bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Insertion Sequence- and Transposon-Mediated Genetic Rearrangements in Genomic Island SGI1 ofSalmonella entericaSerovar Kentucky
Authors: Doublet Benoît , Praud Karine , Bertrand Sophie , Collard Jean-Marc , Weill François-Xavier , Cloeckaert Axel 
Published: August 2008

ABSTRACTSalmonellagenomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemicSalmonella entericaserovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in severalS. entericaserovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array,aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of themermodule similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721containing the tetracycline resistance genestetRandtet(A); (ii) part of Tn5393containing the streptomycin resistance genesstrAB, IS1133, and a truncatedtnpRgene; and (iii) a Tn3-like region containing thetnpRgene and the β-lactamaseblaTEM-1gene flanked by two IS26elements in opposite orientations. The rightmost IS26element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the β-lactamaseblaTEM-1gene flanked by the two IS26elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes.
Penetration of Chlorhexidine into Human Skin
Authors: Karpanen T. J. , Worthington T. , Conway B. R. , Hilton A. C. , Elliott T. S. J. , Lambert P. A. 
Published: August 2008

ABSTRACT
This study evaluated a model of skin permeation to determine the depth of delivery of chlorhexidine into full-thickness excised human skin following topical application of 2% (wt/vol) aqueous chlorhexidine digluconate. Skin permeation studies were performed on full-thickness human skin using Franz diffusion cells with exposure to chlorhexidine for 2 min, 30 min, and 24 h. The concentration of chlorhexidine extracted from skin sections was determined to a depth of 1,500 μm following serial sectioning of the skin using a microtome and analysis by high-performance liquid chromatography. Poor penetration of chlorhexidine into skin following 2-min and 30-min exposures to chlorhexidine was observed (0.157 ± 0.047 and 0.077 ± 0.015 μg/mg tissue within the top 100 μm), and levels of chlorhexidine were minimal at deeper skin depths (less than 0.002 μg/mg tissue below 300 μm). After 24 h of exposure, there was more chlorhexidine within the upper 100-μm sections (7.88 ± 1.37 μg/mg tissue); however, the levels remained low (less than 1 μg/mg tissue) at depths below 300 μm. There was no detectable penetration through the full-thickness skin. The model presented in this study can be used to assess the permeation of antiseptic agents through various layers of skin in vitro. Aqueous chlorhexidine demonstrated poor permeation into the deeper layers of the skin, which may restrict the efficacy of skin antisepsis with this agent. This study lays the foundation for further research in adopting alternative strategies for enhanced skin antisepsis in clinical practice.
Antiviral Effects of Lamivudine, Emtricitabine, Adefovir Dipivoxil, and Tenofovir Disoproxil Fumarate Administered Orally Alone and in Combination to Woodchucks with Chronic Woodchuck Hepatitis Virus Infection
Authors: Menne Stephan , Butler Scott D. , George Andrea L. , Tochkov Ilia A. , Zhu Yuao , Xiong Shelly , Gerin John L. , Cote Paul J. , Tennant Bud C. 
Published: August 2008

ABSTRACTAdefovir dipivoxil (ADV) and tenofovir disoproxil fumarate (TDF) are nucleotide analogs that inhibit the replication of wild-type hepatitis B virus (HBV) and lamivudine (3TC)-resistant virus in HBV-infected patients, including those who are coinfected with human immunodeficiency virus. The combination of ADV or TDF with other nucleoside analogs is a proposed strategy for managing antiviral drug resistance during the treatment of chronic HBV infection. The antiviral effect of oral ADV or TDF, alone or in combination with 3TC or emtricitabine (FTC), against chronic woodchuck hepatitis virus (WHV) infection was evaluated in a placebo-controlled study in the woodchuck, an established and predictive model for antiviral therapy. Once-daily treatment for 48 weeks with ADV plus 3TC or TDF plus FTC significantly reduced serum WHV viremia levels from the pretreatment level by 6.2 log10and 6.1 log10genome equivalents/ml serum, respectively, followed by TDF plus 3TC (5.6 log10genome equivalents/ml), ADV alone (4.8 log10genome equivalents/ml), ADV plus FTC (one survivor) (4.4 log10genome equivalents/ml), TDF alone (2.9 log10genome equivalents/ml), 3TC alone (2.7 log10genome equivalents/ml), and FTC alone (2.0 log10genome equivalents/ml). Individual woodchucks across all treatment groups also demonstrated pronounced declines in serum WHV surface antigen, characteristically accompanied by declines in hepatic WHV replication and the hepatic expression of WHV antigens. Most woodchucks had prompt recrudescence of WHV replication after drug withdrawal, but individual woodchucks across treatment groups had sustained effects. No signs of toxicity were observed for any of the drugs or drug combinations administered. In conclusion, the oral administration of 3TC, FTC, ADV, and TDF alone and in combination was safe and effective in the woodchuck model of HBV infection.
In Vivo Pharmacodynamics of Ceftobiprole against Multiple Bacterial Pathogens in Murine Thigh and Lung Infection Models
Authors: Craig W. A. , Andes D. R. 
Published: August 2008

