bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jasmonate inhibits COP1 activity to suppress hypocotyl elongation and promote cotyledon opening in etiolated Arabidopsis seedlings
Authors: Zheng Yuyu , Cui Xuefei , Su Liang , Fang Shuang , Chu Jinfang , Gong Qingqiu , Yang Jianping , Zhu Ziqiang 
Published: March 2017

SummaryA germinating seedling undergoes skotomorphogenesis to emerge from the soil and reach for light. During this phase, the cotyledons are closed, and the hypocotyl elongates. Upon exposure to light, the seedling rapidly switches to photomorphogenesis by opening its cotyledons and suppressing hypocotyl elongation. The E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) is critical for maintaining skotomorphogenesis. Here, we report that jasmonate (JA) suppresses hypocotyl elongation and stimulates cotyledon opening in etiolated seedlings, partially phenocopying cop1 mutants in the dark. We also find that JA stabilizes several COP1‐targeted transcription factors in a COP1‐dependent manner. RNA‐seq analysis further defines a JA‐light co‐modulated and cop1‐dependent transcriptome, which is enriched for auxin‐responsive genes and genes participating in cell wall modification. JA suppresses COP1 activity through at least two distinct mechanisms: decreasing COP1 protein accumulation in the nucleus; and reducing the physical interaction between COP1 and its activator, SUPPRESSOR OF PHYTOCHROME A‐105 1 (SPA1). Our work reveals that JA suppresses COP1 activity to stabilize COP1 targets, thereby inhibiting hypocotyl elongation and stimulating cotyledon unfolding in etiolated Arabidopsis seedlings.
In Vitro
Activities and Spectrum of the Novel Fluoroquinolone Lascufloxacin (KRP-AM1977)
Authors: Kishii Ryuta , Yamaguchi Yuko , Takei Masaya 
Published: March 2017

ABSTRACT
Lascufloxacin exhibited a broad spectrum of activity against various clinical isolates. Furthermore, lascufloxacin showed the most potent activity against Gram-positive bacteria among the quinolones tested and incomplete cross-resistance against existing quinolone-resistant strains. Enzymatic analysis indicated that lascufloxacin had potent inhibitory activity against both wild-type and mutated target enzymes. These results suggest that lascufloxacin may be useful in treating infections caused by various pathogens, including quinolone-resistant strains.
Piperacillin-Tazobactam versus Other Antibacterial Agents for Treatment of Bloodstream Infections Due to AmpC β-Lactamase-Producing Enterobacteriaceae
Authors: Cheng Lucy , Nelson Brian C. , Mehta Monica , Seval Nikhil , Park Sarah , Giddins Marla J. , Shi Qiuhu , Whittier Susan , Gomez-Simmonds Angela , Uhlemann Anne-Catrin 
Published: March 2017

ABSTRACT

In vivo
induction of AmpC beta-lactamases produces high-level resistance to many beta-lactam antibiotics in
Enterobacteriaceae
, often resulting in the need to use carbapenems or cefepime (FEP). The clinical effectiveness of piperacillin-tazobactam (TZP), a weak inducer of AmpC beta-lactamases, is poorly understood. Here, we conducted a case-control study of adult inpatients with bloodstream infections (BSIs) due to
Enterobacter
,
Serratia
, or
Citrobacter
species from 2009 to 2015 to assess outcomes following treatment with TZP compared to FEP or meropenem (MEM). We collected clinical data and screened all isolates for the presence of
ampC
alleles by PCR. Primary study outcomes were 30-day mortality and persistent bacteremia at ≥72 h from the time of treatment initiation. Of 493 patients with bacteremia, 165 patients met the inclusion criteria, of which 88 were treated with TZP and 77 with FEP or MEM. To minimize differences between covariates, we carried out propensity score matching, which yielded 41 matched pairs. Groups only differed by age, with patients in the TZP group significantly older (
P
= 0.012). There were no significant differences in 30-day mortality, persistent bacteremia, 7-day mortality, or treatment escalation between the two treatment groups, including in the propensity score-matched cohort. PCR amplification and sequencing of
amp
C genes revealed the presence of
amp
C in isolates with cefoxitin MICs below 16 μg/ml, in particular in
Serratia
spp., and demonstrated that these alleles were highly genetically diverse. Taken together, TZP may be a valuable treatment option for BSIs due to AmpC beta-lactamase-producing
Enterobacteriaceae
, diminishing the need for broader-spectrum agents. Future studies are needed to validate these findings.
Antibiotic Effects on Methicillin-Resistant Staphylococcus aureus Cytoplasmic Peptidoglycan Intermediate Levels and Evidence for Potential Metabolite Level Regulatory Loops
Authors: Vemula Harika , Ayon Navid J. , Burton Alloch , Gutheil William G. 
Published: March 2017

