bluuebunny/crossref_metadata_2025 huggingface dataset:
CRITICAL NOTICE: CAUSALITY BY JUDEA PEARL
Authors: Woodward James
Published: November 2003

This is a wonderful book; indeed, it is easily one of the most important and creative books I have ever read on the subject of causation and causal inference. Causality is impressive on many levels and should be of great interest to many different audiences. Philosophers will find of particular interest Pearl's defense of what might be described as a broadly manipulationist or interventionist treatment of causation: Causal claims have to do with what would happen under ideal, suitably surgical experimental manipulations (‘interventions’). But Pearl moves far beyond philosophical generalities on this theme: He makes the case for the approach that he favors by developing a formal apparatus (‘a calculus of interventions’, as he calls it) for talking about interventions and how they relate to causation and information about probabilities that is at once both intuitively compelling and genuinely useful for purposes of calculation and estimation. He also actively engages the philosophical literature on causation at many points – for example, there are illuminating discussions of evidential decision theory, of probabilistic theories of causation of the sort favored by Eells and Cartwright, of Lewisian counterfactual theories of causation, and of the relationship between so-called type and token causal claims, as well as a quite novel treatment of the latter.
REPLY TO WOODWARD
Authors: Pearl Judea
Published: November 2003

I thank Dr. Woodward for his illuminating review of my book Causality, for explicating so clearly the basic contributions of the book, and for giving me the opportunity to further clarify some aspects of the do-calculus, specifically those that pertain to the notion of intervention.
Land subsidence in Houston, Texas, measured by radar interferometry and constrained by extensometers
Authors: Buckley Sean M. , Rosen Paul A. , Hensley Scott , Tapley Byron D.
Published: November 2003

We present results from a radar interferometry study over the Houston‐Galveston, Texas Gulf Coast region. From the nearly 60 potential interferograms considered, an atmospheric artifact assessment is performed and a tractable set of interferograms selected for detailed processing and error analysis. The subsequent interferogram time series spanning 1996–1998 is constrained by coincident extensometer data with root‐mean‐square error less than 2.5 mm. The interferogram time series confirms that historic subsidence in east Houston has stopped. Consistent with current groundwater use patterns, broad‐scale subsidence bowls are observed in west and northwest Houston, where maximum subsidence rates are in excess of 2 and 4 cm yr−1, respectively. Linear interferogram phase signatures associated with approximately 1 cm of differential subsidence across faults, including the Long Point fault in northwest Houston, are observed. Near the Seabrook extensometer, a hereto‐unidentified subsidence bowl with a maximum subsidence rate in excess of 3 cm yr−1 is revealed. This study demonstrates that when used in conjunction with a set of traditional geodetic measurements, radar interferometry can measure the spatial and temporal evolution of urban land subsidence within even the most challenging of environments.
Boussinesq modeling of longshore currents
Authors: Chen Qin , Kirby James T. , Dalrymple Robert A. , Shi Fengyan , Thornton Edward B.
Published: November 2003

A time domain Boussinesq model for nearshore hydrodynamics is improved to obtain the conservation of vertical vorticity correct to second order and extended for use on an open coast using longshore periodic boundary conditions. The model is utilized to simulate surface waves and longshore currents under laboratory and field conditions. Satisfactory agreement is found between numerical results and measurements, including root mean square wave height, mean water level, and longshore current. One striking result of the simulations is the prediction of the strong longshore current in the trough shoreward of the bar as observed during the Duck Experiment on Low‐frequency and Incident‐band Longshore and Across‐shore Hydrodynamics field campaign. The model results give insight into the spatial and temporal variability of wave‐driven longshore currents and the associated vertical vorticity field under the phase‐resolving, random wave forcing with wave/current interaction. Numerical experiments are carried out to examine the response of the modeled longshore currents to the randomness of surface waves and the cross‐shore distributions of bed shear stress coefficient. We find that both regular and irregular waves lead to very similar mean longshore currents, while the input of monochromatic, unidirectional waves results in much more energetic shear waves than does the input of random waves. The model results favor Whitford and Thornton's [1996] finding that the bed shear stress coefficient for the area offshore the bar is larger than that in the trough, as better agreement with the field data for both regular and irregular waves is found if such coefficients are used in the Boussinesq model.
Improved convergence in the analysis of thin metallic gratings with thickness profiles
Authors: Wakabayashi Hideaki , Komatsu Minoru , Yamakita Jiro , Asai Masamitsu
Published: November 2003

A combination of the Fourier series expansion method and the multilayered step method is applied to analysis of the scattering problem by a thin metallic grating with a thickness profile. The extremely large permittivity profiles of metallic gratings may affect accuracy of calculations adversely. The convergence of the Fourier expansion method is improved using the spatial harmonics of flux densities instead of electromagnetic fields normal to the surface of a metallic grating. In using the multilayered step method, the scheme used to partition the grating region and the distribution function of dielectric constant within each layer are examined.
The crustal structure of the East Anatolian plateau (Turkey) from receiver functions
Authors: Zor Ekrem , Sandvol Eric , Gürbüz Cemil , Türkelli Niyazi , Seber Dogan , Barazangi Muawia
Published: November 2003

