bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Novel Composite Staphylococcal Cassette Chromosome
mec
in Methicillin-Resistant Staphylococcus pseudintermedius from Thailand
Authors: Chanchaithong Pattrarat , Prapasarakul Nuvee , Perreten Vincent , Schwendener Sybille 
Published: December 2015

ABSTRACT

A novel staphylococcal cassette chromosome
mec
(SCC
mec
) composite island (SCC
mec
AI16
-SCC
czr
AI16
-CI) was identified in
Staphylococcus pseudintermedius
. Four integration site sequences for SCC subdivided the 60,734-bp island into 41,232-bp SCC
mec
AI16
, 19,400-bp SCC
czr
AI16
, and 102-bp SCC-like
AI16
elements. SCC
mec
AI16
represents a new combination of
ccrA1B3
genes with a class A
mec
complex. SCC
czr
AI16
contains
ccrA1B6
and genes related to restriction modification and heavy metal resistance. SCC
mec
AI16
-SCC
czr
AI16
-CI was found in methicillin-resistant
S. pseudintermedius
sequence type 112 (ST112) and ST111 isolated from dogs and veterinarians in Thailand.
Clinical Candidate VT-1161's Antiparasitic Effect
In Vitro
, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme CYP51 from Trypanosoma cruzi
Authors: Hoekstra William J. , Hargrove Tatiana Y. , Wawrzak Zdzislaw , da Gama Jaen Batista Denise , da Silva Cristiane F. , Nefertiti Aline S. G. , Rachakonda Girish , Schotzinger Robert J. , Villalta Fernando , Soeiro Maria de Nazaré C. , Lepesheva Galina I. 
Published: December 2015

ABSTRACT

A novel antifungal drug candidate, the 1-tetrazole-based agent VT-1161 [(
R
)-2-(2,4-difluorophenyl)-1,1-difluoro-3-(1
H
-tetrazol-1-yl)-1-{5-[4-(2,2,2-trifluoroethoxy)phenyl]pyridin-2-yl}propan-2-ol], which is currently in two phase 2b antifungal clinical trials, was found to be a tight-binding ligand (apparent dissociation constant [

K
d

], 24 nM) and a potent inhibitor of cytochrome P450 sterol 14α-demethylase (CYP51) from the protozoan pathogen
Trypanosoma cruzi
. Moreover, VT-1161 revealed a high level of antiparasitic activity against amastigotes of the Tulahuen strain of
T. cruzi
in cellular experiments (50% effective concentration, 2.5 nM) and was active
in vivo
, causing >99.8% suppression of peak parasitemia in a mouse model of infection with the naturally drug-resistant Y strain of the parasite. The data strongly support the potential utility of VT-1161 in the treatment of Chagas disease. The structural characterization of
T. cruzi
CYP51 in complex with VT-1161 provides insights into the molecular basis for the compound's inhibitory potency and paves the way for the further rational development of this novel, tetrazole-based inhibitory chemotype both for antiprotozoan chemotherapy and for antifungal chemotherapy.
The Asp20-to-Asn Substitution in the Response Regulator AdeR Leads to Enhanced Efflux Activity of AdeB in Acinetobacter baumannii
Authors: Nowak Jennifer , Schneiders Thamarai , Seifert Harald , Higgins Paul G. 
Published: December 2015

