bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization and PprB-Dependent Control of the
Pseudomonas aeruginosa tad
Locus, Involved in Flp Pilus Biology
Authors: Bernard Christophe S. , Bordi Christophe , Termine Elise , Filloux Alain , de Bentzmann Sophie 
Published: January 2009

ABSTRACT

Bacterial attachment to the substratum involves several cell surface organelles, including various types of pili. The
Pseudomonas aeruginosa
Tad machine assembles type IVb pili, which are required for adhesion to abiotic surfaces and to eukaryotic cells. Type IVb pili consist of a major subunit, the Flp pilin, processed by the FppA prepilin peptidase. In this study, we investigated the regulatory mechanism of the
tad
locus. We showed that the
flp
gene is expressed late in the stationary growth phase in aerobic conditions. We also showed that the
tad
locus was composed of five independent transcriptional units. We used transcriptional fusions to show that
tad
gene expression was positively controlled by the PprB response regulator. We subsequently showed that PprB bound to the promoter regions, directly controlling the expression of these genes. We then evaluated the contribution of two genes,
tadF
and
rcpC
, to type IVb pilus assembly. The deletion of these two genes had no effect on Flp production, pilus assembly, or Flp-mediated adhesion to abiotic surfaces in our conditions. However, our results suggest that the putative RcpC protein modifies the Flp pilin, thereby promoting Flp-dependent adhesion to eukaryotic cells.
Genetics and Proteomics of
Aeromonas salmonicida
Lipopolysaccharide Core Biosynthesis
Authors: Jimenez Natalia , Lacasta Anna , Vilches Silvia , Reyes Mercé , Vazquez Judit , Aquillini Eleonora , Merino Susana , Regué Miguel , Tomás Juan M. 
Published: January 2009

ABSTRACT

Comparison between the lipopolysaccharide (LPS) core structures of
Aeromonas salmonicida
subsp.
salmonicida
A450 and
Aeromonas hydrophila
AH-3 shows great similarity in the inner LPS core and part of the outer LPS core but some differences in the distal part of the outer LPS core (residues
ld
-Hep,
d
-Gal, and
d
-GalNAc). The three genomic regions encoding LPS core biosynthetic genes in
A. salmonicida
A450, of which regions 2 and 3 have genes identical to those of
A. hydrophila
AH-3, were fully sequenced.
A. salmonicida
A450 region 1 showed seven genes: three identical to those of
A. hydrophila
AH-3, three similar but not identical to those of
A. hydrophila
AH-3, and one without any homology to any well-characterized gene.
A. salmonicida
A450 mutants with alterations in the genes that were not identical to those of
A. hydrophila
AH-3 were constructed, and their LPS core structures were fully elucidated. At the same time, all the
A. salmonicida
A450 genes identical to those of
A. hydrophila
AH-3 were used to complement the previously obtained
A. hydrophila
AH-3 mutants for each of these genes. Combining the gene sequence and complementation test data with the structural data and phenotypic characterization of the mutant LPSs enabled a presumptive assignment of all LPS core biosynthesis gene functions in
A. salmonicida
A450. Furthermore, hybridization studies with internal probes for the
A. salmonicida
-specific genes using different
A
.
salmonicida
strains (strains of different subspecies or atypical strains) showed a unique or prevalent LPS core type, which is the one fully characterized for
A. salmonicida
A450.
A DNase Encoded by Integrated Element CJIE1 Inhibits Natural Transformation of
Campylobacter jejuni
Authors: Gaasbeek Esther J. , Wagenaar Jaap A. , Guilhabert Magalie R. , Wösten Marc M. S. M. , van Putten Jos P. M. , van der Graaf-van Bloois Linda , Parker Craig T. , van der Wal Fimme J. 
Published: January 2009

