bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of a natural gas fuelled homogeneous charge compression ignition engine with exhaust gas recirculation using a stochastic reactor model
Authors: Bhave A , Balthasar M , Kraft M , Mauss F
Published: February 2004

Combustion and emissions formation in a Volvo TD 100 series diesel engine running in a homogeneous charge compression ignition (HCCI) mode and fuelled with natural gas is simulated and compared with measurements for both with and without external exhaust gas recirculation (EGR). A new stochastic approach is introduced to model the convective heat transfer, which accounts for fluctuations and fluid-wall interaction effects. This model is included in a partially stirred plug flow reactor (PaSPFR) approach, a stochastic reactor model (SRM), and is applied to study the effect of EGR on pressure, autoignition timing and emissions of CO and unburned hydrocarbons (HCs). The model accounts for temperature inhomogeneities and includes a detailed chemical mechanism to simulate the chemical reactions within the combustion chamber. Turbulent mixing is described by the interaction by exchange with the mean (IEM) model. A Monte Carlo method with a second-order time-splitting technique is employed to obtain the numerical solution. The model is validated by comparing the simulated in-cylinder pressure history and emissions with measurements taken from Christensen and Johansson (SAE Paper 982454). Excellent agreement is obtained between the peak pressure, ignition timing and CO and HC emissions predicted by the model and those obtained from the measurements for the non-EGR, 38 per cent EGR and 47 per cent EGR cases. A comparison between the pressure profiles for the cases studied reveals that the ignition timing and the peak pressure are dependent on the EGR. With EGR, the peak pressure reduces and the autoignition is delayed. The trend observed in the measured emissions with varying EGR is also predicted correctly by the model.
Cystic echinococcosis in the Arctic and Sub-Arctic
Authors: RAUSCH R. L.
Published: February 2004

The northern biotype ofEchinococcus granulosusoccurs throughout the holarctic zones of tundra and taiga, from eastern Fennoscandia to the Bering Strait in Eurasia and in North America from arctic Alaska approximately to the northern border of the United States. The cycle of the cestode is complex in taiga at lower latitudes, because of the greater diversity of potential hosts. In the Arctic and Subarctic, however, four patterns of predator/prey relationships may be discerned. Two natural cycles involve the wolf and wild reindeer and the wolf and elk (moose), respectively. Where deer of the two species coexist, both are prey of the wolf; the interactions of the wolf and elk are here described on the basis of long-term observations made on Isle Royale (in Lake Superior near the southern limit of taiga), where only the wolf and elk serve as hosts forE. granulosus. A synanthropic cycle involving herding-dogs and domesticated reindeer caused hyperendemicity of cystic echinococcosis in arctic Eurasia, mainly in northeastern Siberia. The 4th pattern, a semi-synanthropic cycle, formerly existed in Alaska, wherein sled-dogs of the indigenous hunters became infected by consuming the lungs of wild reindeer. The sequence of changes in life-style inherent in the process of acculturation affected the occurrence of cystic echinococcosis among nomadic Iñupiat in arctic Alaska. When those people became sedentary, the environs of their early villages soon became severely contaminated by faeces of dogs, and cases of cystic echinococcosis occurred. Compared to cystic echinococcosis caused byE. granulosusadapted to synanthropic hosts (dog and domestic ungulates), the infection produced by the northern biotype is relatively benign. Nearly all diagnosed cases of cystic echinococcosis (>300) in Alaska have occurred in indigenous people; only one fatality has been recorded (in a non-indigenous person). After sled-dogs were replaced by machines, cases have become rare in Alaska. A similar effect has been observed in Fennoscandia, in the Saami and domesticated reindeer. Recent records indicate that the prevalence of cystic echinococcosis is increasing in Russia, suggesting that dogs are used there in herding.
Perspective on control options forEchinococcus multiloculariswith particular reference to Japan
Authors: ITO A. , ROMIG T. , TAKAHASHI K.
Published: February 2004

Following a brief introduction of recent advances in molecular and immunological technology for detection of persons and animals infected withEchinococcus multilocularisand an overview of the current situation of alveolar echinococcosis (AE) in Japan, perspectives on control options are discussed with reference to different epidemiological situations. AE is considered the most serious parasitic zoonosis in temperate and arctic regions of the northern hemisphere. The number of human cases differs drastically among regions. While high numbers of patients are apparently associated with highE. multilocularisprevalence in domestic dogs, e.g. in parts of Alaska and western China, the number of cases is moderate or low in areas where the parasite is mainly transmitted by wild canid species (e.g. in central Europe or temperate North America). However, the severity of the disease, the absence of curative treatment for most cases, the high cost of long-term chemotherapy and the anxiety caused for the population in highly endemic areas call for the development of preventive strategies even in regions where human AE is rare. Furthermore, in view of (1) drastically increasing numbers and infection rates of foxes involved in transmission ofE. multilocularis, and (2) increasingly close contact between humans and foxes e.g. in Europe and Japan, there is considerable concern that AE incidences may in future increase in these regions. Control options depend on a variety of factors including the species of canid principally responsible for transmission and the socio-economic situation in the region. Where domestic dogs (stray or owned) are the principal hosts forE. multilocularis, control options can include those applicable toE. granulosus, i.e. reduction of the number of stray dogs, registration and regular preventive chemotherapy of owned dogs, and information campaigns for the population promoting low-risk behaviour for man and dogs. WhereE. multilocularisis mainly transmitted by wild canids, the situation is far more difficult with preventive strategies still being in trial stage. Integrated control measures could include prevention information campaigns, restricting access of pet animals (dogs and cats) to rodents, chemotherapy of foxes on local or regional scales, and strategies to minimize contacts between people and foxes.
How do adults and children process referentially ambiguous pronouns?
Authors: SEKERINA IRINA A. , STROMSWOLD KARIN , HESTVIK ARILD
Published: February 2004

