bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled autolysis facilitates the polyhydroxyalkanoate recovery in Pseudomonas putida KT2440
Authors: Martínez Virginia , García Pedro , García José Luis , Prieto María Auxiliadora 
Published: March 2011

SummaryThe development of efficient recovery processes is essential to reduce the cost of polyhydroxyalkanoates (PHAs) production. In this work, a programmed self‐disruptive Pseudomonas putida BXHL strain, derived from the prototype medium‐chain‐length PHA producer bacterium P. putida KT2440, was constructed as a proof of concept for exploring the possibility to control and facilitate the release of PHA granules to the extracellular medium. The new autolytic cell disruption system is based on two simultaneous strategies: the coordinated action of two proteins from the pneumococcal bacteriophage EJ‐1, an endolysin (Ejl) and a holin (Ejh), and the mutation of the tolB gene, which exhibits alterations in outer membrane integrity that induce lysis hypersensitivity. The ejl and ejh coding genes were expressed under a XylS/Pm monocopy expression system inserted into the chromosome of the tolB mutant strain, in the presence of 3‐methylbenzoate as inducer molecule. Our results demonstrate that the intracellular presence of PHA granules confers resistance to cell envelope. Conditions to control the cell autolysis in P. putida BXHL in terms of optimal fermentation, PHA content and PHA recovery have been set up by exploring the sensitivity to detergents, chelating agents and wet biomass solubility in organic solvents such as ethyl acetate.
Membrane proteins of Pseudoalteromonas tunicata during the transition from planktonic to extracellular matrix‐adherent state
Authors: Hoke David E. , Zhang Kunkun , Egan Suhelen , Hatfaludi Tamas , Buckle Ashley M. , Adler Ben 
Published: March 2011

SummaryPseudoalteromonas tunicata is a marine bacterium that was originally isolated from the surface of the tunicate Ciona intestinalis. Since C. intestinalis expresses extracellular matrix (ECM) and P. tunicata has a gene encoding a functional ECM‐binding protein, we hypothesized that P. tunicata could adhere to this host via protein‐ECM interactions and as a result change its membrane proteome. An in vitro adhesion assay was developed to show that P. tunicata adheres strongly to ECM. To further study the adhesion biology of P. tunicata, two‐dimensional (2D) electrophoresis was used to explore the membrane‐associated sub‐proteome of P. tunicata during planktonic, adherent and non‐adherent states. More than 30 proteins were resolved using blue native (BN)/SDS 2D PAGE, many of which were identified by mass spectrometry. BN/SDS PAGE also allowed the identification of several novel protein complexes, which indicate structural and functional relationships for these proteins and related proteins in several other organisms. A proteomic change associated with adhesion was identified by comparison of 2D gels from the three model states. Collectively, these studies explore the membrane proteome of P. tunicata during the transition from planktonic to ECM‐adherent states.
Legionella spp. outdoors: colonization, communication and persistence
Authors: Hilbi Hubert , Hoffmann Christine , Harrison Christopher F. 
Published: March 2011

SummaryBacteria of the genus Legionella persist in a wide range of environmental habitats, including biofilms, protozoa and nematodes. Legionellaceae are ‘accidental’ human pathogens that upon inhalation cause a severe pneumonia termed ‘Legionnaires' disease’. The interactions of L. pneumophila with eukaryotic hosts are governed by the Icm/Dot type IV secretion system (T4SS) and more than 150 ‘effector proteins’, which subvert signal transduction pathways and promote the formation of the replication‐permissive ‘Legionella‐containing vacuole’. The Icm/Dot T4SS is essential to infect free‐living protozoa, such as the amoeba Dictyostelium discoideum, as well as the nematode Caenorhabditis elegans, or mammalian macrophages. To adapt to different niches, L. pneumophila not only responds to exogenous cues, but also to endogenous signals, such as the α‐hydroxyketone compound LAI‐1 (Legionella autoinducer‐1). The long‐term adaptation of Legionella spp. is based on extensive horizontal DNA transfer. In fact, Legionella spp. have acquired canonical ‘genomic islands’ of prokaryotic origin, but also a number of eukaryotic genes. Since many aspects of Legionella virulence against environmental predators and immune phagocytes are similar, an understanding of Legionella ecology provides valuable insights into the pathogenesis of legionellaceae for humans.
Quantification of syntrophic acetate‐oxidizing microbial communities in biogas processes
Authors: Westerholm Maria , Dolfing Jan , Sherry Angela , Gray Neil D. , Head Ian M. , Schnürer Anna 
Published: March 2011

