bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Analysis of the 100 kb Region Containing the Pi-k
h Locus Between Indica and Japonica Rice Lines
Authors: Kumar S.P. , Dalal V. , Singh N.K. , Sharma T.R.
Published: June 2007

We have recently cloned a pathogen inducible blast resistance gene Pi-kh from the indica rice line Tetep using a positional cloning approach. In this study, we carried out structural organization analysis of the Pi-kh locus in both indica and japonica rice lines. A 100 kb region containing 50 kb upstream and 50 kb downstream sequences flanking to the Pi-kh locus was selected for the investigation. A total of 16 genes in indica and 15 genes in japonica were predicted and annotated in this region. The average GC content of indica and japonica genes in this region was 53.15% and 49.3%, respectively. Both indica and japonica sequences were polymorphic for simple sequence repeats having mono-, di-, tri-, tetra-, and pentanucleotides. Sequence analysis of the specific blast resistant Pi-kh allele of Tetep and the susceptible Pi-kh allele of the japonica rice line Nipponbare showed differences in the number and distribution of motifs involved in phosphorylation, resulting in the resistance phenotype in Tetep.
Generation of Synthetic Transcriptome Data with Defined Statistical Properties for the Development and Testing of New Analysis Methods
Authors: Brysbaert Guillaume , Noth Sebastian , Benecke Arndt
Published: June 2007

We have previously developed a combined signal/variance distribution model that accounts for the particular statistical properties of datasets generated on the Applied Biosystems AB1700 transcriptome system. Here we show that this model can be efficiently used to generate synthetic datasets with statistical properties virtually identical to those of the actual data by aid of the JAVA application ace.map creator 1.0 that we have developed. The fundamentally different structure of AB1700 transcriptome profiles requires re-evaluation, adaptation, or even redevelopment of many of the standard microarray analysis methods in order to avoid misinterpretation of the data on the one hand, and to draw full benefit from their increased specificity and sensitivity on the other hand. Our composite data model and the ace.map creator 1.0 application thereby not only present proof of the correctness of our parameter estimation, but also provide a tool for the generation of synthetic test data that will be useful for further development and testing of analysis methods.
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics
Authors: Tamaki Satoshi , Arakawa Kazuharu , Kono Nobuaki , Tomita Masaru
Published: June 2007

Annotations of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http://restauro-g.iab.keio.ac.jp/ under the GNU General Public License.
Genetic Polymorphisms of Nine X-STR Loci in Four Population Groups from Inner Mongolia, China
Authors: Hou Qiao-Fang , Yu Bin , Li Sheng-Bin
Published: June 2007

Nine short tandem repeat (STR) markers on the X chromosome (DXS101, DXS6789, DXS6799, DXS6804, DXS7132, DXS7133, DXS7423, DXS8378, and HPRTB) were analyzed in four population groups (Mongol, Ewenki, Oroqen, and Daur) from Inner Mongolia, China, in order to learn about the genetic diversity, forensic suitability, and possible genetic affinities of the populations. Frequency estimates, Hardy-Weinberg equilibrium, and other parameters of forensic interest were computed. The results revealed that the nine markers have a moderate degree of variability in the population groups. Most heterozygosity values for the nine loci range from 0.480 to 0.891, and there are evident differences of genetic variability among the populations. A UPGMA tree constructed on the basis of the generated data shows very low genetic distance betweent Mongol and Han (Xi’an) populations. Our results based on genetic distance analysis are consistent with the results of earlier studies based on linguistics and the immigration history and origin of these populations. The minisatellite loci on the X chromosome studied here are not only useful in showing significant genetic variation between the populations, but also are suitable for human identity testing among Inner Mongolian populations.
Genetic Analysis of 15 STR Loci in Chinese Han Population from West China
Authors: Deng Ya-Jun , Yan Jiang-Wei , Yu Xiao-Guang , Li Yuan-Zhe , Mu Hao-Fang , Huang Yan-Qing , Shi Xiao-Tie , Sun Wei-Min
Published: June 2007

Allele frequencies for 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001–0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.
Genetic structure analyses of different populations of grass carp (Ctenopharyngodon idella) using the TRAP technique
Authors: Zhi-Wei Zhang , Zhe-Ming Cao , Jing-Song Zhou , Ting-Ting Wu
Published: June 2007

Target region amplified polymorphism (TRAP) was used to compare genetic structures among three populations of grass carp (Ctenopharyngodon idella) – one wild and two cultured populations. Seven out of 15 primer combinations produced good amplification patterns and provided 103 amplified loci from the three populations. Numbers of polymorphic loci in the wild population were higher, indicating a decrease in genetic polymorphism in the two cultured populations. Compared with the wild population, only 39.98% loci gene frequency remained unchanged in the cultured samples, showing a genetic structure change in cultured populations. The genetic distances between wild and cultured populations were 0.0421 and 0.0809. With primer combination Ga5-800-E5, we detected a region in the electrophoretic pattern in which the number of amplified loci apparently decreased in cultured populations. These results establish a good scientific basis for developing molecular markers that can help in distinguishing wild from cultured populations.
Simultaneous observations of nighttime medium‐scale traveling ionospheric disturbances and E region field‐aligned irregularities at midlatitude
Authors: Otsuka Y. , Onoma F. , Shiokawa K. , Ogawa T. , Yamamoto M. , Fukao S.
Published: June 2007