ABSTRACT

Cytoplasmic peptidoglycan (PG) precursor levels were determined in methicillin-resistant
Staphylococcus aureus
(MRSA) after exposure to several cell wall-targeting antibiotics. Three experiments were performed: (i) exposure to 4× MIC levels (acute); (ii) exposure to sub-MIC levels (subacute); (iii) a time course experiment of the effect of vancomycin. In acute exposure experiments, fosfomycin increased UDP-GlcNAc, as expected, and resulted in substantially lower levels of total UDP-linked metabolite accumulation relative to other pathway inhibitors, indicating reduced entry into this pathway. Upstream inhibitors (fosfomycin,
d
-cycloserine, or
d
-boroalanine) reduced UDP-MurNAc-pentapeptide levels by more than fourfold. Alanine branch inhibitors (
d
-cycloserine and
d
-boroalanine) reduced
d
-Ala–
d
-Ala levels only modestly (up to 4-fold) but increased UDP-MurNAc-tripeptide levels up to 3,000-fold. Downstream pathway inhibitors (vancomycin, bacitracin, moenomycin, and oxacillin) increased UDP-MurNAc-pentapeptide levels up to 350-fold and UDP–MurNAc–
l
-Ala levels up to 80-fold, suggesting reduced MurD activity by downstream inhibitor action. Sub-MIC exposures demonstrated effects even at 1/8× MIC which strongly paralleled acute exposure changes. Time course data demonstrated that UDP-linked intermediate levels respond rapidly to vancomycin exposure, with several intermediates increasing three- to sixfold within minutes. UDP-linked intermediate level changes were also multiphasic, with some increasing, some decreasing, and some increasing and then decreasing. The total (summed) UDP-linked intermediate pool increased by 1,475 μM/min during the first 10 min after vancomycin exposure, providing a revised estimate of flux in this pathway during logarithmic growth. These observations outline the complexity of PG precursor response to antibiotic exposure in MRSA and indicate likely sites of regulation (entry and MurD).
A Novel Hybrid Plasmid Carrying Multiple Antimicrobial Resistance and Virulence Genes in Salmonella enterica Serovar Dublin
Authors: Mangat Chand S. , Bekal Sadjia , Irwin Rebecca J. , Mulvey Michael R. 
Published: March 2017

ABSTRACT

Virulence plasmids and antibiotic resistance plasmids are usually maintained separately in
Salmonella
spp.; however, we report an instance of a hybrid plasmid (pN13-01125) in
Salmonella enterica
serovar Dublin. Review of the complete sequence of the 172,265-bp plasmid suggests that pN13-01125 is comprised of the previously described pSDVr and pSH696_135 plasmids and that the mechanism of hybridization likely involves IS
6
(IS
26
) insertion sequence elements. The plasmid has a low conjugation frequency, confers resistance to six classes of antimicrobials, and contains a complete
spv
virulence operon.
Adaptive Upregulation of Clumping Factor A (ClfA) by Staphylococcus aureus in the Obese, Type 2 Diabetic Host Mediates Increased Virulence
Authors: Farnsworth Christopher W. , Schott Eric M. , Jensen Sarah E. , Zukoski Jacob , Benvie Abigail M. , Refaai Majed A. , Kates Stephen L. , Schwarz Edward M. , Zuscik Michael J. , Gill Steven R. , Mooney Robert A. 
Published: March 2017

ABSTRACT

Obesity and associated type 2 diabetes (T2D) are important risk factors for infection following orthopedic implant surgery.
Staphylococcus aureus
, the most common pathogen in bone infections, adapts to multiple environments to survive and evade host immune responses. Whether adaptation of
S. aureus
to the unique environment of the obese/T2D host accounts for its increased virulence and persistence in this population is unknown. Thus, we assessed implant-associated osteomyelitis in normal versus high-fat-diet obese/T2D mice and found that
S. aureus
infection was more severe, including increases in bone abscesses relative to nondiabetic controls.
S. aureus
isolated from bone of obese/T2D mice displayed marked upregulation of four adhesion genes (
clfA
,
clfB
,
bbp
, and
sdrC
), all with binding affinity for fibrin(ogen). Immunostaining of infected bone revealed increased fibrin deposition surrounding bacterial abscesses in obese/T2D mice.
In vitro
coagulation assays demonstrated a hypercoagulable state in obese/T2D mice that was comparable to that of diabetic patients.
S. aureus
with an inactivating mutation in clumping factor A (
clfA
) showed a reduction in bone infection severity that eliminated the effect of obesity/T2D, while infections in control mice were unchanged. In infected mice that overexpress plasminogen activator inhibitor-1 (PAI-1),
S. aureus
clfA
expression and fibrin-encapsulated abscess communities in bone were also increased, further linking fibrin deposition to
S. aureus
expression of
clfA
and infection severity. Together, these results demonstrate an adaptation by
S. aureus
to obesity/T2D with increased expression of
clfA
that is associated with the hypercoagulable state of the host and increased virulence of
S. aureus
.
Optogenetic Module for Dichromatic Control of c-di-GMP Signaling
Authors: Ryu Min-Hyung , Fomicheva Anastasia , Moskvin Oleg V. , Gomelsky Mark 
Published: March 2017