ABSTRACT

Overexpression of the resistance-nodulation-cell division-type efflux pump AdeABC is often associated with multidrug resistance in
Acinetobacter baumannii
and has been linked to mutations in the genes encoding the AdeRS two-component system. In a previous study, we reported that the Asp20→Asn amino acid substitution in the response regulator AdeR is associated with
adeB
overexpression and reduced susceptibility to the antimicrobials levofloxacin, tigecycline, and trimethoprim-sulfamethoxazole. To further characterize the effect of the Asp20→Asn substitution on antimicrobial susceptibility, the expression of the efflux genes
adeB
,
adeJ
, and
adeG
, and substrate accumulation, four plasmid constructs [containing
adeR
(
Asp20
)
S
,
adeR
(
Asn20
)
S
,
adeR
(
Asp20
)
SABC
, and
adeR
(
Asn20
)
SABC
] were introduced into the
adeRSABC
-deficient
A. baumannii
isolate NIPH 60. Neither
adeRS
construct induced changes in antimicrobial susceptibility or substrate accumulation from that for the vector-only control. The
adeR
(
Asp20
)
SABC
transformant showed reduced susceptibility to 6 antimicrobials and accumulated 12% less ethidium than the control, whereas the Asn20 variant showed reduced susceptibility to 6 of 8 antimicrobial classes tested, and its ethidium accumulation was only 72% of that observed for the vector-only construct.
adeB
expression was 7-fold higher in the
adeR
(
Asn20
)
SABC
transformant than in its Asp20 variant. No changes in
adeG
or
adeJ
expression or in acriflavine or rhodamine 6G accumulation were detected. The antimicrobial susceptibility data suggest that AdeRS does not regulate any resistance determinants other than AdeABC. Furthermore, the characterization of the Asp20→Asn20 substitution proves that the reduced antimicrobial susceptibility previously associated with this substitution was indeed caused by enhanced efflux activity of AdeB.
International Evaluation of MIC Distributions and Epidemiological Cutoff Value (ECV) Definitions for Fusarium Species Identified by Molecular Methods for the CLSI Broth Microdilution Method
Authors: Espinel-Ingroff A. , Colombo A. L. , Cordoba S. , Dufresne P. J. , Fuller J. , Ghannoum M. , Gonzalez G. M. , Guarro J. , Kidd S. E. , Meis J. F. , Melhem T. M. S. C. , Pelaez T. , Pfaller M. A. , Szeszs M. W. , Takahaschi J. P. , Tortorano A. M. , Wiederhold N. P. , Turnidge J. 
Published: December 2015

ABSTRACT

The CLSI epidemiological cutoff values (ECVs) of antifungal agents are available for various
Candida
spp.,
Aspergillus
spp., and the Mucorales. However, those categorical endpoints have not been established for
Fusarium
spp., mostly due to the difficulties associated with collecting sufficient CLSI MICs for clinical isolates identified according to the currently recommended molecular DNA-PCR-based identification methodologies. CLSI MIC distributions were established for 53
Fusarium dimerum
species complex (SC), 10
F. fujikuroi
, 82
F. proliferatum
, 20
F. incarnatum-F. equiseti
SC, 226
F. oxysporum
SC, 608
F. solani
SC, and 151
F. verticillioides
isolates originating in 17 laboratories (in Argentina, Australia, Brazil, Canada, Europe, Mexico, and the United States). According to the CLSI guidelines for ECV setting, ECVs encompassing ≥97.5% of pooled statistically modeled MIC distributions were as follows: for amphotericin B, 4 μg/ml (
F. verticillioides
) and 8 μg/ml (
F. oxysporum
SC and
F. solani
SC); for posaconazole, 2 μg/ml (
F. verticillioides
), 8 μg/ml (
F. oxysporum
SC), and 32 μg/ml (
F. solani
SC); for voriconazole, 4 μg/ml (
F. verticillioides
), 16 μg/ml (
F. oxysporum
SC), and 32 μg/ml (
F. solani
SC); and for itraconazole, 32 μg/ml (
F. oxysporum
SC and
F. solani
SC). Insufficient data precluded ECV definition for the other species. Although these ECVs could aid in detecting non-wild-type isolates with reduced susceptibility to the agents evaluated, the relationship between molecular mechanisms of resistance (gene mutations) and MICs still needs to be investigated for
Fusarium
spp.
Clofazimine Prevents the Regrowth of Mycobacterium abscessus and Mycobacterium avium Type Strains Exposed to Amikacin and Clarithromycin
Authors: Ferro Beatriz E. , Meletiadis Joseph , Wattenberg Melanie , de Jong Arjan , van Soolingen Dick , Mouton Johan W. , van Ingen Jakko 
Published: December 2015

