 100 genes receiving orders from DAF-16.
Double Duty
Authors: Leslie Mitch
Published: March 2006

Succeeding at two different jobs is tough. Take basketball superstar Michael Jordan's failed attempt to play baseball or actor Leonard Nimoy's abortive singing career. But according to new research, a metabolic protein adroitly pulls off two disparate tasks: controlling cholesterol concentrations as well as glucose amounts in the blood. The work shows that the protein helps diabetic mice rein in lipids and sugar. The discovery might lead to treatments that allow people with diabetes to do the same.
Dividing to Keep Muscle Together: The Role of Satellite Cells in Aging Skeletal Muscle
Authors: Hepple Russell T.
Published: March 2006

The factors responsible for the atrophy of skeletal muscle with aging remain to be elucidated. Recent evidence points toward an important role for a population of cells located on the surface of skeletal muscle fibers, known as satellite cells, in maintaining the integrity of skeletal myocytes throughout the life span. This Perspective examines the role that these cells are thought to play in aging muscle atrophy, and highlights a recent study by Brack and colleagues that attempts to understand the role of satellite cells in maintaining the ratio of myonuclear number to cytoplasmic volume within myocytes as we age.
Prion 2005: Between Fundamentals and Society's Needs
Authors: Treiber Carina
Published: March 2006

Prion diseases for the most part affect individuals older than 60 years of age and share features with other diseases characterized by protein deposits in the brain, such as Alzheimer's disease and Parkinson's disease. The international conference "Prion 2005: Between Fundamentals and Society's Needs," organized by the German Transmissible Spongiform Encephalopathies Research Platform, aimed to integrate and coordinate the research efforts of participants to better achieve prevention, treatment, control, and management of prion diseases, including Creutzfeldt-Jakob disease and fatal familial insomnia in humans. Several main topics were discussed, such as the molecular characteristics of prion strains, the cell biology of cellular and pathogenic forms of the prion proteins, the pathogenesis of the diseases they cause, emerging problems, and promising approaches for therapy and new diagnostic tools. The presentations at the Prion 2005 conference provided new insights in both basic and applied research, which will have broad implications for society's needs.
Mucking With Metabolism
Authors: Beckman Mary
Published: March 2006

In some family businesses, one heir will strike out in a new direction, rejecting his or her expected fate. Similarly, a protein whose kin protect animals from cancer instead seems to guard mice against a metabolic disruption. The results show that flawed DNA repair could contribute to a condition called metabolic syndrome, and they support a link between the condition and mitochondria.
Craving an Answer
Authors: Leslie Mitch
Published: March 2006

Calorie restriction (CR) tunes up metabolism and makes animals more active. However, the regimen has drawbacks, such as sensitivity to cold and loss of reproduction. Some animals don't gain time, and CR might not work for old individuals. Researchers don't have a full-fledged theory for how CR works, but some scientists postulate that the diet extends life by activating a stress-fighting response. Some researchers argue that we are close to understanding one molecular mechanism behind that effect that involves the enzyme Sir2p. Recent work questions the Sir2p connection and supports an alternative, the TOR pathway. Fat and leaky mitochondria might also play a role in CR. An upcoming study might clarify the diet's benefits for humans.
Buffing Up the Family Jewels
Authors: Beckman Mary
Published: March 2006

Coaches can hurt their athletes by working them out too long or too hard. Similarly, a protein that keeps testicles making sperm wears down the organ, new research shows. The results suggest a new tactic to prevent testicle damage.
Small-Fiber Neuropathy: Answering the Burning Questions
Authors: Fink Ezekiel , Oaklander Anne Louise
Published: March 2006

Small-fiber neuropathy is a peripheral nerve disease that most commonly presents in middle-aged and older people, who develop burning pain in their feet. Although it can be caused by disorders of metabolism such as diabetes, chronic infections (such as with human immunodeficiency virus), genetic abnormalities, toxicity from various drugs, and autoimmune diseases, the cause often remains a mystery because standard electrophysiologic tests for nerve injury do not detect small-fiber function. Inadequate ability to test for and diagnose small-fiber neuropathies has impeded patient care and research, but new tools offer promise. Infrequently, the underlying cause of small-fiber dysfunction is identified and disease-modifying therapy can be instituted. More commonly, the treatments for small-fiber neuropathy involve symptomatic treatment of neuropathic pain.
The Development of Amyloid β Protein Deposits in the Aged Brain
Authors: Thal Dietmar R. , Capetillo-Zarate Estibaliz , Del Tredici Kelly , Braak Heiko
Published: March 2006

