bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term follow up of esophageal varices after balloon‐occluded retrograde transvenous obliteration for gastric varices
Authors: Nakamura Shinichi , Torii Nobuyuki , Yatsuji Satoru , Konishi Hiroyuki , Kishino Maiko , Taniai Makiko , Tokushige Katsutoshi , Hashimoto Etsuko , Shiratori Keiko 
Published: November 2007

Aim:  Because the procedure of balloon‐occluded retrograde transvenous obliteration (B‐RTO) causes extensive thrombosis of the major shunt that connects the spleen and gastric/renal venous systems, an increase in portal pressure is unavoidable. The aim of the present study was to assess the long‐term outcome of B‐RTO, including changes in esophageal varices.Methods:  B‐RTO was conducted in 22 patients with gastric varices, who were divided according to the severity of esophageal varices at baseline; there were no esophageal varices (n = 7), F1 varices (n = 11), and F2 varices (n = 4). The outcome measures included the development/worsening of esophageal varices after B‐RTO and survival rates.Results:  The cumulative bleeding‐free probability for all 22 patients at 3 years after B‐RTO was 100%. The overall 3‐year survival was 94.4%. Seven patients who had no esophageal varices prior to B‐RTO did not develop any after the procedure. Seven (63.6%) of the 11 patients with stage F1 esophageal varices prior to B‐RTO showed no changes in the varices after B‐RTO, while two patients progressed to F2 varices and two developed F3 varices. The cumulative treatment‐free probability of the esophageal varices at 24 months after B‐RTO was 100% for patients without esophageal varices at baseline, 80.8% for patients with pre‐existing F1 varices, and 75% for those with pre‐existing F2 varices.Conclusion:  Although the B‐RTO procedure is considered useful for the treatment of gastric varices, changes in hemodynamics due to obliteration of this major shunt must be taken into account and observed closely.
Direct binding of ligandin to uridine 5'‐diphosphate glucuronosyltransferase 1A1
Authors: Akizawa Emi , Koiwai Kotaro , Hayano Takahide , Maezawa So , Matsushita Toyofumi , Koiwai Osamu 
Published: November 2007

Aim:  Bilirubin, a final degradation product of heme produced mainly in the spleen, is carried to the liver through its binding to albumin in the blood circulation. After its transport to hepatocytes, ligandin (glutathione S‐transferase; GST) carries bilirubin to the endoplasmic reticulum (ER). uridine 5'‐diphosphate‐glucuronosyltransferase 1A1 (UGT1A1) glucuronidates bilirubin for solubilization in the ER.Methods:  By GST pull‐down and co‐immunoprecipitation assays, GSTA2, a member of the α‐class of GST, was observed to directly bind to UGT1A1 through the region present inside the ER.Results:  GSTA2 was detected in the microsomal fraction together with the cytosolic fraction after hepatocyte fractionation.Conclusion:  These results strongly suggest that bilirubin is directly delivered to UGT1A1 from ligandin for glucuronidation.
Interrupted Time Series Analysis of Vancomycin Compared to Cefuroxime for Surgical Prophylaxis in Patients Undergoing Cardiac Surgery
Authors: Garey K. W. , Lai D. , Dao-Tran T. K. , Gentry L. O. , Hwang L. Y. , Davis B. R. 
Published: November 2007

ABSTRACT

The increased incidence of methicillin-resistant
Staphylococcus aureus
(MRSA), the emergence of community-acquired MRSA, and the continued high incidence of methicillin-resistant
Staphylococcus epidermidis
have required that certain institutions choose vancomycin for surgical prophylaxis. However, the data supporting the use of vancomycin for surgical prophylaxis are controversial. The purpose of this project was to assess the effect of the change from cefuroxime to vancomycin for surgical site infection (SSI) rates in patients undergoing coronary artery bypass graft (CABG) surgery. The monthly rates of SSIs from 2001 to 2005 were analyzed before and after a change from cefuroxime to vancomycin antibiotic prophylaxis in patients undergoing CABG by using an interrupted time series analysis. Patients who underwent cardiac valve replacement surgery and who had received vancomycin during the entire study period were used as a comparator group. A total of 6,465 patients underwent CABG surgery (
n
= 4,239) or valve replacement surgery (
n
= 2,226) during the study period. On average, the monthly SSI incidence rate in patients undergoing CABG surgery decreased by 2.1 cases per 100 surgeries after the switch from cefuroxime to vancomycin (
P
= 0.042) when patients undergoing valve replacement were used as a comparator group. The change in SSI rates was associated with a decrease in the incidence of infections caused by coagulase-negative
Staphylococcus
and MRSA isolates, with little change in the incidence of SSIs due to other gram-positive organisms or gram-negative organisms. In institutions with a high incidence of methicillin-resistant
Staphylococcus
species, this study provides evidence for the clinical efficacy of vancomycin prophylaxis for the prevention of postoperative SSIs in patients undergoing CABG surgery.
Comparative Analysis of the σB-Dependent Stress Responses inListeria monocytogenesandListeria innocuaStrains Exposed to Selected Stress Conditions
Authors: Raengpradub Sarita , Wiedmann Martin , Boor Kathryn J. 
Published: November 2007

