bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistence of Antibiotic Resistance: Evaluation of a Probiotic Approach Using Antibiotic-Sensitive Megasphaera elsdenii Strains To Prevent Colonization of Swine by Antibiotic-Resistant Strains
Authors: Stanton Thad B. , Humphrey Samuel B. 
Published: August 2011

ABSTRACTMegasphaera elsdeniiis a lactate-fermenting, obligately anaerobic bacterium commonly present in the gastrointestinal tracts of mammals, including humans. SwineM. elsdeniistrains were previously shown to have high levels of tetracycline resistance (MIC=64 to >256 μg/ml) and to carry mosaic (recombinant) tetracycline resistance genes. Baby pigs inherit intestinal microbiota from the mother sow. In these investigations we addressed two questions. When doM. elsdeniistrains from the sow colonize baby pigs? Can five antibiotic-sensitiveM. elsdeniistrains administered intragastrically to newborn pigs affect natural colonization of the piglets by antibiotic-resistant (AR)M. elsdeniistrains from the mother?M. elsdeniinatural colonization of newborn pigs was undetectable (<104CFU/g [wet weight] of feces) prior to weaning (20 days after birth). After weaning, all pigs became colonized (4 × 105to 2 × 108CFU/g feces). In a separate study, 61% (76/125) ofM. elsdeniiisolates from a gravid sow never exposed to antibiotics were resistant to chlortetracycline, ampicillin, or tylosin. The inoculation of the sow's offspring with mixtures ofM. elsdeniiantibiotic-sensitive strains prevented colonization of the offspring by maternal AR strains until at least 11 days postweaning. At 25 and 53 days postweaning, however, AR strains predominated. Antibiotic susceptibility phenotypes and single nucleotide polymorphism (SNP)-based identities ofM. elsdeniiisolated from sow and offspring were unexpectedly diverse. These results suggest that dosing newborn piglets withM. elsdeniiantibiotic-sensitive strains delays but does not prevent colonization by maternal resistant strains.M. elsdeniisubspecies diversity offers an explanation for the persistence of resistant strains in the absence of antibiotic selection.
Chlortetracycline-Resistant Intestinal Bacteria in Organically Raised and Feral Swine
Authors: Stanton Thad B. , Humphrey Samuel B. , Stoffregen William C. 
Published: August 2011

ABSTRACT

Organically raised swine had high fecal populations of chlortetracycline (CTC)-resistant (growing at 64 μg CTC/ml)
Escherichia coli
,
Megasphaera elsdenii
, and anaerobic bacteria. By comparison, CTC-resistant bacteria in feral swine feces were over 1,000-fold fewer and exhibited lower taxonomic diversity.
Salicylate Functions as an Efflux Pump Inducer and Promotes the Emergence of Fluoroquinolone-Resistant Campylobacter jejuni Mutants
Authors: Shen Zhangqi , Pu Xiao-Ying , Zhang Qijing 
Published: August 2011

ABSTRACT

Salicylate, a nonsteroidal anti-inflammatory compound, has been shown to increase the resistance of
Campylobacter
to antimicrobials. However, the molecular mechanism underlying salicylate-induced resistance has not yet been established. In this study, we determined how salicylate increases antibiotic resistance and evaluated its impact on the development of fluoroquinolone-resistant
Campylobacter
mutants. Transcriptional fusion assays, real-time quantitative reverse transcription-PCR (RT-PCR), and immunoblotting assays consistently demonstrated the induction of the CmeABC multidrug efflux pump by salicylate. Electrophoretic mobility shift assays further showed that salicylate inhibits the binding of CmeR (a transcriptional repressor of the TetR family) to the promoter DNA of
cmeABC
, suggesting that salicylate inhibits the function of CmeR. The presence of salicylate in the culture medium not only decreased the susceptibility of
Campylobacter
to ciprofloxacin but also resulted in an approximately 70-fold increase in the observed frequency of emergence of fluoroquinolone-resistant mutants under selection with ciprofloxacin. Together, these results indicate that in
Campylobacter
, salicylate inhibits the binding of CmeR to the promoter DNA and induces expression of
cmeABC
, resulting in decreased susceptibility to antibiotics and in increased emergence of fluoroquinolone-resistant mutants under selection pressure.
Characterization of Bacillus thuringiensis
l
-Isoleucine Dioxygenase for Production of Useful Amino Acids
Authors: Hibi Makoto , Kawashima Takashi , Kodera Tomohiro , Smirnov Sergey V. , Sokolov Pavel M. , Sugiyama Masakazu , Shimizu Sakayu , Yokozeki Kenzo , Ogawa Jun 
Published: August 2011