ABSTRACTCeftobiprole medocaril is the parenteral prodrug of ceftobiprole, a novel pyrrolidinone broad-spectrum cephalosporin with in vitro and in vivo bactericidal activities against methicillin-resistantStaphylococcus aureus(MRSA) and penicillin-resistantStreptococcus pneumoniae(PRSP). We have used murine thigh and lung infection models in neutropenic and normal mice to characterize the in vivo pharmacokinetic (PK)-pharmacodynamic (PD) activities of ceftobiprole against multiple strains ofS. aureus(including MRSA),S. pneumoniae(including PRSP), and gram-negative bacilli. Serum levels of ceftobiprole following the administration of multiple doses were determined by a microbiological assay. In vivo bactericidal activities and postantibiotic effects (PAEs) of ceftobiprole against MRSA and PRSP strains were determined from serial CFU/thigh values following single doses of ceftobiprole (40 and 160 mg/kg of body weight). Dose fractionation studies were used to determine which PK-PD index correlated best with activity. Magnitudes of the PK-PD indices were calculated from MICs and PK parameters. A sigmoid dose-response model was used to estimate the dose (mg/kg/24 h) required to achieve a static and 2-log10kill effects over 24 h. PK results showed area under the concentration-time curve/dose values of 1.8 to 2.8 and half-lives of 0.29 to 0.51 h. MICs ranged from 0.015 to 2 μg/ml. Ceftobiprole demonstrated time-dependent killing; its in vivo PAEs varied from 3.8 h to 4.8 h for MRSA and from 0 to 0.8 h for PRSP. The time above MIC (T> MIC) correlated best with efficacy for both MRSA and PRSP. TheT> MIC values required for the static doses were significantly longer (P< 0.001) forEnterobacteriaceae(36 to 45%) than forS. aureus(14 to 28%) andS. pneumoniae(15 to 22%). The drug showed activities in the lung model similar to those in the thigh model. The presence of neutrophils significantly enhanced the activity of ceftobiprole againstS. pneumoniaebut only slightly againstKlebsiella pneumoniae. Based on its PD profile, ceftobiprole is a promising new β-lactam agent with activity against gram-negative and gram-positive organisms including MRSA and PRSP.
Regulation ofLactobacillus caseiSorbitol Utilization Genes Requires DNA-Binding Transcriptional Activator GutR and the Conserved Protein GutM
Authors: Alcántara Cristina , Sarmiento-Rubiano Luz Adriana , Monedero Vicente , Deutscher Josef , Pérez-Martínez Gaspar , Yebra María J. 
Published: August 2008