In two eye-tracking experiments, we investigate adults' and children's on-line processing of referentially ambiguous English pronouns. Sixteen adults and 16 four-to-seven-year-olds listened to sentences with either an unambiguous reflexive (himself) or an ambiguous pronoun (him) and chose a picture with two characters that corresponded to those in the sentence. For adults, behavioural data, responses and reaction times indicate that pronouns are referentially ambiguous. Adults' eye movements show a competition between the looks to sentence-internal and -external referents for pronouns, but not for reflexives. Children overwhelmingly prefer the sentence-internal referent in the off-line picture selection task. However, their eye movements reveal implicit awareness of referential ambiguity that develops earlier than their explicit knowledge in the picture selection task. This discrepancy between performance on a looking measure and a pointing measure in the children's processing system is explained by a general dissociation between implicit and explicit knowledge proposed in recent literature on cognitive development.
Sampling children's spontaneous speech: how much is enough?
Authors: TOMASELLO MICHAEL , STAHL DANIEL
Published: February 2004

There has been relatively little discussion in the field of child language acquisition about how best to sample from children's spontaneous speech, particularly with regard to quantitative issues. Here we provide quantitative information designed to help researchers make decisions about how best to sample children's speech for particular research questions (and/or how confident to be in existing analyses). We report theoretical analyses in which the major parameters are: (1) the frequency with which a phenomenon occurs in the real world, and (2) the temporal density with which a researcher samples the child's speech. We look at the influence of these two parameters in using spontaneous speech samples to estimate such things as: (a) the percentage of the real phenomenon actually captured, (b) the probability of capturing at least one target in any given sample, (c) the confidence we can have in estimating the frequency of occurrence of a target from a given sample, and (d) the estimated age of emergence of a target structure. In addition, we also report two empirical analyses of relatively infrequent child language phenomena, in which we sample in different ways from a relatively dense corpus (two children aged 2;0 to 3;0) and compare the different results obtained. Implications of these results for various issues in the study of child language acquisition are discussed.
Speech overlap in Japanese mother–child conversations
Authors: KAJIKAWA SACHIYO , AMANO SHIGEAKI , KONDO TADAHISA
Published: February 2004

This study aimed to clarify the development of conversational style in Japanese mother–child interactions. We focused on the frequency of speech overlap as an index of Japanese conversational style, with particular attention to ne, a particle produced by the speaker, and to backchannels, such as ‘uh-huh’, produced by the listener that support sympathetic conversation. The results of longitudinal observations of two Japanese mother–child dyads from approximately 0;11 to 3;3 suggest that an adultlike conversational style with frequent overlaps emerges in Japanese child-directed speech around the two-word utterance period, and a child's development of ne use is closely related to this shift.
Home range and spatial organization of the marsupial carnivore, Dasyurus maculatus maculatus (Marsupialia: Dasyuridae) in south‐eastern Australia
Authors: Belcher C. A. , Darrant J. P.
Published: February 2004

The tiger quoll or spotted‐tailed quoll Dasyurus maculatus, a nationally threatened species, is the largest surviving carnivorous marsupial on mainland Australia and the sole surviving member of the genus in south‐eastern mainland Australia. Live‐trapping and radio‐tracking studies at three sites in south‐eastern Australia found that tiger quolls were solitary, except when mating, and that male and female tiger quolls occupied very large home ranges, both during and after the breeding season. The mean size of the home range of male tiger quolls (minimum convex polygon (MCP) 1755.4 ha, kernel 3761.7 ha) was significantly larger than the mean size of the home range of females (MCP 495.9 ha, kernel 1113.0 ha). Adult female tiger quolls displayed intrasexual territoriality throughout the year, but they seemed to tolerate the presence of female offspring. Male tiger quolls were not territorial and their home ranges overlapped both with other males and with females throughout the year. Males were recorded regularly moving back and forth between a number of female territories during the breeding season. The spatial organization of the tiger quoll recorded in this study differs markedly from that of the eastern quoll Dasyurus viverrinus and the Tasmanian devil Sarcophilus harrisii, but is similar to that of the western quoll D. geoffroii, northern quoll D. hallucatus and brush‐tailed phascogale Phascogale tapoatafa. The spatial organization and home‐range size of the tiger quoll dictate that conservation of the species requires management across all land tenures at the landscape level.
Editorial
Authors: Tait John , Boguraev Branimir , Jacquemin Christian
Published: February 2004

With this first issue of Volume 10 of Natural Language Engineering we would like to take this opportunity to reflect on the development of the journal, especially over the last year or two, and to look forward to a number of future developments.
Spatiotemporal distribution of interplate coupling in southwest Japan from inversion of geodetic data
Authors: Ito Takeo , Hashimoto Manabu
Published: February 2004