ABSTRACT

We determined the enzymatic characteristics of an industrially important biocatalyst, α-ketoglutarate-dependent
l
-isoleucine dioxygenase (IDO), which was found to be the enzyme responsible for the generation of (2
S
,3
R
,4
S
)-4-hydroxyisoleucine in
Bacillus thuringiensis
2e2. Depending on the amino acid used as the substrate, IDO catalyzed three different types of oxidation reactions: hydroxylation, dehydrogenation, and sulfoxidation. IDO stereoselectively hydroxylated several hydrophobic aliphatic
l
-amino acids, as well as
l
-isoleucine, and produced (
S
)-3-hydroxy-
l
-
allo
-isoleucine, 4-hydroxy-
l
-leucine, (
S
)-4-hydroxy-
l
-norvaline, 4-hydroxy-
l
-norleucine, and 5-hydroxy-
l
-norleucine. The IDO reaction product of
l
-isoleucine, (2
S
,3
R
,4
S
)-4-hydroxyisoleucine, was again reacted with IDO and dehydrogenated into (2
S
,3
R
)-2-amino-3-methyl-4-ketopentanoate, which is also a metabolite found in
B. thuringiensis
2e2. Interestingly, IDO catalyzed the sulfoxidation of some sulfur-containing
l
-amino acids and generated
l
-methionine sulfoxide and
l
-ethionine sulfoxide. Consequently, the effective production of various modified amino acids would be possible using IDO as the biocatalyst.
Microbial Dynamics during Aerobic Exposure of Corn Silage Stored under Oxygen Barrier or Polyethylene Films
Authors: Dolci Paola , Tabacco Ernesto , Cocolin Luca , Borreani Giorgio 
Published: August 2011

ABSTRACT

The aims of this study were to compare the effects of sealing forage corn with a new oxygen barrier film with those obtained by using a conventional polyethylene film. This comparison was made during both ensilage and subsequent exposure of silage to air and included chemical, microbiological, and molecular (DNA and RNA) assessments. The forage was inoculated with a mixture of
Lactobacillus buchneri
,
Lactobacillus plantarum
, and
Enterococcus faecium
and ensiled in polyethylene (PE) and oxygen barrier (OB) plastic bags. The oxygen permeability of the PE and OB films was 1,480 and 70 cm
3
m
−2
per 24 h at 23°C, respectively. The silages were sampled after 110 days of ensilage and after 2, 5, 7, 9, and 14 days of air exposure and analyzed for fermentation characteristics, conventional microbial enumeration, and bacterial and fungal community fingerprinting via PCR-denaturing gradient gel electrophoresis (DGGE) and reverse transcription (RT)-PCR-DGGE. The yeast counts in the PE and OB silages were 3.12 and 1.17 log
10
CFU g
−1
, respectively, with corresponding aerobic stabilities of 65 and 152 h.
Acetobacter pasteurianus
was present at both the DNA and RNA levels in the PE silage samples after 2 days of air exposure, whereas it was found only after 7 days in the OB silages. RT-PCR-DGGE revealed the activity of
Aspergillus fumigatus
in the PE samples from the day 7 of air exposure, whereas it appeared only after 14 days in the OB silages. It has been shown that the use of an oxygen barrier film can ensure a longer shelf life of silage after aerobic exposure.
Unique Regulatory Mechanism for
d
-Galactose Utilization in Aspergillus nidulans
Authors: Christensen Ulla , Gruben Birgit S. , Madrid Susan , Mulder Harm , Nikolaev Igor , de Vries Ronald P. 
Published: August 2011