ABSTRACTSequence analysis of the five genes (gutRMCBA) downstream from the previously described sorbitol-6-phosphate dehydrogenase-encodingLactobacillus casei gutFgene revealed that they constitute a sorbitol (glucitol) utilization operon. ThegutRMgenes encode putative regulators, while thegutCBAgenes encode the EIIC, EIIBC, and EIIA proteins of a phosphoenolpyruvate-dependent sorbitol phosphotransferase system (PTSGut). Thegutoperon is transcribed as a polycistronicgutFRMCBAmessenger, the expression of which is induced by sorbitol and repressed by glucose.gutRencodes a transcriptional regulator with two PTS-regulated domains, a galactitol-specific EIIB-like domain (EIIBGatdomain) and a mannitol/fructose-specific EIIA-like domain (EIIAMtldomain). Its inactivation abolishedgutoperon transcription and sorbitol uptake, indicating that it acts as a transcriptional activator. In contrast, cells carrying agutBmutation expressed thegutoperon constitutively, but they failed to transport sorbitol, indicating that EIIBCGutnegatively regulates GutR. A footprint analysis showed that GutR binds to a 35-bp sequence upstream from thegutpromoter. A sequence comparison with the presumed promoter region ofgutoperons from various firmicutes revealed a GutR consensus motif that includes an inverted repeat. The regulation mechanism of theL. casei gutoperon is therefore likely to be operative in other firmicutes. Finally,gutMcodes for a conserved protein of unknown function present in all sequencedgutoperons. AgutMmutant, the first constructed in a firmicute, showed drastically reducedgutoperon expression and sorbitol uptake, indicating a regulatory role also for GutM.
Effects of Hypercapnic Hypoxia on Inactivation and Elimination of
Vibrio campbellii
in the Eastern Oyster,
Crassostrea virginica
Authors: Macey Brett M. , Achilihu Ikenna O. , Burnett Karen G. , Burnett Louis E. 
Published: August 2008

ABSTRACT

The Eastern oyster,
Crassostrea virginica
, inhabits shallow coastal waters that frequently experience periods of low dissolved oxygen (hypoxia) and elevated CO
2
(hypercapnia) levels. Bacteria are extremely abundant in these environments and accumulate in large numbers in filter-feeding oysters, which can act as passive carriers of human pathogens. Although hypercapnic hypoxia (HH) can affect certain specific immune mechanisms, its direct effect on the inactivation, degradation and elimination of bacteria in oysters is unknown. This research was conducted to determine whether exposure to HH reduces the ability of
C. virginica
to inactivate and eliminate
Vibrio campbellii
following its injection into the adductor muscle. Oysters were held in fully air-saturated (normoxic; partial O
2
pressure [P
O2
] = 20.7 kPa, CO
2
< 0.06 kPa, pH 7.8 to 8.0) or HH (P
O2
= 4 kPa, CO
2
= 1.8 kPa, pH 6.5 to 6.8) seawater at 25°C for 4 h before being injected in the adductor muscle with 10
5
live
Vibrio campbellii
bacteria and remained under these conditions for the remainder of the experiment (up to 24 h postinjection). Real-time PCR was used to quantify the number of intact
V. campbellii
bacteria, while selective plating was used to quantify the number of injected bacteria remaining culturable in whole-oyster tissues, seawater, and feces/pseudofeces at 0, 1, 4, and 24 h postinjection. We found that oysters maintained under normoxic conditions were very efficient at inactivating and degrading large numbers of injected bacteria within their tissues. Moreover, a small percentage (∼10%) of injected bacteria were passed into the surrounding seawater, while less than 1% were recovered in the feces/pseudofeces. In contrast, HH increased the percentage of culturable bacteria recovered from the tissues of oysters, suggesting an overall decrease in bacteriostasis. We suggest that poor water quality may increase the risk that oysters will harbor and transmit bacterial pathogens hazardous to human and ecosystem health.
Engineering of an
Escherichia coli
Strain for the Production of 3-Methyl-1-Butanol
Authors: Connor Michael R. , Liao James C. 
Published: August 2008

ABSTRACT

3-Methyl-1-butanol is a potential fuel additive or substitute. Previously this compound was identified in small quantities in yeast fermentation as one of the fusel alcohols. In this work, we engineered an
Escherichia coli
strain to produce 3-methyl-1-butanol from glucose via the host's amino acid biosynthetic pathways. Strain improvement with the removal of feedback inhibition and competing pathways increased the selectivity and productivity of 3-methyl-1-butanol. This work demonstrates the feasibility of production of 3-methyl-1-butanol as a biofuel and shows promise in using
E. coli
as a host for production.
Transformation of
N
-Phenylpiperazine by Mixed Cultures from a Municipal Wastewater Treatment Plant
Authors: Jung Carina M. , Heinze Thomas M. , Deck Joanna , Strakosha Ruth , Sutherland John B. 
Published: August 2008

ABSTRACT

Samples from a wastewater treatment plant were used as inocula for mixed cultures dosed with
N
-phenylpiperazine (NPP), a model compound containing the piperazine ring found in many fluoroquinolones. Chemical analyses showed that NPP (50 mg liter
−1
) disappeared in 12 days, with the appearance of a transient metabolite and two nitrosated compounds.
Assessment of Inhibitory Effects of Fluoride-Coated Tubes on Biofilm Formation by Using the In Vitro Dental Unit Waterline Biofilm Model
Authors: Yabune Toshiaki , Imazato Satoshi , Ebisu Shigeyuki 
Published: August 2008

