bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection, Optimization, and Pharmacokinetic Properties of a Novel, Potent Antiviral Locked Nucleic Acid-Based Antisense Oligomer Targeting Hepatitis C Virus Internal Ribosome Entry Site
Authors: Laxton Carl , Brady Kevin , Moschos Sterghios , Turnpenny Paul , Rawal Jaiessh , Pryde David C. , Sidders Ben , Corbau Romu , Pickford Chris , Murray E. J. 
Published: April 2011

ABSTRACTWe have screened 47 locked nucleic acid (LNA) antisense oligonucleotides (ASOs) targeting conserved (>95% homology) sequences in the hepatitis C virus (HCV) genome using the subgenomic HCV replicon assay and generated both antiviral (50% effective concentration [EC50]) and cytotoxic (50% cytotoxic concentration [CC50]) dose-response curves to allow measurement of the selectivity index (SI). This comprehensive approach has identified an LNA ASO with potent antiviral activity (EC50= 4 nM) and low cytotoxicity (CC50>880 nM) targeting the 25- to 40-nucleotide region (nt) of the HCV internal ribosome entry site (IRES) containing the distal and proximal miR-122 binding sites. LNA ASOs targeting previously known accessible regions of the IRES, namely, loop III and the initiation codon in loop IV, had poor SI values. We optimized the LNA ASO sequence by performing a 1-nucleotide walk through the 25- to 40-nt region and show that the boundaries for antiviral efficacy are extremely precise. Furthermore, we have optimized the format for the LNA ASO using different gapmer and mixomer patterns and show that RNase H is required for antiviral activity. We demonstrate that RNase H-refractory ASOs targeting the 25- to 40-nt region have no antiviral effect, revealing important regulatory features of the 25- to 40-nt region and suggesting that RNase H-refractory LNA ASOs can act as potential surrogates for proviral functions of miR-122. We confirm the antisense mechanism of action using mismatched LNA ASOs. Finally, we have performed pharmacokinetic experiments to demonstrate that the LNA ASOs have a very long half-life (>5 days) and attain hepatic maximum concentrations >100 times the concentration required forin vitroantiviral activity.
In Vivo
Efficacy of Glycopeptide-Colistin Combination Therapies in a
Galleria mellonella
Model of
Acinetobacter baumannii
Infection
Authors: Hornsey M. , Wareham D. W. 
Published: April 2011

ABSTRACT

The treatment of
Acinetobacter baumannii
infections poses a significant clinical challenge, with isolates resistant to all commonly used agents increasingly being reported. With few new agents in the pipeline, clinicians are increasingly turning to combinations of antimicrobials in the hope that they may act synergistically together. In this study we assessed the activities of two glycopeptide-colistin combinations both
in vitro
and using a
Galleria mellonella
caterpillar model of
A. baumannii
infection. In checkerboard assays both vancomycin and teicoplanin were highly active against susceptible and multidrug-resistant strains of
A. baumannii
when combined with colistin (fractional inhibitory concentration [FIC] of <0.25). Treatment of
G. mellonella
caterpillars infected with lethal doses of
A. baumannii
resulted in significantly enhanced survival rates when either vancomycin or teicoplanin was given with colistin compared to colistin treatment alone (
P
< 0.05). This effect was most marked when vancomycin was the glycopeptide administered, although this agent was also highly effective as monotherapy, possibly through an immunomodulatory action on the
G. mellonella
response to
A. baumannii
infection. This work suggests that glycopeptide-colistin combinations are highly active against
A. baumannii
both
in vitro
and in a simple animal model of infection. They should be considered further as potential treatments for difficult-to-treat
A. baumannii
infections.
Dose Range Evaluation of Mycograb C28Y Variant, a Human Recombinant Antibody Fragment to Heat Shock Protein 90, in Combination with Amphotericin B-Desoxycholate for Treatment of Murine Systemic Candidiasis
Authors: Louie Arnold , Stein Daniel S. , Zack Julia Z. , Liu Weiguo , Conde Haley , Fregeau Christine , VanScoy Brian D. , Drusano George L. 
Published: April 2011