We determine the spatiotemporal distribution of slip (or slip deficit) on the subduction interface of the Nankai trough over an entire earthquake cycle using geodetic data (including leveling, triangulation, and trilateration, sea level, and GPS surveys) obtained during the past 100 years in southwest Japan. We develop a new inversion method that accounts for long‐term crustal deformation, coseismic (earthquake) displacements, and stress relaxation of the viscoelastic asthenosphere. From this analysis we obtain a model that shows postseismic afterslip on the deeper part of the plate interface following the 1946 Nankaido earthquake. Significant afterslip is found beneath central Shikoku that totals about 0.8 m. The slip deficit rate during the interseismic period is 5–6 cm/year in the N50°W–N60°W direction, which is consistent with the relative plate motion between the Philippine and Amurian plates. A fully locked region is found in the shallower portion (<30 km), and the slip deficit rate has a maximum at a depth of about 20 km. The plate interface deeper than 30 km is slowly slipping. The amount of slip deficit reaches about 3.3 m off Shikoku and about 2 m off the Kii peninsula 50 years after the 1946 earthquake. This suggests that fault healing and full interplate coupling has occurred by this time along the Nankai trough.
High‐resolution far ultraviolet spectrum of electron‐excited SO2
Authors: Vatti Palle Prahlad , Ajello Joseph , Bhardwaj Anil
Published: February 2004

The high‐resolution UV capabilities (λ/Δλ = 105) of the Hubble Space Telescope (HST) equipped with the Space Telescope Imaging Spectrograph (STIS) reflects a need for a high‐resolution laboratory UV spectral data base for comparison with observation. For the purpose of interpreting the astronomical observations of Io by HST the electron‐excited UV spectrum of SO2 gas has been studied from 800–1700 Å at medium (λ/Δλ ∼ 103) and high resolution (λ/Δλ ∼ 5 × 104) . The far ultraviolet (FUV) laboratory spectrum consists entirely of S I, II and O I, II multiplets. From a measurement of the medium resolution spectrum at 1.5 Å FWHM we are able to provide new detail in the 200 eV emission cross sections for all the FUV features. At 30 and 100 eV electron‐impact energy we have measured high resolution emission spectra of the fine structure lines of the atomic multiplets at 1256 Å from S II, at 1304 Å from O I, 1479 Å from S I and at 1429 Å from S I at 100 eV electron‐impact energy. At 100 eV electron‐impact energy we compare the optically thin laboratory spectrum of the atomic multiplet S I at 1479 Å with the model spectrum of electron excitation of atomic sulfur. In addition, we compare a HST STIS observation of Io with the G140M grating (FWHM ∼ 0.5 Å) at 1479 Å with a laboratory spectrum after transmission through a layer of atomic S. We have also compared our laboratory spectrum to FUV observations by STIS reported by Roesler et al. [1999]. The relative intensities of the strongest lines of S I and O I are compared with the laboratory emission cross sections for SO2 near 40 eV (3 Ryd) electron energy. The Doppler line profiles of individual fine structure lines of atomic sulfur and oxygen were used to ascertain the kinetic energy distribution from dissociative excitation at 30 and 100 eV. At 100 eV electron‐impact energy we find the kinetic energy distribution of the oxygen and sulfur atoms to be in the range of 2 eV to 3 eV. At 30 eV electron‐impact energy we place an upper limit on the kinetic energy of sulfur and oxygen atoms as <1 eV. We provide the first measurement of the O I] 1356 Å absolute excitation function and the estimate of the cross section ratio O I] 1356 Å/1304 Å as a function of energy. We establish the absolute cross section of O I 1304 Å as 2.3 ± 0.5 × 10−18 cm2 at 100 eV and the estimated cross section of O I] 1356 Å as 2.1 ± 1 × 10−18 cm2 at 100 eV.
Physical Electron Belt Model from Jupiter's surface to the orbit of Europa
Authors: Sicard Angélica , Bourdarie Sébastien
Published: February 2004

The three‐dimensional model, Salammbô‐3D, which was initially developed to model the Earth's radiation belts, has been adapted to Jupiter's radiation environment. As a first step, this model has been validated between L = 1 and L = 6 (L: MacIlwain parameter), just inside Io's obit. In order to extend our three‐dimensional (3‐D) code up to L = 9.5, just inside Europa's orbit, a more realistic magnetic field than the dipole field used before has been introduced in Salammbô. Two magnetic field models are available: The model of Connerney [1981] and the one of Khurana [1997]. Both of them are composed of two parts: An internal magnetic field, intrinsic to the planet, and an external magnetic field, due to the current sheet. Results deduced from Salammbô‐3D, using these two different models, will be shown and compared. Then, to validate our 3‐D code, from Jupiter up to Europa's orbit, comparisons between simulations and two kinds of observations will be done. Firstly, Salammbô results will be compared with spacecraft data (Pioneer 10 and 11) and secondly with radio observations (Very Large Array: VLA). Indeed, with the help of Salammbô‐3D and a synchrotron model, two‐dimensional images of Jupiter's synchrotron emission can be deduced. It is then possible to investigate the global radiation belt shape by comparing simulations and VLA observations. Two important results emerge from this study. First, the extension of our model outside Io's orbit aims to show that Io does not play any role on relativistic electron dynamics, i.e., it does not create losses of particles like the inner moons (Metis, Adrastea, Amalthea, and Thebe). The second important result is that contrary to Io, Europa seems to play a significant role in determining the electron distribution in the Jovian radiation belts.
Circulation of summer Pacific halocline water in the Arctic Ocean
Authors: Steele Michael , Morison James , Ermold Wendy , Rigor Ignatius , Ortmeyer Mark , Shimada Koji
Published: February 2004