ABSTRACT

This study describes two novel regulators, GalX and GalR, that control
d
-galactose utilization in
Aspergillus nidulans
. This system is unique for
A. nidulans
since no GalR homologs were found in other ascomycetes. GalR shares significant sequence identity with the arabinanolytic and xylanolytic regulators AraR and XlnR, but GalX is more distantly related.
Cloning, Expression, and Characterization of a New β-Agarase from
Vibrio
sp. Strain CN41
Authors: Liao Li , Xu Xue-Wei , Jiang Xia-Wei , Cao Yi , Yi Na , Huo Ying-Yi , Wu Yue-Hong , Zhu Xu-Fen , Zhang Xin-qi , Wu Min 
Published: August 2011

ABSTRACT

A new agarase, AgaA
CN41
, cloned from
Vibrio
sp. strain CN41, consists of 990 amino acids, with only 49% amino acid sequence identity with known β-agarases. AgaA
CN41
belongs to the GH50 (glycoside hydrolase 50) family but yields neoagarotetraose as the end product. AgaA
CN41
was expressed and characterized.
Inhibition of Escherichia coli CFT073
fliC
Expression and Motility by Cranberry Materials
Authors: Hidalgo Gabriela , Chan Michelle , Tufenkji Nathalie 
Published: August 2011

ABSTRACT

In humans, uropathogenic
Escherichia coli
(UPEC) is the most common etiological agent of uncomplicated urinary tract infections (UTIs). Cranberry extracts have been linked to the prevention of UTIs for over a century; however, a mechanistic understanding of the way in which cranberry derivatives prevent bacterial infection is still lacking. In this study, we used a
fliC-lux
reporter as well as quantitative reverse transcription-PCR to demonstrate that when UPEC strain CFT073 was grown or exposed to dehydrated, crushed cranberries or to purified cranberry-derived proanthocyanidins (cPACs), expression of the flagellin gene (
fliC
) was inhibited. In agreement with these results, transmission electron microscopy imaging of bacteria grown in the presence of cranberry materials revealed fewer flagella than those in bacteria grown under control conditions. Furthermore, we showed that swimming and swarming motilities were hindered when bacteria were grown in the presence of the cranberry compounds. Because flagellum-mediated motility has been suggested to enable UPEC to disseminate to the upper urinary tract, we propose that inhibition of flagellum-mediated motility might be a key mechanism by which cPACs prevent UTIs. This is the first report to show that cranberry compounds inhibit UPEC motility via downregulation of the
fliC
gene. Further studies are required to establish whether these inhibitors play a role
in vivo
.
Comparison of Surface Sampling Methods for Virus Recovery from Fomites
Authors: Julian Timothy R. , Tamayo Francisco J. , Leckie James O. , Boehm Alexandria B. 
Published: August 2011

ABSTRACT
The role of fomites in infectious disease transmission relative to other exposure routes is difficult to discern due, in part, to the lack of information on the level and distribution of virus contamination on surfaces. Comparisons of studies intending to fill this gap are difficult because multiple different sampling methods are employed and authors rarely report their method's lower limit of detection. In the present study, we compare a subset of sampling methods identified from a literature review to demonstrate that sampling method significantly influences study outcomes. We then compare a subset of methods identified from the review to determine the most efficient methods for recovering virus from surfaces in a laboratory trial using MS2 bacteriophage as a model virus. Recoveries of infective MS2 and MS2 RNA are determined using both a plaque assay and quantitative reverse transcription-PCR, respectively. We conclude that the method that most effectively recovers virus from nonporous fomites uses polyester-tipped swabs prewetted in either one-quarter-strength Ringer's solution or saline solution. This method recovers a median fraction for infective MS2 of 0.40 and for MS2 RNA of 0.07. Use of the proposed method for virus recovery in future fomite sampling studies would provide opportunities to compare findings across multiple studies.
Oxidoreductive Cellulose Depolymerization by the Enzymes Cellobiose Dehydrogenase and Glycoside Hydrolase 61
Authors: Langston James A. , Shaghasi Tarana , Abbate Eric , Xu Feng , Vlasenko Elena , Sweeney Matt D. 
Published: August 2011

