bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Analysis of Antigen 43 in UropathogenicEscherichia coliReveals a Role in Long-Term Persistence in the Urinary Tract
Authors: Ulett Glen C. , Valle Jaione , Beloin Christophe , Sherlock Orla , Ghigo Jean-Marc , Schembri Mark A. 
Published: April 2007

ABSTRACTEscherichia coliis the primary cause of urinary tract infection (UTI) in the developed world. The major factors associated with the virulence of uropathogenicE. coli(UPEC) are fimbrial adhesins, which mediate specific attachment to host receptors and trigger innate host responses. Another group of adhesins is represented by the autotransporter subgroup of proteins. The best characterized of these proteins, antigen 43 (Ag43), is a self-recognizing adhesin that is associated with cell aggregation and biofilm formation inE. coliK-12. The sequenced genome of prototype UPEC strain CFT073 contains two variant Ag43-encoding genes located on pathogenicity islands. The biological significance of both of these genes and their role in UPEC pathogenesis have not been investigated previously. Here we performed a detailed molecular characterization analysis of Ag43a (c3655) and Ag43b (c1273) from UPEC CFT073. Expression of Ag43a and Ag43b in a K-12 background revealed that they possess different functional properties. Ag43a produced a strong aggregation phenotype and promoted significant biofilm growth. Deletion mutants and strains constitutively expressing Ag43a and Ag43b were also constructed using CFT073. When these mutants were analyzed in a mouse model of UTI, Ag43a (but not Ag43b) promoted long-term persistence in the urinary bladder. Our findings demonstrate that Ag43a contributes to UPEC disease pathogenesis and reveal that there are pathogenicity-adapted variants of Ag43 with distinct virulence-related functions.
Evading the Proteasome: Absence of Lysine Residues Contributes to Pertussis Toxin Activity by Evasion of Proteasome Degradation
Authors: Worthington Zoë E. V. , Carbonetti Nicholas H. 
Published: April 2007

ABSTRACT

Pertussis toxin (PT) is an important virulence factor produced by
Bordetella pertussis
. PT holotoxin comprises one enzymatically active A subunit (S1), associated with a pentamer of B subunits. PT is an ADP-ribosyltransferase that modifies several mammalian heterotrimeric G proteins. Some bacterial toxins are believed to undergo retrograde intracellular transport through the Golgi apparatus to the endoplasmic reticulum (ER). The ER-associated degradation (ERAD) pathway involves the removal of misfolded proteins from the ER and degradation upon their return to the cytosol; this pathway may be exploited by PT and other toxins. In the cytosol, ERAD substrates are ubiquitinated at lysine residues, targeting them to the proteasome for degradation. We hypothesize that S1 avoids ubiquitination and proteasome degradation due to its lack of lysine residues. We predicted that the addition of lysine residues would reduce PT toxicity by allowing ubiquitination and degradation to occur. Variant forms of PT were engineered, replacing one, two, or three arginines with lysines in a variety of locations on S1. Several variants were identified with wild-type in vitro enzymatic activity but reduced cellular activity, consistent with our hypothesis. Significant recovery of the cellular activity of these variants was observed when CHO cells were pretreated with a proteasome inhibitor. We concluded that the replacement of arginine residues with lysine in the S1 subunit of PT renders the toxin subject to proteasomal degradation, suggesting that wild-type PT avoids proteasome degradation due to an absence of lysine residues.
Isolation and characterization of the pea cytochrome c oxidase Vb gene
Authors: Kubo Nakao , Arimura Shin-ichi , Tsutsumi Nobuhiro , Kadowaki Koh-ichi , Hirai Masashi 
Published: April 2007

Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.
Construction and characterization of the first bacterial artificial chromosome library for the cotton species Gossypium barbadense L.
Authors: Wang X.F. , Ma J. , Wang W.S. , Zheng Y.M. , Zhang G.Y. , Liu C.J. , Ma Z.Y. 
Published: April 2007