ABSTRACTThe alternative sigma factor σBcontributes to transcription of stress response and virulence genes in diverse gram-positive bacterial species. The composition and functions of theListeria monocytogenesandListeria innocuaσBregulons were hypothesized to differ due to virulence differences between these closely related species. Transcript levels in stationary-phase cells and in cells exposed to salt stress were characterized by microarray analyses for both species. InL. monocytogenes, 168 genes were positively regulated by σB; 145 of these genes were preceded by a putative σBconsensus promoter. InL. innocua, 64 genes were positively regulated by σB. σBcontributed to acid stress survival in log-phase cells for both species but to survival in stationary-phase cells only forL. monocytogenes. In summary, (i) theL. monocytogenesσBregulon includes >140 genes that are both directly and positively regulated by σB, including genes encoding proteins with importance in stress response, virulence, transcriptional regulation, carbohydrate metabolism, and transport; (ii) a number ofL. monocytogenesgenes encoding flagellar proteins show higher transcript levels in the ΔsigBmutant, and bothL. monocytogenesandL. innocuaΔsigBnull mutants have increased motility compared to the respective isogenic parent strains, suggesting that σBaffects motility and chemotaxis; and (iii) althoughL. monocytogenesandL. innocuadiffer in σB-dependent acid stress resistance and have species-specific σB-dependent genes, theL. monocytogenesandL. innocuaσBregulons show considerable conservation, with a common set of at least 49 genes that are σBdependent in both species.
Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities
Authors: Smith Nancy R. , Kishchuk Barbara E. , Mohn William W. 
Published: November 2007

ABSTRACT

Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH
4
+
and NO
3
−
due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments.
Gamma
- and
Alphaproteobacteria
were highly characteristic of the unburned treatments, while
Betaproteobacteria
and members of
Bacillus
were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.
Production and Characterization of
Bacillus thuringiensis
Cry1Ac-Resistant Cotton Bollworm
Helicoverpa zea
(Boddie)
Authors: Anilkumar Konasale J. , Rodrigo-Simón Ana , Ferré Juan , Pusztai-Carey Marianne , Sivasupramaniam Sakuntala , Moar William J. 
Published: November 2007

ABSTRACT

Laboratory-selected
Bacillus thuringiensis
-resistant colonies are important tools for elucidating
B. thuringiensis
resistance mechanisms. However, cotton bollworm,
Helicoverpa zea
, a target pest of transgenic corn and cotton expressing
B. thuringiensis
Cry1Ac (Bt corn and cotton), has proven difficult to select for stable resistance. Two populations of
H. zea
(AR and MR), resistant to the
B. thuringiensis
protein found in all commercial Bt cotton varieties (Cry1Ac), were established by selection with Cry1Ac activated toxin (AR) or MVP II (MR). Cry1Ac toxin reflects the form ingested by
H. zea
when feeding on Bt cotton, whereas MVP II is a Cry1Ac formulation used for resistance selection and monitoring. The resistance ratio (RR) for AR exceeded 100-fold after 11 generations and has been maintained at this level for nine generations. This is the first report of stable Cry1Ac resistance in
H. zea
. MR crashed after 11 generations, reaching only an RR of 12. AR was only partially cross-resistant to MVP II, suggesting that MVP II does not have the same Cry1Ac selection pressure as Cry1Ac toxin against
H. zea
and that proteases may be involved with resistance. AR was highly cross-resistant to Cry1Ab toxin but only slightly cross-resistant to Cry1Ab expressing corn leaf powder. AR was not cross-resistant to Cry2Aa2, Cry2Ab2-expressing corn leaf powder, Vip3A, and cypermethrin. Toxin-binding assays showed no significant differences, indicating that resistance was not linked to a reduction in binding. These results aid in understanding why this pest has not evolved
B. thuringiensis
resistance, and highlight the need to choose carefully the form of
B. thuringiensis
protein used in experiments.
Degradation of Bis(4-Hydroxyphenyl)Methane (Bisphenol F) by
Sphingobium yanoikuyae
Strain FM-2 Isolated from River Water
Authors: Inoue Daisuke , Hara Shoji , Kashihara Mari , Murai Yusaku , Danzl Erica , Sei Kazunari , Tsunoi Shinji , Fujita Masanori , Ike Michihiko 
Published: November 2007