SummaryChanges in communities of syntrophic acetate‐oxidizing bacteria (SAOB) and methanogens caused by elevated ammonia levels were quantified in laboratory‐scale methanogenic biogas reactors operating at moderate temperature (37°C) using quantitative polymerase chain reaction (qPCR). The experimental reactor was subjected to gradually increasing ammonia levels (0.8–6.9 g NH4+‐N l−1), whereas the level of ammonia in the control reactor was kept low (0.65–0.90 g NH4+‐N l−1) during the entire period of operation (660 days). Acetate oxidation in the experimental reactor, indicated by increased production of 14CO2 from acetate labelled in the methyl carbon, occurred when ammonia levels reached 5.5 and 6.9 g NH4+‐N l−1. Syntrophic acetate oxidizers targeted by newly designed qPCR primers were Thermacetogenium phaeum, Clostridium ultunense, Syntrophaceticus schinkii and Tepidanaerobacter acetatoxydans. The results showed a significant increase in abundance of all these bacteria except T. phaeum in the ammonia‐stressed reactor, coincident with the shift to syntrophic acetate oxidation. As the abundance of the bacteria increased, a simultaneous decrease was observed in the abundance of aceticlastic methanogens from the families Methanosaetaceae and Methanosarcinaceae. qPCR analyses of sludge from two additional high ammonia processes, in which methane production from acetate proceeded through syntrophic acetate oxidation (reactor SB) or through aceticlastic degradation (reactor DVX), demonstrated that SAOB were significantly more abundant in the SB reactor than in the DVX reactor.
Biochemical response to ursodeoxycholic acid predicts long‐term outcome in Japanese patients with primary biliary cirrhosis
Authors: Azemoto Nobuaki , Kumagi Teru , Abe Masanori , Konishi Ichiro , Matsuura Bunzo , Hiasa Yoichi , Onji Morikazu 
Published: March 2011

Aim:  There is an ongoing need for predictors of long‐term outcomes for patients with primary biliary cirrhosis (PBC). Biochemical response to ursodeoxycholic acid (UDCA) has been introduced to predict development of symptoms by our group (Ehime criteria) and to predict long‐term outcomes in Western countries (Paris, Barcelona and Rotterdam criteria). The aim of this study was to evaluate whether these criteria are also useful to predict long‐term outcomes in Japanese patients with PBC.Methods:  A retrospective chart review was conducted for 227 Japanese patients with PBC. Patients taking UDCA with an observation period of more than 6 months were included in the study. Data collection included demographics, biochemical and serological markers, and histological stage. Four different criteria regarding biochemical response to UDCA were compared and evaluated.Results:  In total, 138 patients met the inclusion criteria and underwent analysis. Using the Ehime criteria, the transplant‐free survival rate was significantly higher in responders than in non‐responders (P = 0.010). The Paris criteria also predicted long‐term outcomes in our population (P = 0.003), whereas the Barcelona and Rotterdam criteria showed no such association (P = 0.282 and P = 0.553, respectively).Conclusion:  Good biochemical response to UDCA according to the Ehime and Paris criteria is associated with long‐term outcome in Japanese patients with PBC and allows identification of non‐responders who may benefit from further trials. Finally, Ehime criteria should be validated in a different patient cohort.
Off-Target Gene Regulation Mediated by Transcriptional Repressors of Antimicrobial Efflux Pump Genes in Neisseria gonorrhoeae
Authors: Johnson Paul J. T. , Stringer Virginia A. , Shafer William M. 
Published: March 2011

ABSTRACT

DNA-binding proteins that control expression of drug efflux pump genes have been termed “local regulators” as their encoding gene is often located adjacent to the gene(s) that they regulate. However, results from recent studies indicate that they can control genes outside efflux pump-encoding loci, which we term as being “off target.” For example, the MtrR repressor was initially recognized for its ability to repress transcription of the
mtrCDE
-encoded efflux pump operon in the strict human pathogen
Neisseria gonorrhoeae
, but recent results from genetic and microarray studies have shown that it can control expression of nearly 70 genes scattered throughout the chromosome. One of the off-target MtrR-repressed genes is
glnA
, which encodes glutamine synthetase. Herein, we confirm the capacity of MtrR to repress
glnA
expression and provide evidence that such repression is due to its ability to negatively influence the binding of a second DNA-binding protein (FarR), which activates
glnA
. FarR was previously recognized as a transcriptional repressor of the
farAB
-encoded efflux pump operon. Thus, two DNA-binding proteins previously characterized as repressors of genes encoding efflux pumps that contribute to gonococcal resistance to antimicrobials can act in an opposing manner to modulate expression of a gene involved in basic metabolism.
Sequential Population Pharmacokinetic Modeling of Lopinavir and Ritonavir in Healthy Volunteers and Assessment of Different Dosing Strategies
Authors: Dickinson Laura , Boffito Marta , Back David , Else Laura , von Hentig Nils , Davies Geraint , Khoo Saye , Pozniak Anton , Moyle Graeme , Aarons Leon 
Published: March 2011

