bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of Failure in Vancomycin-Treated Methicillin-Resistant Staphylococcus aureus Bloodstream Infection: a Clinically Useful Risk Stratification Tool
Authors: Moore Carol L. , Lu Mei , Cheema Faiqa , Osaki-Kiyan Paola , Perri Mary Beth , Donabedian Susan , Haque Nadia Z. , Zervos Marcus J.
Published: August 2011

Methicillin-resistant
Staphylococcus aureus
(MRSA) is a common cause of bloodstream infection (BSI) and is often associated with invasive infections and high rates of mortality. Vancomycin has remained the mainstay of therapy for serious Gram-positive infections, particularly MRSA BSI; however, therapeutic failures with vancomycin have been increasingly reported. We conducted a comprehensive evaluation of the factors (patient, strain, infection, and treatment) involved in the etiology and management of MRSA BSI to create a risk stratification tool for clinicians. This study included consecutive patients with MRSA BSI treated with vancomycin over 2 years in an inner-city hospital in Detroit, MI. Classification and regression tree analysis (CART) was used to develop a risk prediction model that characterized vancomycin-treated patients at high risk of clinical failure. Of all factors, the Acute Physiology and Chronic Health Evaluation II (APACHE-II) score, with a cutoff point of 14, was found to be the strongest predictor of failure and was used to split the population into two groups. Forty-seven percent of the population had an APACHE-II score < 14, a value that was associated with low rates of clinical failure (11%) and mortality (4%). Fifty-four percent of the population had an APACHE-II score ≥ 14, which was associated with high rates of clinical failure (35%) and mortality (23%). The risk stratification model identified the interplay of three other predictors of failure, including the vancomycin MIC as determined by Vitek 2 analysis, the risk level of the source of BSI, and the USA300 strain type. This model can be a useful tool for clinicians to predict the likelihood of success or failure in vancomycin-treated patients with MRSA bloodstream infection.
Impaired Parasite Attachment as Fitness Cost of Metronidazole Resistance in Giardia lamblia
Authors: Tejman-Yarden Noa , Millman Maya , Lauwaet Tineke , Davids Barbara J. , Gillin Frances D. , Dunn Linda , Upcroft Jacqueline A. , Miyamoto Yukiko , Eckmann Lars
Published: August 2011

Infections with the diarrheagenic protozoan pathogen
Giardia lamblia
are most commonly treated with metronidazole (Mz). Treatment failures with Mz occur in 10 to 20% of cases and Mz resistance develops in the laboratory, yet clinically, Mz-resistant (Mz
r
)
G. lamblia
has rarely been isolated from patients. To understand why clinical Mz
r
isolates are rare, we questioned whether Mz resistance entails fitness costs to the parasite. Our studies employed several newly generated and established isogenic Mz
r
cell lines with stable, high-level resistance to Mz and significant cross-resistance to tinidazole, nitazoxanide, and furazolidone. Oral infection of suckling mice revealed that three of five Mz
r
cell lines could not establish infection, while two Mz
r
cell lines infected pups, albeit with reduced efficiencies. Failure to colonize resulted from a diminished capacity of the parasite to attach to the intestinal mucosa
in vivo
and to epithelial cells and plastic surfaces
in vitro
. The attachment defect was related to impaired glucose metabolism, since the noninfectious Mz
r
lines consumed less glucose, and glucose promoted ATP-independent parasite attachment in the parental lines. Thus, resistance of
Giardia
to Mz is accompanied by a glucose metabolism-related attachment defect that can interfere with colonization of the host. Because glucose-metabolizing pathways are important for activation of the prodrug Mz, it follows that a fitness trade-off exists between diminished Mz activation and reduced infectivity, which may explain the observed paucity of clinical Mz
r
isolates of
Giardia
. However, the data also caution that some forms of Mz resistance do not markedly interfere with
in vivo
infectivity.
Comparison of Drug Resistance Scores for Tipranavir in Protease Inhibitor-Naïve Patients Infected with HIV-1 B and Non-B Subtypes
Authors: Stürmer Martin , Stephan Christoph , Gute Peter , Knecht Gaby , Bickel Markus , Brodt Hans-Reinhard , Doerr Hans W. , Gürtler Lutz , Lecocq Pierre , van Houtte Margriet
Published: August 2011