ABSTRACT

Multidrug therapy is a standard practice when treating infections by nontuberculous mycobacteria (NTM), but few treatment options exist. We conducted this study to define the drug-drug interaction between clofazimine and both amikacin and clarithromycin and its contribution to NTM treatment.
Mycobacterium abscessus
and
Mycobacterium avium
type strains were used. Time-kill assays for clofazimine alone and combined with amikacin or clarithromycin were performed at concentrations of 0.25× to 2× MIC. Pharmacodynamic interactions were assessed by response surface model of Bliss independence (RSBI) and isobolographic analysis of Loewe additivity (ISLA), calculating the percentage of statistically significant Bliss interactions and interaction indices (I), respectively. Monte Carlo simulations with predicted human lung concentrations were used to calculate target attainment rates for combination and monotherapy regimens. Clofazimine alone was bacteriostatic for both NTM. Clofazimine-amikacin was synergistic against
M. abscessus
(I = 0.41; 95% confidence interval [CI], 0.29 to 0.55) and
M. avium
(I = 0.027; 95% CI, 0.007 to 0.048). Based on RSBI analysis, synergistic interactions of 28.4 to 29.0% and 23.2 to 56.7% were observed at 1× to 2× MIC and 0.25× to 2× MIC for
M. abscessus
and
M. avium
, respectively. Clofazimine-clarithromycin was also synergistic against
M. abscessus
(I = 0.53; 95% CI, 0.35 to 0.72) and
M. avium
(I = 0.16; 95% CI, 0.04 to 0.35), RSBI analysis showed 23.5% and 23.3 to 53.3% at 2× MIC and 0.25× to 0.5× MIC for
M. abscessus
and
M. avium
, respectively. Clofazimine prevented the regrowth observed with amikacin or clarithromycin alone. Target attainment rates of combination regimens were >60% higher than those of monotherapy regimens for
M. abscessus
and
M. avium
. The combination of clofazimine with amikacin or clarithromycin was synergistic
in vitro
. This suggests a potential role for clofazimine in treatment regimens that warrants further evaluation.
Molecular Characterization by Using Next-Generation Sequencing of Plasmids Containing
bla
NDM-7
in Enterobacteriaceae from Calgary, Canada
Authors: Chen L. , Peirano G. , Lynch T. , Chavda K. D. , Gregson D. B. , Church D. L. , Conly J. , Kreiswirth B. N. , Pitout J. D. 
Published: December 2015

ABSTRACT

Enterobacteriaceae
with
bla
NDM-7
are relatively uncommon and had previously been described in Europe, India, the United States, and Japan. This study describes the characteristics of
Enterobacteriaceae
(
Klebsiella pneumoniae
[
n
= 2],
Escherichia coli
[
n
= 2],
Serratia marcescens
[
n
= 1], and
Enterobacter hormaechei
[
n
= 1] isolates) with
bla
NDM-7
obtained from 4 patients from Calgary, Canada, from 2013 to 2014. The 46,161-bp IncX3 plasmids with
bla
NDM-7
are highly similar to other
bla
NDM
-harboring IncX3 plasmids and, interestingly, showed identical structures within the different isolates. This finding may indicate horizontal transmission within our health region, or it may indicate contact with individuals from areas of endemicity within the hospital setting. Patients infected or colonized with bacteria containing
bla
NDM-7
IncX3 plasmids generate infection control challenges. Epidemiological and molecular studies are required to better understand the dynamics of transmission, the risk factors, and the reservoirs for bacteria harboring
bla
NDM-7
. To the best of our knowledge, this is the first report of
S. marcescens
and
E. hormaechei
with
bla
NDM-7
.
HexR Controls Glucose-Responsive Genes and Central Carbon Metabolism in Neisseria meningitidis
Authors: Antunes Ana , Golfieri Giacomo , Ferlicca Francesca , Giuliani Marzia M. , Scarlato Vincenzo , Delany Isabel 
Published: December 2015

