bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Safety of Danoprevir-Ritonavir plus Peginterferon Alfa-2a–Ribavirin in Hepatitis C Virus Genotype 1 Prior Null Responders
Authors: Gane Edward J. , Rouzier Régine , Wiercinska-Drapalo Alicja , Larrey Dominique G. , Morcos Peter N. , Brennan Barbara J. , Le Pogam Sophie , Nájera Isabel , Petric Rosemary , Tran Jonathan Q. , Kulkarni Rohit , Zhang Ying , Smith Patrick , Yetzer Ellen S. , Shulman Nancy S. 
Published: December 2013

ABSTRACT

Danoprevir (DNV) is a hepatitis C virus (HCV) protease inhibitor that achieves high sustained virologic response (SVR) rates in combination with peginterferon alfa-2a–ribavirin in treatment-naive HCV genotype 1 (G1)-infected patients. This study explored the efficacy and safety of ritonavir-boosted DNV (DNVr) plus peginterferon alfa-2a–ribavirin in G1-infected prior peginterferon-ribavirin null responders. Null responders (<2-log
10
reduction in HCV RNA level at week 12) were given an open-label combination of 100 mg of ritonavir and 100 mg of DNV (100/100 mg DNVr) every 12 h (q12h) plus peginterferon alfa-2a–ribavirin for 12 weeks. All patients achieving an early virologic response (EVR; ≥2-log
10
decrease in HCV RNA by week 12) continued treatment with peginterferon alfa-2a–ribavirin; those without an EVR discontinued all study drugs. Twenty-four prior null responders were enrolled; 16 patients (67%) were infected with HCV G1b, and 8 (33%) were infected with G1a. Ninety-six percent of patients had an
IL28B
non-CC genotype. A sustained virologic response at 24 weeks posttreatment (SVR24) was achieved in 67% of patients, with a higher rate in G1b-infected (88%) than G1a-infected (25%) patients. Resistance-related breakthrough occurred in 4/8 G1a and 1/16 G1b patients through the DNV resistance-associated variant (RAV) NS3 R155K. NS3 R155K was also detected in 2/2 G1a patients who relapsed. Treatment was well tolerated. Two patients withdrew prematurely from study medications due to adverse events. Two serious adverse events were reported; both occurred after completion of DNVr therapy and were considered unrelated to treatment. No grade 3 or 4 alanine aminotransferase (ALT) elevations were observed. DNVr plus peginterferon alfa-2a–ribavirin demonstrated high SVR24 rates in HCV G1b-infected prior null responders and was well tolerated. (This study has been registered at
ClinicalTrials.gov
under registration no. NCT01185860.)
Detection of Carbapenemase-Producing Bacteria by Using an Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry Method
Authors: Carricajo Anne , Verhoeven Paul O. , Guezzou Salim , Fonsale Nathalie , Aubert Gerald 
Published: December 2013

ABSTRACT

The emergence of carbapenemase-producing bacteria poses a new challenge in the management of antibiotic therapies for patients. This report describes a new method using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) for rapid detection of carbapenemase activity in enterobacteria,
Pseudomonas aeruginosa
, and
Acinetobacter baumannii
. In a panel of 78 isolates, including 41 carbapenemase-producing strains, the ULPC-MS/MS assay showed 100% agreement with molecular characterization, whereas six carbapenemase-producing isolates were not detected by the modified Hodge test.
Oxacillin Alters the Toxin Expression Profile of Community-Associated Methicillin-Resistant Staphylococcus aureus
Authors: Rudkin Justine K. , Laabei Maisem , Edwards Andrew M. , Joo Hwang-Soo , Otto Michael , Lennon Katrina L. , O'Gara James P. , Waterfield Nicholas R. , Massey Ruth C. 
Published: December 2013