The crustal structure of the Anatolian plateau in Eastern Turkey is investigated using receiver functions obtained from the teleseismic recordings of a 29 broadband PASSCAL temporary network, i.e., the Eastern Turkey Seismic Experiment [ETSE]. The S‐wave velocity structure was estimated from the stacked receiver functions by performing a 6‐plane layered grid search scheme in order to model the first order features in the receiver functions with minimum trade‐off. We found no significant crustal root beneath the western portion of the network, but there is some evidence of crustal thickening in the northern portion of the network. We found an average crustal thickness of 45 km and an average crustal shear velocity of 3.7 km/s for the entire eastern Anatolian plateau. Within the Anatolian plateau we found evidence of a prominent low velocity zone where the crust thickness is approximately 46 km. These results suggests that the 2 km high topography across the Anatolian plateau is dynamically supported because most of the plateau appears to be isostatically under‐compensated. Also, there appears to be a region of thin crust at the easternmost edge of the Anatolian plateau that may be a relic from the accretion of island arcs to the Eurasian plate.
The impact of decadal‐scale Indian Ocean sea surface temperature anomalies on Sahelian rainfall and the North Atlantic Oscillation
Authors: Bader J. , Latif M.
Published: November 2003

The sea surface temperatures (SSTs) of the tropical Indian Ocean show a pronounced warming since the 1950s. We have analyzed the impact of this warming on Sahelian rainfall and on the North Atlantic Oscillation (NAO) by conducting ensemble experiments with an atmospheric general circulation model. Additionally, we investigate the impact of the other two tropical oceans on these two climate parameters. Our results suggest that the warming trend in the Indian Ocean played a crucial role for the drying trend over the West Sahel from the 1950s to 1990s and may also have contributed to the strengthening of the NAO during the most recent decades.
An optical technique for the measurement of longshore currents
Authors: Chickadel C. C. , Holman R. A. , Freilich M. H.
Published: November 2003

We present an optical method (optical current meter) to measure the longshore component of nearshore surface currents by measuring the alongshore drift of persistent sea foam in the surf zone. The method uses short time series of video data collected from an alongshore array of pixels. These space‐time data are first Fourier transformed to a frequency‐wave number spectrum and, finally, to a velocity spectrum. A model of the velocity spectrum is fit to the observed spectrum to estimate the foam drift velocity. Confidence intervals and other measures of the input and output data quality are calculated. Field test comparisons were made against an in situ bidirectional electromagnetic current meter on the basis of 1 month of video data from the 1997 Sandy Duck field experiment. The root mean square error between the two approaches was 0.10 m/s. Linear regression analysis showed the gain between the two instruments to not be statistically different from one. Differences between the surface and interior measurements were compared to forcing mechanisms that may cause surface velocity shear. Velocity offsets and alongshore wind stress were well correlated for cases when waves and wind were not aligned to within ±45°, when wind‐ and wave‐forced currents are reasonably separable. Calculated wind‐dependent surface current shear, modeled as a surface boundary layer, correlated well with the observed velocity offsets for observations of nonalignment between wind and waves. This technique can be applied to study large‐scale coastal behavior.
Equilibrium ranges in surf zone wave spectra
Authors: Smith Jane McKee , Vincent Charles L.
Published: November 2003

Laboratory measurements of two wave trains breaking on a plane slope demonstrate dramatic changes in spectral shape in the surf zone. The higher‐frequency spectral peak is completely eliminated in the surf zone, and the resulting spectral shape is similar regardless of the peak frequency and relative energy content of the higher‐frequency peak. Examination of both laboratory and field data show that surf zone wave number (k) spectra evolve to contain two equilibrium ranges. The higher‐frequency range is similar to that proposed by Toba in deeper water with the form k−5/2 and is valid for approximately k > 1/depth. The second range falls between the peak wave number and k = 1/depth and has a wave number dependence of k−4/3, similar to that proposed by Zakharov on theoretical grounds. The equilibrium range coefficients, which are a function of wind speed in deep and finite water depths, are a function of the water depth in the surf zone. The laboratory and field data sets used in these analyses covered a broad range of conditions (unidirectional and multidirectional waves, plane and barred beaches, two orders of magnitude variation in wave height, and one order of magnitude variation in wave period), yet the equilibrium ranges identified were consistent and provide a robust parameterization of surf zone wave spectra.
Effect of different rootstock on plant growth, yield and quality of watermelon
Authors: Yetisir H. , Sari N.
Published: November 2003