As the second most widely cultivated cotton, Gossypium barbadense is well known for its superior fiber properties and its high levels of resistance to Fusarium and Verticillium wilts. To enhance our ability to exploit these properties in breeding programs, we constructed the first bacterial artificial chromosome (BAC) library for this species. The library contains 167 424 clones (49 920 BamHI and 117 504 HindIII clones), with an estimated average insert size of 130 kb. About 94.0% of the clones had inserts over 100 kb, and the empty clones accounted for less than 4.0%. Contamination of the library with chloroplast clones was very low (0.2%). Screening the library with locus-specific probes showed that BAC clones represent 6.5-fold genome equivalents. This high-quality library provides an additional asset with which to exploit genetic variation for cotton improvement.
Mapping of FHB resistance QTLs in tetraploid wheat
Authors: Somers Daryl J. , Fedak George , Clarke John , Cao Wenguang 
Published: April 2007

Triticum turgidum L var. durum is known to be particularly susceptible to infection by Fusarium graminearum, the causal agent for Fusarium head blight (FHB), which results in severe yield losses and grain contaminated with mycotoxins. This research was aimed at identifying FHB resistance in tetraploid wheat and mapping the location of FHB resistance genes. A tetraploid cross of durum wheat (‘Strongfield’) × Triticum carthlicum (‘Blackbird’) was used to generate a doubled-haploid (DH) population. This population was evaluated for type II resistance to F. graminearum in replicated greenhouse trials, in which heads were innoculated and the percent of infected spikelets was determined 21 days later. The population was also genotyped with microsatellite markers to construct a map of 424 loci, covering 2 052 cM. The FHB reaction and genotypic data were used to identify FHB resistance quantitative trait loci (QTLs). It was determined that 2 intervals on chromosomes 2BL and 6BS controlled FHB resistance in this tetraploid cross. The FHB resistance allele on chromosome 2BL (r2 = 0.26, logarithm of odds (LOD) = 8.5) was derived from ‘Strongfield’, and the FHB resistance allele on chromosome 6BS (r2 = 0.23, LOD = 6.6) was derived from ‘Blackbird’. Two other loci, on chromosomes 5AS and 2AL, were shown to regulate FHB infection and to have an epistatic effect on the FHB resistance QTL on chromosome 6BS. Further, the FHB resistance QTL peak on chromosome 6BS was clearly coincident with the known FHB resistance gene Fhb2, derived from Sumai 3. The results show that FHB resistance can be expressed in durum wheat, and that T. carthlicum and Triticum aestivum likely share a common FHB resistance gene on chromosome 6BS.
WATER SUPPLY VULNERABILITY ASSESSMENT FOR SUSTAINABLE LIVELIHOODS
Authors: HADIPURO WIJANTO 
Published: April 2007

All the United Nations' members have already committed to achieve the Millennium Development Goals (MDGs) to reduce by half the proportion of 1.1 billion people without sustainable access to safe drinking water by 2015. The problem is that with all the limiting capacities, which half should be prioritized and what kind of policy intervention can be used to achieve the goal. This paper proposes a methodology on water supply vulnerability assessment, specifically for meeting basic human needs. Based on the impacts to the five assets owned by a certain household and the causes of the lack of access, the policy intervention can be tailored made as to what problems the community faces. Hopefully the method can be used by multilateral donors or agencies and all levels of government to focus on a certain community or area that should be prioritized to meet the MDG target.
Targeted Imaging of Colonic Tumors in Smad3−/− Mice Discriminates Cancer and Inflammation
Authors: Deane Natasha G. , Manning H. Charles , Foutch A. Coe , Washington M. Kay , Aronow Bruce A. , Bornhop Darryl J. , Coffey Robert J. 
Published: April 2007