We report on simultaneous observations of very high frequency (VHF) radar backscatter from field‐aligned irregularities (FAI) in the E region and medium‐scale traveling ionospheric disturbances (MSTID) in 630‐nm airglow images. On the night of 6 August 2002, the powerful 46.5‐MHz middle and upper atmosphere (MU) radar with five beam directions at Shigaraki, Japan, observed typical quasiperiodic (QP) echoes from FAI in the E region. During this QP echo event, an all‐sky charge‐coupled device imager at the MU radar site detected MSTID in 630‐nm airglow images. The MSTID also propagated southwestward at 80 m/s with fluctuation amplitudes of 50% from the background intensity and a wavelength of 380 km. Period of the MSTID was almost same as that of the Doppler velocity in the QP echoes. The airglow enhancement (depletion) caused by the MSTID coincided with southeastward (northwestward) velocity in the QP echo. These results indicate that the electric fields associated with the F region MSTID could be closely coupled to those associated with QP echoes in the E region.
Finding the Lyon‐Fedder‐Mobarry magnetopause: A statistical perspective
Authors: García K. S. , Hughes W. J.
Published: June 2007

The determination of the location and global structure of the magnetopause is not a well‐defined problem, either in satellite data or in magnetohydrodynamic (MHD) models. Assessing the accuracy of MHD models by comparing single‐point crossings of the magnetopause cannot provide a complete picture of the accuracy of the model. We evaluate the accuracy of magnetopause location in the Lyon‐Fedder‐Mobarry (LFM) MHD model by examining LFM behavior on a statistical, rather than single event basis. Empirical magnetopause models seek to fit a functional form to large data sets of magnetopause crossings parameterized by controlling factors such as solar wind ram pressure and interplanetary magnetic field orientation. By comparing the LFM magnetopause with the empirical magnetopause models in their region of greatest accuracy, we determine the overall accuracy of the LFM magnetopause position in the dayside equatorial plane. We find the LFM magnetopause to be earthward of the empirical models by, on average, 0.5 to 1.0 RE at noon and 1.0 to 2.0 RE at dusk. This observed discrepancy is shown to be, at least in part, due to the insufficient ring current in the LFM.
Dependence of the high‐latitude lower thermospheric momentum forcing on the interplanetary magnetic field
Authors: Kwak Y.‐S. , Richmond A. D. , Roble R. G.
Published: June 2007

We analyze the forces acting on the high‐latitude lower thermospheric wind system below 170 km for Southern Hemisphere summer conditions, as a function of the interplanetary magnetic field (IMF) direction, on the basis of numerical simulations. The pattern and magnitude of the forces and their relative contributions to the wind system vary strongly with respect to the direction of the IMF. At higher altitudes, above 130 km, for negative By, strong anticyclonic winds are accelerated primarily by rotational Pedersen ion drag and are maintained by an approximate balance among the divergent/convergent Coriolis, horizontal advection, and relatively weak pressure‐gradient accelerations. For positive By, the pressure‐gradient acceleration is increased, while the inertial forces are reduced. For negative Bz, in comparison with negative and positive By, the winds and forces extend to lower latitudes. The patterns of the accelerations for positive Bz are similar to those for negative Bz, but the magnitudes tend to be significantly smaller. At lower altitudes, below 120 km, the horizontal advection acceleration is less important but still contributes significantly to the maintenance of the neutral circulation in the polar cap region for positive By. The difference of winds and forces above 130 km for negative and positive By, with respect to winds and forces for zero IMF, show a simple structure with a strong anticyclonic or cyclonic vortex near the pole, respectively, centered differently for the two By directions. The difference of winds and forces for negative and positive Bz are more complex than those for negative and positive By and extend to lower latitudes. Below 120 km, the difference of winds and forces for negative and positive By are much stronger near the pole than for negative and positive Bz, indicating that the IMF By component tends to dominate effects on the neutral winds in the polar cap at low thermospheric altitudes. For all IMF conditions, at higher altitudes, the rotational ion‐drag acceleration makes the dominant contribution to the neutral velocity tendency. This feature is most pronounced when the IMF Bz is negative.
One‐dimensional hybrid simulations of obliquely propagating ion cyclotron waves: Application to ion pickup at Io
Authors: Cowee M. M. , Russell C. T. , Strangeway R. J. , Blanco‐Cano X.
Published: June 2007