ABSTRACTNonlinear mixed-effects modeling was applied to explore the relationship between lopinavir and ritonavir concentrations over 72 h following drug cessation and also to assess other lopinavir and ritonavir dosing strategies compared to the standard 400-mg–100-mg twice-daily dose. Data from 16 healthy volunteers were included. Possible covariates influencing lopinavir and ritonavir pharmacokinetics were also assessed. Data were modeled first separately and then together by using individually predicted ritonavir pharmacokinetic parameters in the final lopinavir model. The model was evaluated by means of a visual predictive check and external validation. A maximum-effect model in which ritonavir inhibited the elimination of lopinavir best described the relationship between ritonavir concentrations and lopinavir clearance (CL/F). A ritonavir concentration of 0.06 mg/liter was associated with a 50% maximum inhibition of the lopinavir CL/F. The population prediction of the lopinavir CL/Fin the absence of ritonavir was 21.6 liters/h (relative standard error, 14.0%), and the apparent volume of distribution and absorption rate constant were 55.3 liters (relative standard error, 10.2%) and 0.57 h−1(relative standard error, 0.39%), respectively. Overall, 92% and 94% of the observed concentrations were encompassed by the 95% prediction intervals for lopinavir and ritonavir, respectively, which is indicative of an adequate model. Predictions of concentrations from an external data set (HIV infected) (n= 12) satisfied predictive performance criteria. Simulated lopinavir exposures at lopinavir-ritonavir doses of 200 mg-150 mg and 200 mg-50 mg twice daily were 38% and 65% lower, respectively, than that of the standard dose. The model allows a better understanding of the interaction between lopinavir and ritonavir and may allow a better prediction of lopinavir concentrations and assessments of different dosing strategies.
Paradoxical Effect of Caspofungin against Candida Bloodstream Isolates Is Mediated by Multiple Pathways but Eliminated in Human Serum
Authors: Shields Ryan K. , Nguyen M. Hong , Du Chen , Press Ellen , Cheng Shaoji , Clancy Cornelius J. 
Published: March 2011

ABSTRACT

Paradoxical growth of
Candida in vitro
at echinocandin concentrations exceeding the MIC is well described, but the clinical relevance is unknown. We assessed echinocandin paradoxical effects against
Candida
bloodstream isolates (BSI) in the presence or absence of human serum and investigated regulatory mechanisms. As determined by broth microdilution, a paradoxical effect was evident for 60% (18/30), 23% (7/30), and 13% (4/30) of
Candida albicans
BSI exposed to caspofungin, anidulafungin, and micafungin, respectively, at achievable human serum concentrations (≤8 μg/ml). A paradoxical effect was not evident among 34
C. glabrata
BSI and was observed only for caspofungin against
C. parapsilosis
(4%, 1/23). As determined in time-kill studies, a caspofungin paradoxical effect was demonstrated by
C. albicans
(2/3),
C. glabrata
(1/3), and
C. parapsilosis
(1/3), including BSI that were determined to be negative by microdilution. In 50% human serum, a paradoxical effect was eliminated at caspofungin concentrations up to 64 μg/ml for 100% (8/8) of the
C. albicans
BSI. A caspofungin paradoxical effect was also eliminated by chitin synthase inhibitor nikkomycin Z and at achievable concentrations of calcineurin pathway inhibitors, tacrolimus and cyclosporine. Moreover, these agents were synergistic with caspofungin against 100, 100, and 88% (7/8) of
C. albicans
, respectively, and exerted their own paradoxical effects. Finally, paradoxical growth was eliminated in
C. albicans irs4
- and
inp51
-null mutants, which lack phosphatidylinositol-(4,5)-bisphosphate 5′-phosphatase. Our findings suggest that the paradoxical effect is unlikely to be important
in vivo
but remains an important tool to study cell wall stress responses. We implicate the Irs4-Inp51 phosphatidylinositol-(4,5)-bisphosphate 5′-phosphatase as a novel regulator of paradoxical growth.
Decrease in Penicillin Susceptibility Due to Heat Shock Protein ClpL in Streptococcus pneumoniae
Authors: Tran Thao Dang-Hien , Kwon Hyog-Young , Kim Eun-Hye , Kim Ki-Woo , Briles David E. , Pyo Suhkneung , Rhee Dong-Kwon 
Published: March 2011