Abstract
The peripheral benzodiazepine receptor (PBR) is a trans-mitochondrial membrane protein that modulates steroid biosynthesis. Recently, up-regulation and nuclear localization of PBR has been shown to be associated with colon, prostate, and breast cancer. PBR has been targeted by the exogenous synthetic ligand, PK11195, for various purposes including imaging. To capitalize on these observations, we developed a high-throughput, noninvasive, in vivo imaging approach to detect spontaneously arising colonic tumors in mice using a novel PBR-targeted molecular imaging agent (NIR-conPK11195). NIR-conPK11195 localized and was retained in colonic adenomas and carcinomas in Smad3−/− mice but not in non-neoplastic hamartomas or chronically inflamed colonic tissue. Using a fluorescence signal-to-noise ratio of ≥4-fold 13 h after injection of the agent, we detected colonic tumors with a sensitivity of 67% and a specificity of 86% in a cohort of 37 Smad3−/− mice and control littermates. Furthermore, using oral administration of dextran sulfate to induce colonic inflammation, we showed that the clearance profile of NIR-conPK11195 distinguished transient uptake in inflammatory tissue from longer term retention in tumors. Taken together, these results indicate that NIR-conPK11195 is a promising optical molecular imaging tool to rapidly screen for colonic tumors in mice and to discriminate inflammation from cancer. (Mol Cancer Res 2007;5(4):341–9)
Loss of p53 Expression Correlates with Metastatic Phenotype and Transcriptional Profile in a New Mouse Model of Head and Neck Cancer
Authors: Ku Tony K.S. , Nguyen Dan C. , Karaman Mazen , Gill Parkash , Hacia Joseph G. , Crowe David L. 
Published: April 2007

AbstractSquamous cell carcinoma of the head and neck (HNSCC) is the sixth most frequent cancer worldwide. Because HNSCC is largely acquired by environmental carcinogen exposure rather than through germ line mutations, there are no known familial forms of the disease in humans nor are there inbred rodent strains prone to spontaneous head and neck tumors. Transgenic animals with inactivation of tumor suppressor genes commonly mutated in human cases of HNSCC provide attractive models for studying the pathogenesis of head and neck cancer. p53 is the most frequently inactivated tumor suppressor gene in HNSCC. We used a chemical induction protocol in mice heterozygous for the p53 gene to evaluate how p53 inactivation contributed to head and neck carcinogenesis the mouse model. Metastatic squamous cell carcinomas developed in 100% of animals. Histopathologically, the tumors ranged from well to poorly differentiated and showed many molecular features of human HNSCC. Mice carrying only one p53 allele developed tumors with significantly reduced latency compared with wild-type controls (average, 18 versus 22 weeks). Metastatic cancer cells showed complete loss of p53 expression when compared with primary tumors. Transcriptional profiling showed not only distinct genetic differences between primary and metastatic tumors, but also when cancers from heterozygous null and wild-type animals were compared. Our results provide novel insights into the molecular genetics of tumor progression in head and neck cancer. (Mol Cancer Res 2007;5(4):351–62)
HMGA2 Regulates Transcription of the Imp2 Gene via an Intronic Regulatory Element in Cooperation with Nuclear Factor-κB
Authors: Cleynen Isabelle , Brants Jan R. , Peeters Kristel , Deckers Rob , Debiec-Rychter Maria , Sciot Raf , Van de Ven Wim J.M. , Petit Marleen M.R. 
Published: April 2007

Abstract
IMP2 (insulin-like growth factor-II mRNA binding protein 2) is an oncofetal protein that is aberrantly expressed in several types of cancer. We recently identified the Imp2 gene as a target gene of the architectural transcription factor HMGA2 (high mobility group A2) and its tumor-specific truncated form HMGA2Tr. In this study, we investigated the mechanism via which HMGA2 regulates Imp2 gene expression. We show that HMGA2 and HMGA2Tr directly regulate transcription of the Imp2 gene by binding to an AT-rich regulatory region located in the first intron. In reporter experiments, we show that this AT-rich regulatory region mimics the response of the endogenous Imp2 gene to HMGA2 and HMGA2Tr. Furthermore, we show that a consensus nuclear factor-κB (NF-κB) binding site located immediately adjacent to the AT-rich regulatory region binds NF-κB and that NF-κB and HMGA2 cooperate to regulate Imp2 gene expression. Finally, we provide evidence that there is a strong and statistically significant correlation between HMGA2 and IMP2 gene expression in human liposarcomas. (Mol Cancer Res 2007;5(4):363–72)
Inversion Variability in the Hawaiian Trade Wind Regime
Authors: Cao Guangxia , Giambelluca Thomas W. , Stevens Duane E. , Schroeder Thomas A. 
Published: April 2007