In Jupiter and Saturn's magnetospheres, ionization of neutrals produced by the satellites and rings results in populations of newborn pickup ions with T⊥ > T∥, which are unstable to the generation of electromagnetic ion cyclotron waves. Linear dispersion analysis of this anisotropy instability finds maximum growth at parallel propagation, with decreasing growth rates at wave vector angles, θ, oblique to the ambient magnetic field, B0. Observed S+ and SO+ ion cyclotron waves near the Jovian moon, Io, propagate at a variety of angles within 60° of B0. Using one‐dimensional hybrid simulation, we study the properties of the obliquely propagating waves in the Io plasma torus environment for θ ≤ 60°. We find that the maximum growth rate decreases with increasing angle from B0, as predicted by linear theory, with the growth rate at θ = 60° equal to ∼70% the growth rate at parallel propagation. At the oblique angles, cyclotron harmonics of S+ and SO+ are excited and grow larger with θ. At θ = 60°, the fundamental mode saturation amplitude is roughly four times that of the first harmonic. However, we do not expect to see these harmonics in the Io torus because thermalized O+ and S+ damps their growth. We also find that SO+ cyclotron waves may dominate over S+ if > 2.5 – 3.
A historical reconstruction of ships' fuel consumption and emissions
Authors: Endresen Øyvind , Sørgård Eirik , Behrens Hanna Lee , Brett Per Olaf , Isaksen Ivar S. A.
Published: June 2007

Shipping activity has increased considerably over the last century and currently represents a significant contribution to the global emissions of pollutants and greenhouse gases. Despite this, information about the historical development of fuel consumption and emissions is generally limited, with little data published pre‐1950 and large deviations reported for estimates covering the last 3 decades. To better understand the historical development in ship emissions and the uncertainties associated with the estimates, we present fuel‐based CO2 and SO2 emission inventories from 1925 up to 2002 and activity‐based estimates from 1970 up to 2000. The global CO2 emissions from ships in 1925 have been estimated to 229 Tg (CO2), growing to about 634 Tg (CO2) in 2002. The corresponding SO2 emissions are about 2.5 Tg (SO2) and 8.5 Tg (SO2), respectively. Our activity‐based estimates of fuel consumption from 1970 to 2000, covering all oceangoing civil ships above or equal to 100 gross tonnage (GT), are lower compared to previous activity‐based studies. We have applied a more detailed model approach, which includes variation in the demand for sea transport, as well as operational and technological changes of the past. This study concludes that the main reason for the large deviations found in reported inventories is the applied number of days at sea. Moreover, our modeling indicates that the ship size and the degree of utilization of the fleet, combined with the shift to diesel engines, have been the major factors determining yearly fuel consumption. Interestingly, the model results from around 1973 suggest that the fleet growth is not necessarily followed by increased fuel consumption, as technical and operational characteristics have changed. Results from this study indicate that reported sales over the last 3 decades seems not to be significantly underreported as previous simplified activity‐based studies have suggested. The results confirm our previously reported modeling estimates for year 2000. Previous activity‐based studies have not considered ships less than 100 GT (e.g., today some 1.3 million fishing vessels), and we suggest that this fleet could account for an important part of the total fuel consumption (∼10%).
Toward understanding the double Intertropical Convergence Zone pathology in coupled ocean‐atmosphere general circulation models
Authors: Zhang Xuehong , Lin Wuyin , Zhang Minghua
Published: June 2007

This paper first analyzes structures of the double Intertropical Convergence Zone (ITCZ) in the central equatorial Pacific simulated by three coupled ocean‐atmosphere general circulation models in terms of sea surface temperatures, surface precipitation, and surface winds. It then describes the projection of the double ITCZ in the equatorial upper ocean. It is shown that the surface wind convergences, associated with the zonally oriented double rainbands on both sides of the equator, also correspond to surface wind curls that are favorable to Ekman pumping immediately poleward of the rainbands. The pumping results in a thermocline ridge south of the equator in the central equatorial Pacific, causing a significant overestimation of the eastward South Equatorial Counter Current that advects warm water eastward. A positive feedback mechanism is then described for the amplification of the double ITCZ in the coupled models from initial biases in stand‐alone atmospheric models through the following chain of interactions: precipitation (atmospheric latent heating), surface wind convergences, surface wind curls, Ekman pumping, South Equatorial Counter Current, and eastward advection of ocean temperature. This pathology provides a possible means to address the longstanding double ITCZ problem in coupled models.
Atmospheric CO2 modeling at the regional scale: Application to the CarboEurope Regional Experiment
Authors: Sarrat C. , Noilhan J. , Lacarrère P. , Donier S. , Lac C. , Calvet J. C. , Dolman A. J. , Gerbig C. , Neininger B. , Ciais P. , Paris J. D. , Boumard F. , Ramonet M. , Butet A.
Published: June 2007