ABSTRACT

Neisseria meningitidis
, an exclusively human pathogen and the leading cause of bacterial meningitis, must adapt to different host niches during human infection.
N. meningitidis
can utilize a restricted range of carbon sources, including lactate, glucose, and pyruvate, whose concentrations vary in host niches. Microarray analysis of
N. meningitidis
grown in a chemically defined medium in the presence or absence of glucose allowed us to identify genes regulated by carbon source availability. Most such genes are implicated in energy metabolism and transport, and some are implicated in virulence. In particular, genes involved in glucose catabolism were upregulated, whereas genes involved in the tricarboxylic acid cycle were downregulated. Several genes encoding surface-exposed proteins, including the MafA adhesins and
Neisseria
surface protein A, were upregulated in the presence of glucose. Our microarray analysis led to the identification of a glucose-responsive
hexR
-like transcriptional regulator that controls genes of the central carbon metabolism of
N. meningitidis
in response to glucose. We characterized the HexR regulon and showed that the
hexR
gene is accountable for some of the glucose-responsive regulation;
in vitro
assays with the purified protein showed that HexR binds to the promoters of the central metabolic operons of the bacterium. Based on DNA sequence alignment of the target sites, we propose a 17-bp pseudopalindromic consensus HexR binding motif. Furthermore,
N. meningitidis
strains lacking
hexR
expression were deficient in establishing successful bacteremia in an infant rat model of infection, indicating the importance of this regulator for the survival of this pathogen
in vivo
.

IMPORTANCE
Neisseria meningitidis
grows on a limited range of nutrients during infection. We analyzed the gene expression of
N. meningitidis
in response to glucose, the main energy source available in human blood, and we found that glucose regulates many genes implicated in energy metabolism and nutrient transport, as well as some implicated in virulence. We identified and characterized a transcriptional regulator (HexR) that controls metabolic genes of
N. meningitidis
in response to glucose. We generated a mutant lacking HexR and found that the mutant was impaired in causing systemic infection in animal models. Since
N. meningitidis
lacks known bacterial regulators of energy metabolism, our findings suggest that HexR plays a major role in its biology by regulating metabolism in response to environmental signals.
Inactivation of Cell Division Protein FtsZ by SulA Makes Lon Indispensable for the Viability of a ppGpp
0
Strain of Escherichia coli
Authors: Nazir Aanisa , Harinarayanan Rajendran 
Published: December 2015

ABSTRACT

The modified nucleotides (p)ppGpp play an important role in bacterial physiology. While the accumulation of the nucleotides is vital for adaptation to various kinds of stress, changes in the basal level modulates growth rate and vice versa. Studying the phenotypes unique to the strain lacking (p)ppGpp (ppGpp
0
) under overtly unstressed growth conditions may be useful to understand functions regulated by basal levels of (p)ppGpp and its physiological significance. In this study, we show that the ppGpp
0
strain, unlike the wild type, requires the Lon protease for cell division and viability in LB. Our results indicate the decrease in FtsZ concentration in the ppGpp
0
strain makes cell division vulnerable to SulA inhibition. We did not find evidence for SOS induction contributing to the cell division defect in the ppGpp
0
Δ
lon
strain. Based on the results, we propose that basal levels of (p)ppGpp are required to sustain normal cell division in
Escherichia coli
during growth in rich medium and that the basal SulA level set by Lon protease is important for insulating cell division against a decrease in FtsZ concentration and conditions that can increase the susceptibility of FtsZ to SulA.