ABSTRACT

Systemic candidiasis causes significant mortality in patients despite amphotericin B (AMB) therapy. Mycograb C28Y variant, a human recombinant antibody fragment to heat shock protein 90, is closely related to Mycograb, which showed a survival advantage in combination with AMB in a phase III human trial. The Mycograb C28Y variant could potentially increase the antifungal effect of AMB. In our study, the interaction between AMB-desoxycholate (DAMB) and the Mycograb C28Y variant was characterized
in vitro
by using a checkerboard method. Quantitative cultures of kidneys, livers, and spleens of neutropenic mice with systemic
Candida albicans
infections were used to assess the
in vivo
interaction between 1.4 mg/kg of body weight/day of DAMB and 0.15, 1.5, and 15 mg/kg/day of the Mycograb C28Y variant after 1, 3, and 5 days of therapy. DAMB and Mycograb C28Y variant monotherapies, vehicle, and a no-treatment arm served as controls. Also, single- and multidose pharmacokinetics for the Mycograb C28Y variant were determined. Indifference or synergy between DAMB and the Mycograb C28Y variant was seen in two trials by the checkerboard method. The pharmacokinetics of the Mycograb C28Y variant was best described by a 2-compartment model with a median serum
t
1/2
α
of ∼0.198 h and a
t
1/2
β
of ∼1.77 h. In mice, DAMB together with the Mycograb C28Y variant was no more effective than AMB alone (
P
> 0.05 by analysis of variance). The Mycograb C28Y variant alone had no antifungal activity. We therefore conclude that the Mycograb C28Y variant in combination with DAMB offered no benefit over DAMB monotherapy in a neutropenic murine model of systemic candidiasis.
Posaconazole in Human Serum: a Greater Pharmacodynamic Effect than Predicted by the Non-Protein-Bound Serum Concentration
Authors: Lignell Anders , Löwdin Elisabeth , Cars Otto , Chryssanthou Erja , Sjölin Jan 
Published: April 2011

ABSTRACT

It is generally accepted that only the unbound fraction of a drug is pharmacologically active. Posaconazole is an antifungal agent with a protein binding of 98 to 99%. Taking into account the degree of protein binding, plasma levels in patients, and MIC levels of susceptible strains, it can be assumed that the free concentration of posaconazole sometimes will be too low to exert the expected antifungal effect. The aim was therefore to test the activity of posaconazole in serum in comparison with that of the calculated unbound concentrations in protein-free media. Significant differences (
P
< 0.05) from the serum control were found at serum concentrations of posaconazole of 1.0 and 0.10 mg/liter, with calculated free concentrations corresponding to 1× MIC and 0.1× MIC, respectively, against one
Candida lusitaniae
strain selected for proof of principle. In RPMI 1640, the corresponding calculated unbound concentration of 0.015 mg/liter resulted in a significant effect, whereas that of 0.0015 mg/liter did not. Also, against seven additional
Candida
strains tested, there was an effect of the low posaconazole concentration in serum, in contrast to the results in RPMI 1640. Fluconazole, a low-grade-protein-bound antifungal, was used for comparison at corresponding concentrations in serum and RPMI 1640. No effect was observed at the serum concentration, resulting in a calculated unbound concentration of 0.1× MIC. In summary, there was a substantially greater pharmacodynamic effect of posaconazole in human serum than could be predicted by the non-protein-bound serum concentration. A flux from serum protein-bound to fungal lanosterol 14α-demethylase-bound posaconazole is suggested.
Genetic Resistance Elements Carrying
mef
Subclasses Other than
mef
(A) in Streptococcus pyogenes
Authors: Del Grosso Maria , Camilli Romina , Barbabella Giada , Blackman Northwood John , Farrell David J. , Pantosti Annalisa 
Published: April 2011