Abstract
Using 1979–2003 radiosonde data at Hilo and Līhu‘e, Hawaii, the trade wind inversion (TWI) is found to occur approximately 82% of the time at each station, with average base heights of 2225 m (781.9 hPa) for Hilo and 2076 m (798.8 hPa) for Līhu‘e. A diurnal pattern in base height of nighttime high and afternoon low is consistently found during summer at Hilo. Inversion base height has a September maximum and a secondary maximum in April. Frequency of inversion occurrence was found to be higher during winters and lower during summers of El Niño years than non–El Niño years. Significant upward trends were found for inversion frequency at Hilo for March–May (MAM), June–August (JJA), and September–November (SON) seasons, and at Līhu‘e for all seasons and for annual values.
The Spatial and Temporal Distribution of Lightning Strikes and Their Relationship with Vegetation Type, Elevation, and Fire Scars in the Northern Territory
Authors: Kilinc Musa , Beringer Jason 
Published: April 2007

Abstract
In this paper the authors explore the spatial and temporal patterns of lightning strikes in northern Australia for the first time. In particular, the possible relationships between lightning strikes and elevation, vegetation type, and fire scars (burned areas) are examined. Lightning data provided by the Bureau of Meteorology were analyzed for a 6-yr period (1998–2003) over the northern, southern, and coastal regions of the Northern Territory (NT) through the use of Geographical Information Systems (GIS) to determine the spatial and temporal characteristics of lightning strikes. It was determined that the highest densities of lightning strikes occurred during the monsoon transitional period (dry to wet) and during the active monsoon periods, when atmospheric moisture is highest. For the period of this study, lightning was far more prevalent over the northern region (1.21 strikes per km2 yr−1) than over the southern (0.58 strikes per km2 yr−1) and coastal regions (0.71 strikes per km2 yr−1). Differences in vegetation cover were suggested to influence the lightning distribution over the northern region of the NT, but no relationship was found in the southern region. Lightning strikes in the southern region showed a positive relationship with elevations above 800 m, but no relationship was found in the northern region, which could be due to the low-lying topography of the area. A comparison of lightning densities between burned and unburned areas showed high variability; however, the authors suggest that, under ideal atmospheric conditions, large-scale fire scars (&gt;500 m) could produce lightning strikes triggered by either enhanced free convection or mesoscale circulations.
The Influence of Amazon Rainfall on the Atlantic ITCZ through Convectively Coupled Kelvin Waves
Authors: Wang Hui , Fu Rong 
Published: April 2007

Abstract
Using outgoing longwave radiation (OLR) and Tropical Rainfall Measuring Mission (TRMM) daily rain-rate data, systematic changes in intensity and location of the Atlantic intertropical convergence zone (ITCZ) were detected along the equator during boreal spring. It is found that the changes in convection over the tropical Atlantic may be induced by deep convection in equatorial South America. Lagged regression analyses demonstrate that the anomalies of convection developed over the land propagate eastward across the Atlantic and then into Africa. The eastward-propagating disturbances appear to be convectively coupled Kelvin waves with a period of 6–7.5 days and a phase speed of around 15 m s−1. These waves modulate the intensity and location of the convection in the tropical Atlantic and result in a zonal variation of the Atlantic ITCZ on synoptic time scales. The convectively coupled Kelvin wave has substantial signals in both the lower and upper troposphere. Both a reanalysis dataset and the Quick Scatterometer (QuikSCAT) ocean surface wind are used to characterize the Kelvin wave. This study suggests that synoptic-scale variation of the Atlantic ITCZ may be linked to precipitation anomalies in South America through the convectively coupled Kelvin wave. The results imply that the changes of Amazon convection could contribute to the large variability of the tropical Atlantic ITCZ observed during boreal spring.
Robust Bayesian Uncertainty Analysis of Climate System Properties Using Markov Chain Monte Carlo Methods
Authors: Tomassini Lorenzo , Reichert Peter , Knutti Reto , Stocker Thomas F. , Borsuk Mark E. 
Published: April 2007

AbstractA Bayesian uncertainty analysis of 12 parameters of the Bern2.5D climate model is presented. This includes an extensive sensitivity study with respect to the major statistical assumptions. Special attention is given to the parameter representing climate sensitivity. Using the framework of robust Bayesian analysis, the authors first define a nonparametric set of prior distributions for climate sensitivity S and then update the entire set according to Bayes’ theorem. The upper and lower probability that S lies above 4.5°C is calculated over the resulting set of posterior distributions. Furthermore, posterior distributions under different assumptions on the likelihood function are computed. The main characteristics of the marginal posterior distributions of climate sensitivity are quite robust with regard to statistical models of climate variability and observational error. However, the influence of prior assumptions on the tails of distributions is substantial considering the important political implications. Moreover, the authors find that ocean heat change data have a considerable potential to constrain climate sensitivity.
Formation Mechanism for Isopycnal Temperature–Salinity Anomalies Propagating from the Eastern South Pacific to the Equatorial Region
Authors: Nonaka Masami , Sasaki Hideharu 
Published: April 2007