ABSTRACT

This study aimed to establish an in vitro model to simulate biofilms formed in dental unit waterlines (DUWLs) and to investigate the ability of polyvinylidene fluoride (PVDF)-coated tubes to inhibit biofilm formation using this model. The water and biofilm samples were obtained from DUWLs which had been clinically used for 2.5 years, and the predominant bacteria were identified. A conventional polyurethane tube was incubated for 24 to 96 h in the mixed flora of isolated bacteria, and the optimal incubation conditions to simulate a clinically formed biofilm were determined by observation with a scanning electron microscope. Biofilm formation on a PVDF-coated tube was observed using this in vitro model, and the adherence of different bacterial species to conventional and PVDF-coated tubes was assessed.
Sphingomonas paucimobilis
,
Acinetobacter haemolytics
, and
Methylobacterium mesophilicum
were predominantly isolated from contaminated DUWLs. Incubation of the polyurethane tube with the mixed flora containing these three species for 96 h resulted in the formation of a mature biofilm similar to the one clinically observed. The PVDF-coated tube was significantly less adhesive to all three bacterial species than the polyurethane tube (
P
< 0.05 by the Mann-Whitney U test), and the attachment of small amounts of rods was observed even after incubation with the mixed flora for 96 h. In conclusion, an in vitro biofilm model was obtained by using a mixed flora of bacteria isolated from DUWLs, and the PVDF-coated tube was found to be effective in preventing biofilm formation using this model.
Evaluation of a Low-Cost Electrostatic Dust Fall Collector for Indoor Air Endotoxin Exposure Assessment
Authors: Noss Ilka , Wouters Inge M. , Visser Maaike , Heederik Dick J. J. , Thorne Peter S. , Brunekreef Bert , Doekes Gert 
Published: August 2008

ABSTRACTExposure to endotoxin in home environments has become a key issue in asthma and allergy research. Most studies have analyzed floor or mattress dust endotoxin, but its validity as a proxy for airborne exposure is unknown, while active airborne dust sampling is not feasible in large-scale population studies because of logistic and financial limitations. We therefore developed and evaluated a simple passive airborne dust collection method for airborne endotoxin exposure assessment. We explored an electrostatic dust fall collector (EDC), consisting of a 42- by 29.6-cm-sized folder with four electrostatic cloths exposed to the air. The EDC was tested during two 14-day periods in seven nonfarm and nine farm homes and in farm stables. In parallel, active airborne dust sampling was performed with Harvard impactors and floor dust collected by vacuuming, using nylon sampling socks. The endotoxin levels could be measured in all EDC cloth extracts. The levels (in EU/m2) between EDCs used simultaneously or in different sampling periods in the same home correlated strongly (r> 0.8). EDC endotoxin also correlated moderately to strongly (r= 0.6 to 0.8) with the endotoxin measured by active airborne dust sampling and living room floor dust sampling and—in farm homes—with the endotoxin captured by the EDC in stables. In contrast, endotoxin levels measured by floor dust sampling showed only a poor correlation with the levels measured by active airborne dust sampling. We therefore conclude that measuring endotoxin levels with the EDC is a valid measure of average airborne endotoxin exposure, while reproducibility over time is at least equivalent to that of reservoir dust analyses.
Preferential Colonization ofSolanum tuberosumL. Roots by the FungusGlomus intraradicesin Arable Soil of a Potato Farming Area
Authors: Cesaro Patrizia , van Tuinen Diederik , Copetta Andrea , Chatagnier Odile , Berta Graziella , Gianinazzi Silvio , Lingua Guido 
Published: August 2008