ABSTRACT

The species
Campylobacter jejuni
is considered naturally competent for DNA uptake and displays strong genetic diversity. Nevertheless, nonnaturally transformable strains and several relatively stable clonal lineages exist. In the present study, the molecular mechanism responsible for the nonnatural transformability of a subset of
C. jejuni
strains was investigated. Comparative genome hybridization indicated that
C. jejuni
Mu-like prophage integrated element 1 (CJIE1) was more abundant in nonnaturally transformable
C. jejuni
strains than in naturally transformable strains. Analysis of CJIE1 indicated the presence of
dns
(CJE0256), which is annotated as a gene encoding an extracellular DNase. DNase assays using a defined
dns
mutant and a
dns
-negative strain expressing Dns from a plasmid indicated that Dns is an endogenous DNase. The DNA-hydrolyzing activity directly correlated with the natural transformability of the knockout mutant and the
dns
-negative strain expressing Dns from a plasmid. Analysis of a broader set of strains indicated that the majority of nonnaturally transformable strains expressed DNase activity, while all naturally competent strains lacked this activity. The inhibition of natural transformation in
C. jejuni
via endogenous DNase activity may contribute to the formation of stable lineages in the
C. jejuni
population.
Comparative Structural and Molecular Characterization of Ribitol-5-Phosphate-Containing
Streptococcus oralis
Coaggregation Receptor Polysaccharides
Authors: Yang Jinghua , Ritchey Mary , Yoshida Yasuo , Bush C. Allen , Cisar John O. 
Published: January 2009

ABSTRACT

The antigenically related coaggregation receptor polysaccharides (RPS) of
Streptococcus oralis
strains C104 and SK144 mediate recognition of these bacteria by other members of the dental plaque biofilm community. In the present study, the structure of strain SK144 RPS was established by high resolution NMR spectroscopy as [6Gal
f
β1-6GalNAcβ1-3Galα1-2ribitol-5-PO
4
−
-6Gal
f
β1-3Galβ1]
n
, thereby indicating that this polysaccharide and the previously characterized RPS of strain C104 are identical, except for the linkage between Gal and ribitol-5-phosphate, which is α1-2 in strain SK144 versus α1-1 in strain C104. Studies to define the molecular basis of RPS structure revealed comparable genes for six putative transferases and a polymerase in the
rps
loci of these streptococci. Cell surface RPS production was abolished by disrupting the gene for the first transferase of strain C104 with a nonpolar
erm
cassette. It was restored in the resulting mutant by plasmid-based expression of either
wcjG
, the corresponding gene of
S. pneumoniae
for serotype 10A capsular polysaccharide (CPS) biosynthesis or
wbaP
for the transferase of
Salmonella enterica
that initiates O-polysaccharide biosynthesis. Thus, WcjG, like WbaP, appears to initiate polysaccharide biosynthesis by transferring galactose-1-phosphate to a lipid carrier. In further studies, the structure of strain C104 RPS was converted to that of strain SK144 by replacing the gene (
wefM
) for the fourth transferase in the
rps
locus of strain C104 with the corresponding gene (
wcrC
) of strain SK144 or
Streptococcus pneumoniae
serotype 10A. These findings identify genetic markers for the different ribitol-5-phosphate-containing types of RPS present in
S. oralis
and establish a close relationship between these polysaccharides and serogroup 10 CPSs of
S. pneumoniae
.
Seawater-Regulated Genes for Two-Component Systems and Outer Membrane Proteins in
Myxococcus
Authors: Pan Hong-wei , Liu Hong , Liu Ting , Li Cheng-yun , Li Zhi-feng , Cai Ke , Zhang Cui-ying , Zhang Yong , Hu Wei , Wu Zhi-hong , Li Yue-zhong 
Published: January 2009

ABSTRACT

When salt-tolerant
Myxococcus
cells are moved to a seawater environment, they change their growth, morphology, and developmental behavior. Outer membrane proteins and signal transduction pathways may play important roles in this shift. Chip hybridization targeting the genes predicted to encode 226 two-component signal transduction pathways and 74 outer membrane proteins of
M. xanthus
DK1622 revealed that the expression of 55 corresponding genes in the salt-tolerant strain
M. fulvus
HW-1 was significantly modified (most were downregulated) by the presence of seawater. Sequencing revealed that these seawater-regulated genes are highly homologous in both strains, suggesting that they have similar roles in the lifestyle of
Myxococcus
. Seven of the genes that had been reported in
M. xanthus
DK1622 are involved in different cellular processes, such as fruiting body development, sporulation, or motility. The outer membrane (Om) gene Om031 had the most significant change in expression (downregulated) in response to seawater, while the two-component system (Tc) gene Tc105 had the greatest increase in expression. Their homologues MXAN3106 and MXAN4042 were knocked out in DK1622 to analyze their functions in response to changes in salinity. In addition to having increased salt tolerance, sporulation of the MXAN3106 mutant was enhanced compared to that of DK1622, whereas mutating gene MXAN4042 produced contrary results. The results indicated that the genes that are involved in the cellular processes that are significantly changed in response to salinity may also be involved the salt tolerance of
Myxococcus
cells. Regulating the expression levels of these multifunctional genes may allow cells to quickly and efficiently respond to changing conditions in coastal environments.
Differential Binding Profiles of StpA in Wild-Type and
hns
Mutant Cells: a Comparative Analysis of Cooperative Partners by Chromatin Immunoprecipitation-Microarray Analysis
Authors: Uyar Ebru , Kurokawa Ken , Yoshimura Mika , Ishikawa Shu , Ogasawara Naotake , Oshima Taku 
Published: January 2009