This study was conducted in Department of Horticulture, Faculty of Agriculture, University of Cukurova in 1999 and 2000. Watermelon [Citrullus lanatus (Thunb.) Matsum and Nakai] cultivar Crimson Tide was grafted onto 10 different rootstocks. Cucurbita moschata, Cucurbita maxima and Lagenaria siceraria were open pollinated cultivars, and Strong Tosa, Gold Tosa, P360 (Cucurbita maxima × Cucurbita moschata), Skopje, Emphasis, 216 and FRG (Lagenaria spp.) were hybrid cultivars. The ungrafted Crimson Tide watermelon cultivar was used as the control. Plants were grown under low tunnel conditions until the outdoor temperature was suitable (22–25°C) for watermelon growth. Our results showed that while survival rate was low (65%) in Cucurbita type rootstocks, it was high (95%) in Lagenaria type rootstocks. Grafted plants flowered about 10 days earlier and showed more vigorous vegetative growth than the control plants. Grafted plants had up to 148% higher fresh weights than control plants. Similarly, grafted plants showed 42–180% higher dry weight, 58–100% more leaves and larger leaf area as compared with the control. In total yield, Lagenaria type rootstocks produced a higher yield but Cucurbita type rootstocks produced a lower yield than the control. While control plants had 6.43 kg/m2 yield, Lagenaria type rootstocks produced 27–106% higher yield than the control. In contrast, Cucurbita type rootstocks had 127–240% less yield than the control. This could be attributed to incompatibility of Cucurbita rootstocks because some of the plants died before harvest. The study showed that rootstock choices influence plant growth as well as yield and quality of scion fruit, suggesting an important consideration in the potential use of grafting applications in watermelon.
Performance of lot-fed Bos indicus steers exposed to aspects of a feedlot environment before lot-feeding
Authors: Petherick J. C. , Holroyd R. G. , Swain A. J.
Published: November 2003

Fifty Bos indicus steers, 2–3 years old, were exposed to aspects of a feedlot environment on their home property for 9 days (pre-exposed). A further 50 steers were placed in a holding paddock for the 9 days (naïve). Twenty steers in each group became 'focal animals' for periodic blood sampling and behaviour observations. The cattle were transported for 15 h (950 km) to an experimental feedlot where they were lot-fed for 100 days, with productivity (liveweight, body condition and feed intakes) and flight speeds recorded at intervals. A subjective fear of humans test was conducted on the pre-exposed group during the 9 days in the yards on the home property and carcass traits were measured on all cattle.Both groups lost substantial weight on the property and during transportation. On the property, the pre-exposed steers lost about 12% of their original liveweight and the naïve about 9%. Transit losses were a further 5 and 4% of pre-transport liveweights, respectively. The steers did not reach their initial liveweights until day 41 of feedlotting. The pre-exposure treatment did not affect final liveweight, but feed intakes were lower for the pre-exposed animals than the naïve ones during the first 16 days of feedlotting, and the pre-exposed steers had superior average daily gains and feed conversion efficiencies. These effects were probably due to a combination of compensation and improved feed digestibility, as a result of the pre-exposed animals being under-fed on the property, but receiving concentrated grain supplement. There was no effect of focal status on productivity.Flight speed and the subjective fear of humans test were significantly correlated. Neither treatment nor focal status affected flight speeds, but flight speeds decreased in the latter part of feedlotting, were highly correlated between days and negatively correlated with average daily gain and intakes.
Sprouting elimination of decapitated peach trees
Authors: Tsipouridis C. , Thomidis T.
Published: November 2003

The effects of the herbicides Garlon, Roundup, ammonium sulfate (as dry fertiliser or sprayed liquid), fresh manure, and organic matter derived from wild grass, on elimination of re-sprouting by cut peach trees cv.��Papagianni, grafted on the rootstock GF677, were recorded. Complete elimination of re-sprouting from decapitated peach trees was achieved following treatment with Garlon, Roundup or ammonium sulfate (as dry fertiliser). Treatment with fresh manure or organic matter eliminated 70–80% of re-sprouting. Spray application of ammonium sulfate delayed re-sprouting, but did not eliminate it. The use of manure and 'yard waste' can provide organic growers with a certified tool to control re-sprouting of decapitated trees.
Kinetics of ammonium and nitrate uptake by eucalypt roots and associated proton fluxes measured using ion selective microelectrodes
Authors: Garnett Trevor P. , Shabala Sergey N. , Smethurst Philip J. , Newman Ian A.
Published: November 2003

Ion-selective microelectrodes were used non-invasively to measure the concentration dependence of NH4+ and NO3– fluxes around the roots of intact solution-cultured Eucalyptus nitens (Deane & Maiden) Maiden. In addition, NH4+ and H+ fluxes were measured simultaneously at a range of NH4+ concentrations, and NO3– and H+ fluxes were measured simultaneously at a range of NO3– concentrations. Nitrogen concentrations ranged from 10–250 μM, i.e. in the range corresponding to the high affinity transport system (HATS). Both NH4+ and NO3– fluxes exhibited saturating Michaelis–Menten-style kinetics. The Km was 16 μM for NH4+ and 18 μM for NO3–. Values of Vmax were 53 nmol m–2 s–1 for NH4+ and 37 nmol m–2 s–1 for NO3–. Proton fluxes were highly correlated with NH4+ and NO3– fluxes, but the relationships were different. Proton efflux increased with increasing NH4+ concentration and mirrored the changing NH4+ fluxes. The ratio between NH4+ and H+ fluxes was 1 : –1.6. Proton influx was evident with initial exposure to NO3–, with the flux stoichiometry for NO3– : H+ being 1 : 1.4. Subsequent increases in NO3– concentration caused a gradual increase in H+ efflux such that the flux stoichiometry for NO3– : H+ became 1 : –0.8. The presence of 100 μM NH4+ greatly reduced NO3– fluxes and caused a large and constant H+ efflux. These results are evidence that E. nitens has a preference for NH4+ as a source of N, and that the fluxes of NH4+ and NO3– are quantitatively linked to H+ flux.
The effect of calcium on the antioxidant enzymes from salt-treated loquat and anger plants
Authors: Hernández Jose A. , Aguilar Ana Belén , Portillo Bruno , López-Gómez Elvira , Beneyto Jorge Mataix , García-Legaz Manuel F.
Published: November 2003