We present an analysis of Arctic Ocean hydrographic and sea ice observations from the 1990s, with a focus on the circulation of water that originates in the North Pacific Ocean. Previous studies have shown the presence of two varieties of relatively warm “summer halocline water” in the vicinity of the Chukchi Sea, i.e., the relatively fresh Alaskan Coastal Water (ACW) and the relatively saltier summer Bering Sea Water (sBSW). Here we extend these studies by tracing the circulation of these waters downstream into the Arctic Ocean. We find that ACW is generally most evident in the southern Beaufort Gyre, while sBSW is strongest in the northern portion of the Beaufort Gyre and along the Transpolar Drift Stream. We find that this separation is most extreme during the early mid‐1990s, when the Arctic Oscillation was at historically high index values. This leads us to speculate that the outflow to the North Atlantic Ocean (through the Canadian Archipelago and Fram Strait) may be similarly separated. As Arctic Oscillation index values fell during the later 1990s, ACW and sBSW began to overlap in their regions of influence. These changes are evident in the area north of Ellesmere Island, where the influence of sBSW is highly correlated, with a 3‐year lag, with the Arctic Oscillation index. We also note the presence of winter Bering Sea Water (wBSW), which underlies the summer varieties. All together, this brings the number of distinct Pacific water types in our Arctic Ocean inventory to three: ACW, sBSW, and wBSW.
Temporal interpolation of global surface skin temperature diurnal cycle over land under clear and cloudy conditions
Authors: Aires F. , Prigent C. , Rossow W. B.
Published: February 2004

The surface skin temperature is a key parameter at the land‐atmosphere interface. An accurate description of its diurnal cycle would not only help estimate the energy exchanges at the interface, it would also enable an analysis of the global surface skin diurnal cycle and its variability within the last 20 years. This study is based on the 3‐hourly surface skin temperature estimated by the International Satellite Cloud Climatology Project (ISCCP) from the infrared measurements collected by the polar and geostationary meteorological satellites. The diurnal cycle of surface skin temperature is analyzed almost globally (60N–60S snow‐free areas), using a Principal Component Analysis. The first three components are identifyed as the amplitude, the phase, and the width (i.e., daytime duration) of the diurnal cycle and represent 97% of the variability. PCA is used to regularize estimates of the diurnal cycle at a higher time resolution. A new temporal interpolation algorithm, designed to work when only a few measurements of surface temperature are available, is developed based on the PCA representation and an iterative optimization algorithm. This method is very flexible: only temperature measurements are used (no ancillary data), no surface model constraints are used, and the time and number of measurements are not fixed. The performance of this interpolation algorithm is tested for various diurnal sampling configurations. In particular, the potential to use the satellite microwave observations to provide a full diurnal surface temperature cycle in cloudy conditions is investigated.
Genetic and biophysical studies of diphtheria toxin repressor (DtxR) and the hyperactive mutant DtxR(E175K) support a multistep model of activation
Authors: Love John F. , vanderSpek Johanna C. , Marin Vedrana , Guerrero Luis , Logan Timothy M. , Murphy John R.
Published: February 2004

The diphtheria toxin repressor (DtxR) from
Corynebacterium diphtheriae
is the prototypic member of a superfamily of transition metal ion-activated transcriptional regulators that have been isolated from Gram-positive prokaryotes. Upon binding divalent transition metal ions, the N-terminal domain of DtxR undergoes a dynamic structural organization leading to homodimerization and target DNA binding. We have used site-directed mutagenesis and NMR analysis to probe the mechanism by which apo-DtxR transits from an inactive to a fully active repressor upon metal ion binding. We demonstrate that the ancillary metal-binding site mutant DtxR(H79A) requires higher concentrations of metal ions for activation both
in vivo
and
in vitro
, providing a functional correlation to the proposed cooperativity between ancillary and primary binding sites. We also demonstrate that the C-terminal
src
homology 3 (SH3)-like domain of DtxR functions to modulate repressor activity by (
i
) binding to the polyprolyl tether region between the N- and C-terminal domains, and (
ii
) destabilizing the ancillary binding site, leading to full inactivation of the repressor. Finally, we show by NMR analysis that the hyperactive phenotype of DtxR(E175K) results from the stabilization of a structural intermediate in the activation process. Taken together, the data presented support a multistep model for the activation of apo-DtxR by transition metal ions.
Membrane and acto-myosin tension promote clustering of adhesion proteins
Authors: Delanoë-Ayari H. , Al Kurdi R. , Vallade M. , Gulino-Debrac D. , Riveline D.
Published: February 2004

Physicists have studied the aggregation of adhesive proteins, giving a central role to the elastic properties of membranes, whereas cell biologists have put the emphasis on the cytoskeleton. However, there is a dramatic lack of experimental studies probing both contributions on cellular systems. Here, we tested both mechanisms on living cells. We compared, for the same cell line, the growth of cadherin-GFP patterns on recombinant cadherin-coated surfaces, with the growth of vinculin-GFP patterns on extracellular matrix protein-coated surfaces by using evanescent wave microscopy. In our setup, cadherins are not linked to actin, whereas vinculins are. This property allows us to compare formation of clusters with proteins linked or not to the cytoskeleton and thus study the role of membrane versus cytoskeleton in protein aggregation. Strikingly, the motifs we obtained on both surfaces share common features: they are both elongated and located at the cell edges. We showed that a local force application can impose this symmetry breaking in both cases. However, the origin of the force is different as demonstrated by drug treatment (butanedione monoxime) and hypotonic swelling. Cadherins aggregate when membrane tension is increased, whereas vinculins (cytoplasmic proteins of focal contacts) aggregate when acto-myosin stress fibers are pulling. We propose a mechanism by which membrane tension is localized at cell edges, imposing flattening of membrane and enabling aggregation of cadherins by diffusion. In contrast, cytoplasmic proteins of focal contacts aggregate by opening cryptic sites in focal contacts under acto-myosin contractility.
Regulation of canonical transient receptor potential isoform 3 (TRPC3) channel by protein kinase G
Authors: Kwan Hiu-Yee , Huang Yu , Yao Xiaoqiang
Published: February 2004