ABSTRACT

The emergence of community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) is a growing cause for concern. These strains are more virulent than health care-associated MRSA (HA-MRSA) due to higher levels of toxin expression. In a previous study, we showed that the high-level expression of PBP2a, the alternative penicillin binding protein encoded by the
mecA
gene on type II staphylococcal cassette chromosome
mec
(SCC
mec
) elements, reduced toxicity by interfering with the Agr quorum sensing system. This was not seen in strains carrying the CA-MRSA-associated type IV SCC
mec
element. These strains express significantly lower levels of PBP2a than the other MRSA type, which may explain their relatively high toxicity. We hypothesized that as oxacillin is known to increase
mecA
expression levels, it may be possible to attenuate the toxicity of CA-MRSA by using this antibiotic. Subinhibitory oxacillin concentrations induced PBP2a expression, repressed Agr activity, and, as a consequence, decreased phenol-soluble modulin (PSM) secretion by CA-MRSA strains. However, consistent with other studies, oxacillin also increased the expression levels of alpha-toxin and Panton-Valentine leucocidin (PVL). The net effect of these changes on the ability to lyse diverse cell types was tested, and we found that where the PSMs and alpha-toxin are important, oxacillin reduced overall lytic activity, but where PVL is important, it increased lytic activity, demonstrating the pleiotropic effect of oxacillin on toxin expression by CA-MRSA.
Intersubspecific Recombination in Xylella fastidiosa Strains Native to the United States: Infection of Novel Hosts Associated with an Unsuccessful Invasion
Authors: Nunney Leonard , Hopkins Donald L. , Morano Lisa D. , Russell Stephanie E. , Stouthamer Richard 
Published: December 2013

ABSTRACT

The bacterial pathogen
Xylella fastidiosa
infects xylem and causes disease in many plant species in the Americas. Different subspecies of this bacterium and different genotypes within subspecies infect different plant hosts, but the genetics of host adaptation are unknown. Here we examined the hypothesis that the introduction of novel genetic variation via intersubspecific homologous recombination (IHR) facilitates host shifts. We investigated IHR in 33
X. fastidiosa
subsp.
multiplex
isolates previously identified as recombinant based on 8 loci (7 multilocus sequence typing [MLST] loci plus 1 locus). We found significant evidence of introgression from
X. fastidiosa
subsp.
fastidiosa
in 4 of the loci and, using published data, evidence of IHR in 6 of 9 additional loci. Our data showed that IHR regions in 2 of the 4 loci were inconsistent (12 mismatches) with
X. fastidiosa
subsp.
fastidiosa
alleles found in the United States but consistent with alleles from Central America. The other two loci were consistent with alleles from both regions. We propose that the recombinant forms all originated via genomewide recombination of one
X. fastidiosa
subsp.
multiplex
ancestor with one
X. fastidiosa
subsp.
fastidiosa
donor from Central America that was introduced into the United States but subsequently disappeared. Using all of the available data, 5 plant hosts of the recombinant types were identified, 3 of which also supported non-IHR
X. fastidiosa
subsp.
multiplex
, but 2 were unique to recombinant types from blueberry (7 isolates from Georgia, 3 from Florida); and blackberry (1 each from Florida and North Carolina), strongly supporting the hypothesis that IHR facilitated a host shift to blueberry and possibly blackberry.
Ingestibility, Digestibility, and Engineered Biological Control Potential of Flavobacterium
hibernum
, Isolated from Larval Mosquito Habitats
Authors: Chen Shicheng , Kaufman Michael G. , Korir Michelle L. , Walker Edward D. 
Published: December 2013

ABSTRACT

Flavobacterium
hibernum
, isolated from larval habitats of the eastern tree hole mosquito,
A. triseriatus
, remained suspended in the larval feeding zone much longer (8 days) than other bacteria. Autofluorescent protein markers were developed for the labeling of
F. hibernum
with a strong flavobacterial expression system. Green fluorescent protein (GFP)-tagged
F. hibernum
cells were quickly consumed by larval mosquitoes at an ingestion rate of 9.5 × 10
4
/larva/h. The ingested
F. hibernum
cells were observed mostly in the foregut and midgut and rarely in the hindgut, suggesting that cells were digested and did not pass the gut viably. The NanoLuc luciferase reporter system was validated for quantitative larval ingestion rate and bacterial fate analyses. Larvae digested 1.87 × 10
5
cells/larva/h, and few
F. hibernum
cells were excreted intact. Expression of the GFP::Cry11A fusion protein with the P20 chaperone protein from
Bacillus thuringiensis
H-14 was successfully achieved in
F. hibernum
. Whole-cell bioassays of recombinant
F. hibernum
exhibited high larvicidal activity against
A. triseriatus
in microplates and in microcosms simulating tree holes.
F. hibernum
cells persisted in microcosms at 100, 59, 30, and 10% of the initial densities at days 1, 2, 3, and 6, respectively, when larvae were absent, while larvae consumed nearly all of the
F. hibernum
cells within 3 days of their addition to microcosms.
Use of Limited Proteolysis and Mutagenesis To Identify Folding Domains and Sequence Motifs Critical for Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase Activity
Authors: Villa Juan A. , Cabezas Matilde , de la Cruz Fernando , Moncalián Gabriel 
Published: December 2013