ABSTRACT

Three bacteria capable of utilizing bis(4-hydroxyphenyl)methane (bisphenol F [BPF]) as the sole carbon source were isolated from river water, and they all belonged to the family
Sphingomonadaceae
. One of the isolates, designated
Sphingobium yanoikuyae
strain FM-2, at an initial cell density of 0.01 (optical density at 600 nm) completely degraded 0.5 mM BPF within 9 h without any lag period under inductive conditions. Degradation assays of various bisphenols revealed that the BPF-metabolizing system of strain FM-2 was effective only on the limited range of bisphenols consisting of two phenolic rings joined together through a bridging carbon without any methyl substitution on the rings or on the bridging structure. A BPF biodegradation pathway was proposed on the basis of metabolite production patterns and identification of the metabolites. The initial step of BPF biodegradation involves hydroxylation of the bridging carbon to form bis(4-hydroxyphenyl)methanol, followed by oxidation to 4,4′-dihydroxybenzophenone. The 4,4′-dihydroxybenzophenone appears to be further oxidized by the Baeyer-Villiger reaction to 4-hydroxyphenyl 4-hydroxybenzoate, which is then cleaved by oxidation to form 4-hydroxybenzoate and 1,4-hydroquinone. Both of the resultant simple aromatic compounds are mineralized.
Evaluation of
Escherichia coli
Host Strain CB390 for Simultaneous Detection of Somatic and F-Specific Coliphages
Authors: Guzmán Carolina , Mocé-Llivina Laura , Lucena Francisco , Jofre Juan 
Published: November 2007

ABSTRACT

Escherichia coli
WG5, the strain recommended by the International Organization for Standardization (ISO) to detect somatic coliphages, was transformed to F
+
by introducing the plasmid Famp, which rendered it capable of simultaneously detecting both somatic and F-specific coliphages. Indeed, this strain, CB390, proved as effective in detecting similar numbers of phages as the sum of somatic and F-specific bacteriophages detected by the host strains recommended by both the ISO and the U.S. Environmental Protection Agency standardized methods.
Methyl Sulfide Production by a Novel Carbon Monoxide Metabolism inMethanosarcina acetivorans
Authors: Moran James J. , House Christopher H. , Vrentas Jennifer M. , Freeman Katherine H. 
Published: November 2007

ABSTRACTWe observed dimethyl sulfide and methanthiol production in pure incubations of the methanogenMethanosarcina acetivoranswhen carbon monoxide (CO) served as the only electron donor. Energy conservation likely uses sodium ion gradients for ATP synthesis. This novel metabolism permits utilization of CO by the methanogen, resulting in quantitative sulfide methylation.
The Cytochrome P450 Lanosterol 14α-Demethylase Gene Is a Demethylation Inhibitor Fungicide Resistance Determinant in
Monilinia fructicola
Field Isolates from Georgia
Authors: Luo Chao-Xi , Schnabel Guido 
Published: November 2007