Canonical transient receptor potential (TRPC) channels are Ca2+-permeable nonselective cation channels that are widely expressed in numerous cell types. Seven different members of TRPC channels have been isolated. The activity of these channels is regulated by the filling state of intracellular Ca2+stores and/or diacylglycerol and/or Ca2+/calmodulin. However, no evidence is available as to whether TRPC channels are regulated by direct phosphorylation on the channels. In the present study, TRPC isoform 3 (TRPC3) gene was overexpressed in HEK293 cells that were stably transfected with protein kinase G (PKG). We found that the overexpressed TRPC3 mediated store-operated Ca2+influx and that this type of Ca2+influx was inhibited by cGMP. The inhibitory effect of cGMP was abolished by KT5823 or H8. Point mutations at two consensus PKG phosphorylation sites (T11A and S263Q) of TRPC3 channel markedly reduced the inhibitory effect of cGMP. In addition, TRPC3 proteins were purified from HEK293 cells that were transfected with either wild-type or mutant TRPC3 constructs, andin vitroPKG phosphorylation assay was carried out. It was found that wild-type TRPC3 could be directly phosphorylated by PKGin vitroand that the phosphorylation was abolished in the presence of KT5823. The phosphorylation signal was greatly reduced in mutant protein T11A or S263Q. Taken together, TRPC3 channels could be directly phosphorylated by PKG at position T11 and S263, and this phosphorylation abolished the store-operated Ca2+influx mediated by TRPC3 channels in HEK293 cells.
Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in
Arabidopsis
Authors: Ohgishi Maki , Saji Kensuke , Okada Kiyotaka , Sakai Tatsuya
Published: February 2004

Blue light receptors in
Arabidopsis
include two types of proteins, cryptochromes and phototropins. Previous studies have suggested that the cryptochromes cry1 and cry2 function mainly in photomorphogenic responses and that the phototropins phot1 and phot2 mainly regulate photo-induced movements. Receptors in the same family have redundant functions, although their responses to the fluence rate of blue light differ. To uncover functions of blue light receptors that may be concealed by their functional redundancy, we conducted analyses of combinatorial multiple mutants of blue light receptors. Comparison of the responses of the quadruple mutant
cry1 cry2 phot1 phot2
to blue light with those of related triple mutants revealed that cryptochromes function in blue light-dependent, random hypocotyl-bending and that phototropins function in one photomorphogenic response, cotyledon expansion. Microarray analysis suggested that cry1 and cry2 independently function as key regulators of early blue light-induced genes, whereas phot1 and phot2 play subsidiary roles in transcriptional regulation by blue light.
IκB-kinaseβ-dependent NF-κB activation provides radioprotection to the intestinal epithelium
Authors: Egan Laurence J. , Eckmann Lars , Greten Florian R. , Chae Sungwon , Li Zhi-Wei , Myhre Gennett M. , Robine Sylvie , Karin Michael , Kagnoff Martin F.
Published: February 2004

Acute injury to the intestinal mucosa is a major dose-limiting complication of abdominal radiation therapy. We studied the role of the transcription factor NF-κB in protection against radiation-induced apoptosis in the intestinal epithelium
in vivo
. We use mice in which NF-κB signaling through IκB-kinase (IKK)-β is selectively ablated in intestinal epithelial cells to show that failure to activate epithelial cell NF-κB
in vivo
results in a significant increase in radiation-induced epithelial cell apoptosis. Furthermore, bacterial lipopolysaccharide, which is normally a radioprotective agent, is radiosensitizing in IKKβ-deficient intestinal epithelial cells. Increased apoptosis in IKKβ-deficient intestinal epithelial cells was accompanied by increased expression and activation of the tumor suppressor p53 and decreased expression of antiapoptotic Bcl-2 family proteins. These results demonstrate the physiological importance of the NF-κB system in protection against radiation-induced death in the intestinal epithelium
in vivo
and identify IKKβ as a key molecular target for radioprotection in the intestine. Selective preactivation of NF-κB through IKKβ in intestinal epithelial cells could provide a therapeutic modality that allows higher doses of radiation to be tolerated during cancer radiotherapy.
Potent neutralization of severe acute respiratory syndrome (SARS) coronavirus by a human mAb to S1 protein that blocks receptor association
Authors: Sui Jianhua , Li Wenhui , Murakami Akikazu , Tamin Azaibi , Matthews Leslie J. , Wong Swee Kee , Moore Michael J. , Tallarico Aimee St. Clair , Olurinde Mobolaji , Choe Hyeryun , Anderson Larry J. , Bellini William J. , Farzan Michael , Marasco Wayne A.
Published: February 2004