ABSTRACT
Triacylglycerols and wax esters are synthesized as energy storage molecules by some proteobacteria and actinobacteria under stress. The enzyme responsible for neutral lipid accumulation is the bifunctional wax ester synthase/acyl-coenzyme A (CoA):diacylglycerol acyltransferase (WS/DGAT). Structural modeling of WS/DGAT suggests that it can adopt an acyl-CoA-dependent acyltransferase fold with the N-terminal and C-terminal domains connected by a helical linker, an architecture demonstrated experimentally by limited proteolysis. Moreover, we found that both domains form an active complex when coexpressed as independent polypeptides. The structural prediction and sequence alignment of different WS/DGAT proteins indicated catalytically important motifs in the enzyme. Their role was probed by measuring the activities of a series of alanine scanning mutants. Our study underscores the structural understanding of this protein family and paves the way for their modification to improve the production of neutral lipids.
Characterization of Biofilm Formation and the Role of
BCR1
in Clinical Isolates of Candida parapsilosis
Authors: Pannanusorn Srisuda , Ramírez-Zavala Bernardo , Lünsdorf Heinrich , Agerberth Birgitta , Morschhäuser Joachim , Römling Ute 
Published: December 2013

ABSTRACT

In
Candida parapsilosis
, biofilm formation is considered to be a major virulence factor. Previously, we determined the ability of 33 clinical isolates causing bloodstream infection to form biofilms and identified three distinct groups of biofilm-forming strains (negative, low, and high). Here, we establish two different biofilm structures among strains forming large amounts of biofilm in which strains with complex spider-like structures formed robust biofilms on different surface materials with increased resistance to fluconazole. Surprisingly, the transcription factor Bcr1, required for biofilm formation in
Candida albicans
and
C. parapsilosis
, has an essential role only in strains with low capacity for biofilm formation. Although
BCR1
leads to the formation of more and longer pseudohyphae, it was not required for initial adhesion and formation of mature biofilms in strains with a high level of biofilm formation. Furthermore, an additional phenotype affected by
BCR1
was the switch in colony morphology from rough to crepe, but only in strains forming high levels of biofilm. All
bcr1
Δ/Δ mutants showed increased proteolytic activity and increased susceptibility to the antimicrobial peptides protamine and RP-1 compared to corresponding wild-type and complemented strains. Taken together, our results demonstrate that biofilm formation in clinical isolates of
C. parapsilosis
is both dependent and independent of
BCR1
, but even in strains which showed a
BCR1
-independent biofilm phenotype,
BCR1
has alternative physiological functions.
Giardia intestinalis Incorporates Heme into Cytosolic Cytochrome
b
5
Authors: Pyrih Jan , Harant Karel , Martincová Eva , Sutak Robert , Lesuisse Emmanuel , Hrdý Ivan , Tachezy Jan 
Published: December 2013

ABSTRACT

The anaerobic intestinal pathogen
Giardia intestinalis
does not possess enzymes for heme synthesis, and it also lacks the typical set of hemoproteins that are involved in mitochondrial respiration and cellular oxygen stress management. Nevertheless,
G. intestinalis
may require heme for the function of particular hemoproteins, such as cytochrome
b
5
(cyt
b
5
). We have analyzed the sequences of eukaryotic cyt
b
5
proteins and identified three distinct cyt
b
5
groups: group I, which consists of C-tail membrane-anchored cyt
b
5
proteins; group II, which includes soluble cyt
b
5
proteins; and group III, which comprises the fungal cyt
b
5
proteins. The majority of eukaryotes possess both group I and II cyt
b
5
proteins, whereas three
Giardia
paralogs belong to group II. We have identified a fourth
Giardia
cyt
b
5
paralog (gCYTb5-IV) that is rather divergent and possesses an unusual 134-residue N-terminal extension. Recombinant
Giardia
cyt
b
5
proteins, including gCYTb5-IV, were expressed in
Escherichia coli
and exhibited characteristic UV-visible spectra that corresponded to heme-loaded cyt
b
5
proteins. The expression of the recombinant gCYTb5-IV in
G. intestinalis
resulted in the increased import of extracellular heme and its incorporation into the protein, whereas this effect was not observed when gCYTb5-IV containing a mutated heme-binding site was expressed. The electrons for
Giardia
cyt
b
5
proteins may be provided by the NADPH-dependent Tah18-like oxidoreductase GiOR-1. Therefore, GiOR-1 and cyt
b
5
may constitute a novel redox system in
G. intestinalis
. To our knowledge,
G. intestinalis
is the first anaerobic eukaryote in which the presence of heme has been directly demonstrated.
The
phtC-phtD
Locus Equips Legionella pneumophila for Thymidine Salvage and Replication in Macrophages
Authors: Fonseca Maris V. , Sauer John-Demian , Crepin Sebastien , Byrne Brenda , Swanson Michele S. 
Published: December 2013