ABSTRACT

In
Streptococcus pyogenes
, efflux-mediated erythromycin resistance is associated with the
mef
gene, represented mostly by
mef
(A), although a small portion of strains carry different
mef
subclasses. We characterized the composite genetic elements, including
mef
subclasses other than
mef
(A), associated with other resistance genes in
S. pyogenes
isolates. Determination of the genetic elements was performed by PCR mapping. The strains carrying mosaic
mef
(A/E), in which the 5′ region was identical to
mef
(A) and the 3′ region was identical to
mef
(E), also carried
tet
(O). The two genes were found enclosed in an element similar to
S. pyogenes
prophage Φm46.1, designated the Φm46.1-like element. In
S. pyogenes
strains carrying
mef
(E) and
tet
(M),
mef
(E) was included in a typical mega element, and in some strains, it was physically associated with
tet
(M) in the composite element Tn
2009
.
S. pyogenes
strains carrying
mef
(I) also carried
catQ
; the two genes were linked in a fragment representing a portion of the 5216IQ complex of
Streptococcus pneumoniae
, designated the defective IQ element. In the only isolate carrying a novel
mef
gene, this was associated with
catQ
and
tet
(M) in a genetic element similar to the 5216IQ complex of
S. pneumoniae
(5216IQ-like complex), suggesting that the novel
mef
is in fact a variant of
mef
(I). This study demonstrates that the composite elements containing
mef
are shared between
S. pyogenes
and
S. pneumoniae
and suggests that it is important to distinguish the
mef
subclass on the basis of the genetic element containing it.
Significant Natural Product Biosynthetic Potential of Actinorhizal Symbionts of the Genus Frankia, as Revealed by Comparative Genomic and Proteomic Analyses
Authors: Udwary Daniel W. , Gontang Erin A. , Jones Adam C. , Jones Carla S. , Schultz Andrew W. , Winter Jaclyn M. , Yang Jane Y. , Beauchemin Nicholas , Capson Todd L. , Clark Benjamin R. , Esquenazi Eduardo , Eustáquio Alessandra S. , Freel Kelle , Gerwick Lena , Gerwick William H. , Gonzalez David , Liu Wei-Ting , Malloy Karla L. , Maloney Katherine N. , Nett Markus , Nunnery Joshawna K. , Penn Kevin , Prieto-Davo Alejandra , Simmons Thomas L. , Weitz Sara , Wilson Micheal C. , Tisa Louis S. , Dorrestein Pieter C. , Moore Bradley S. 
Published: April 2011

ABSTRACT

Bacteria of the genus
Frankia
are mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genus
Frankia
has largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences of
Frankia
strains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from other
Frankia
strains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis of
Frankia
sp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed in
Frankia
sp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in the
Frankia
genus.
Distribution of Bacillus thuringiensis subsp. israelensis in Soil of a Swiss Wetland Reserve after 22 Years of Mosquito Control
Authors: Guidi Valeria , Patocchi Nicola , Lüthy Peter , Tonolla Mauro 
Published: April 2011

ABSTRACT

Recurrent treatments with
Bacillus thuringiensis
subsp.
israelensis
are required to control the floodwater mosquito
Aedes vexans
that breeds in large numbers in the wetlands of the Bolle di Magadino Reserve in Canton Ticino, Switzerland. Interventions have been carried out since 1988. In the present study, the spatial distribution of resting
B. thuringiensis
subsp.
israelensis
spores in the soil was measured. The
B. thuringiensis
subsp.
israelensis
concentration was determined in soil samples collected along six transects covering different elevations within the periodically flooded zones. A total of 258 samples were processed and analyzed by quantitative PCR that targeted an identical fragment of 159 bp for the
B. thuringiensis
subsp.
israelensis cry4Aa
and
cry4Ba
genes.
B. thuringiensis
subsp.
israelensis
spores were found to persist in soils of the wetland reserve at concentrations of up to 6.8 log per gram of soil. Continuous accumulation due to regular treatments could be excluded, as the decrease in spores amounted to 95.8% (95% confidence interval, 93.9 to 97.7%). The distribution of spores was correlated to the number of
B. thuringiensis
subsp.
israelensis
treatments, the elevation of the sampling point, and the duration of the flooding periods. The number of
B. thuringiensis
subsp.
israelensis
treatments was the major factor influencing the distribution of spores in the different topographic zones (
P
< 0.0001). These findings indicated that
B. thuringiensis
subsp.
israelensis
spores are rather immobile after their introduction into the environment.
Extracellular Reduction of Hexavalent Chromium by Cytochromes MtrC and OmcA of Shewanella oneidensis MR-1
Authors: Belchik Sara M. , Kennedy David W. , Dohnalkova Alice C. , Wang Yuanmin , Sevinc Papatya C. , Wu Hong , Lin Yuehe , Lu H. Peter , Fredrickson James K. , Shi Liang 
Published: April 2011