Effective prophylaxis and antiviral therapies are urgently needed in the event of reemergence of the highly contagious and often fatal severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) infection. We have identified eight recombinant human single-chain variable region fragments (scFvs) against the S1 domain of spike (S) protein of the SARS-CoV from two nonimmune human antibody libraries. One scFv 80R efficiently neutralized SARS-CoV and inhibited syncytia formation between cells expressing the S protein and those expressing the SARS-CoV receptor angiotensin-converting enzyme 2 (ACE2). Mapping of the 80R epitope showed it is located within the N-terminal 261–672 amino acids of S protein and is not glycosylation-dependent. 80R scFv competed with soluble ACE2 for association with the S1 domain and bound S1 with high affinity (equilibrium dissociation constant,
K
d
= 32.3 nM). A human IgG1 form of 80R bound S1 with a 20-fold higher affinity of 1.59 nM comparable to that of ACE2 (
K
d
= 1.70 nM), and neutralized virus 20-fold more efficiently than the 80R scFv. These data suggest that the 80R human monoclonal antibody may be a useful viral entry inhibitor for the emergency prophylaxis and treatment of SARS, and that the ACE2-binding site of S1 could be an attractive target for subunit vaccine and drug development.
The genome sequence of the probiotic intestinal bacterium
Lactobacillus johnsonii
NCC 533
Authors: Pridmore R. David , Berger Bernard , Desiere Frank , Vilanova David , Barretto Caroline , Pittet Anne-Cecile , Zwahlen Marie-Camille , Rouvet Martine , Altermann Eric , Barrangou Rodolphe , Mollet Beat , Mercenier Annick , Klaenhammer Todd , Arigoni Fabrizio , Schell Mark A.
Published: February 2004

Lactobacillus johnsonii
NCC 533 is a member of the acidophilus group of intestinal lactobacilli that has been extensively studied for their “probiotic” activities that include, pathogen inhibition, epithelial cell attachment, and immunomodulation. To gain insight into its physiology and identify genes potentially involved in interactions with the host, we sequenced and analyzed the 1.99-Mb genome of
L. johnsonii
NCC 533. Strikingly, the organism completely lacked genes encoding biosynthetic pathways for amino acids, purine nucleotides, and most cofactors. In apparent compensation, a remarkable number of uncommon and often duplicated amino acid permeases, peptidases, and phosphotransferase-type transporters were discovered, suggesting a strong dependency of NCC 533 on the host or other intestinal microbes to provide simple monomeric nutrients. Genome analysis also predicted an abundance (>12) of large and unusual cell-surface proteins, including fimbrial subunits, which may be involved in adhesion to glycoproteins or other components of mucin, a characteristic expected to affect persistence in the gastrointestinal tract (GIT). Three bile salt hydrolases and two bile acid transporters, proteins apparently critical for GIT survival, were also detected.
In silico
genome comparisons with the >95% complete genome sequence of the closely related
Lactobacillus gasseri
revealed extensive synteny punctuated by clear-cut insertions or deletions of single genes or operons. Many of these regions of difference appear to encode metabolic or structural components that could affect the organisms competitiveness or interactions with the GIT ecosystem.
Relationship between the frequency of HIV-specific CD8+T cells and the level of CD38+CD8+T cells in untreated HIV-infected individuals
Authors: Chun Tae-Wook , Justement J. Shawn , Sanford Christina , Hallahan Claire W. , Planta Marie A. , Loutfy Mona , Kottilil Shyam , Moir Susan , Kovacs Colin , Fauci Anthony S.
Published: February 2004

CD8+T cells are critical for effective host defenses against viral infections. Studies addressing HIV-induced immune responses in infected individuals have suggested that CD8+T cells play an important role in controlling viral replication. However, despite an abundance of HIV-specific CD8+T cells, HIV is not contained in many untreated patients. Active HIV replication is associated with numerous immunologic changes, the most notable and consistent of which is an increase in CD8+T cells expressing CD38. Previous studies have demonstrated that the expression of CD38 on CD8+T cells is associated with poor prognostic outcome in infected individuals with detectable plasma viremia; however, the relationship between the expression of CD38 and the frequency of HIV-specific CD8+T cells is unclear. We demonstrate a correlation between levels of HIV-specific CD8+T cells and levels of CD8+T cells expressing CD38 in untreated patients. The distribution of HIV-specific CD8+T cells was heavily skewed toward CD38+CD8+T cells in patients with a high percentage of CD38+CD8+T cells. Spontaneous/Fas-mediated apoptosis in CD38+CD8+T cells was significantly higher in patients with high percentages of CD38+CD8+T cells. Our data suggest that a substantial proportion of the HIV-specific CD8+T cells present in CD38+CD8+T cells in patients with active viral replication arise by HIV-driven aberrant immune activation and may not manifest effective cytolytic activity against infected targets due to a high degree of susceptibility to apoptosis, thus providing an explanation of why HIV is not successfully contained by CD8+T cells in such individuals.
Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution
Authors: Yeh Shiou-Hwei , Wang Hurng-Yi , Tsai Ching-Yi , Kao Chuan-Liang , Yang Jyh-Yuan , Liu Hwan-Wun , Su Ih-Jen , Tsai Shih-Feng , Chen Ding-Shinn , Chen Pei-Jer ,   the National Taiwan University SARS Research Team§§
Published: February 2004