The deposition of amyloid β protein (Aβ) in the human brain and the generation of neurofibrillary tangles are the histopathological hallmarks of Alzheimer's disease. Accumulation of Aβ takes place in senile plaques and in cerebrovascular deposits as a result of an imbalance between Aβ production and clearance. This Review describes the different types of Aβ deposits, which can be distinguished by their morphology and by the hierarchical involvement of distinct areas of the brain in Aβ deposition. The role of intracellular Aβ in Aβ deposition and the mechanism of Aβ toxicity are also discussed.
The Nature and Dynamics of Bacterial Genomes
Authors: Ochman Howard , Davalos Liliana M.
Published: March 2006

Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result, the coding potential of bacterial genomes can be substantially lower than originally predicted. Whereas only a single pseudogene was included in the original annotation of the bacterium
Escherichia coli
, we estimate that this genome harbors hundreds of inactivated and otherwise functionless genes. Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell.
General Strategies for Nanoparticle Dispersion
Authors: Mackay Michael E. , Tuteja Anish , Duxbury Phillip M. , Hawker Craig J. , Van Horn Brooke , Guan Zhibin , Chen Guanghui , Krishnan R. S.
Published: March 2006

Traditionally the dispersion of particles in polymeric materials has proven difficult and frequently results in phase separation and agglomeration. We show that thermodynamically stable dispersion of nanoparticles into a polymeric liquid is enhanced for systems where the radius of gyration of the linear polymer is greater than the radius of the nanoparticle. Dispersed nanoparticles swell the linear polymer chains, resulting in a polymer radius of gyration that grows with the nanoparticle volume fraction. It is proposed that this entropically unfavorable process is offset by an enthalpy gain due to an increase in molecular contacts at dispersed nanoparticle surfaces as compared with the surfaces of phase-separated nanoparticles. Even when the dispersed state is thermodynamically stable, it may be inaccessible unless the correct processing strategy is adopted, which is particularly important for the case of fullerene dispersion into linear polymers.
A Voltage Sensor-Domain Protein Is a Voltage-Gated Proton Channel
Authors: Sasaki Mari , Takagi Masahiro , Okamura Yasushi
Published: March 2006

Voltage-gated proton channels have been widely observed but have not been identified at a molecular level. Here we report that a four-transmembrane protein similar to the voltage-sensor domain of voltage-gated ion channels is a voltage-gated proton channel. Cells overexpressing this protein showed depolarization-induced outward currents accompanied by tail currents. Current reversal occured at equilibrium potentials for protons. The currents exhibited pH-dependent gating and zinc ion sensitivity, two features which are characteristic of voltage-gated proton channels. Responses of voltage dependence to sequence changes suggest that mouse voltage-sensor domain–only protein is itself a channel, rather than a regulator of another channel protein.
An Integrated Logic Circuit Assembled on a Single Carbon Nanotube
Authors: Chen Zhihong , Appenzeller Joerg , Lin Yu-Ming , Sippel-Oakley Jennifer , Rinzler Andrew G. , Tang Jinyao , Wind Shalom J. , Solomon Paul M. , Avouris Phaedon
Published: March 2006

Single-walled carbon nanotubes (SWCNTs) have been shown to exhibit excellent electrical properties, such as ballistic transport over several hundred nanometers at room temperature. Field-effect transistors (FETs) made from individual tubes show dc performance specifications rivaling those of state-of-the-art silicon devices. An important next step is the fabrication of integrated circuits on SWCNTs to study the high-frequency ac capabilities of SWCNTs. We built a five-stage ring oscillator that comprises, in total, 12 FETs side by side along the length of an individual carbon nanotube. A complementary metal-oxide semiconductor‐type architecture was achieved by adjusting the gate work functions of the individual p-type and n-type FETs used.
A Population of Comets in the Main Asteroid Belt
Authors: Hsieh Henry H. , Jewitt David
Published: March 2006

Comets are icy bodies that sublimate and become active when close to the Sun. They are believed to originate in two cold reservoirs beyond the orbit of Neptune: the Kuiper Belt (equilibrium temperatures of ∼40 kelvin) and the Oort Cloud (∼10 kelvin). We present optical data showing the existence of a population of comets originating in a third reservoir: the main asteroid belt. The main-belt comets are unlike the Kuiper Belt and Oort Cloud comets in that they likely formed where they currently reside and may be collisionally activated. The existence of the main-belt comets lends new support to the idea that main-belt objects could be a major source of terrestrial water.
RNA Interference Directs Innate Immunity Against Viruses in Adult
Drosophila
Authors: Wang Xiao-Hong , Aliyari Roghiyh , Li Wan-Xiang , Li Hong-Wei , Kim Kevin , Carthew Richard , Atkinson Peter , Ding Shou-Wei
Published: March 2006