Genotypes of samples from protease inhibitor-naïve patients in Frankfurt's HIV Cohort were analyzed with five tipranavir resistance prediction algorithms. Mean scores were higher in non-B than in B subtypes. The proportion of non-B subtypes increased with increasing scores, except in weighted algorithms. Virtual andin vitrophenotype analyses of samples with increased scores showed no reduced tipranavir susceptibility. Current algorithms appear suboptimal for interpretation of resistance to tipranavir in non-B subtypes; increased scores might reflect algorithm bias rather than “natural resistance.”
Effect of the Hepatitis C Virus Protease Inhibitor Telaprevir on the Pharmacokinetics of Amlodipine and Atorvastatin
Authors: Lee Jee Eun , van Heeswijk Rolf , Alves Katia , Smith Frances , Garg Varun
Published: August 2011

Telaprevir is a hepatitis C virus protease inhibitor that is both a substrate and an inhibitor of CYP3A. Amlodipine and atorvastatin are both substrates of CYP3A and are among the drugs most frequently used by patients with hepatitis C. This study was conducted to examine the effect of telaprevir on atorvastatin and amlodipine pharmacokinetics (PK). This was an open-label, single sequence, nonrandomized study involving 21 healthy male and female volunteers. A coformulation of 5 mg amlodipine and 20 mg atorvastatin was administered on day 1. Telaprevir was taken with food as a 750-mg dose every 8 h from day 11 until day 26, and a single dose of the amlodipine-atorvastatin combination was readministered on day 17. Plasma samples were collected for determination of the PK of telaprevir, amlodipine, atorvastatin,
ortho
-hydroxy atorvastatin, and
para
-hydroxy atorvastatin. When administration with telaprevir was compared with administration without telaprevir, the least-square mean ratios (90% confidence limits) for amlodipine were 1.27 (1.21, 1.33) for the maximum drug concentration in serum (
C
max
) and 2.79 (2.58, 3.01) for the area under the concentration-time curve from 0 h to infinity (AUC
0-∞
); for atorvastatin, they were 10.6 (8.74, 12.9) for the
C
max
and 7.88 (6.84, 9.07) for the AUC
0-∞
. Telaprevir significantly increased exposure to amlodipine and atorvastatin, consistent with the inhibitory effect of telaprevir on the CYP3A-mediated metabolism of these agents.
Adjunctive Rifampin Is Crucial to Optimizing Daptomycin Efficacy against Rabbit Prosthetic Joint Infection Due to Methicillin-Resistant Staphylococcus aureus
Authors: Saleh-Mghir Azzam , Muller-Serieys Claudette , Dinh Aurélien , Massias Laurent , Crémieux Anne-Claude
Published: August 2011

Daptomycin is an attractive option for treating prosthetic joint infection, but the 6-mg/kg of body weight/day dose was linked to clinical failure and emergence of resistance. Using a methicillin-resistant
Staphylococcus aureus
(MRSA) knee prosthesis infection in rabbits, we studied the efficacies of high-dose daptomycin (22 mg/kg given intravenously [i.v.] once daily [o.d.]; equivalent to 8 mg/kg/day in humans) or vancomycin (60 mg/kg given intramuscularly [i.m.] twice daily [b.i.d.]), both either alone or with adjunctive rifampin (10 mg/kg i.m. b.i.d.). After partial knee replacement with a silicone implant, 10
7
MRSA CFU was injected into the knees. Treatment started 7 days postinoculation and lasted 7 days. Positive cultures were screened for the emergence of mutant strains, defined as having 3-fold-increased MICs. Although
in vivo
mean log
10
CFU/g of daptomycin-treated (4.23 ± 1.44;
n
= 12) or vancomycin-treated (4.63 ± 1.08;
n
= 12) crushed bone was significantly lower than that of controls (5.93 ± 1.15;
n
= 9) (
P
< 0.01), neither treatment sterilized bone (2/12 and 0/12 rabbits with sterile bone, respectively). Daptomycin mutant strains were found in 6/12, 3/12, and 2/9 daptomycin-treated, vancomycin-treated, and control rabbits, respectively; no resistant strains emerged (MIC was always <1 mg/liter). Adjunctive rifampin with daptomycin (1.47 ± 0.04 CFU/g of bone [detection threshold]; 11/11 sterile bones) or vancomycin (1.5 ± 0.12 CFU/g of bone; 6/8 sterile bones) was significantly more effective than monotherapy (
P
< 0.01) and prevented the emergence of daptomycin mutant strains. In this MRSA joint prosthesis infection model, combining rifampin with daptomycin was highly effective. Daptomycin mutant strains were isolated
in vivo
even without treatment, but adjunctive rifampin prevented this phenomenon, previously found after monotherapy in humans.
Impact of Carbapenem Resistance and Receipt of Active Antimicrobial Therapy on Clinical Outcomes of Acinetobacter baumannii Bloodstream Infections
Authors: Esterly John S. , Griffith Milena , Qi Chao , Malczynski Michael , Postelnick Michael J. , Scheetz Marc H.
Published: August 2011