Since early March 2003, the severe acute respiratory syndrome (SARS) coronavirus (CoV) infection has claimed 346 cases and 37 deaths in Taiwan. The epidemic occurred in two stages. The first stage caused limited familial or hospital infections and lasted from early March to mid-April. All cases had clear contact histories, primarily from Guangdong or Hong Kong. The second stage resulted in a large outbreak in a municipal hospital, and quickly spread to northern and southern Taiwan from late April to mid-June. During this stage, there were some sporadic cases with untraceable contact histories. To investigate the origin and transmission route of SARS-CoV in Taiwan's epidemic, we conducted a systematic viral lineage study by sequencing the entire viral genome from ten SARS patients. SARS-CoV viruses isolated from Taiwan were found closely related to those from Guangdong and Hong Kong. In addition, all cases from the second stage belonged to the same lineage after the municipal hospital outbreak, including the patients without an apparent contact history. Analyses of these full-length sequences showed a positive selection occurring during SARS-CoV virus evolution. The mismatch distribution indicated that SARS viral genomes did not reach equilibrium and suggested a recent introduction of the viruses into human populations. The estimated genome mutation rate was ≈0.1 per genome, demonstrating possibly one of the lowest rates among known RNA viruses.
Bilirubin protects astrocytes from its own toxicity by inducing up-regulation and translocation of multidrug resistance-associated protein 1 (Mrp1)
Authors: Gennuso Florinda , Fernetti Cristina , Tirolo Cataldo , Testa Nuccio , L'Episcopo Francesca , Caniglia Salvo , Morale Maria Concetta , Ostrow J. Donald , Pascolo Lorella , Tiribelli Claudio , Marchetti Bianca
Published: February 2004

Unconjugated bilirubin (UCB) causes encephalopathy in severely jaundiced neonates by damaging astrocytes and neurons. Astrocytes, which help defend the brain against cytotoxic insults, express the ATP-dependent transporter, multidrug resistance-associated protein 1 (Mrp1), which mediates export of organic anions, probably including UCB. We therefore studied whether exposure to UCB affects the expression and intracellular localization of Mrp1 in cultured mouse astroglial cells (>95% astrocytes). Mrp1 was localized and quantitated by confocal laser scanning microscopy and double immunofluorescence labeling by using specific antibodies against Mrp1 and the astrocyte marker glial fibrillary acidic protein, plus the Golgi marker wheat germ agglutinin (WGA). In unexposed astrocytes, Mrp1 colocalized with WGA in the Golgi apparatus. Exposure to UCB at a low unbound concentration (Bf)of 40 nM caused rapid redistribution of Mrp1 from the Golgi throughout the cytoplasm to the plasma membrane, with a peak 5-fold increase in Mrp1 immunofluorescence intensity from 30 to 120 min.Bfabove aqueous saturation produced a similar but aborted response. Exposure to this higherBffor 16 h markedly decreased Trypan blue exclusion and methylthiazoletetrazoilum activity and increased apoptosis 5-fold by terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling assay. These toxic effects were modestly increased by inhibition of Mrp1 activity with 3-([3-(2-[7-chloro-2-quinolinyl]ethenyl)phenyl-(3-dimethylamino-3-oxopropyl)-thio-methyl]thio)propanoic acid (MK571). By contrast,Bf= 40 nM caused injury only if Mrp1 activity was inhibited by MK571, which also blocked translocation of Mrp1. Our conclusion is that in astrocytes, UCB up-regulates expression of Mrp1 and promotes its trafficking from the Golgi to the plasma membrane, thus moderating cytotoxicity from UCB, presumably by limiting its intracellular accumulation.
Unexpected Ca
2+
-binding properties of synaptotagmin 9
Authors: Shin Ok-Ho , Maximov Anton , Lim Byung Kook , Rizo Josep , Südhof Thomas C.
Published: February 2004

Synaptotagmin 1 (Syt 1) functions as an essential Ca
2+
sensor for the fast but not slow component of Ca
2+
-triggered exocytosis. One hypothesis to account for this selective function, based on the close homology of Syt 1 with synaptotagmin 9 (Syt 9), is that these Syts are redundant for the slow but not the fast component of release. We now show, however, that Syt 9 has unique properties that set it apart from Syt 1. Different from Syt 1, endogenous Syt 9 does not associate Ca
2+
dependently or independently with soluble
N
-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) protein complexes, and the Syt 9 C
2
B domain does not form Ca
2+
/phospholipid complexes, whereas such complexes are essential for Syt 1 function. Nevertheless, the C
2
A domain of Syt 9 functions as a Ca
2+
-binding module, suggesting that Syts 1 and 9 are Ca
2+
sensors with similar Ca
2+
-binding sequences but distinct properties that indicate nonoverlapping functions.
Exceptional conservation of horse–human gene order on X chromosome revealed by high-resolution radiation hybrid mapping
Authors: Raudsepp Terje , Lee Eun-Joon , Kata Srinivas R. , Brinkmeyer Candice , Mickelson James R. , Skow Loren C. , Womack James E. , Chowdhary Bhanu P.
Published: February 2004

Development of a dense map of the horse genome is key to efforts aimed at identifying genes controlling health, reproduction, and performance. We herein report a high-resolution gene map of the horse (Equus caballus) X chromosome (ECAX) generated by developing and typing 116 gene-specific and 12 short tandem repeat markers on the 5,000-rad horse × hamster whole-genome radiation hybrid panel and mapping 29 gene loci by fluorescencein situhybridization. The human X chromosome sequence was used as a template to select genes at 1-Mb intervals to develop equine orthologs. Coupled with our previous data, the new map comprises a total of 175 markers (139 genes and 36 short tandem repeats, of which 53 are fluorescencein situhybridization mapped) distributed on average at ≈880-kb intervals along the chromosome. This is the densest and most uniformly distributed chromosomal map presently available in any mammalian species other than humans and rodents. Comparison of the horse and human X chromosome maps shows remarkable conservation of gene order along the entire span of the chromosomes, including the location of the centromere. An overview of the status of the horse map in relation to mouse, livestock, and companion animal species is also provided. The map will be instrumental for analysis of X linked health and fertility traits in horses by facilitating identification of targeted chromosomal regions for isolation of polymorphic markers, building bacterial artificial chromosome contigs, or sequencing.
Thioredoxin links redox to the regulation of fundamental processes of plant mitochondria
Authors: Balmer Yves , Vensel William H. , Tanaka Charlene K. , Hurkman William J. , Gelhaye Eric , Rouhier Nicolas , Jacquot Jean-Pierre , Manieri Wanda , Schürmann Peter , Droux Michel , Buchanan Bob B.
Published: February 2004