ABSTRACTTo characterize the roles of cytochromes MtrC and OmcA ofShewanella oneidensisMR-1 in Cr(VI) reduction, the effects of deleting themtrCand/oromcAgene on Cr(VI) reduction and the cellular locations of reduced Cr(III) precipitates were investigated. Compared to the rate of reduction of Cr(VI) by the wild type (wt), the deletion ofmtrCdecreased the initial rate of Cr(VI) reduction by 43.5%, while the deletion ofomcAor bothmtrCandomcAlowered the rate by 53.4% and 68.9%, respectively. In wt cells, Cr(III) precipitates were detected by transmission electron microscopy in the extracellular matrix between the cells, in association with the outer membrane, and inside the cytoplasm. No extracellular matrix-associated Cr(III) precipitates, however, were found in the cytochrome mutant cell suspension. In mutant cells without either MtrC or OmcA, most Cr(III) precipitates were found in association with the outer membrane, while in mutant cells lacking both MtrC and OmcA, most Cr(III) precipitates were found inside the cytoplasm. Cr(III) precipitates were also detected by scanning election microscopy on the surfaces of the wt and mutants without MtrC or OmcA but not on the mutant cells lacking both MtrC and OmcA, demonstrating that the deletion ofmtrCandomcAdiminishes the extracellular formation of Cr(III) precipitates. Furthermore, purified MtrC and OmcA reduced Cr(VI) with apparentkcatvalues of 1.2 ± 0.2 (mean ± standard deviation) and 10.2 ± 1 s−1andKmvalues of 34.1 ± 4.5 and 41.3 ± 7.9 μM, respectively. Together, these results consistently demonstrate that MtrC and OmcA are the terminal reductases used byS. oneidensisMR-1 for extracellular Cr(VI) reduction where OmcA is a predominant Cr(VI) reductase.
Dynamics of Flagellum- and Pilus-Mediated Association of Pseudomonas aeruginosa with Contact Lens Surfaces
Authors: Tran Victoria B. , Fleiszig Suzanne M. J. , Evans David J. , Radke Clayton J. 
Published: April 2011

ABSTRACT

Flagella and pili are appendages that modulate attachment of
Pseudomonas aeruginosa
to solid surfaces. However, previous studies have mostly reported absolute attachment. Neither the dynamic roles of these appendages in surface association nor those of attachment phenotypes have been quantified. We used video microscopy to address this issue. Unworn, sterile, soft contact lenses were placed in a laminar-flow optical chamber. Initial lens association kinetics for
P. aeruginosa
strain PAK were assessed in addition to lens-surface association phenotypes. Comparisons were made to strains with mutations in flagellin (
fliC
) or pilin (
pilA
) or those in flagellum (
motAB
) or pilus (
pilU
) function. PAK and its mutants associated with the contact lens surface at a constant rate according to first-order kinetics. Nonswimming mutants associated ∼30 to 40 times slower than the wild type. PAK and its
pilA
mutant associated at similar rates, but each ∼4 times faster than the
pilU
mutant. Lens attachment by wild-type PAK induced multiple phenotypes (static, lateral, and rotational surface movement), each showing only minor detachment. Flagellin (
fliC
) and flagellar-motility (
motAB
) mutants did not exhibit surface rotation. Conversely, strains with mutations in pilin (
pilA
) and pilus retraction (
pilU
) lacked lateral-surface movement but displayed enhanced surface rotation. Slower surface association of swimming-incapable
P. aeruginosa
mutants was ascribed to lower convective-diffusion-arrival rates, not to an inability to adhere. Flagellum function (swimming) enhanced lens association, attachment, and rotation; hyperpiliation hindered lens association.
P. aeruginosa
bound through three different adhesion sites: flagellum, pili, and body. Reduction of bacterial attachment to contact lenses thus requires blockage of multiple adhesion phenotypes.
Determining Thermal Inactivation of Escherichia coli O157:H7 in Fresh Compost by Simulating Early Phases of the Composting Process
Authors: Singh Randhir , Kim Jinkyung , Shepherd Marion W. , Luo Feng , Jiang Xiuping 
Published: April 2011

ABSTRACT

A three-strain mixture of
Escherichia coli
O157:H7 was inoculated into fresh dairy compost (ca. 10
7
CFU/g) with 40 or 50% moisture and was placed in an environmental chamber (ca. 70% humidity) that was programmed to ramp from room temperature to selected composting temperatures in 2 and 5 days to simulate the early composting phase. The surviving
E. coli
O157:H7 population was analyzed by direct plating and enrichment. Optimal and suboptimal compost mixes, with carbon/nitrogen (C/N) ratios of 25:1 and 16:1, respectively, were compared in this study. In the optimal compost mix,
E. coli
O157:H7 survived for 72, 48, and 24 h in compost with 40% moisture and for 72, 24, and 24 h with 50% moisture at 50, 55, and 60°C, respectively, following 2 days of come-up time (rate of heating up). However, in the suboptimal compost mix, the pathogen survived for 288, 72, and 48 h in compost with 40% moisture and for 240, 72, 24 h in compost with 50% moisture at the same temperatures, respectively. Pathogen survival was longer, with 5 days of come-up time compared with 2 days of come-up. Overall,
E. coli
O157:H7 was inactivated faster in the compost with 50% moisture than in the compost with 40% at 55 and 60°C. Both moisture and come-up time were significant factors affecting Weibull model parameters. Our results suggest that slow come-up time at the beginning of composting can extend pathogen survival during composting. Additionally, both the C/N ratio and the initial moisture level in the compost mix affect the rate of pathogen inactivation as well.
Antimicrobial Effect of Chitosan Nanoparticles on Streptococcus mutans Biofilms
Authors: Chávez de Paz Luis E. , Resin Anton , Howard Kenneth A. , Sutherland Duncan S. , Wejse Peter L. 
Published: April 2011