ABSTRACT

Resistance in
Monilinia fructicola
to demethylation inhibitor (DMI) fungicides is beginning to emerge in North America, but its molecular basis is unknown. Two potential genetic determinants of DMI fungicide resistance including the 14α-demethylase gene (Mf
CYP51
) and the ATP-binding cassette transporter gene Mf
ABC1
, were investigated in six resistant (DMI-R) and six sensitive (DMI-S) field isolates. No point mutations leading to an amino acid change were found in the Mf
CYP51
gene. The constitutive expression of the Mf
CYP51
gene in DMI-R isolates was significantly higher compared to DMI-S isolates. Gene expression was not induced in mycelium of DMI-R or DMI-S isolates treated with 0.3 μg of propiconazole/ml. A slightly higher average Mf
CYP51
copy number value was detected in DMI-R isolates (1.35) compared to DMI-S isolates (1.13); however, this difference could not be verified in Southern hybridization experiments or explain the up to 11-fold-increased Mf
CYP51
mRNA levels in DMI-R isolates. Analysis of the upstream nucleotide sequence of the Mf
CYP51
gene revealed a unique 65-bp repetitive element at base pair position −117 from the translational start site in DMI-R isolates but not in DMI-S isolates. This repetitive element contained a putative promoter and was named Mona. The link between Mona and the DMI resistance phenotype became even more apparent after studying the genetic diversity between the isolates. In contrast to DMI-S isolates, DMI-R isolates contained an Mf
CYP51
gene of identical nucleotide sequence associated with Mona. Still, DMI-R isolates were not genetically identical as revealed by Microsatellite-PCR analysis. Also, real-time PCR analysis of genomic DNA indicated that the relative copy number of Mona among DMI-S and DMI-R isolates varied, suggesting its potential for mobility. Interestingly, constitutive expression of the Mf
ABC1
gene in DMI-R isolates was slightly lower than that of DMI-S isolates, but expression of the Mf
ABC1
gene in DMI-R isolates was induced in mycelium after propiconazole treatment. Therefore, the Mf
ABC1
gene may play a minor role in DMI fungicide resistance in
M. fructicola
. Our results strongly suggest that overexpression of the Mf
CYP51
gene is an important mechanism in conferring DMI fungicide resistance in
M. fructicola
field isolates from Georgia and that this overexpression is correlated with Mona located upstream of the Mf
CYP51
gene.
Protein Kinases Involved in Mating and Osmotic Stress in the Yeast
Kluyveromyces lactis
Authors: Kawasaki Laura , Castañeda-Bueno María , Sánchez-Paredes Edith , Velázquez-Zavala Nancy , Torres-Quiroz Francisco , Ongay-Larios Laura , Coria Roberto 
Published: November 2007

ABSTRACT

Systematic disruption of genes encoding kinases and mitogen-activated protein kinases (MAPKs) was performed in
Kluyveromyces lactis
haploid cells. The mutated strains were assayed by their capacity to mate and to respond to hyperosmotic stress. The
K. lactis
Ste11p (KlSte11p) MAPK kinase kinase (MAPKKK) was found to act in both mating and osmoresponse pathways while the scaffold KlSte5p and the MAPK KlFus3p appeared to be specific for mating. The p21-activated kinase KlSte20p and the kinase KlSte50p participated in both pathways. Protein association experiments showed interaction of KlSte50p and KlSte20p with Gα and Gβ, respectively, the G protein subunits involved in the mating pathway. Both KlSte50p and KlSte20p also showed interaction with KlSte11p. Disruption mutants of the
K. lactis PBS2
(Kl
PBS2
) and Kl
HOG1
genes of the canonical osmotic response pathway resulted in mutations sensitive to high salt and high sorbitol but dispensable for mating. Mutations that eliminate the MAPKK KlSte7p activity had a strong effect on mating and also showed sensitivity to osmotic stress. Finally, we found evidence of physical interaction between KlSte7p and KlHog1p, in addition to diminished Hog1p phosphorylation after a hyperosmotic shock in cells lacking KlSte7p. This study reveals novel roles for components of transduction systems in yeast.
Fitting Periplasmic Membrane Fusion Proteins to Inner Membrane Transporters: Mutations That Enable
Escherichia coli
AcrA To Function with
Pseudomonas aeruginosa
MexB
Authors: Krishnamoorthy Ganesh , Tikhonova Elena B. , Zgurskaya Helen I. 
Published: November 2007