ABSTRACT

We performed chromatin immunoprecipitation-microarray analysis to investigate differences in function between StpA and H-NS in
Escherichia coli
cells. StpA binding regions essentially overlap those of H-NS in wild-type cells, while they are reduced to one-third in the
hns
mutant. The H-NS binding profile was unaffected by
stpA
inactivation.
The NS4A Protein of Hepatitis C Virus Promotes RNA-Coupled ATP Hydrolysis by the NS3 Helicase
Authors: Beran Rudolf K. F. , Lindenbach Brett D. , Pyle Anna Marie 
Published: January 2009

ABSTRACT
Nonstructural protein 3 (NS3) is an essential replicative component of the hepatitis C virus (HCV) and a member of the DExH/D-box family of proteins. The C-terminal region of NS3 (NS3hel) exhibits RNA-stimulated NTPase and helicase activity, while the N-terminal serine protease domain of NS3 enhances RNA binding and unwinding by NS3hel. The nonstructural protein 4A (NS4A) binds to the NS3 protease domain and serves as an obligate cofactor for NS3 serine protease activity. Given its role in stimulating protease activity, we sought to determine whether NS4A also influences the activity of NS3hel. Here we show that NS4A enhances the ability of NS3hel to bind RNA in the presence of ATP, thereby acting as a cofactor for helicase activity. This effect is mediated by amino acids in the C-terminal acidic domain of NS4A. When these residues are mutated, one observes drastic reductions in ATP-coupled RNA binding and duplex unwinding by NS3. These same mutations are lethal in HCV replicons, thereby establishing in vitro and in vivo that NS4A plays an important role in the helicase mechanism of NS3 and its function in replication.
Distribution, host preference, and impact of parasitic mistletoes (Loranthaceae) in young eucalypt plantations in New South Wales, AustraliaThis article is one of a collection of papers based on a presentation from the Stem and Shoot Fungal Pathogens and Parasitic Plants: the Values of Biological Diversity session of the XXII International Union of Forestry Research Organization World Congress meeting held in Brisbane, Queensland, Australia, in 2005.
Authors: Carnegie Angus J. , Bi Huiquan , Arnold Scott , Li Yun , Binns Doug 
Published: January 2009

Mistletoe is a common sight in mature eucalypt trees in Australia, especially in remnant stands in agricultural and pastoral areas, where they have been associated with debility and death. We surveyed over 450 eucalypt plantations in New South Wales, Australia, for mistletoe, and report for the first time that mistletoe infestation is becoming a problem in young eucalypt plantations. Forty-three plantations were infected, but only 9 of these had levels of mistletoe of 20% or more trees infected; 4 had levels of 38%, 40%, 65%, and 68%. Mistletoe was observed in plantations ranging in age from 3–10 years old. Species of Corymbia ( Corymbia maculata (Hook.) K.D. Hill & L.A.S. Johnson and Corymbia citriodora subsp. variegata (F. Muell.) K.D. Hill & L.A.S. Johnson) were the most susceptible to mistletoe. The mistletoe species Dendrophthoe vitellina (F. Muell.) Tiegh. was commonly observed in plantations in both lower and upper northeast New South Wales, while Amyema bifurcata (Benth.) Tiegh. was only observed in the upper northeast. We observed a significant impact on growth of mistletoe, affecting tree growth as young as four years old. Simulated analysis indicated that mistletoe infection can reduce stand basal area by 10% and stand volume by 13%. However, the impact of mistletoe on tree growth was variable across space and time.
Association between polymorphisms in the β2-adrenergic receptor gene with myocardial infarction and ischaemic stroke in women
Authors: Kurth Tobias , Ridker Paul , Buring Julie , Zee Robert , Schürks Markus 
Published: January 2009