The CarboEurope Regional Experiment Strategy (CERES) experiment took place in May and June 2005 in France and offers a comprehensive database on atmospheric CO2 and boundary layer processes at the regional scale. One “golden” day of CERES is interpreted with the mesoscale atmospheric model Meso‐NH coupled on‐line with the Interactions between Soil, Biosphere and Atmosphere, CO2‐reactive (ISBA‐A‐gs) surface scheme, allowing a full interaction of CO2 between the surface and the atmosphere. The rapid diurnal cycle of carbon coupled with water and energy fluxes is parameterized including, e.g., plant assimilation, respiration, anthropogenic emissions, and sea fluxes. During the analyzed day, frequent vertical profiles and aircraft transects revealed high spatial and temporal variabilities of CO2 concentrations within the boundary layer at the regional scale: a 10‐ppm gradient of CO2‐mixing ratio is observed during the day by the aircraft measurements. The Meso‐NH model proved able to simulate very well the CO2 concentration variability as well as the spatial and temporal evolution of the surface fluxes and the boundary layer in the domain. The model is used to explain the CO2 variability as a result of two complementary processes: (1) the regional heterogeneity of CO2 surface fluxes related to the land cover (e.g., winter crops versus a pine forest) and (2) the variability of mesoscale circulation across the boundary layer: development of the sea breeze in the western part of the domain and dominating wind flow in the eastern part of the domain.
On the variability of summer air temperature during the last 28 years in Athens
Authors: Livada I. , Santamouris M. , Assimakopoulos M. N.
Published: June 2007

The increase of living standards in buildings and the high, summer maximum air‐temperature values during the last years have important economic, technical, social, and environmental consequences. Analysis of the summer ambient temperatures is thus necessary to investigate, among others, the important impact on energy consumption. Ambient temperature data from the National Observatory of Athens station for the period 1950–2004 are presented. The number of hours with air temperature above 30°C, as well as the degree hour values (DH) in base of 30°C are estimated and statistically analyzed in order to evaluate passive, hybrid, and conventional cooling systems and techniques. The general conclusion of this study is that during the last 15 years there is a dramatic increase of the number of hours with high air temperatures that leads to an increasing persistence of hot weather conditions. This corresponds, however, to the rising part of the air temperature cyclic change which does not verify yet the estimated significant increasing tendency.
A case study of a frontal system simulated by a climate model: Clouds and radiation
Authors: Wu Jingbo , Zhang Minghua , Lin Wuyin
Published: June 2007

A case study is carried out to evaluate the capability of the Community Atmosphere Model (CAM3) in simulating frontal clouds over the Southern Great Plains (SGP). It focuses on a midlatitude cyclonic storm system observed during the March 2000 Intensive Observation Period (IOP) of the Atmospheric Radiation Measurement Program (ARM). Cloud biases are found to be consistent with climate model biases in this region: overestimation of optically thick clouds and shortwave cooling at the top‐of‐the‐atmosphere (TOA), underestimation of optically thin middle clouds. Satellite observations, NOAA ETA analysis and a suite of ARM measurements are used to analyze the model cloud biases. We found two independent causes of model errors during two stages of the evolution of the cyclone. In the first stage, the biases are from cloud microphysical properties. The model significantly overpredicted cloud liquid water path, while it underpredicted cloud ice water path. As a result, it overestimated the magnitude of shortwave cloud forcing. In the second stage, the model cloud biases are primarily caused by a faster eastward propagation of the 500 mbar ridge behind the cyclone, which dissipated the high‐ and middle‐level clouds but favored low clouds, leading to biases in cloud forcing. Averaged over the cyclone domain and period, the model simulated shortwave and longwave TOA cloud forcing of −113 W/m2 and 30 W/m2, respectively, while the corresponding observations are −69 W/m2 and 38 W/m2. Our results illustrated the feasibility of using synoptic cases to understand and eventually eliminate systematic cloud biases in climate models.
Associations between large‐scale atmospheric circulation and polar low developments over the North Atlantic during winter
Authors: Claud Chantal , Duchiron Bertrand , Terray Pascal
Published: June 2007

Polar lows are intense mesoscale weather systems which develop in response to combinations of upper tropospheric vorticity advection, low‐level baroclinicity near the sea ice‐ocean margin and strong air‐sea thermodynamical fluxes. In this paper, an evaluation of the associations between dominant patterns of low‐frequency variability in the atmospheric circulation and polar low developments over the North Atlantic during winter is presented. Because polar lows are rather poorly represented in reanalyses, the temperature (T500) and geopotential height at 500 hPa, the wind at 925 hPa, the SST, and the difference (SST‐T500), which are critical for their formation, are considered. The North Atlantic Oscillation (NAO) has a strong impact on all these variables, but it is contrasted spatially and temporally. Polar low formation is stimulated in the Labrador Sea for a positive NAO phase, while over the Norwegian Sea, there is an increase of polar lows forming on the flank of synoptic storms. Still over the Norwegian Sea, higher SST from January on favor the formation of polar lows of predominantly convective nature, while to the east of Greenland, the reduction of sea ice plus the northerly low‐level flow lead to a larger number of polar lows. Other teleconnection patterns also exhibit associations with polar low developments. The Scandinavia pattern shows a strong negative association with the studied variables over the Norwegian and Barents seas, but only marginally affects the Labrador Sea. The formation of polar lows is encouraged over the Norwegian and Greenland seas when the Polar/Eurasia pattern is in its negative phase.
Mars Express High Resolution Stereo Camera spectrophotometric data: Characteristics and science analysis
Authors: McCord T. B. , Adams J. B. , Bellucci G. , Combe J.‐P. , Gillespie A. R. , Hansen G. , Hoffmann H. , Jaumann R. , Neukum G. , Pinet P. , Poulet F. , Stephan K.
Published: June 2007