Salt treatment (50 mM NaCl) reduced plant growth of loquat (Eribotria japonica Lindl.) (by up to 40%) but not that of anger (Cydonia oblonga Mill.). Salt stress induced a strong leaf Na+ accumulation in both species. However, the observed increase in leaf Cl– level was higher in loquat (13-fold) than in anger plants (3.8-fold). Addition of Ca2+ (25 mM) significantly reduced Na+ and Cl– concentrations in both salt-treated species. In anger leaves, calcium addition to the nutrient media did not change the leaf calcium contents in salt-treated or untreated plants, this value being lower in salt-treated plants. However, in loquat plants, an increase in leaf Ca2+ was observed after the calcium addition. Surprisingly, an increase in Ca2+ concentration was also observed in salt-treated loquat plants. In general, anger plants had higher constitutive antioxidant enzyme levels in both control and salt-treated plants. Salt stress did not change antioxidant enzyme levels in loquat plants. A similar effect was observed in anger plants, but in this case a 2-fold induction of monodehydroascorbate reductase (MDHAR) activity was observed.In both species, salinity produced an oxidative stress, indicated by an increase in lipid peroxidation, this value being much higher in loquat (83%) than in anger (40%) plants. In salt-treated plants, Ca2+ addition provided some protection to the membranes, because the increases observed in thiobarbituric-acid-reactive substances (TBARS) were not significant.In contrast, in control plants Ca2+ treatments increased glutathione reductase (GR) and decreased catalase activity in anger, but increased MDHAR, dehydroascorbate reductase (DHAR), GR and superoxide dismutase (SOD) in loquat plants. In salt-treated plants, Ca2+ additions decreased catalase (CAT) and ascorbate peroxidase (APX) for anger and raised DHAR, GR and SOD for loquat. However, the mechanism by which Ca2+ regulates antioxidant enzymes remains to be determined.These results suggest that anger plants have a higher capacity to scavenge AOS, both under saline and non-saline conditions. Accordingly, and related to the smaller Cl– increase observed, anger plants are more salt-tolerant, at least partly owing to the higher antioxidant enzyme levels observed.
Morphological development of rice caryopses located at the different positions in a panicle from early to middle stage of grain filling
Authors: Ishimaru Tsutomu , Matsuda Toshiaki , Ohsugi Ryu , Yamagishi Tohru
Published: November 2003

Rice caryopses show different patterns of grain filling depending on position within a panicle. Caryopses located on the upper primary rachis branches generally accumulate larger amounts of starch at maturity than caryopses located on the secondary rachis branches of the lower primary rachis. In this study, the former and latter types of caryopses were defined as superior and inferior caryopses, respectively. Superior caryopses elongated soon after flowering, whereas inferior caryopses hardly elongated and were morphologically stagnant until the first 4 d after flowering (DAF). However, once inferior caryopses began elongation, their morphological development was the same as superior caryopses until the middle stage of grain filling. Cell division of the inner integument ceased before endosperm cellularization, pericarp functioned as a transient starch storage tissue until endosperm accumulated starch, and endosperm cell number was determined concomitantly with nucellus disintegration. These results implied the coordinated development of the endosperm with maternal tissues. In addition, differences of inner-integument cell number and endosperm cell number were related to a difference of endosperm size between superior and inferior caryopses.
Multiple effects of antibiotics on chloroplast and nuclear gene expression
Authors: Mulo Paula , Pursiheimo Saijaliisa , Hou Cai-Xia , Tyystjärvi Taina , Aro Eva-Mari
Published: November 2003

Antibiotics are widely used to monitor signalling cascades within a plant cell, for example between the nucleus and chloroplasts, and to study the function of the photosynthetic machinery. In the present study, we attempted to test various antibiotics with respect to their expected modes of function and also to monitor their possible side effects on metabolic processes in mature leaves of pea (Pisum sativum L.). Streptomycin, despite its reported prokaryotic nature, prevented translation not only in the chloroplast, but also in the cytosol. Application of puromycin, an inhibitor of protein synthesis in both the pro- and eukaryotes, resulted in severe photoinhibition of photosystem II upon illumination, yet had no effect on plastid translation, thus implying a severe side effect on plastid metabolism. Prokaryotic-type translation inhibitors lincomycin, spectinomycin and erythromycin blocked translation in the chloroplast without any direct effects on cytoplasmic protein synthesis. More detailed studies with lincomycin, however, revealed a strong modulation of the expression of nuclear-encoded genes by slowing down the transcription rate of photosynthesis-related Lhcb and RbcS genes, and furthermore, lincomycin clearly decreased the phosphorylation level of the LHCII proteins.
Evolutionary dynamics of an
Arabidopsis
insect resistance quantitative trait locus
Authors: Kroymann Juergen , Donnerhacke Susanne , Schnabelrauch Domenica , Mitchell-Olds Thomas
Published: November 2003