SummaryResults from studies investigating the association between polymorphisms in the β2-adrenergic receptor gene (ADRB2) and cardiovascular disease (CVD) are controversial. Using haplo-type-based analysis, we have previously shown a protective effect of the Gly16-Gln27-Ile164 haplotype on myocardial infarction in men. We sought to replicate these findings in women and further investigated whether the gene variants exert differential effects on myocardial infarction and ischaemic stroke. We performed a prospective study among 25,224 women, participating in the Women’s Health Study and free of CVD at study entry. We had information on polymorphisms Gly16Arg, Gln27Glu, and Thr164Ile in the ADRB2. Incident CVD was self-reported and confirmed after medical record review. We used proportional hazards models to investigate the association between genotypes and haplotypes with any myocardial infarction, any ischaemic stroke, and CVD death. During a mean of 11.8 years of follow-up, 274 myocardial infarctions, 299 ischaemic strokes, and 159 CVD deaths occurred. Among the whole cohort genotypeand haplotype-based analyses did not show an association for any of the gene variants with any of the CVD outcomes. When we focused on Caucasian women, the haplotype-based analysis, however, suggested an inverse association of the haplotype Gly16-Gln27-Thr164 with incident myocardial infarction (multivariable-adjusted hazard ratio 0.75; 95% confidence interval 0.58–0.97; p=0.03). We did not find associations in the haplo-type-based analyses with incident ischaemic stroke or CVD death. Our results suggest that the haplotype Gly16-Gln27-Thr164 is associated with reduced risk of incident myocardial infarction but not ischaemic stroke in Caucasian women and suggest differential pathophysiologies for myocardial infarction and stroke.
Association study between variants in the fibrinogen gene cluster, fibrinogen levels and hypertension: Results from the MONICA/ KORA study
Authors: Kolz Melanie , Baumert Jens , Gohlke Henning , Grallert Harald , Döring Angela , Peters Annette , Wichmann Erich , Illig Thomas , Koenig Wolfgang 
Published: January 2009

SummaryPrevious studies reported a gender-specific association between plasma fibrinogen concentrations and incident hypertension. We systematically analysed polymorphisms and haplotypes across the fibrinogen gene cluster with fibrinogen levels and assessed their contribution to prevalent hypertension in 2,200 men and 2,159 women from the population-based MONICA/KORA Augsburg study. Eleven tagging single nucleotide polymorphisms (SNPs) were systematically selected in the three fibrinogen genes and haplotypes were reconstructed. The minor alleles of two SNPs, rs2227401 (FGB) and rs2070016 (FGA) and the haplotypes tagged by those variants, were significantly associated with higher fibrinogen concentrations in both, men and women, explaining 1% of the total variance of fibrinogen concentrations. In addition, a FGG haplotype, tagged by rs1049636, was associated with lower concentrations of fibrinogen in women, but not in men. Regarding hypertension, we detected a significant association with a FGA promoter variant (rs2070008) in women only, whereas fibrinogen haplotypes were not associated with hyper-tension after correction for multiple comparisons in either men or women. In conclusion, our results suggest that variants in all three fibrinogen genes are significantly associated with differences in fibrinogen concentrations with modest contribution to phenotypic variance. It is likely that other genetic variants outside the fibrinogen gene loci are involved in the regulation of fibrinogen concentrations. In addition, one FGA promoter variant was significantly associated with hypertension in women. Confirmation of these findings by future studies is warranted.
The Dead Sea Scrolls and Violence: Sectarian Formation and Eschatological Imagination
Authors: Jassen Alex 
Published: January 2009

AbstractThis article analyzes two interconnected narratives of violence in the Dead Sea Scrolls by drawing upon some recent treatments of religious violence employing social-scientific approaches—in particular, the "scarce resources" theory—and more general sociological approaches to sectarianism. The first narrative of violence revolves around the origins of the community's violent worldview as embodied in its debates with its opponents. Early sectarian literature represents sectarian debates and polemics in terms of an exclusive understanding of the meaning of Scripture, the application of ritual and cultic law, and the identity of God's elect. These aspects become focal points of ideological debate as the community attempted to convince the "outsiders" of the correctness of the sectarian way. By tracing the development of these debates in sectarian literature, however, I reveal how they are transformed from innocuous elements of disagreement into focal points for the emergence of violence as a central preoccupation of the Qumran community. The "scarce resources" theory explains why these specific points of disagreement become infused with violence. The second narrative of violence involves the continued appearance of these debates within the community's eschatological literature as a rhetorical device to legitimize its violent expectations. Unlike related groups in Second Temple Judaism (e.g., the Zealots), for the Qumran community, violence outside of the framework of the eschatological battle is not legitimized and presumably did not exist. By delaying all punishment until the eschaton, the community simultaneously defused its own violent worldview. The simultaneous infusion and defusion of violence is explained in the context of the sectarian structure of the community.
Verification with Variograms
Authors: Marzban Caren , Sandgathe Scott 
Published: January 2009