ABSTRACT

Several members of the glycoside hydrolase 61 (GH61) family of proteins have recently been shown to dramatically increase the breakdown of lignocellulosic biomass by microbial hydrolytic cellulases. However, purified GH61 proteins have neither demonstrable direct hydrolase activity on various polysaccharide or lignacious components of biomass nor an apparent hydrolase active site. Cellobiose dehydrogenase (CDH) is a secreted flavocytochrome produced by many cellulose-degrading fungi with no well-understood biological function. Here we demonstrate that the binary combination of
Thermoascus aurantiacus
GH61A (TaGH61A) and
Humicola insolens
CDH (HiCDH) cleaves cellulose into soluble, oxidized oligosaccharides. TaGH61A-HiCDH activity on cellulose is shown to be nonredundant with the activities of canonical endocellulase and exocellulase enzymes in microcrystalline cellulose cleavage, and while the combination of TaGH61A and HiCDH cleaves highly crystalline bacterial cellulose, it does not cleave soluble cellodextrins. GH61 and CDH proteins are coexpressed and secreted by the thermophilic ascomycete
Thielavia terrestris
in response to environmental cellulose, and the combined activities of
T. terrestris
GH61 and
T. terrestris
CDH are shown to synergize with
T. terrestris
cellulose hydrolases in the breakdown of cellulose. The action of GH61 and CDH on cellulose may constitute an important, but overlooked, biological oxidoreductive system that functions in microbial lignocellulose degradation and has applications in industrial biomass utilization.
Pseudomonas aeruginosa Suppresses Interferon Response to Rhinovirus Infection in Cystic Fibrosis but Not in Normal Bronchial Epithelial Cells
Authors: Chattoraj Sangbrita S. , Ganesan Shyamala , Faris Andrea , Comstock Adam , Lee Wai-Ming , Sajjan Umadevi S. 
Published: August 2011

ABSTRACT

Despite increased morbidity associated with secondary respiratory viral infections in cystic fibrosis (CF) patients with chronic
Pseudomonas aeruginosa
infection, the underlying mechanisms are not well understood. Here, we investigated the effect of
P. aeruginosa
infection on the innate immune responses of bronchial epithelial cells to rhinovirus (RV) infection. CF cells sequentially infected with mucoid
P. aeruginosa
(MPA) and RV showed lower levels of interferons (IFNs) and higher viral loads than those of RV-infected cells. Unlike results for CF cells, normal bronchial epithelial cells coinfected with MPA/RV showed higher IFN expression than RV-infected cells. In both CF and normal cells, the RV-stimulated IFN response requires phosphorylation of Akt and interferon response factor 3 (IRF3). Preinfection with MPA inhibited RV-stimulated Akt phosphorylation and decreased IRF3 phosphorylation in CF cells but not in normal cells. Compared to normal, unstimulated CF cells or normal cells treated with CFTR inhibitor showed increased reactive oxygen species (ROS) production. Treatment of CF cells with antioxidants prior to MPA infection partially reversed the suppressive effect of MPA on the RV-stimulated IFN response. Together, these results suggest that MPA preinfection inhibits viral clearance by suppressing the antiviral response particularly in CF cells but not in normal cells. Further, increased oxidative stress in CF cells appears to modulate the innate immune responses to coinfection.
Anaerobic Respiration of Escherichia coli in the Mouse Intestine
Authors: Jones Shari A. , Gibson Terri , Maltby Rosalie C. , Chowdhury Fatema Z. , Stewart Valley , Cohen Paul S. , Conway Tyrrell 
Published: August 2011