The High Resolution Stereo Camera (HRSC) on the Mars Express (MEx) spacecraft in orbit about Mars is delivering images of the Mars surface and atmosphere from its high‐inclination, elliptical orbit that are intended to cover most of the Mars surface by the end of the mission. These are acquired in four specific spectral passbands that sample the scene at different parts of the extended visual spectrum from near 0.4 μm to about 1μm and in five additional channels, four used for stereo and one nadir, that use the same fifth spectral passband. These channels view from different angles and can be used for photometric and spectral analysis. The data allow a variety of studies of the surface and atmosphere of Mars, but these require detailed understanding of the data characteristics, as there are several effects, including of the observation geometry and the atmosphere, that need to be treated. This article is a report to the science community on the current understanding of the HRSC color data after an initial analysis and also a demonstration of their capabilities for study of Mars, which, from this study, appear to be considerable. We first discuss the characteristics and calibration of the HRSC spectral data. The atmospheric influence on the photometric appearance of the surface materials is explored, and methods of compensating are considered. Reflectances are calculated for surface units by assuming the dark material is basalt and scaling the entire HRSC scene using a laboratory basalt spectrum for the selected dark material area; the results and the correction factors for different orbits are compared. We present several examples of what could become a large volume of future science results utilizing the HRSC spectrophotometric data in conjunction with photo‐interpretation. For example, we find relatively few but very important distinct spectral components at the HRSC resolution, including what we interpret as iron oxide‐rich material, unoxidized basalt, and polar ice, consistent with past works. The major spectral components are distributed in ways that suggest compositional mixing and the need to revise the current geologic understanding of major regions.
Combinations of processes responsible for Martian impact crater “layered ejecta structures” emplacement
Authors: Komatsu Goro , Ori Gian Gabriele , Di Lorenzo Stefano , Rossi Angelo Pio , Neukum Gerhard
Published: June 2007

We utilized images and stereo‐derived topographic data acquired by the High Resolution Stereo Camera (HRSC) and Thermal Emission Imaging System (THEMIS) images together with other data in order to study the geology of “layered ejecta structures” associated with relatively pristine Martian impact craters. The geomorphology and morphometric properties indicate their origin as complex combinations of a variety of impact processes. The studied (inner) layered ejecta structures often exhibit ground‐hugging characteristics, and many of them do not have topographic profiles expected from simple ballistic emplacement. Such profiles include ones that are plateau‐shaped or thickening outward. We think that water‐rich fluidized flows driven by the momentum due to the impact and by gravity, together with ballistic emplacement and vortex produced by the atmosphere‐ejecta curtain interaction, were essential to the (inner) layered ejecta structure formation. We hypothesize that the thinner outer layered ejecta structures were formed by various combinations of shockwave‐induced liquefaction of water‐rich near‐surface sediments, ballistic emplacement of ejecta‐entraining water, and strong winds (expanding vapor, vortex, base surge) related to the impact. The contribution of each proposed layered ejecta structure formation mechanism should have been variable depending on the condition of the impact.
Changes in the Arctic Oscillation under increased atmospheric greenhouse gases
Authors: Wu Aiming , Hsieh William W. , Boer George J. , Zwiers Francis W.
Published: June 2007

The Arctic Oscillation (AO) under increased atmospheric concentration of greenhouse gases (GHG) was studied by comparing an ensemble of simulations from 13 coupled general circulation models with GHG at the pre‐industrial level and at the late 20th century level, for November to March. The change in the linear AO pattern as GHG increased reveals positive sea level pressure (SLP) anomalies centered over the Gulf of Alaska, and weaker negative SLP anomalies over eastern Canada and North Atlantic – a pattern resembling the nonlinear AO pattern arising from a quadratic relation to the AO index. This quadratic AO pattern itself has positive SLP anomalies receding from Europe but strengthening over the Gulf of Alaska and surrounding areas as GHG increased. This study points to the importance of the nonlinear structure in determining how the linear oscillatory pattern changes when there is a change in the mean climate.
An explanation for the seasonal dependence of midlatitude sporadic E layers
Authors: Haldoupis C. , Pancheva D. , Singer W. , Meek C. , MacDougall J.
Published: June 2007