Abstract
The verification of a gridded forecast field, for example, one produced by numerical weather prediction (NWP) models, cannot be performed on a gridpoint-by-gridpoint basis; that type of approach would ignore the spatial structures present in both forecast and observation fields, leading to misinformative or noninformative verification results. A variety of methods have been proposed to acknowledge the spatial structure of the fields. Here, a method is examined that compares the two fields in terms of their variograms. Two types of variograms are examined: one examines correlation on different spatial scales and is a measure of texture; the other type of variogram is additionally sensitive to the size and location of objects in a field and can assess size and location errors. Using these variograms, the forecasts of three NWP model formulations are compared with observations/analysis, on a dataset consisting of 30 days in spring 2005. It is found that within statistical uncertainty the three formulations are comparable with one another in terms of forecasting the spatial structure of observed reflectivity fields. None, however, produce the observed structure across all scales, and all tend to overforecast the spatial extent and also forecast a smoother precipitation (reflectivity) field. A finer comparison suggests that the University of Oklahoma 2-km resolution Advanced Research Weather Research and Forecasting (WRF-ARW) model and the National Center for Atmospheric Research (NCAR) 4-km resolution WRF-ARW slightly outperform the 4.5-km WRF-Nonhydrostatic Mesoscale Model (NMM), developed by the National Oceanic and Atmospheric Administration/National Centers for Environmental Prediction (NOAA/NCEP), in terms of producing forecasts whose spatial structures are closer to that of the observed field.
Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi
Authors: Lewis Samantha C , Dyal Leslie A , Hilburn Caroline F , Weitz Stephanie , Liau Wei-Siang , LaMunyon Craig W , Denver Dee R 
Published: January 2009

Abstract

Background
As exemplified by the famously successful model organism Caenorhabditis elegans, nematodes offer outstanding animal systems for investigating diverse biological phenomena due to their small genome sizes, short generation times and ease of laboratory maintenance. Nematodes in the genus Panagrolaimus have served in comparative development and anhydrobiosis studies, and the Antarctic species P. davidi offers a powerful paradigm for understanding the biological mechanisms of extreme cold tolerance. Panagrolaimus nematodes are also unique in that examples of gonochoristic, hermaphroditic and parthenogenetic reproductive modes have been reported for members of this genus. The evolutionary origins of these varying reproductive modes and the Antarctic species P. davidi, however, remain enigmatic.

Results
We collected nuclear ribosomal RNA gene and mitochondrial protein-coding gene sequences from diverse Panagrolaimus species and strains, including newly discovered isolates from Oregon, to investigate phylogenetic relationships in this nematode genus. Nuclear phylogenies showed that the species and strains historically identified as members of Panagrolaimus constitute a paraphyletic group, suggesting that taxonomic revision is required for Panagrolaimus and related nematode lineages. Strain-specific reproductive modes were mapped onto the molecular phylogeny to show a single origin of parthenogenesis from a presumably gonochoristic ancestor. The hermaphroditic strains were all placed outside a major monophyletic clade that contained the majority of other Panagrolaimus nematodes. Phylogenetic analyses of mitochondrial sequences showed that substantial molecular and geographic diversity exists within the clade of parthenogenetic strains. The Antarctic species P. davidi was found to be very closely related to two Panagrolaimus strains from southern California. Phylogenetic and molecular clock analyses suggested that P. davidi and the California strain PS1579 shared a common ancestor in the very recent evolutionary past.

Conclusion
Our study provides a phylogenetic framework for understanding the evolutionary origins and diversification patterns of varying reproductive modes within Panagrolaimus and important insights into the origin of the Antarctic species P. davidi. Panagrolaimus offers a powerful nematode model for understanding diverse evolutionary phenomena including the evolution of asexuality and the adaptive evolution of extreme cold tolerance.