Innate immunity against bacterial and fungal pathogens is mediated by Toll and immune deficiency (Imd) pathways, but little is known about the antiviral response in
Drosophila
. Here, we demonstrate that an RNA interference pathway protects adult flies from infection by two evolutionarily diverse viruses. Our work also describes a molecular framework for the viral immunity, in which viral double-stranded RNA produced during infection acts as the pathogen trigger whereas
Drosophila
Dicer-2 and Argonaute-2 act as host sensor and effector, respectively. These findings establish a
Drosophila
model for studying the innate immunity against viruses in animals.
The Significance of Interferon-γ–Triggered Internalization of Tight-Junction Proteins in Inflammatory Bowel Disease
Authors: Chiba Hideki , Kojima Takashi , Osanai Makoto , Sawada Norimasa
Published: March 2006

Disruption of the epithelial barrier function of tight junctions by the proinflammatory cytokine interferon (IFN)–γ plays a fundamental role in the pathogenesis of inflammatory bowel disease and other gastrointestinal disorders, but its precise mechanism has not been established. This Perspective provides an overview of how IFN-γ triggers barrier dysfunction and bacterial translocation in intestinal epithelial cells, and highlights the roles of internalization of tight-junction transmembrane proteins, as well as rearrangements of the cortical actin cytoskeleton, in intestinal inflammation.
Phosphatidylserine and Signal Transduction: Who Needs Whom?
Authors: Martínez M. Carmen , Kunzelmann Corinne , Freyssinet Jean-Marie
Published: March 2006

The plasma membrane, long considered a simple barrier between the extracellular and intracellular compartments, is now thought to play a pivotal role in many physiological processes that regulate the communication of cells with their environment. On one hand, the plasma membrane directly participates in intracellular signaling; on the other hand, changes in membrane structure contribute to the transcellular transfer of biological information. Among the membrane constituents, phosphatidylserine is a major actor implicated in these effects. Evidence now exists for a role for phosphatidylserine redistribution in modulating the activities of several membrane proteins during signaling in nonapoptotic T lymphocytes.
Endothelin Action on Pituitary Lactotrophs: One Receptor, Many GTP-Binding Proteins
Authors: Bertram Richard , Tabak Joel , Toporikova Natalia , Freeman Marc E.
Published: March 2006

The endothelins are a family of hormones that have a biphasic action on pituitary lactotrophs. The initial effect is stimulatory, followed later by inhibition that persists long after the agonist has been removed. Recent research has uncovered several G protein pathways that mediate these effects.
A Tale of Two Signals: Wnt and Hedgehog in Dentate Neurogenesis
Authors: Pozniak Christine D. , Pleasure Samuel J.
Published: March 2006

It is now widely accepted that discrete regions of the adult brain contain stem cells that continue to generate new neurons. However, it remains unclear what molecular signals define the neurogenic niche and how such signals act on the heterogeneous cell populations within these regions. Here we discuss two recent studies that demonstrate the role of Wnt and Sonic Hedgehog signaling in neurogenic zones. Wnts act on neuronal precursors that mature and contribute to the dentate gyrus (DG), whereas Sonic Hedgehog affects the bona fide stem cells and transit amplifying cells (the partially committed progeny of stem cells). These studies further define how discrete populations of cells react to specific extracellular signals provided within the neurogenic niche to survive, proliferate, and form functional mature cell types.
Inhibition of Immune Responses by ITAM-Bearing Receptors
Authors: Hamerman Jessica A. , Lanier Lewis L.
Published: March 2006

Cells of the immune system possess many multisubunit receptors that are composed of a ligand-binding subunit associated with distinct signaling adaptors containing one or more immunoreceptor tyrosine-based activation motifs (ITAMs). These receptors include the T cell receptor, the B cell receptor, and many Fc receptors, as well as families of activating receptors on myeloid and natural killer cells. Receptors that associate with ITAM-containing adaptors classically have been viewed as transducing activating signals involving phosphorylation of the tyrosines within the ITAM and recruitment of Syk family tyrosine kinases. Receptors associated with ITAM-containing adaptors in myeloid cells have also been implicated in inhibition of cellular activation. Here, we discuss these new negative roles for signaling by receptors that associate with ITAM-bearing adaptors in myeloid and other cell types within the immune system.
Focus Issue: Signaling Lipids
Authors: Gough Nancy R.
Published: March 2006

Membranes are dynamic and specific contributors to cell signaling. Cellular membranes play a key structural role in creating sites for the formation of signaling complexes. Changes in membrane phospholipids can regulate the activity of transmembrane and peripheral membrane proteins. Modification of membrane lipids can result in formation of dynamic signaling molecules.
Science
's STKE highlights new insights into the roles that lipids and membranes play in cell signaling.
Building Signaling Complexes at the Membrane
Authors: Cho Wonhwa
Published: March 2006

Cell membranes, the plasma membrane in particular, serve as the hub of various cellular signaling networks. In response to receptor activation, many cytosolic proteins are reversibly recruited to membranes to form dynamic signaling complexes. Membranes provide a unique microenvironment in which the formation of signaling complexes can be exquisitely modulated by the fine interplay between protein-protein and lipid-protein interactions.