ABSTRACTThe symbiosis between plant roots and arbuscular mycorrhizal (AM) fungi has been shown to affect both the diversity and productivity of agricultural communities. In this study, we characterized the AM fungal communities ofSolanum tuberosumL. (potato) roots and of the bulk soil in two nearby areas of northern Italy, in order to verify if land use practices had selected any particular AM fungus with specificity to potato plants. The AM fungal large-subunit (LSU) rRNA genes were subjected to nested PCR, cloning, sequencing, and phylogenetic analyses. One hundred eighty-three LSU rRNA sequences were analyzed, and eight monophyletic ribotypes, belonging toGlomusgroups A and B, were identified. AM fungal communities differed between bulk soil and potato roots, as one AM fungal ribotype, corresponding toGlomus intraradices, was much more frequent in potato roots than in soils (accounting for more than 90% of sequences from potato samples and less than 10% of sequences from soil samples). A semiquantitative heminested PCR with specific primers was used to confirm and quantify the AM fungal abundance observed by cloning. Overall results concerning the biodiversity of AM fungal communities in roots and in bulk soils from the two studied areas suggested that potato roots were preferentially colonized by one AM fungal species,G. intraradices.
Characterization of an Endoglucanase Belonging to a New Subfamily of Glycoside Hydrolase Family 45 of the BasidiomycetePhanerochaete chrysosporium
Authors: Igarashi Kiyohiko , Ishida Takuya , Hori Chiaki , Samejima Masahiro 
Published: August 2008

ABSTRACTThe wood decay fungusPhanerochaete chrysosporiumhas served as a model system for the study of lignocellulose conversions, but aspects of its cellulolytic system remain uncertain. Here, we report identifying the gene that encodes the glycoside hydrolase (GH) family 45 endoglucanase (EG) from the fungus, cloning the cDNA, determining its heterologous expression in the methylotrophic yeastPichia pastoris, and characterizing the recombinant protein. The cDNA consisted of 718 bp, including an open reading frame encoding a 19-amino-acid signal peptide, a 7-amino-acid presequence at the N-terminal region, and a 180-amino-acid mature protein, which has no cellulose binding domain. Analysis of the amino acid sequence revealed that the protein has a low similarity (<22%) to known fungal EGs belonging to the GH family 45 (EGVs). No conserved domain of this family was found by a BLAST search, suggesting that the protein should be classified into a new subdivision of this GH family. The recombinant protein has hydrolytic activity toward amorphous cellulose, carboxylmethyl cellulose, lichenan, barley β-glucan, and glucomannan but not xylan. Moreover, a synergistic effect was observed with the recombinant GH family 6 cellobiohydrolase from the same fungus toward amorphous cellulose as a substrate, indicating that the enzyme may act in concert with other cellulolytic enzymes to hydrolyze cellulosic biomass in nature.
Persistence of
Helicobacter pylori
in Heterotrophic Drinking-Water Biofilms
Authors: Gião M. S. , Azevedo N. F. , Wilks S. A. , Vieira M. J. , Keevil C. W. 
Published: August 2008

ABSTRACT

Although the route of transmission of
Helicobacter pylori
remains unknown, drinking water has been considered a possible transmission vector. It has been shown previously that, in water, biofilms are a protective niche for several pathogens, protecting them from stressful conditions, such as low carbon concentration, shear stress, and less-than-optimal temperatures. In this work, the influence of these three parameters on the persistence and cultivability of
H. pylori
in drinking-water biofilms was studied. Autochthonous biofilm consortia were formed in a two-stage chemostat system and then inoculated with the pathogen. Total numbers of
H. pylori
cells were determined by microscopy using a specific
H. pylori
16S rRNA peptide nucleic acid probe, whereas cultivable cells were assessed by standard plating onto selective
H. pylori
medium. Cultivable
H. pylori
could not be detected at any time point, but the ability of
H. pylori
cells to incorporate, undergo morphological transformations, persist, and even agglomerate in biofilms for at least 31 days without a noticeable decrease in the total cell number (on average, the concentration was between 1.54 × 10
6
and 2.25 × 10
6
cells cm
−2
) or in the intracellular rRNA content may indicate that the loss of cultivability was due to entry into a viable but noncultivable state. Unlike previous results obtained for pure-culture
H. pylori
biofilms, shear stress did not negatively influence the numbers of
H. pylori
cells attached, suggesting that the autochthonous aquatic bacteria have an important role in retaining this pathogen in the sessile state, possibly by providing suitable microaerophilic environments or linking biomolecules to which the pathogen adheres. Therefore, biofilms appear to provide not only a safe haven for
H. pylori
but also a concentration mechanism so that subsequent sloughing releases a concentrated bolus of cells that might be infectious and that could escape routine grab sample microbiological analyses and be a cause of concern for public health.