Nosocomial
Acinetobacter baumannii
bloodstream infections occur with significant prevalence and mortality. The relationship between carbapenem resistance in
A. baumannii
and patient outcomes remains unclear. A retrospective cohort study was conducted on patients with
A. baumannii
bacteremia. Outcomes, controlling for confounders, were compared for carbapenem-nonresistant
A. baumannii
(CNRAB) and carbapenem-resistant
A. baumannii
(CRAB). The primary outcome studied was all-cause hospital mortality, and the secondary endpoints evaluated were time to mortality, time to negative cultures, and length of stay postinfection for survivors. A total of 79 patients, 37 infected with CRAB and 42 with CNRAB, were studied. Hospital mortality was greater in the CRAB group as determined based on bivariate analysis (
P
< 0.01); however, this effect was nullified when controlling for relevant confounders with logistic regression and a Cox proportional-hazards model (
P
= 0.71 and 0.75, respectively). Values for time to mortality and time to negative cultures did not differ between the groups. The median number of days of stay postinfection for survivors was greater for the CRAB group than the CNRAB group (14 versus 6.5;
P
< 0.01). Patients who received active antimicrobial therapy were less likely to die (93.5% versus 74.2%;
P
= 0.02), regardless of carbapenem susceptibility classifications, and this result was robust in the multivariate model (
P
= 0.02). Trends existed for improved outcomes in patients receiving an active beta-lactam, and patients fared worse if they had received a polymyxin as an active agent. Patients with CRAB bloodstream infections were more chronically ill and had more comorbidities. Inactive therapy was more important than carbapenem susceptibility with respect to outcomes, was a strong predictor of death, and is potentially modifiable.
Macroscopic Biofilms in Fracture-Dominated Sediment That Anaerobically Oxidize Methane
Authors: Briggs B. R. , Pohlman J. W. , Torres M. , Riedel M. , Brodie E. L. , Colwell F. S.
Published: August 2011

Methane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 10
7
to 10
8
cells cm
−3
. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated by
Deltaproteobacteria
, candidate division WS3, and
Chloroflexi
, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade,
Thermoplasmatales
, and
Desulfurococcales
, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla of
Methanosarcinales
and
Desulfurococcales
. The stable carbon isotope composition of the biofilm from the SMT (−35 to −43‰) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments.
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

Megasphaera 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

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

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

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

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

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

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

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

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

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

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

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

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

Our 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

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.
Altering light availability to the plant host determined the identity of the dominant ectomycorrhizal fungal partners and mediated mycorrhizal effects on plant growth
Authors: Kummel Miroslav , Lostroh Phoebe
Published: August 2011

Variation in light availability likely impacts the processes that determine the identity of ectomycorrhizal fungi associated with the host plant, and the resulting changes in fungal composition may modify the plant’s growth response to light. Our two field surveys and two field experiments using Abies balsamea (L.) Mill. seedlings show that the identity of the dominant ectomycorrhizal fungus changed in response to natural and experimentally induced variation in light. Plants in low light were mostly dominated by a Cenococcum -like morphotype, and plants in high light were mostly dominated by a Lactarius -like morphotype. The patterns of absolute abundance show the key role of plant size: the absolute abundance of the Lactarius-like morphotype increased with increasing light and increasing root system size, whereas the absolute abundance of the Cenococcum-like morphotype was unrelated to both variables. Root system size increased with light availability. With increasing light, growth of plants dominated by the Lactarius-like morphotype decreased with respect to average plants, and therefore, as the Lactarius-like morphotype was increasing in dominance, it was decreasing in mutualistic effectiveness. Plants dominated by Cenococcum had lower growth compared with plants dominated by Lactarius in low light. However, the effects of the two morphotypes were indistinguishable in high light. Our results are likely driven by an interaction of priority effects and light-limited plant growth.
Impact of elevated CO2 on carbohydrate and ureide concentrations in soybean inoculated with different strains of Bradyrhizobium japonicum
Authors: Bertrand Annick , Prévost Danielle , Juge Christine , Chalifour François-P.
Published: August 2011