ABSTRACT

The phagosomal transporter (Pht) family of the major facilitator superfamily (MFS) is encoded by phylogenetically related intracellular gammaproteobacteria, including the opportunistic pathogen
Legionella pneumophila
. The location of the
pht
genes between the putative thymidine kinase (
tdk
) and phosphopentomutase (
deoB
) genes suggested that the
phtC
and
phtD
loci contribute to thymidine salvage in
L. pneumophila
. Indeed, a
phtC

+

allele in
trans
restored pyrimidine uptake to an
Escherichia coli
mutant that lacked all known nucleoside transporters, whereas a
phtD

+

allele did not. The results of phenotypic analyses of
L. pneumophila
strains lacking
phtC
or
phtD
strongly indicate that
L. pneumophila
requires PhtC and PhtD function under conditions where sustained dTMP synthesis is compromised. First, in broth cultures that mimicked thymidine limitation or starvation,
L. pneumophila
exhibited a marked requirement for PhtC function. Conversely, mutation of
phtD
conferred a survival advantage. Second, in medium that lacked thymidine, multicopy
phtC

+

or
phtD

+

alleles enhanced the survival of
L. pneumophila
thymidylate synthase (
thyA
)-deficient strains, which cannot synthesize dTMP endogenously. Third, under conditions in which transport of the pyrimidine nucleoside analog 5-fluorodeoxyuridine (FUdR) would inhibit growth, PhtC and PhtD conferred a growth advantage to
L. pneumophila
thyA

+

strains. Finally, when cultured in macrophages,
L. pneumophila
required the
phtC-phtD
locus to replicate. Accordingly, we propose that PhtC and PhtD contribute to protect
L. pneumophila
from dTMP starvation during its intracellular life cycle.
Host-Nonspecific Iron Acquisition Systems and Virulence in the Zoonotic Serovar of Vibrio vulnificus
Authors: Pajuelo David , Lee Chung-Te , Roig Francisco J. , Lemos Manuel L. , Hor Lien-I , Amaro Carmen 
Published: December 2013

ABSTRACT

The zoonotic serovar of
Vibrio vulnificus
(known as biotype 2 serovar E) is the etiological agent of human and fish vibriosis. The aim of the present work was to discover the role of the vulnibactin- and hemin-dependent iron acquisition systems in the pathogenicity of this zoonotic serovar under the hypothesis that both are host-nonspecific virulence factors. To this end, we selected three genes for three outer membrane receptors (
vuuA
, a receptor for ferric vulnibactin, and
hupA
and
hutR
, two hemin receptors), obtained single and multiple mutants as well as complemented strains, and tested them in a series of
in vitro
and
in vivo
assays, using eels and mice as animal models. The overall results confirm that
hupA
and
vuuA
, but not
hutR
, are host-nonspecific virulence genes and suggest that a third undescribed host-specific plasmid-encoded system could also be used by the zoonotic serovar in fish.
hupA
and
vuuA
were expressed in the internal organs of the animals in the first 24 h of infection, suggesting that they may be needed to achieve the population size required to trigger fatal septicemia.
vuuA
and
hupA
were sequenced in strains representative of the genetic diversity of this species, and their phylogenies were reconstructed by multilocus sequence analysis of selected housekeeping and virulence genes as a reference. Given the overall results, we suggest that both genes might form part of the core genes essential not only for disease development but also for the survival of this species in its natural reservoir, the aquatic environment.
Response to Metronidazole and Oxidative Stress Is Mediated through Homeostatic Regulator HsrA (HP1043) in Helicobacter pylori
Authors: Olekhnovich Igor N. , Vitko Serhiy , Valliere Meaghan , Hoffman Paul S. 
Published: December 2013