Mitochondria contain thioredoxin (Trx), a regulatory disulfide protein, and an associated flavoenzyme, NADP/Trx reductase, which provide a link to NADPH in the organelle. Unlike animal and yeast counterparts, the function of Trx in plant mitochondria is largely unknown. Accordingly, we have applied recently devised proteomic approaches to identify soluble Trx-linked proteins in mitochondria isolated from photosynthetic (pea and spinach leaves) and heterotrophic (potato tubers) sources. Application of the mitochondrial extracts to mutant Trx affinity columns in conjunction with proteomics led to the identification of 50 potential Trx-linked proteins functional in 12 processes: photorespiration, citric acid cycle and associated reactions, lipid metabolism, electron transport, ATP synthesis/transformation, membrane transport, translation, protein assembly/folding, nitrogen metabolism, sulfur metabolism, hormone synthesis, and stress-related reactions. Almost all of these targets were also identified by a fluorescent gel electrophoresis procedure in which reduction by Trx can be observed directly. In some cases, the processes targeted by Trx depended on the source of the mitochondria. The results support the view that Trx acts as a sensor and enables mitochondria to adjust key reactions in accord with prevailing redox state. These and earlier findings further suggest that, by sensing redox in chloroplasts and mitochondria, Trx enables the two organelles of photosynthetic tissues to communicate by means of a network of transportable metabolites such as dihydroxyacetone phosphate, malate, and glycolate. In this way, light absorbed and processed by means of chlorophyll can be perceived and function in regulating fundamental mitochondrial processes akin to its mode of action in chloroplasts.
Postsynaptic
N
-methyl-
d
-aspartate receptor function requires α-neurexins
Authors: Kattenstroth Gunnar , Tantalaki Evangelia , Südhof Thomas C. , Gottmann Kurt , Missler Markus
Published: February 2004

α-Neurexins are neuron-specific cell-surface molecules that are essential for the functional organization of presynaptic Ca
2+
channels and release sites. We have now examined postsynaptic glutamate receptor function in α-neurexin knockout (KO) mice by using whole-cell recordings in cultured neocortical slices. Unexpectedly, we find that α-neurexins are required for normal activity of
N
-methyl-
d
-aspartate (NMDA)- but not α-amino-3-hydroxy-5-methyl-4-isoxyzolepropionic acid (AMPA)-type glutamate receptors. In α-neurexin-deficient mice, the ratio of NMDA- to AMPA-receptor currents, recorded as evoked synaptic responses, was diminished ≈50%. Furthermore, the NMDA-receptor-dependent component of spontaneous synaptic miniature responses was reduced ≈50%, whereas the AMPA-receptor-dependent component was unaffected. No alterations in the levels of NMDA- or AMPA-receptor proteins were detected. These results suggest that α-neurexins are required to maintain normal postsynaptic NMDA-receptor function. The decrease in NMDA-receptor activity in α-neurexin-deficient synapses could be due to a transsynaptic effect on the postsynaptic neuron (i.e., α-neurexins on the presynaptic inputs guide postsynaptic NMDA-receptor function) or to a cell-autonomous postsynaptic effect of α-neurexins on NMDA-receptor activity. To distinguish between these two possibilities, we cocultured WT GFP-labeled neurons with neocortical slices from α-neurexin-deficient or control mice. No difference was found between WT neurons innervated by inputs that contained or lacked α-neurexins, indicating that the absence of presynaptic α-neurexins alone does not depress postsynaptic NMDA-receptor function. Our data suggest that, in addition to the previously described presynaptic impairments, loss of α-neurexins induces postsynaptic changes by a cell-autonomous mechanism.
Evolutionary comparisons suggest many novel cAMP response protein binding sites in
Escherichia coli
Authors: Brown C. T. , Callan C. G.
Published: February 2004

The cAMP response protein (CRP) is a transcription factor known to regulate many genes in
Escherichia coli
. Computational studies of transcription factor binding to DNA are usually based on a simple matrix model of sequence-dependent binding energy. For CRP, this model predicts many binding sites that are not known to be functional. If they are indeed spurious, the underlying binding model is called into question. We use a species comparison method to assess the functionality of a population of such predicted CRP sites in
E. coli
. We compare them with orthologous sites in
Salmonella typhimurium
identified independently by
clustalw
alignment, and find a dependence of mutation probability on position in the site. This dependence increases with predicted site binding energy. The positions where mutation is most strongly suppressed are those where mutation would have the biggest effect on predicted binding energy. This finding suggests that many of the novel sites are functional, that the matrix model correctly estimates their binding strength, and that calculated CRP binding strength is the quantity that is conserved between species. The analysis also identifies many new
E. coli
binding sites and genes likely to be functional for CRP.