Glucosinolate profiles differ among
Arabidopsis thaliana
ecotypes, caused by the composition of alleles at several glucosinolate biosynthetic loci. One of these,
GS-Elong
, harbors a family of methylthioalkylmalate synthase (MAM) genes that determine the side chain length of aliphatic glucosinolate structures. Fine mapping reveals that
GS-Elong
constitutes an insect resistance quantitative trait locus, caused by variation in glucosinolate profiles conferred by polymorphism of
MAM
alleles in this region. A sequence survey of randomly chosen ecotypes indicates that
GS-Elong
is highly variable among
A. thaliana
ecotypes: indel polymorphisms are frequent, as well as gene conversion events between gene copies arranged in tandem. Furthermore, statistical methods of molecular population genetics suggest that one of the genes,
MAM2
, is subject to balancing selection. This may be caused by ecological tradeoffs, i.e., by contrasting physiological effects of glucosinolates on generalist vs. specialist insects.
A20, a regulator of NFκB, maps to an atherosclerosis locus and differs between parental sensitive C57BL/6J and resistant FVB/N strains
Authors: Idel Susanne , Dansky Hayes M. , Breslow Jan L.
Published: November 2003

An intercross between atherosclerosis susceptible (C57BL/6J ApoE0) and resistant (FVB/N ApoE0) mice revealed a susceptibility locus on chromosome 10 (11 cM, logarithm of odds 7.8). Surprisingly, the genotypic means for this locus revealed that heterozygosity or homozygosity for the C57BL/6J allele was associated with decreased atherosclerosis. A candidate gene in this region is A20, which is involved in the feedback suppression of NFκB activation induced by tumor necrosis factor α (TNFα). We sequenced the A20 gene coding region from the parental strains and found a single-nucleotide polymorphism resulting in a single amino acid exchange, Glu627Ala (C57BL/6J vs. FVB/N). This mutation introduces a putative casein kinase 2 phosphorylation site in C57BL/6J-A20 not present in FVB/N-A20. NFκB reporter gene assays showed that this amino acid change results in less effective termination of TNFα-stimulated NFκB activation by C57BL/6J-A20. In accordance, the TNFα-induced expression of NFκB target genes (A20, IκBα) in vascular smooth muscle cells was prolonged in cells isolated from C57BL/6J compared with FVB/N mice. In light of the genotypic means for atherosclerosis at the chromosome 10 locus in F
2
mice from this intercross, the observations now reported suggest that prolonged expression of genes induced by NFκB might be antirather than proatherogenic.
RNA backbone is rotameric
Authors: Murray Laura J. W. , Arendall W. Bryan , Richardson David C. , Richardson Jane S.
Published: November 2003

Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic
B
factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for α-β-γ and for δ-ε-ζ are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into “suites” to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures.
Dissection of K
+
currents in
Caenorhabditis elegans
muscle cells by genetics and RNA interference
Authors: Santi C. M. , Yuan A. , Fawcett G. , Wang Z.-W. , Butler A. , Nonet M. L. , Wei A. , Rojas P. , Salkoff L.
Published: November 2003

GFP-promoter experiments have previously shown that at least nine genes encoding potassium channel subunits are expressed in
Caenorhabditis elegans
muscle. By using genetic, RNA interference, and physiological techniques we revealed the molecular identity of the major components of the outward K
+
currents in body wall muscle cells in culture. We found that under physiological conditions, outward current is dominated by the products of only two genes,
Shaker
(Kv1) and
Shal
(Kv4), both expressing voltage-dependent potassium channels. Other channels may be held in reserve to respond to particular circumstances. Because GFP-promoter experiments indicated that
slo-2
expression is prominent, we created a deletion mutant to identify the SLO-2 current
in vivo
. In both whole-cell and single-channel modes,
in vivo
SLO-2 channels were active only when intracellular Ca
2+
and Cl
-
were raised above normal physiological conditions, as occurs during hypoxia. Under such conditions, SLO-2 is the largest outward current, contributing up to 87% of the total current. Other channels are present in muscle, but our results suggest that they are unlikely to contribute a large outward component under physiological conditions. However, they, too, may contribute currents conditional on other factors. Hence, the picture that emerges is of a complex membrane with a small number of household conductances functioning under normal circumstances, but with additional conductances that are activated during unusual circumstances.
Disulfide bond formation involves a quinhydrone-type charge–transfer complex
Authors: Regeimbal James , Gleiter Stefan , Trumpower Bernard L. , Yu Chang-An , Diwakar Mithun , Ballou David P. , Bardwell James C. A.
Published: November 2003