ABSTRACT

Metronidazole (MTZ) is often used in combination therapies to treat infections caused by the gastric pathogen
Helicobacter pylori
. Resistance to MTZ results from loss-of-function mutations in genes encoding RdxA and FrxA nitroreductases. MTZ-resistant strains, when cultured at sub-MICs of MTZ (5 to 20 μg/ml), show dose-dependent defects in bacterial growth; depressed activities of many Krebs cycle enzymes, including pyruvate:ferredoxin oxidoreductase (PFOR); and low transcript levels of
porGDAB
(primer extension), phenotypes consistent with an involvement of a transcriptional regulator. Using a combination of protein purification steps, electrophoretic mobility shift assays (EMSAs), and mass spectrometry analyses of proteins bound to
porG
promoter sequences, we identified HP1043, an essential homeostatic global regulator (HsrA [for
h
omeostatic
s
tress
r
egulator]). Competition EMSAs and supershift analyses with HsrA-enriched protein fractions confirmed specific binding to
porGDAB
and
hsrA
promoter sequences. Exposure to MTZ resulted in >10-fold decreases in levels of HsrA and in levels of the HsrA-regulated gene products PFOR and TlpB. Exposure to paraquat (PQ), hydrogen peroxide, or organic peroxides showed near equivalence with MTZ, revealing a common oxidative stress response pathway. Finally, direct superoxide dismutase (SOD) assays showed an inverse relationship between HsrA levels and SOD activity, suggesting that HsrA may serve as a repressor of
sodB
. As a homeostatic sentinel, HsrA appears to be ideally positioned to enable rapid shutdown of genes associated with metabolism and growth while activating (directly or indirectly) oxidative defense genes in response to low levels of toxic metabolites (MTZ or oxygen) before they reach DNA-damaging levels.
Amino-4-Imidazolecarboxamide Ribotide Directly Inhibits Coenzyme A Biosynthesis in Salmonella enterica
Authors: Bazurto Jannell V. , Downs Diana M. 
Published: December 2013

ABSTRACT

Aminoimidazole carboxamide ribotide (AICAR) is a purine biosynthetic intermediate and a by-product of histidine biosynthesis. In bacteria, yeast, and humans, accumulation of AICAR has been shown to affect an array of cellular processes by both direct and indirect mechanisms. In purine biosynthesis, AICAR is the substrate of the bifunctional protein phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (PurH, EC 2.1.2.3/3.5.4.10). Strains lacking PurH accumulate AICAR and have a defect in the synthesis of the 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) moiety of thiamine. The formation of HMP is also compromised
in vivo
when coenzyme A (CoA) levels are reduced. Our results show that the
in vivo
accumulation of AICAR decreased total CoA pools and, further, that AICAR inhibited the activity of pantoate β-alanine ligase
in vitro
(PanC, EC 6.3.2.1). These results demonstrated a mechanism of AICAR action and provide new insights into the metabolic consequences of disrupting purine metabolism.
Dynamics of late Cenozoic aeolian deposition along the South African coast: a record of evolving climate and ecosystems
Authors: Roberts Dave , Cawthra Hayley , Musekiwa Chiedza 
Published: December 2013

Abstract
Dune systems along the South African coast are sensitive barometers of fluctuations in palaeoenvironments, as archived in their orientation, geometry, internal architecture, composition, granulometry, diagenesis, palaeontology and archaeological content. Presently, the pronounced climatic/oceanographic gradients around the southern African coastline, including the west coast Mediterranean climate type, with cold upwelling to progressively warmer in terms of climate and sea temperatures eastwards, are mirrored by variations in these parameters. Here, we review and contribute new information concerning their fluctuations from the Miocene to the present to track changes in the bio-, hydro- and geospheres through time. West coast dunes take the form of dune plumes, which have an orientation since the Miocene that mirrors the southerlies of the South Atlantic Anticyclone (SAA), muted during the warm Pliocene, as reflected by intense bioturbation. Shoreline-parallel, vertically aggraded dune cordons dominate along the southern and eastern coasts, formed by (winter) polar westerlies since the Miocene. The contrasting dunefield morphologies relate to seasonality of wind strength and precipitation. Subtropical east coast dunes are profoundly weathered – on the shelf, glacial-period dunes indicate different atmospheric circulations. The long-term stability of the warm Agulhas Current contrasts with variability in the Benguela. The aeolianites host a rich human and faunal archive, including human ichnofossils.

Supplementary material:

Tables S1 and S2, which provide details of the data and data sources for Figure
9
in the text, are available at
http://www.geolsoc.org.uk/SUP18711
.