ABSTRACT

Antibiotic resistance and tolerance are increasing threats to global health as antibiotic-resistant bacteria can cause severe morbidity and mortality and can increase treatment cost 10-fold. Although several genes contributing to antibiotic tolerance among pneumococci have been identified, we report here that ClpL, a major heat shock protein, could modulate cell wall biosynthetic enzymes and lead to decreased penicillin susceptibility. On capsular type 1, 2, and 19 genetic backgrounds, mutants lacking ClpL were more susceptible to penicillin and had thinner cell walls than the parental strains, whereas a ClpL-overexpressing strain showed a higher resistance to penicillin and a thicker cell wall. Although exposure of
Streptococcus pneumoniae
D39 to penicillin inhibited expression of the major cell wall synthesis gene
pbp2x
, heat shock induced a ClpL-dependent increase in the mRNA levels and protein synthesized by
pbp2x
. Inducible ClpL expression correlated with PBP2x expression and penicillin susceptibility. Fractionation and electron micrograph data revealed that ClpL induced by heat shock is localized at the cell wall, and the Δ
clpL
showed significantly reduced net translocation of PBP2x into the cell wall. Moreover, coimmunoprecipitation with either ClpL or PBP2x antibody followed by reprobing with ClpL or PBP2x antibody showed an interaction between ClpL and PBP2x after heat stress. This interaction was confirmed by His tag pulldown assay with either ClpLHis
6
or PBP2xHis
6
. Thus, ClpL stabilized
pbp2x
expression, interacted with PBP2x, and facilitated translocation of PBP2x, a key protein of cell wall synthesis process, contributing to the decrease of antibiotic susceptibility in
S. pneumoniae
.
Double-Carbapenem Therapy for Carbapenemase-Producing Klebsiella pneumoniae
Authors: Bulik Catharine C. , Nicolau David P. 
Published: March 2011

ABSTRACT

The limited treatment options available for carbapenemase-producing
Klebsiella pneumoniae
(KPC) have made it a formidable pathogen. Previously we have shown the enhanced activity of pharmacodynamically optimized doripenem against KPC. Capitalizing on KPC's increased affinity for ertapenem, we evaluated the efficacy of a combination of ertapenem and doripenem in both an
in vitro
chemostat and an
in vivo
murine thigh infection model. Overall, the combination of doripenem plus ertapenem demonstrated enhanced efficacy over either agent alone.
Novel Types of Staphylococcal Cassette Chromosome
mec
Elements Identified in Clonal Complex 398 Methicillin-Resistant Staphylococcus aureus Strains
Authors: Li Shanshuang , Skov Robert Leo , Han Xiao , Larsen Anders Rhod , Larsen Jesper , Sørum Marit , Wulf Mireille , Voss Andreas , Hiramatsu Keiichi , Ito Teruyo 
Published: March 2011

ABSTRACT

The structures of staphylococcal cassette chromosome
mec
(SCC
mec
) elements carried by 31 clonal complex 398 (CC398) methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from the participants at a conference were analyzed. The SCC
mec
s were classified into novel types, namely, IX, X, V(5C2&5) subtype c, and IVa. Type V(5C2&5) subtype c, IX, and X SCC
mec
s carried genes conferring resistance to metals. The structures of SCC
mec
s from CC398 strains were distinct from those normally found in humans, adding to the evidence that humans are not the original host for CC398.
Antimicrobial Peptoids Are Effective against Pseudomonas aeruginosa Biofilms
Authors: Kapoor Rinki , Wadman Mayken W. , Dohm Michelle T. , Czyzewski Ann M. , Spormann Alfred M. , Barron Annelise E. 
Published: March 2011