Elevated CO2 increases soybean growth and photosynthesis, and the resulting additional supply of photosynthates stimulates nodule activity. To characterize its biochemical response to both CO2 and bradyrhizobial strains, soybean inoculated with three strains of Bradyrhizobium japonicum was grown in growth chambers under ambient (400 µmol·mol–1) or elevated (800 µmol·mol–1) CO2. Soluble sugars were generally more abundant in leaves and nodules under elevated CO2, while starch and pinitol were depleted, indicating that additional photosynthates were rapidly used, in particular for nodule growth (dry mass increased by 65%). Ureides (allantoin and allantoic acid) increased under elevated CO2 in leaves, while this increase was not significant in nodules. The indigenous strain 12NS14 induced the highest ureides concentration in nodules under elevated CO2 along with the highest nitrogenase activity and increase in shoot dry mass, indicating a positive-feedback stimulation: soybean mobilized energy reserves to support more nodules, and in return nodules synthesized more ureides to support plant growth. In contrast, the commercial strain 532c resulted in the highest ureide concentrations in leaves, coupled with the lowest nitrogenase activity and nodules yield, suggesting a feedback inhibition of nodule activity. Our results show that selection of B. japonicum strains better adapted to elevated CO2 could improve soybean performance.
Natural plant colonization of borrow pits in boreal forest highlands of eastern Canada
Authors: Hugron Sandrine , Andersen Roxane , Poulin Monique , Rochefort Line
Published: August 2011

Plant colonization after gravel extraction for road construction is slow and is often considered to be primary succession. The goal of this study was to identify the plant communities that spontaneously colonized borrow pits located in boreal climate zones and to assess how environmental variables influenced this colonization process. It also helped identifying potential combinations of plants to use as well as environmental factors to improve to restore borrow pits. A total of 505 plots were inventoried in 117 borrow pits located in the boreal forest highlands 120 km northeast of Quebec City, Quebec, Canada (Parc national des Grands Jardins). Species cover was visually estimated for different plant communities within each borrow pit where slope and soil characteristics were also evaluated. We used multivariate analyses, including clustering, redundancy, and regression tree analyses. The borrow pits studied were undergoing primary succession processes decades after abandonment. The main pioneer species were bryophytes and lichens. Soil water content and soil physicochemistry had the greatest influence on the natural colonization of borrow pits. We observed that, based on the prevailing conditions, the bryophytes Polytrichum piliferum Hedw. and Niphotrichum canescens (Hedw.) Bednarek-Ochyra & Ochyra, lichens of the genus Stereocaulon , and the lichen Trapeliopsis granulosa (Hoffm.) Lumbsch could potentially act as nurse species and could initiate the restoration of borrow pits located in boreal forests.
Motif-based evidence that a plastid translocon component acts like a rhomboid protease substrate in yeast mitochondria
Authors: Powles Joshua , Savage Paul , Wu Edwin , Karakasis Katherine , Ko Kenton
Published: August 2011