ABSTRACT
Nanoparticle complexes were prepared from chitosans of various molecular weights (MW) and degrees of deacetylation (DD). The antimicrobial effect was assessed by the Live/Dead BacLight technique in conjunction with confocal scanning laser microscopy (CSLM) and image analysis. Nanocomplexes prepared from chitosans with high MW showed a low antimicrobial effect (20 to 25% of cells damaged), whereas those prepared from low-MW chitosans showed high antimicrobial effect (>95% of cells damaged).
Protein Targeting to the Parasitophorous Vacuole Membrane of Plasmodium falciparum
Authors: Eksi Saliha , Williamson Kim C. 
Published: April 2011

ABSTRACTRed blood cell (RBC) invasion and parasitophorous vacuole (PV) formation byPlasmodium falciparumare critical for the development and pathogenesis of malaria, a continuing global health problem. Expansion of the PV membrane (PVM) during growth is orchestrated by the parasite. This is particularly important in mature RBCs, which lack internal organelles and no longer actively synthesize membranes. Pfs16, a 16-kDa integral PVM protein expressed by gametocytes, was chosen as a model for studying the trafficking of material from the parasite across the PV space to the PVM. The locations of Pfs16-green fluorescent protein (GFP) reporter proteins containing distinct regions of Pfs16 were tracked from RBC invasion to emergence. Inclusion of the 53 C-terminal amino acids (aa) of Pfs16 to a GFP reporter construct already containing the N-terminal secretory signal sequence was sufficient for targeting to and retention on the PVM. An amino acid motif identified in this region was also found in seven other known PVM proteins. Removal of the 11 C-terminal aa did not affect PVM targeting, but membrane retention was decreased. Additionally, during emergence from the PVM and RBC, native Pfs16 and the full-length Pfs16-GFP reporter protein were found to concentrate on the ends of the gametocyte. Capping was not observed in constructs lacking the amino acids between the N-terminal secretory signal sequence and the transmembrane domain, suggesting that this region, which is not required for PVM targeting, is involved in capping. This is the first report to define the amino acid domains required for targeting to theP. falciparumPVM.
Campylobacter jejuni Lipooligosaccharides Modulate Dendritic Cell-Mediated T Cell Polarization in a Sialic Acid Linkage-Dependent Manner
Authors: Bax Marieke , Kuijf Mark L. , Heikema Astrid P. , van Rijs Wouter , Bruijns Sven C. M. , García-Vallejo Juan J. , Crocker Paul R. , Jacobs Bart C. , van Vliet Sandra J. , van Kooyk Yvette 
Published: April 2011

ABSTRACTCarbohydrate mimicry betweenCampylobacter jejunilipooligosaccharides (LOS) and host neural gangliosides plays a crucial role in the pathogenesis of Guillain-Barré syndrome (GBS).Campylobacter jejuniLOS may mimic various gangliosides, which affects the immunogenicity and the type of neurological deficits in GBS patients. Previous studies have shown the interaction of LOS with sialic acid-specific siglec receptors, although the functional consequences remain unknown. Cells that express high levels of siglecs include dendritic cells (DCs), which are crucial for initiation and differentiation of immune responses. We confirm that α2,3-sialylated GD1a/GM1a mimic and α2,8-sialylated GD1c mimic LOS structures interact with recombinant Sn and siglec-7, respectively. Although the linkage of the terminal sialic acid of LOS did not regulate expression of DC maturation markers, it displayed clear opposite expression levels of interleukin-12 (IL-12) and OX40L, molecules involved in DC-mediated Th cell differentiation. Accordingly, targeting DC-expressed siglec-7 with α2,8-linked sialylated LOS resulted in Th1 responses, whereas Th2 responses were induced by targeting with LOS containing α2,3-linked sialic acid. Thus, our data demonstrate for the first time that depending on the sialylated composition ofCampylobacter jejuniLOS, specific Th differentiation programs are initiated, possibly through targeting of distinct DC-expressed siglecs.