ABSTRACT

The intestine is inhabited by a large microbial community consisting primarily of anaerobes and, to a lesser extent, facultative anaerobes, such as
Escherichia coli
, which we have shown requires aerobic respiration to compete successfully in the mouse intestine (S. A. Jones et al., Infect. Immun. 75:4891-4899, 2007). If facultative anaerobes efficiently lower oxygen availability in the intestine, then their sustained growth must also depend on anaerobic metabolism. In support of this idea, mutants lacking nitrate reductase or fumarate reductase have extreme colonization defects. Here, we further explore the role of anaerobic respiration in colonization using the streptomycin-treated mouse model. We found that respiratory electron flow is primarily via the naphthoquinones, which pass electrons to cytochrome
bd
oxidase and the anaerobic terminal reductases. We found that
E. coli
uses nitrate and fumarate in the intestine, but not nitrite, dimethyl sulfoxide, or trimethylamine
N
-oxide. Competitive colonizations revealed that cytochrome
bd
oxidase is more advantageous than nitrate reductase or fumarate reductase. Strains lacking nitrate reductase outcompeted fumarate reductase mutants once the nitrate concentration in cecal mucus reached submillimolar levels, indicating that fumarate is the more important anaerobic electron acceptor in the intestine because nitrate is limiting. Since nitrate is highest in the absence of
E. coli
, we conclude that
E. coli
is the only bacterium in the streptomycin-treated mouse large intestine that respires nitrate. Lastly, we demonstrated that a mutant lacking the NarXL regulator (activator of the NarG system), but not a mutant lacking the NarP-NarQ regulator, has a colonization defect, consistent with the advantage provided by NarG. The emerging picture is one in which gene regulation is tuned to balance expression of the terminal reductases that
E. coli
uses to maximize its competitiveness and achieve the highest possible population in the intestine.
Tegumental Phosphodiesterase SmNPP-5 Is a Virulence Factor for Schistosomes
Authors: Bhardwaj Rita , Krautz-Peterson Greice , Da'dara Akram , Tzipori Saul , Skelly Patrick J. 
Published: August 2011

ABSTRACT

The intravascular trematode
Schistosoma mansoni
is a causative agent of schistosomiasis, a disease that constitutes a major health problem globally. In this study we cloned and characterized the schistosome tegumental phosphodiesterase SmNPP-5 and evaluated its role in parasite virulence. SmNPP-5 is a 52.5-kDa protein whose gene is rapidly turned on in the intravascular parasitic life stages, following invasion of the definitive host. Highest expression is found in mated adult males. As revealed by immunofluorescence analysis, SmNPP-5 protein is found prominently in the dorsal surface of the tegument of males. Localization by immuno-electron microscopy illustrates a unique pattern of immunogold-labeled SmNPP-5 within the tegument; some immunogold particles are scattered throughout the tissue, but many are clustered in tight arrays. To determine the importance of the protein for the parasites, RNA interference (RNAi) was employed to knock down expression of the SmNPP-5-encoding gene in schistosomula and adult worms. Both quantitative real-time PCR (qRT-PCR) and Western blotting confirmed successful and robust gene suppression. In addition, the suppression and the ectolocalization of this enzyme in live parasites were evident because of a significantly impaired ability of the suppressed parasites to hydrolyze exogenously added phosphodiesterase substrate
p
-nitrophenyl 5′-dTMP (
p
-Nph-5′-TMP). The effects of suppressing expression of the SmNPP-5 gene
in vivo
were tested by injecting parasites into mice. It was found that, unlike controls, parasites whose SmNPP-5 gene was demonstrably suppressed at the time of host infection were greatly impaired in their ability to establish infection. These results demonstrate that SmNPP-5 is a virulence factor for schistosomes.
Enhanced Neutrophil Longevity and Recruitment Contribute to the Severity of Oviduct Pathology during Chlamydia muridarum Infection
Authors: Frazer Lauren C. , O'Connell Catherine M. , Andrews Charles W. , Zurenski Matthew A. , Darville Toni 
Published: August 2011