The chemistry of disulfide exchange in biological systems is well studied. However, the detailed mechanism of how oxidizing equivalents are derived to form disulfide bonds in proteins is not clear. In prokaryotic organisms, it is known that DsbB delivers oxidizing equivalents through DsbA to secreted proteins. DsbB becomes reoxidized by reducing quinones that are part of the membrane-bound electron-transfer chains. It is this quinone reductase activity that links disulfide bond formation to the electron transport system. We show here that purified DsbB contains the spectral signal of a quinhydrone, a charge–transfer complex consisting of a hydroquinone and a quinone in a stacked configuration. We conclude that disulfide bond formation involves a stacked hydroquinone–benzoquinone pair that can be trapped on DsbB as a quinhydrone charge–transfer complex. Quinhydrones are known to be redox-active and are commonly used as redox standards, but, to our knowledge, have never before been directly observed in biological systems. We also show kinetically that this quinhydrone-type charge–transfer complex undergoes redox reactions consistent with its being an intermediate in the reaction mechanism of DsbB. We propose a simple model for the action of DsbB where a quinhydrone-like complex plays a crucial role as a reaction intermediate.
Characterization of the requirements for localization of phytochrome B to nuclear bodies
Authors: Chen Meng , Schwab Rebecca , Chory Joanne
Published: November 2003

Phytochromes are red- and far-red-sensing photoreceptors that detect the quantity, quality, and duration of light throughout the entire life cycle of plants. Phytochromes accumulate in the cytoplasm in the dark. As one of the earliest responses after light illumination, phytochromes localize to the nucleus where they become associated with discrete nuclear bodies (NBs). Here, we describe the steady-state dynamics of
Arabidopsis
phytochrome B (phyB) localization in response to different light conditions and define four phyB subnuclear localization patterns: diffuse nuclear localization, small and numerous NBs only, both small and large NBs, and large NBs only. We show that phyB nuclear import is not sufficient for phyB NB formation. Rather, phyB accumulation in NBs is mainly determined by the percentage of the total amount of phyB protein that is in the active phyB conformer, with large NBs always correlating with strong phyB responses. A genetic screen to identify determinants required for subnuclear localization of phyB resulted in several phyB mutants, mutants deficient in phytochrome chromophore biosynthesis, and mutations in at least one previously uninvestigated locus. This study lays the groundwork for future investigations to identify the molecular mechanisms of light-regulated partitioning of plant photoreceptors to discrete subnuclear domains.
Cardioprotection specific for the G protein G
i2
in chronic adrenergic signaling through β
2
-adrenoceptors
Authors: Foerster Katharina , Groner Ferdi , Matthes Jan , Koch Walter J. , Birnbaumer Lutz , Herzig Stefan
Published: November 2003

Two subtypes of β-adrenoceptors, β
1
and β
2
, mediate cardiac catecholamine effects. These two types differ qualitatively, e.g., regarding G protein coupling and calcium channel stimulation. Transgenic mice overexpressing human β
2
-adrenoceptors survive high-expression levels, unlike mice overexpressing β
1
-adrenoceptors. We examined the role of inhibitory G
i
proteins, known to be activated by β
2
- but not β
1
-adrenoceptors, on the chronic effects of human β
2
-adrenoreceptor overexpression in transgenic mice. These mice were crossbred with mice where Gα
i2
, a functionally important cardiac G
i
α-subunit, was inactivated by targeted gene deletion. Survival of β
2
-adrenoreceptor transgenic mice was reduced by heterozygous inactivation of Gα
i2
. Homozygous knockout/β
2
-adrenoreceptor transgenic mice died within 4 days after birth. Heterozygous knockout/β
2
-adrenoreceptor transgenic mice developed more pronounced cardiac hypertrophy and earlier heart failure compared with β
2
-adrenoreceptor transgenic mice. Single calcium-channel activity was strongly suppressed in heterozygous knockout/β
2
-adrenoreceptor transgenic mice. In cardiomyocytes from these mice, pertussis toxin treatment
in vitro
fully restored channel activity and enhanced channel activity in cells from homozygous Gα
i2
knockout animals. Cardiac Gα
i3
protein was increased in all Gα
i2
knockout mouse strains. Our results demonstrate that Gα
i2
takes an essential protective part in chronic signaling of overexpressed β
2
-adrenoceptors, leading to prolonged survival and delayed cardiac pathology. However, reduction of calcium-channel activity by β
2
-adrenoreceptor overexpression is due to a different pertussis-toxin-sensitive pathway, most likely by Gα
i3
. This result indicates that subtype-specific signaling of β
2
-adrenoreceptor functionally bifurcates at the level of G
i
, leading to different effects depending on the Gα isoform.
Development of an enhanced GFP-based dual-color reporter to facilitate genetic screens for the recovery of mutations in mice
Authors: Frank Aubrey C. , Meyers Kimberly A. , Welsh Ian C. , O'Brien Timothy P.
Published: November 2003