The midlatitude sporadic E layers form when metallic ions of meteoric origin in the lower thermosphere are converged vertically in a wind shear. The occurrence and strength of sporadic E follow a pronounced seasonal dependence marked by a conspicuous summer maximum. Although this is known since the early years of ionosonde studies, its cause has remained a mystery as it cannot be accounted for by the windshear theory ofEs formation. We show here that the marked seasonal dependence of sporadic E correlates well with the annual variation of sporadic meteor deposition in the upper atmosphere. The later has been established recently from long‐term measurements using meteor radar interferometers in the Northern and Southern Hemispheres. Knowing that the occurrence and strength of sporadic E layers depends directly on the metal ion content, which apparently is determined primarily by the meteoric deposition, the present study offers a cause‐and‐effect explanation for the long‐going mystery of sporadic E layer seasonal dependence.
Transcription factor AP‐1, and the role of Fra‐2
Authors: FOLETTA VICTORIA C
Published: June 2007

Transcription factors function to regulate gene transcription. They may be constitutively expressed or may only be activated during specific situations. Activator protein‐1 (AP‐1) is an inducible transcription factor, and is comprised of multiple protein complexes that include the gene products of the fos and jun gene families. Numerous cellular and viral genes contain AP‐1 binding sites within their promoters and, accordingly, AP‐1 has been shown to play a role in the regulation of both basal and inducible transcription of these genes, fos‐related antigen‐2 (fra‐2) has been found to have both similar and unique properties to that of other fos gene members in terms of its regulation and expression. The analysis and determination of the function of Fra‐2 will provide further information on the role of AP‐1.
Gonadotropin‐releasing hormone agonist influences absolute levels of lymphocyte subsets in vivo in male mice
Authors: RAO LV , CLEVELAND RP , KIMMEL RJ , ATAYA KM
Published: June 2007

Our earlier studies have demonstrated that gonadotropin‐releasing hormone (GnRH) agonists suppress immune system function in female mice. No systematic studies regarding the effect of gender on immune system function following GnRH agonist treatment, however, have been reported. This study, therefore, investigated sequential changes in lymphocyte subsets in 3‐ and 10‐week‐old male mice following agonist or placebo administration. Changes in immunophenotypic expression of lymphocytes from thymus, bone marrow, spleen, and blood were analysed at periodic intervals. Upon agonist administration, plasma testosterone levels were significantly increased in pre‐pubertal mice, but were significantly decreased in post‐pubertal males. Absolute thymic weights, thymocytes and T subsets were significantly increased from the third week regardless of gonadal status. Blood lymphocyte subsets showed a decreasing trend after agonist administration in pre‐pubertal males, whereas no differences were observed in post‐pubertal males. No significant differences were observed in spleen cells after agonist administration. These studies, together with earlier observations in female mice indicate that GnRH agonist effects on the immune system, are independent of steroid hormone levels. In contrast to suppressive effects in females, GnRH agonists induce no change or ultimately enhanced lymphocyte counts in males, indicating differential effects on the immune system between males and females. This may have important implications for the treatment of various diseases.
Control of scarring in adult wounds using antisense transforming growth factor‐β1 oligodeoxynucleotides
Authors: CHOI BYUNG‐MIN , KWAK HYUN‐JEONG , JUN CHANG‐DUK , PARK SEOK‐DON , KIM KI‐YOUNG , KIM HYUNG‐RYUN , CHUNG HUN‐TAEG
Published: June 2007

Adult wounds heal with scar formation, whereas fetal wounds heal without scarring and with a lesser inflammatory and cytokine response. We reasoned that a strategy employing antisense oligodeoxynucleotides (ODN) complementary to transforming growth factor (TGF)‐β1 mRNA might decrease the scarring of dermal wounds in the mouse. To evaluate this concept, we tested the effects of antisense ODN targeted to TGF‐β1 mRNA by topical application of the ODN on the skin wound. Phosphorothioation of ODN to retard their degradation. When antisense TGF‐βl ODN were applied on the wound site, there was a marked reduction of scarring compared with a control wound site. This effect of antisense TGF‐β1 ODN on scar formation was associated with decreased expression of the TGF‐β1 gene. However, sense TGF‐pl ODN had no effect on the expression of the TGF‐β1 gene. In addition, control wounds healed with excessive fibrosis compared with the antisense‐treated wounds. In conclusion, our results indicate that antisense TGF‐β1 ODN could be used for ameliorating scar formation during wound healing.
Molecular cloning and characterization of tumour necrosis factor alpha (TNF‐α) from the Australian common brushtail possum, Trichosurus vulpecula
Authors: WEDLOCK D NEIL , ALDWELL FRANK E , BUDDLE BRYCE M
Published: June 2007