Abstract
Equatorward propagation of temperature–salinity (or spiciness) anomalies on an isopycnal surface emanating from the eastern subtropical South Pacific and their formation mechanism are investigated based on a hindcast simulation with an eddy-resolving quasi-global ocean general circulation model. Because of density-compensating meridional distributions of temperature and salinity, the meridional density gradient is weak at the sea surface in the eastern subtropical South Pacific. With these mean fields, cool sea surface temperature anomalies (SSTAs) can make the outcrop line of an isopycnal surface migrate equatorward more than 5° and induce warm and salty anomalies on the isopycnal surface. Subducted warm, salty anomalies propagate to the equatorial region over approximately 5 yr and may influence equatorial isopycnal temperature–salinity anomalies. Although the associated effects are unclear, if these anomalies could further induce warm eastern equatorial SSTAs that are positively correlated with eastern South Pacific SSTAs, opposite sign temperature–salinity anomalies would be formed in the subtropical South Pacific, and a closed cycle having a decadal time scale might be induced.
Observed Relationship of Spring and Summer East Asian Rainfall with Winter and Spring Eurasian Snow
Authors: Wu Renguang , Kirtman Ben P. 
Published: April 2007

AbstractThis study investigates the relationship between spring and summer rainfall in East Asia and the preceding winter and spring snow cover/depth over Eurasia, using station rainfall observations, satellite-observed snow cover, satellite-derived snow water equivalent, and station observations of the number of days of snow cover and snow depth. Correlation analysis shows that snow-depth anomalies can persist from winter to spring whereas snow cover anomalies cannot in most regions of Eurasia. Locally, snow cover and snow-depth anomalies in February are not related in most regions to the north of 50°N, but those anomalies in April display consistent year-to-year variations. The results suggest that the winter snow cover cannot properly represent all the effects of snow and it is necessary to separate the winter and spring snow cover in addressing the snow–monsoon relationship.Spring snow cover in western Siberia is positively correlated with spring rainfall in southern China. The circulation anomalies associated with the western Siberian spring snow cover variations show an apparent wave pattern over the eastern Atlantic through Europe and midlatitude Asia. Spring snow cover over the Tibetan Plateau shows a moderate positive correlation with spring rainfall in southern China. Analysis shows that this correlation includes El Niño–Southern Oscillation (ENSO) effects. In contrast to the Indian summer monsoon rainfall for which the ENSO interferes with the snow effects, the Tibetan Plateau snow cover and ENSO work cooperatively to enhance spring rainfall anomalies in southern China. In comparison, ENSO has larger impacts than the snow on spring rainfall in southern China.
Influence of Low-Frequency Indonesian Throughflow Transport on Temperatures in the Indian Ocean in a Coupled Model*
Authors: Potemra James T. , Schneider Niklas 
Published: April 2007

Abstract
The relationship between 3- and 10-yr variability in Indian Ocean temperatures and Indonesian throughflow (ITF) volume transport is examined using results from a 300-yr integration of the coupled NCAR Parallel Climate Model (PCM). Correlation and regression analyses are used with physical reasoning to estimate the relative contributions of changes in ITF volume transport and Indian Ocean surface atmospheric forcing in determining low-frequency temperature variations in the Indian Ocean. In the PCM, low-frequency variations in ITF transport are small, 2 Sv (1 Sv ≡ 106 m3 s−1), and have a minimal impact on sea surface temperatures (SSTs). Most of the low-frequency variance in Indian Ocean temperature (rms &gt; 0.5°C) occurs in the upper thermocline (75–100 m). These variations largely reflect concurrent atmospheric forcing; ITF-induced temperature variability at this depth is limited to the outflow region between Java and Australia extending westward along a band between 10° and 15°S.