Mutagenesis screens to isolate a variety of alleles leading to null and non-null phenotypes represent an important approach for the characterization of gene function. Genetic schemes that use visible markers permit the efficient recovery of chemically induced mutations. We have developed a universal reporter system to visibly mark chromosomes for genetic screens in the mouse. The dualcolor reporter is based on a single vector that drives the ubiquitous coexpression of the enhanced GFP (EGFP) spectral variants yellow and cyan. We show that widespread expression of the dual-color reporter is readily detected in embryonic stem cells, mice, and throughout developmental stages. CRE-
loxP
- and FLPe-
FRT
-mediated deletion of each color cassette demonstrates the modular design of the marker system. Random integration followed by plasmid rescue and sequence-based mapping was used to introduce the marker to a defined genomic location. Thus, single-step placement will simplify the construction of a genomewide bank of marked chromosomes. The dual-color nature of the marker permits complete identification of genetic classes of progeny as embryos or mice in classic regionally directed screens. The design also allows for more efficient and novel schemes, such as marked suppressor screens, in the mouse. The result is a versatile reporter that can be used independently or in combination with the growing sets of deletion and inversion resources to enhance the design and application of a wide variety of genetic schemes for the functional dissection of the mammalian genome.
Channelrhodopsin-2, a directly light-gated cation-selective membrane channel
Authors: Nagel Georg , Szellas Tanjef , Huhn Wolfram , Kateriya Suneel , Adeishvili Nona , Berthold Peter , Ollig Doris , Hegemann Peter , Bamberg Ernst
Published: November 2003

Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 (ChR1), a recently identified light-gated proton channel from the green alga
Chlamydomonas reinhardtii
. ChR1 and ChR2, a related microbial-type rhodopsin from
C. reinhardtii
, were shown to be involved in generation of photocurrents of this green alga. We demonstrate by functional expression, both in oocytes of
Xenopus laevis
and mammalian cells, that ChR2 is a directly light-switched cation-selective ion channel. This channel opens rapidly after absorption of a photon to generate a large permeability for monovalent and divalent cations. ChR2 desensitizes in continuous light to a smaller steady-state conductance. Recovery from desensitization is accelerated by extracellular H
+
and negative membrane potential, whereas closing of the ChR2 ion channel is decelerated by intracellular H
+
. ChR2 is expressed mainly in
C. reinhardtii
under low-light conditions, suggesting involvement in photoreception in dark-adapted cells. The predicted seven-transmembrane α helices of ChR2 are characteristic for G protein-coupled receptors but reflect a different motif for a cation-selective ion channel. Finally, we demonstrate that ChR2 may be used to depolarize small or large cells, simply by illumination.
Association of the Mediator complex with enhancers of active genes
Authors: Kuras Laurent , Borggrefe Tilman , Kornberg Roger D.
Published: November 2003

The multiprotein Mediator complex has been shown to interact with gene-specific regulatory proteins and RNA polymerase II
in vitro
. Here, we use chromatin immunoprecipitation to analyze the recruitment of Mediator to
GAL
genes of yeast
in vivo
. We find that Mediator associates exclusively with transcriptionally active and not inactive
GAL
genes. This association maps to the upstream activating sequence, rather than the core promoter, and is independent of RNA polymerase II, general transcription factors, and core promoter sequences. These findings support the idea of Mediator as a primary conduit of regulatory information from enhancers to promoters in eukaryotic cells.
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
Authors: Nymeyer Hugh , García Angel E.
Published: November 2003

We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent model with simulations using explicit solvent (transferable intermolecular potential 3 point, TIP3P) to test the GB/SA algorithm. We use the replica exchange molecular dynamics method to sample the conformational phase space of two α-helical peptides, A21and the Fs, by using two different classical potentials and both water models. We find that when using GB/SA: (i) A21is predicted to be more helical than the Fspeptide at all temperatures; (ii) the native structure of the Fspeptide is predicted to be a helical bundle instead of a single helix; and (iii) the persistence length and most probable end-to-end distance are too large in the unfolded state when compared against the explicit solvent simulations. We find that the potential of mean force in the ϕψ plane is markedly different in the two solvents, making the two simulated peptides respond differently when the backbone torsions are perturbed. A fit of the temperature melting curves obtained in these simulations to a Lifson–Roig model finds that the GB/SA model has an unphysically large nucleation parameter, whereas the explicit solvent model produces values similar to experiment.
Biomolecular mimicry in the actin cytoskeleton: Mechanisms underlying the cytotoxicity of kabiramide C and related macrolides
Authors: Tanaka Junichi , Yan Yuling , Choi Jeongeun , Bai Jihong , Klenchin Vadim A. , Rayment Ivan , Marriott Gerard
Published: November 2003

This study characterizes the interactions between kabiramide C (KabC) and related macrolides and actin and establishes the mechanisms that underlie their inhibition of actin filament dynamics and cytotoxicity. The G-actin–KabC complex is formed through a two-step binding reaction and is extremely stable and long-lived. Competition-binding studies show that KabC binds to the same site on G-actin as Gelsolin domain 1 and CapG. KabC also binds to protomers within F-actin and results in the severing and capping of the (+) end; these studies suggest that free KabC and related macrolides act as biomimetics of Gelsolin. The G-actin–KabC complex binds to the (+) end of a growing filament, where it functions as a novel, unregulated, (+)-end capper and is largely responsible for the inhibition of motility and cytokinesis in ≈10 –100 nM KabC-treated cells. KabC and related macrolides are useful probes to study the regulation of the actin filament (+) end and may lead to new therapies to treat diseases of the actin cytoskeleton.
Estrogen-related receptor α1 up-regulates endothelial nitric oxide synthase expression
Authors: Sumi Daigo , Ignarro Louis J.
Published: November 2003