IMPORTANCE
The physiology of the stringent response has been the subject of investigation for more than 4 decades, with the majority of the work carried out using the bacterial model organism
Escherichia coli
. These studies have revealed that the accumulation of (p)ppGpp, the effector of the stringent response, is associated with growth retardation and changes in gene expression that vary with the intracellular concentration of (p)ppGpp. By studying a synthetic lethal phenotype, we have uncovered a function modulated by the basal levels of (p)ppGpp and studied its physiological significance. Our results show that (p)ppGpp and Lon protease contribute to the robustness of the cell division machinery in
E. coli
during growth in rich medium.
Proteome Profiling of the Rhodobacter capsulatus Molybdenum Response Reveals a Role of IscN in Nitrogen Fixation by Fe-Nitrogenase
Authors: Hoffmann Marie-Christine , Wagner Eva , Langklotz Sina , Pfänder Yvonne , Hött Sina , Bandow Julia E. , Masepohl Bernd 
Published: December 2015

ABSTRACT

Rhodobacter capsulatus
is capable of synthesizing two nitrogenases, a molybdenum-dependent nitrogenase and an alternative Mo-free iron-only nitrogenase, enabling this diazotroph to grow with molecular dinitrogen (N
2
) as the sole nitrogen source. Here, the Mo responses of the wild type and of a mutant lacking ModABC, the high-affinity molybdate transporter, were examined by proteome profiling, Western analysis, epitope tagging, and
lacZ
reporter fusions. Many Mo-controlled proteins identified in this study have documented or presumed roles in nitrogen fixation, demonstrating the relevance of Mo control in this highly ATP-demanding process. The levels of Mo-nitrogenase, NifHDK, and the Mo storage protein, Mop, increased with increasing Mo concentrations. In contrast, Fe-nitrogenase, AnfHDGK, and ModABC, the Mo transporter, were expressed only under Mo-limiting conditions. IscN was identified as a novel Mo-repressed protein. Mo control of Mop, AnfHDGK, and ModABC corresponded to transcriptional regulation of their genes by the Mo-responsive regulators MopA and MopB. Mo control of NifHDK and IscN appeared to be more complex, involving different posttranscriptional mechanisms. In line with the simultaneous control of IscN and Fe-nitrogenase by Mo, IscN was found to be important for Fe-nitrogenase-dependent diazotrophic growth. The possible role of IscN as an A-type carrier providing Fe-nitrogenase with Fe-S clusters is discussed.

IMPORTANCE
Biological nitrogen fixation is a central process in the global nitrogen cycle by which the abundant but chemically inert dinitrogen (N
2
) is reduced to ammonia (NH
3
), a bioavailable form of nitrogen. Nitrogen reduction is catalyzed by nitrogenases found in diazotrophic bacteria and archaea but not in eukaryotes. All diazotrophs synthesize molybdenum-dependent nitrogenases. In addition, some diazotrophs, including
Rhodobacter capsulatus
, possess catalytically less efficient alternative Mo-free nitrogenases, whose expression is repressed by Mo. Despite the importance of Mo in biological nitrogen fixation, this is the first study analyzing the proteome-wide Mo response in a diazotroph. IscN was recognized as a novel member of the molybdoproteome in
R. capsulatus
. It was dispensable for Mo-nitrogenase activity but supported diazotrophic growth under Mo-limiting conditions.
Disulfide-Bond-Forming Pathways in Gram-Positive Bacteria
Authors: Reardon-Robinson Melissa E. , Ton-That Hung 
Published: December 2015