Of the organisms with sequenced genomes, plants appear to possess the most rhomboid protease-encoding genes. However, our knowledge of processes in plants that involve rhomboid proteases and regulated intramembrane proteolysis (RIP) remains low. As expressed recently by other researchers, finding and establishing a natural substrate for a rhomboid protease represents the biggest experimental challenge. Using yeast mitochondria-based assays, a potential link between the plastid translocon component Tic40 and organellar rhomboid proteases was recently uncovered. In this particular link, rhomboid proteases appear capable of influencing the pattern of imported Tic40 in yeast mitochondria. Here, we obtained motif-oriented evidence that Tic40 acts like a rhomboid protease substrate in yeast mitochondria. A comparative analysis of sequences revealed that Tic40 may also possess similar transmembrane domain motifs found in the model substrate, Spitz. Rhomboid proteases often require these motifs to cleave substrates within intramembrane environments. Using site-directed mutagenesis and yeast mitochondria assays, the impact of mutations occurring in the motifs ASISS, GV, QP, and GVGVG of Tic40 was assessed. In terms of cleavage and changing the pattern of imported Tic40, some of the mutations showed decreased activity and a few showed enhancement. More importantly, the overall observed pattern associated with select Tic40 mutations resembled the characteristics reported for the model substrates. In particular, mutations in the Tic40 GV motif produced similar results as those observed with the Spitz GA motif, by drastically decreasing or increasing cleavage as a function of the amino acid sequence.
Retro-arc extension and continental rifting: a model for the Paleoproterozoic Baker Lake Basin, Nunavut1Geological Survey of Canada Contribution 20100436.
Authors: Hadlari T. , Rainbird R.H.
Published: August 2011

Within Baker Lake sub-basin, the ca. 1.84–1.78 Ga Baker Sequence formed in two stages. At the start of the first stage, during rift initiation, half-graben were host to siliciclastic alluvial, eolian, and lacustrine deposits and to localized felsic minette volcanics. Back-stepping of facies indicate high accommodation rates and areal expansion, which, combined with extrusion of voluminous minette volcanic rocks, are interpreted to record increased extension and rift climax. Low accommodation post-rift deposits from the second stage of basin development are relatively thin and coeval felsite domes spatially restricted. Volcanic rocks and some siliciclastic units correlate between sub-basins, and hence the interpreted history of Baker Lake sub-basin is extended across greater Baker Lake Basin. This implies that the basin formed in response to regional extension and crustal thinning. The Baker Lake Basin marks the northern extent of a series of basins that trend northeastward along the Snowbird Tectonic Zone, including an inlier of the correlative Martin Group in northern Saskatchewan. The high accommodation first stage of basin development is proposed to have been the result of intra-continental retro-arc extension during ca. 1.85–1.84 Ga formation of the Kisseynew back-arc basin of the Trans-Hudson Orogen. Upon closure of the Kisseynew back-arc basin and collision of the Superior Province with the western Churchill Province, Baker Lake Basin was subject to strike-slip faulting. The second, low accommodation stage of basin development and strike-slip faulting is proposed to record lateral tectonic escape between the Saskatchewan–Manitoba and Baffin Island – Committee Bay foci of the western Churchill – Superior Province collision.
Quartz arenites of the Cambro-Ordovician Kamouraska Formation, Quebec Appalachians, Canada: I. Deep-water depositional processes in a continental-slope environment
Authors: Malhame Pierre , Hesse Reinhard
Published: August 2011

The Kamouraska Formation is an uppermost Cambrian – lowermost Ordovician quartz-arenite-dominated unit of controversial origin deposited on the southeastern slope of Laurentia bordering the Iapetus Ocean. It is exposed in the Quebec Appalachians on the south shore of the St. Lawrence Estuary. The formation consists of basal polymictic conglomerate and overlying massive sheet-like quartz arenite. The conglomerate beds are reversely and reversely to normally graded. The quartz arenite beds are generally massive, although they may show coarse-tail grading. Beds containing full or partial Bouma sequences are rare. Paleoflow directions from ripple-cross lamination, ripple marks on bed surfaces, and sole marks point towards southeast, south, and southwest. The clastic sediments of the Kamouraska were transported into the deep sea by sediment gravity flows that evolved from hyperconcentrated to concentrated density flows, and then to turbidity currents. The depositional environment is interpreted to have been a southwest-trending meandering submarine canyon. The exposed part of the canyon deposits is slightly oblique to the strike of slope. If correct, our interpretation establishes the preservation of continental-slope deposits in more distal deep-water siliciclastic sedimentary rocks of the Taconian orogen in Quebec, which traditionally have been interpreted as submarine-fan and (or) basin-plain deposits. The orientation of a canyon near parallel-to strike of the slope may have been controlled by syn-depositional growth faults. The coarsest hyperconcentrated flows, which deposited the conglomerate, were restricted to the deepest parts of the canyon during its early stages of development, whereas the concentrated density flows that deposited the massive quartz-arenite beds covered a wider area.