The human estrogen-related receptor α1 (ERRα1) is a member of an orphan receptor family closely related to the estrogen receptor. It has been demonstrated that estrogen modulates endothelial nitric oxide synthase (eNOS) expression through the estrogen receptor in endothelial cells. However, little is known about the relationship between ERRα1 and eNOS. In this study, we show that ERRα1 activates the estrogen response element (ERE) and eNOS promoter-dependent luciferase activity in COS-7 cells and bovine pulmonary artery endothelial cells. The endogenous ligand for ERRα1 has not been identified, but we show that these actions are dependent on serum constituents because ERRα1 fails to stimulate eNOS promoter-dependent luciferase activity in charcoal-treated serum. Furthermore, through the use of truncated eNOS promoter luciferase constructs, we demonstrate that the activation of eNOS transcription by ERRα1 is mediated via three regions: base pairs -1001 to -743, base pairs -743 to -265, and downstream from base pair -265 on the eNOS promoter. In addition, ERRα1 up-regulates eNOS mRNA and protein expression and stimulates eNOS activity in bovine pulmonary artery endothelial cells. These results suggest that ERRα1 has a potential role in the regulation of eNOS expression and may stimulate NO production by endothelial cells, which may in turn result in a protective effect against atherosclerosis.
Ovarian cystocytes can repopulate the embryonic germ line and produce functional gametes
Authors: Niki Yuzo , Mahowald Anthony P.
Published: November 2003

Ovarian tumors are formed either in the absence of Bam (bag-of-marbles) in germ-line cells or the overexpression of Dpp (decapentaplegic) in ovarian somatic cells. These tumor cells contain spectrosomes characteristic of ovarian germ-line stem cells and the immediate descendents called cystoblasts. We show that pole cells can successfully populate the gonad after transplantation to the dorsal mesoderm of host embryos following germ-band extension. By using this approach, we demonstrate that
bam
–
cells can populate the gonad and become established as germ-line stem cells. Tumor cells containing the wild-type
bam
gene under heat shock transcriptional control are able to produce functional oocytes. Thus, stem cells/cystoblasts of the adult ovary are capable of forming stem cells in the embryonic ovary and recapitulating the development of the female germ line.
Resting and daily energy expenditures of free-living field voles are positively correlated but reflect extrinsic rather than intrinsic effects
Authors: Speakman J. R. , Ergon T. , Cavanagh R. , Reid K. , Scantlebury D. M. , Lambin X.
Published: November 2003

Resting metabolic rates at thermoneutral (RMRts) are unexpectedly variable. One explanation is that high RMRts intrinsically potentiate a greater total daily energy expenditure (DEE), but recent work has suggested that DEE is extrinsically defined by the environment, which independently affects RMRt. This extrinsic effect could occur because expenditure is forced upwards in poor habitats or enabled to rise in good habitats. We provide here an intraspecific test for an association between RMRt and DEE that separates intrinsic from extrinsic effects and forcing from enabling effects. We measured the DEE and RMRt of 75 free-living short-tailed field voles at two time points in late winter. Across all sites, there was a positive link between individual variation in RMRt and DEE. This correlation, however, emerged only because of an effect across sites, rather than because of an intrinsic association within sites. We defined site quality from the survivorship of voles at the sites and the time at which they commenced breeding in spring. The associations between DEE/RMRt and site quality suggested that in February voles in poorer sites had higher energy demands, indicating that DEE was forced upwards, but in March the opposite was true, with higher demands in good sites, indicating that high expenditure was enabled. These data show that daily energy demands are extrinsically defined, with a link to RMRt that is secondary or independent. Both forcing and enabling effects of the environment may pertain at different times of year.
Pneumococcal carriage results in ganglioside-mediated olfactory tissue infection
Authors: van Ginkel Frederik W. , McGhee Jerry R. , Watt James M. , Campos-Torres Antonio , Parish Lindsay A. , Briles David E.
Published: November 2003

Streptococcus pneumoniaecause considerable morbidity and mortality, with persistent neurological sequelae, particularly in young children and the elderly. It is widely assumed that carriage occurs through direct mucosal colonization from the environment whereas meningitis results from invasion from the blood. However, the results of published studies can be interpreted that pneumococci may enter the brain directly from the nasal cavity by axonal transport through olfactory nerves. This hypothesis is based on findings that (i) teichoic acid of the pneumococcal cell wall interact with gangliosides (GLS), (ii) the interaction of GLS with cholera toxin leads to axonal transport through the olfactory nerves into the brain, and (iii) viruses enter the brain through axonal transport into olfactory nerves. After nasal inoculation, we observe high numbers of pneumococci in nasal washes and the olfactory nerves and epithelium. Significant numbers of pneumococci also infected the olfactory bulbs, brain, and the trigeminal ganglia. The absence of bacteremia in this model makes it unlikely that the bacteria entered the brain from the blood stream. Recovery of colony-forming units from the brain, lungs, olfactory nerves, and epithelium and nasal washes was inhibited by incubating pneumococci with GLS before nasal inoculation. These findings, confirmed by PCR and immunohistochemistry, support a GLS-mediated process of infection and are consistent with pneumococci reaching the brain through retrograde axonal transport.