Immune responses in the Australian common brushtail possum (Trichosurus vulpecula) and in particular the role of cytokines are poorly understood. We have undertaken to isolate cytokine genes using reverse transcriptase‐polymerase chain reaction (RT‐PCR) and in this study describe the molecular cloning of TNF‐α. Primers were designed from consensus sequences at the N‐terminus end of eutherian mammalian TNF‐α and the possum cDNA, derived from spleen RNA, identified by RT‐PCR. The complete cDNA encoding possum TNF‐α was amplified from lymphocyte RNA by 5′ and 3′ rapid amplification of cDNA ends (RACE). The nucleotide sequence of the protein coding region of this cDNA shared 66‐69% identity with other mammalian TNF‐α genes. The predicted protein of 233 amino acids shared 56‐58% identity with eutherian mammalian TNF‐α. Possum TNF‐α was expressed in both Saceharomyces cerevisiae and Escherichia coli by constructing expression plasmid derivatives of the vectors pYES2 and pGEX‐2T respectively. Cell extracts prepared from transformants and the purified GST/TNF‐α fusion protein exhibited cytotoxic activity on the TNF‐α‐sensitive murine fibroblast L929 cells and stimulated proliferation of possum thymocyte cells. The induction of possum TNF‐α mRNA in alveolar macrophages was analysed by RT‐PCR using possumspecific TNF‐α primers. Macrophages cultured in the presence of LPS showed enhanced transcription of TNF‐α mRNA. This is the first report of the cloning and sequence analysis of the cDNA encoding a marsupial cytokine gene.
Uncontrolled triggering of programmed cell death (apoptosis) in haematopoietic stem cells: A new hypothesis for the pathogenesis of aplastic anaemia
Authors: LAVEDER FRANCESCO , MARCOLONGO RENZO
Published: June 2007

The cause of bone marrow failure in aplastic anaemia (AA) is still unknown: however, it is clear that acquired AA is a heterogeneous disease including basically different pathophysiological conditions. Causative agents, clinically associated with AA, possibly exert their action through restricted pathways. Some theoretical and experimental data show that programmed cell death (PCD) or apoptosis is physiologically important in normal haematopoiesis and could be involved in the pathophysiological events responsible for the development of AA. Therefore, it is intriguing to hypothesize that the pathogenetic mechanism underlying most cases of acquired AA could be represented by an excessive and/or uncontrolled triggering of PCD in haematopoietic stem cells. Investigations to test this hypothesis are proposed.
Antigen presentation in allergic sensitization
Authors: MUDDE GEERT C , REISCHL ILONA G , CORVAIA NATHALIE , HREN ANDREA , POELLABAUER EVA‐MARIA
Published: June 2007

IgE antibodies, when cross‐linked by allergen on the surface of effector cells such as mast cells and basophils, are known to be directly responsible for immediate type hypersensitivity reactions. In addition, IgE may be involved in other, indirect, mechanisms, fundamental to the pathogenesis of allergic diseases, such as enhancement of the antigen capturing capacity of antigen presenting cells. IgE mediated antigen presentation could lead to a continuous activation of the immune system by very low concentrations of allergen. As a result, Th2 cell populations may expand and may induce more B cells to switch to IgE production. Subsequently, the overproduction of IgE and Th2 cells in a patient may explain the clinical observation that certain allergic patients deteriorate from sensitivity to a single group of allergens to sensitivity to multiple groups of allergens. Therefore, control of IgE production is not only important for the treatment of allergic symptoms, but may also regulate deterioration of allergy via the mechanism of CD23/IgE mediated allergen presentation by native B cells. The role that monocytes, which have recently been found to express FCERL play in the pathogenesis of allergy, remains speculative. We hypothesize that their role may be to remove IgE from the circulation and re‐direct the immune response from naive B cells. IgG antibodies which cannot be used for antigen uptake by B cells also direct the immune response to monocytes.
Peptide‐mediated regulation of the allergic immune response
Authors: HOYNE GERARD F , LAMB JONATHAN R
Published: June 2007

A major key to successful immunotherapy may depend on altering the qualitative nature of the immune response in allergic patients. In this review we examine how immune responses to environmental allergens are regulated, and the mechanisms used by the immune system to prevent allergic sensitization. We also discuss future prospects of using allergen‐derived peptides in immunotherapy and the possibility of‘reprogramming’the immune responses by immunizing under conditions that promote Th1 responses instead of Th2 responses.
Immunological and structural similarities among allergens: Prerequisite for a specific and component‐based therapy of allergy
Authors: VALENTA RUDOLF , STEINBERGER PETER , DUCHÊNE MICHAEL , KRAFT DIETRICH
Published: June 2007

It is known that allergic patients are frequently co‐sensitized against different allergen sources. Progress made in the field of allergen characterization by molecular biological techniques has now revealed that sensitization against different allergen sources can be explained as cross‐reactivity of IgE antibodies with structurally and immunologically related components present in these allergen sources. This review defines groups of cross‐reactive plant allergens with significant sequence homology. The similarities among allergens may facilitate allergy diagnosis by using a few representative cross‐reactive allergens to determine the patient's IgE reactivity profile (allergogram). According to that typing, a few cross‐reactive allergens, carrying most of the relevant IgE epitopes, may then be selected for patient‐tailored specific therapy.
Atopy and the ectopic immune response
Authors: AALBERSE ROB C
Published: June 2007