ABSTRACTDisulfide bonds are important for the stability and function of many secreted proteins. In Gram-negative bacteria, these linkages are catalyzed by thiol-disulfide oxidoreductases (Dsb) in the periplasm. Protein oxidation has been well studied in these organisms, but it has not fully been explored in Gram-positive bacteria, which lack traditional periplasmic compartments. Recent bioinformatics analyses have suggested that the high-GC-content bacteria (i.e., actinobacteria) rely on disulfide-bond-forming pathways. In support of this, Dsb-like proteins have been identified inMycobacterium tuberculosis, but their functions are not known.Actinomyces orisandCorynebacterium diphtheriaehave recently emerged as models to study disulfide bond formation in actinobacteria. In both organisms, disulfide bonds are catalyzed by the membrane-bound oxidoreductase MdbA. Remarkably, unlike known Dsb proteins, MdbA is important for pathogenesis and growth, which makes it a potential target for new antibacterial drugs. This review will discuss disulfide-bond-forming pathways in bacteria, with a special focus on Gram-positive bacteria.
Sensitivity of Real-Data Simulations of the 3 May 1999 Oklahoma City Tornadic Supercell and Associated Tornadoes to Multimoment Microphysics. Part II: Analysis of Buoyancy and Dynamic Pressure Forces in Simulated Tornado-Like Vortices
Authors: Dawson Daniel T. , Xue Ming , Shapiro Alan , Milbrandt Jason A. , Schenkman Alexander D. 
Published: December 2015

Abstract
Vortex stretching by intense upward accelerations is a critical process for tornadogenesis and maintenance. Two high-resolution (250-m grid spacing) real-data simulations of the 3 May 1999 Oklahoma City, Oklahoma, supercell and associated tornadoes, using single- and triple-moment microphysics parameterization schemes, respectively, are examined. Microphysical, thermodynamic, and dynamic impacts on the vertical accelerations near and within simulated tornado-like vortices (TLVs) are analyzed. Systematic differences in behavior of the TLVS between the two experiments are found; the TLV in the triple-moment simulation is substantially more intense and longer lived than in the single-moment case. The triple-moment scheme in this case produces less rain and hail mass in the low levels and drop size distributions of rain shifted toward larger drops, relative to the single-moment scheme, leading to less latent cooling and warmer outflow. Trajectory analyses reveal that more parcels entering the TLV in the triple-moment simulation have a history of dynamically induced descent, whereas buoyantly driven descent is more prevalent in the single-moment experiment. It is found that the intensity and longevity of the TLV are tied to weaker negative or neutral thermal buoyancy in the air flowing into the TLV in the triple-moment case, consistent with previous observational and modeling studies. Finally, the contribution to buoyancy from pressure perturbations is found to be of prime importance within the TLV, where strong negative pressure perturbations lead to substantial positive buoyancy. This contribution compensates for the slight negative thermal buoyancy and negative dynamic pressure gradient acceleration in the triple-moment case.
Sensitivity Study on the Influence of Cloud Microphysical Parameters on Mixed-Phase Cloud Thermodynamic Phase Partitioning in CAM5
Authors: Tan Ivy , Storelvmo Trude 
Published: December 2015

Abstract
The influence of six CAM5.1 cloud microphysical parameters on the variance of phase partitioning in mixed-phase clouds is determined by application of a variance-based sensitivity analysis. The sensitivity analysis is based on a generalized linear model that assumes a polynomial relationship between the six parameters and the two-way interactions between them. The parameters, bounded such that they yield realistic cloud phase values, were selected by adopting a quasi–Monte Carlo sampling approach. The sensitivity analysis is applied globally, and to 20°-latitude-wide bands, and over the Southern Ocean at various mixed-phase cloud isotherms and reveals that the Wegener–Bergeron–Findeisen (WBF) time scale for the growth of ice crystals single-handedly accounts for the vast majority of the variance in cloud phase partitioning in mixed-phase clouds, while its interaction with the WBF time scale for the growth of snowflakes plays a secondary role. The fraction of dust aerosols active as ice nuclei in latitude bands, and the parameter related to the ice crystal fall speed and their interactions with the WBF time scale for ice are also significant. All other investigated parameters and their interactions with each other are negligible (&lt;3%). Further analysis comparing three of the quasi–Monte Carlo–sampled simulations with spaceborne lidar observations by CALIOP suggests that the WBF process in CAM5.1 is currently parameterized such that it occurs too rapidly due to failure to account for subgrid-scale variability of liquid and ice partitioning in mixed-phase clouds.