ABSTRACT

AcrAB-TolC from
Escherichia coli
is a multidrug efflux complex capable of transenvelope transport. In this complex, AcrA is a periplasmic membrane fusion protein that establishes a functional connection between the inner membrane transporter AcrB of the RND superfamily and the outer membrane channel TolC. To gain insight into the mechanism of the functional association between components of this complex, we replaced AcrB with its close homolog MexB from
Pseudomonas aeruginosa
. Surprisingly, we found that AcrA is promiscuous and can form a partially functional complex with MexB and TolC. The chimeric AcrA-MexB-TolC complex protected cells from sodium dodecyl sulfate, novobiocin, and ethidium bromide but failed with other known substrates of MexB. We next identified single and double mutations in AcrA and MexB that enabled the complete functional fit between AcrA, MexB, and TolC. Mutations in either the α-helical hairpin of AcrA making contact with TolC or the β-barrel domain lying on MexB improved the functional alignment between components of the complex. Our results suggest that three components of multidrug efflux pumps do not associate in an “all-or-nothing” fashion but accommodate a certain degree of flexibility. This flexibility in the association between components affects the transport efficiency of RND pumps.
Effects of Glycosylation on Swimming Ability and Flagellar Polymorphic Transformation in
Pseudomonas syringae
pv. tabaci 6605
Authors: Taguchi Fumiko , Shibata Satoshi , Suzuki Tomoko , Ogawa Yujiro , Aizawa Shin-Ichi , Takeuchi Kasumi , Ichinose Yuki 
Published: November 2007

ABSTRACT

The role of flagellin glycosylation on motility was investigated in
Pseudomonas syringae
pv. tabaci. The swimming activity of glycosylation-defective mutants was prominently decreased in a highly viscous medium. The mutants showed differences in polymorphic transitions and in the bundle formation of flagella, indicating that glycosylation stabilizes the filament structure and lubricates the rotation of the bundle.
Identification and Characterization of Two Novel Methyltransferase Genes That Determine the Serotype 12-Specific Structure of Glycopeptidolipids of
Mycobacterium intracellulare
Authors: Nakata Noboru , Fujiwara Nagatoshi , Naka Takashi , Yano Ikuya , Kobayashi Kazuo , Maeda Shinji 
Published: November 2007

ABSTRACT

The
Mycobacterium avium
complex is distributed ubiquitously in the environment. It is an important cause of pulmonary and extrapulmonary diseases in humans and animals. The species in this complex produce polar glycopeptidolipids (GPLs); of particular interest is their serotype-specific antigenicity. Several reports have described that GPL structure may play an important role in bacterial physiology and pathogenesis and in the host immune response. Recently, we determined the complete structure of the GPL derived from
Mycobacterium intracellulare
serotype 7 and characterized the serotype 7 GPL-specific gene cluster. The structure of serotype 7 GPL closely resembles that of serotype 12 GPL, except for O methylation. In the present study, we isolated and characterized the serotype 12-specific gene cluster involved in glycosylation of the GPL. Ten open reading frames (ORFs) and one pseudogene were observed in the cluster. The genetic organization of the serotype 12-specific gene cluster resembles that of the serotype 7-specific gene cluster, but two novel ORFs (
orfA
and
orfB
) encoding putative methyltransferases are present in the cluster. Functional analyses revealed that
orfA
and
orfB
encode methyltransferases that synthesize
O
-methyl groups at the C-4 position in the rhamnose residue next to the terminal hexose and at the C-3 position in the terminal hexose, respectively. Our results show that these two methyltransferase genes determine the structural difference of serotype 12-specific GPL from serotype 7-specific GPL.
PhyR Is Involved in the General Stress Response ofMethylobacterium extorquensAM1
Authors: Gourion Benjamin , Francez-Charlot Anne , Vorholt Julia A. 
Published: November 2007

ABSTRACTPhyR represents a novel alphaproteobacterial family of response regulators having a structure consisting of two domains; a predicted amino-terminal extracytoplasmic function (ECF) sigma factor-like domain and a carboxy-terminal receiver domain. PhyR was first described inMethylobacterium extorquensAM1, in which it has been shown to be essential for plant colonization, probably due to its suggested involvement in the regulation of a number of stress proteins. Here we investigated the PhyR regulon using microarray technology. We found that the PhyR regulon is rather large and that most of the 246 targets are under positive control. Mapping of transcriptional start sites revealed candidate promoters for PhyR-mediated regulation. One of these promoters, an ECF-type promoter, was identified upstream of one-third of the target genes by in silico analysis. Among the PhyR targets are genes predicted to be involved in multiple stress responses, includingkatE,osmC,htrA,dnaK,gloA,dps, anduvrA. The induction of these genes is consistent with our phenotypic analyses which revealed that PhyR is involved in resistance to heat shock and desiccation, as well as oxidative, UV, ethanol, and osmotic stresses, inM. extorquensAM1. The finding that PhyR is involved in the general stress response was further substantiated by the finding that carbon starvation induces protection against heat shock and that this protection is at least in part dependent on PhyR.