A hypothesis if formulated for the mode of action of the ‘atopy gene’: the gene(s) causing an increased tendency to mount an IgE immune response to trivial environmental antigens. It is postulated that some antigens are not efficiently transported to the lymphoid organs, the location of the ‘eutopic’ immune system; migratory lymphoid cells may occasionally react and start an inefficient immune response in sites not so destined. This is called an ectopic immune response. This response lacks the regulatory influences prevailing in the lymphoid organs, which results in approximately equal quantities of the various immunoglobulin isotypes, including IgE. The atopy gene(s) work by increasing the risk of such an ectopic immune response.
How is expression of the interleukin‐5 gene regulated?
Authors: KARLEN STEPHANE , MORDVINOV VIATCHESLAV A , SANDERSON COLIN J
Published: June 2007

Eosinophilia is a uniquely specific phenomenon regulated by interleukin‐5 (IL‐5), suggesting specific control for IL‐5 expression. However in eosinophilia IL‐5 is often co‐expressed with other lymphokines such as IL‐4, indicating that common, as well as independent, control mechanisms must exist. IL‐5 gene expression is regulated at the transcriptional level. The molecular analysis of the IL‐5 promoter region reveals the presence of positive regulatory sites that are common to many lymphokine genes. Results from immunosuppression studies suggest that the key control mechanism of IL‐5 regulation may not depend on specific regulatory factors but on how gene expression is activated.
The structure and function of hyaluronan: An overview
Authors: LAURENT TORVARD C , LAURENT ULLA BG , FRASER J ROBERT E
Published: June 2007

Hyaluronan is a major component of synovial tissue and fluid as well as other soft connective tissues. It is a high‐Mr polysaccharide which forms entangled networks already at dilute concentrations (< 1 mg/mL) and endows its solutions with unique rheological properties. Physiological functions of hyaluronan (lubrication, water homeostasis. macromolecular filtering, exclusion, etc.) have been ascribed to the properties of these networks. Recently a number of specific interactions between hyaluronan and a group of proteins named hyaladherins have also pointed towards a role of hyaluronan in recognition and the regulation of cellular activities. Many more or less well documented hypotheses have been proposed for the function of hyaluronan in joints, for example, that it should lubricate, protect cartilage surfaces, scavenge free radicals and debris, keep the joint cavities open, form flow barriers in the synovium and prevent capillary growth.
Susceptibility to Leishmania major in IL‐4 transgenic mice is not correlated with the lack of a Th1 immune response
Authors: ERB KLAUS J. , BLANK CHRISTINE , MOLL HEIDRUN
Published: June 2007

IL‐4 transgenic mice of C3H genetic background expressing IL‐4 under the control of an MHC class I promoter were infected with Leishmania major and the immune response was assessed. In contrast to littermate control mice, the transgenic mice were unable to restrict the growth of the parasites as shown by the strong increase in footpad swelling and parasite numbers in the spleen. The observed susceptibility was markedly less severe than that observed in BALB/c mice. Restimulation of lymph node cells with L. major antigen in vitro and subsequent analysis of cytokine secretion revealed that, in contrast to BALB/c mice, the cells from the IL‐4 transgenic mice secreted more IL‐5 and similar amounts of IFN‐γ as did the cells from litter mate control mice. These results demonstrate that the transgenic expression of IL‐4 in vivo leads to the generation of more Th2 cells without affecting the generation of IFN‐γ‐producing Th1 cells. This indicates that under certain conditions Th1 and Th2 immune responses during infection with L. majorare not mutually exclusive, and that other factors besides the secretion of IL‐4 determine whether only a Th1 or a Th2 immune response develops. The observed susceptibility of IL‐4 transgenic mice to L. major was not due to the lack of IFN‐γ production but presumably to the transgenic and Th2 cell‐derived IL‐4 counteracting the otherwise protective effect of IFN‐γ on infected macrophages. Our results might help explain why humans develop cutaneous leishmaniasis even though IFN‐γ‐producing ceils are readily detectable in the lesions.
Gene family use and somatic mutation in primary and secondary fluorescein‐specific IgM antibody responses
Authors: VAN DER KEYL H , HSU C , TOLAT A , KANSIL S , DALESANDRO MR , DORER DR , CATON A , OWEN JA
Published: June 2007

A comparative analysis of the DNA sequences of primary and secondary IgM, fluorescein‐ specific antibodies was performed. These antibodies were secreted by hybridomas generated following fusion of immunized BALB/c mouse lymphocytes and SP2/0 myeloma cells. Our results show that primary and secondary fluorescein‐specific IgM antibodies use a variety of segments from the variable region of the immunoglobulin heavy chain locus (VH), with members of the J558 and 7183 VH gene families predominating in both populations, D regions from the DF116 and DSP2 families were used exclusively in our primary antibody sample and predominated in the secondary response. In the primary antibodies, 15 out of 18 definable D regions were transcribed in reading frame one, but in the secondary antibodies the three reading frames were used stochastically. Secondary IgM antibodies showed a higher frequency of somatic mutation than their primary counterparts, but we could detect no evidence of selection for mutations in the complementarity determining regions as compared with the framework regions. It appears that fusion of secondary cells, 3‐6 days after immunization, is able to‘capture’the IgM‐producing population of B cells at a stage in their development following mutation but prior to antigenic selection.