ABSTRACT

The resistance of biofilms to conventional antibiotics complicates the treatment of chronic cystic fibrosis (CF). We investigated the effects of peptoids, peptides, and conventional antibiotics on the biomass and cell viability within
Pseudomonas aeruginosa
biofilms. At their MICs, peptoids 1 and 1-C13
4mer
caused maximum reductions in biomass and cell viability, respectively. These results suggest that peptoids of this class could be worth exploring for the treatment of pulmonary infections occurring in CF patients.
In Vitro Activities of Anidulafungin and Other Antifungal Agents against Biofilms Formed by Clinical Isolates of Different Candida and Aspergillus Species
Authors: Fiori Barbara , Posteraro Brunella , Torelli Riccardo , Tumbarello Mario , Perlin David S. , Fadda Giovanni , Sanguinetti Maurizio 
Published: March 2011

ABSTRACT

We tested the activities of anidulafungin and other antifungal agents against clinical isolates of different fungal species. For
Candida
species, high sessile MIC
90
s (SMIC
90
s) were obtained for fluconazole, voriconazole, and amphotericin B, whereas the anidulafungin SMIC
90
s were very low, as were those for caspofungin. Comparatively, for
Aspergillus
species, higher SMIC
90
values were obtained not only for amphotericin B and voriconazole but also for the echinocandins.
A Novel Gene Cassette,
aacA43
, in a Plasmid-Borne Class 1 Integron
Authors: Partridge Sally R. , Thomas Lee C. , Ginn Andrew N. , Wiklendt Agnieszka M. , Kyme Pierre , Iredell Jonathan R. 
Published: March 2011

ABSTRACT

A novel gene cassette,
aacA43
, was identified in the
aadB-aacA43-oxa10-smr2
cassette array in a class 1 integron. Like related aminoglycoside-(6′)-acetyltransferases, AacA43 confers clinically relevant resistance to kanamycin, tobramycin, and some less-used aminoglycosides but not to gentamicin. Although transferable on an IncL/M plasmid,
aacA43
was identified in only two different
Klebsiella pneumoniae
strains (14 isolates), one
Escherichia coli
strain (2 isolates), and one
Enterobacter cloacae
strain in a survey of patients in a Sydney intensive care unit in 2004-2005.
Saturability of Granulocyte Kill of Pseudomonas aeruginosa in a Murine Model of Pneumonia
Authors: Drusano G. L. , VanScoy B. , Liu W. , Fikes S. , Brown D. , Louie A. 
Published: March 2011

ABSTRACT

Outcomes for patients with dense bacterial burdens, such as ventilator-associated pneumonia (VAP) patients, are often critically influenced by the adequacy of antimicrobial chemotherapy and by the response of the immune system, particularly the granulocytes. Little information is available about the quantitation of kill of organisms over time by granulocytes. In this investigation, we examined the impact of the baseline bacterial burden on the ability of granulocytes alone (without chemotherapy) to keep the number of organisms in check or to kill them over a 24-h period.
Pseudomonas aeruginosa
ATCC 27853 was the study organism, and we employed a murine pneumonia model (granulocyte replete) for the study. We found that the ability of the immune system to kill
P. aeruginosa
was saturable. The burden at which the system was half saturated was 2.15 × 10
6
± 2.66 × 10
6
CFU/g. Burdens greater than 10
7
CFU/g demonstrated net growth over 24 h. These findings suggest the need for aggressive chemotherapy early in the treatment of VAP to keep the burden from saturating the granulocytes. This should optimize the outcome for these seriously infected patients.
In Vitro Activity of Ceftazidime Combined with NXL104 versus Pseudomonas aeruginosa Isolates Obtained from Patients in Canadian Hospitals (CANWARD 2009 Study)
Authors: Walkty A. , DeCorby M. , Lagacé-Wiens P. R. S. , Karlowsky J. A. , Hoban D. J. , Zhanel G. G. 
Published: March 2011

ABSTRACT

The
in vitro
activity of ceftazidime in combination with NXL104 versus 470
Pseudomonas aeruginosa
clinical isolates was evaluated using Clinical and Laboratory Standards Institute (CLSI) broth microdilution methods. Ceftazidime had MIC
90
s of 8 μg/ml and 32 μg/ml in the presence and absence of NXL104, respectively. Of 25 multidrug-resistant
P. aeruginosa
isolates, the percentages with a ceftazidime MIC of ≤8 μg/ml with and without NXL104 were 60% and 4%, respectively. These data suggest that the ceftazidime-NXL104 combination may prove useful for treating many
P. aeruginosa
infections.