ABSTRACTOur previous studies revealed that intravaginal infection of mice with a plasmid-deficient strain ofChlamydia muridarum, CM3.1, does not induce the development of oviduct pathology. In this study, we determined that infection with CM3.1 resulted in a significantly reduced frequency and absolute number of neutrophils in the oviducts during acute infection. This reduction in neutrophils was associated with significantly lower levels of neutrophil chemokines in the oviducts and decreased production of neutrophil chemokines by oviduct epithelial cells infected with CM3.1in vitro. Infection with CM3.1 also resulted in an increased frequency of late apoptotic/dead neutrophils in the oviduct. Examination of the ability ofChlamydia trachomatisto prevent neutrophil apoptosisin vitrorevealed thatC. trachomatisstrain D/UW-3/Cx exhibited an enhanced ability to prevent neutrophil apoptosis compared to plasmid-deficient CTD153, and this effect was dependent on the presence of CD14highmonocytes. The presence of monocytes also resulted in enhanced neutrophil cytokine production and increased production of tissue-damaging molecules in response to D/UW-3/Cx relative to results with CTD153. Attempts to use antibody-mediated depletion to discern the specific role of neutrophils in infection control and pathologyin vivorevealed that although Ly6Ghighneutrophils were eliminated from the blood and oviducts with this treatment, immature neutrophils and high levels of tissue-damaging molecules were still detectable in the upper genital tract. These data support the role of neutrophils in chlamydia-induced pathology and reveal that novel methods of depletion must be developed before their role can be specifically determinedin vivo.
Retracted Science and the Retraction Index
Authors: Fang Ferric C. , Casadevall Arturo 
Published: August 2011

ABSTRACT
Articles may be retracted when their findings are no longer considered trustworthy due to scientific misconduct or error, they plagiarize previously published work, or they are found to violate ethical guidelines. Using a novel measure that we call the “retraction index,” we found that the frequency of retraction varies among journals and shows a strong correlation with the journal impact factor. Although retractions are relatively rare, the retraction process is essential for correcting the literature and maintaining trust in the scientific process.
Progress towards a reference genome for sunflower
Authors: Kane N.C. , Gill N. , King M.G. , Bowers J.E. , Berges H. , Gouzy J. , Bachlava E. , Langlade N.B. , Lai Z. , Stewart M. , Burke J.M. , Vincourt P. , Knapp S.J. , Rieseberg L.H. 
Published: August 2011

The Compositae is one of the largest and most economically important families of flowering plants and includes a diverse array of food crops, horticultural crops, medicinals, and noxious weeds. Despite its size and economic importance, there is no reference genome sequence for the Compositae, which impedes research and improvement efforts. We report on progress toward sequencing the 3.5 Gb genome of cultivated sunflower ( Helianthus annuus ), the most important crop in the family. Our sequencing strategy combines whole-genome shotgun sequencing using the Solexa and 454 platforms with the generation of high-density genetic and physical maps that serve as scaffolds for the linear assembly of whole-genome shotgun sequences. The performance of this approach is enhanced by the construction of a sequence-based physical map, which provides unique sequence-based tags every 5–6 kb across the genome. Thus far, our physical map covers ∼85% of the sunflower genome, and we have generated ∼80× genome coverage with Solexa reads and 15.5× with 454 reads. Preliminary analyses indicated that ∼78% of the sunflower genome consists of repetitive sequences. Nonetheless, ∼76% of contigs >5 kb in size can be assigned to either the physical or genetic map or to both, suggesting that our approach is likely to deliver a highly accurate and contiguous reference genome for sunflower.