ABSTRACT

Many aspects of bacterial physiology and behavior, including motility, surface attachment, and the cell cycle, are controlled by cyclic di-GMP (c-di-GMP)-dependent signaling pathways on the scale of seconds to minutes. Interrogation of such processes in real time requires tools for introducing rapid and reversible changes in intracellular c-di-GMP levels. Inducing the expression of genes encoding c-di-GMP-synthetic (diguanylate cyclases) and -degrading (c-di-GMP phosphodiesterase) enzymes by chemicals may not provide adequate temporal control. In contrast, light-controlled diguanylate cyclases and phosphodiesterases can be quickly activated and inactivated. A red/near-infrared-light-regulated diguanylate cyclase, BphS, was engineered previously, yet a complementary light-activated c-di-GMP phosphodiesterase has been lacking. In search of such a phosphodiesterase, we investigated two homologous proteins from
Allochromatium vinosum
and
Magnetococcus marinus
, designated BldP, which contain C-terminal EAL-BLUF modules, where EAL is a c-di-GMP phosphodiesterase domain and BLUF is a blue light sensory domain. Characterization of the BldP proteins in
Escherichia coli
and
in vitro
showed that they possess light-activated c-di-GMP phosphodiesterase activities. Interestingly, light activation in both enzymes was dependent on oxygen levels. The truncated EAL-BLUF fragment from
A. vinosum
BldP lacked phosphodiesterase activity, whereas a similar fragment from
M. marinus
BldP, designated EB1, possessed such activity that was highly (>30-fold) upregulated by light. Following light withdrawal, EB1 reverted to the inactive ground state with a half-life of ∼6 min. Therefore, the blue-light-activated phosphodiesterase EB1 can be used in combination with the red/near-infrared-light-regulated diguanylate cyclase BphS for the bidirectional regulation of c-di-GMP-dependent processes in
E. coli
as well as other bacterial and nonbacterial cells.

IMPORTANCE
Regulation of motility, attachment to surfaces, the cell cycle, and other bacterial processes controlled by the c-di-GMP signaling pathways occur at a fast (seconds-to-minutes) pace. Interrogation of these processes at high temporal and spatial resolution using chemicals is difficult or impossible, while optogenetic approaches may prove useful. We identified and characterized a robust, blue-light-activated c-di-GMP phosphodiesterase (hydrolase) that complements a previously engineered red/near-infrared-light-regulated diguanylate cyclase (c-di-GMP synthase). These two enzymes form a dichromatic module for manipulating intracellular c-di-GMP levels in bacterial and nonbacterial cells.
The Pseudomonas aeruginosa Two-Component Regulator AlgR Directly Activates
rsmA
Expression in a Phosphorylation-Independent Manner
Authors: Stacey Sean D. , Williams Danielle A. , Pritchett Christopher L. 
Published: March 2017

ABSTRACT

Pseudomonas aeruginosa
is an important pathogen of the immunocompromised, causing both acute and chronic infections. In cystic fibrosis (CF) patients,
P. aeruginosa
causes chronic disease. The impressive sensory network of
P. aeruginosa
allows the bacterium to sense and respond to a variety of stimuli found in diverse environments. Transcriptional regulators, including alternative sigma factors and response regulators, integrate signals changing gene expression, allowing
P. aeruginosa
to cause infection. The two-component transcriptional regulator AlgR is important in
P. aeruginosa
pathogenesis in both acute and chronic infections. In chronic infections, AlgR and the alternative sigma factor AlgU activate the genes responsible for alginate production. Previous work demonstrated that AlgU controls
rsmA
expression. RsmA is a posttranscriptional regulator that is antagonized by two small RNAs, RsmY and RsmZ. In this work, we demonstrate that AlgR directly activates
rsmA
expression from the same promoter as AlgU. In addition, phosphorylation was not necessary for AlgR activation of
rsmA
using
algR
and
algZ
mutant strains. AlgU and AlgR appear to affect the antagonizing small RNAs
rsmY
and
rsmZ
indirectly. RsmA was active in a
mucA22
mutant strain using leader fusions of two RsmA targets,
tssA1
and
hcnA
. AlgU and AlgR were necessary for posttranscriptional regulation of
tssA1
and
hcnA
. Altogether, our work demonstrates that the alginate regulators AlgU and AlgR are important in the control of the RsmA posttranscriptional regulatory system. These findings suggest that RsmA plays an unknown role in mucoid strains due to AlgU and AlgR activities.

IMPORTANCE
P. aeruginosa
infections are difficult to treat and frequently cause significant mortality in CF patients. Understanding the mechanisms of persistence is important. Our work has demonstrated that the alginate regulatory system also significantly impacts the posttranscriptional regulator system RsmA/Y/Z. We demonstrate that AlgR directly activates
rsmA
expression, and this impacts the RsmA regulon. This leads to the possibility that the RsmA/Y/Z system plays a role in helping
P. aeruginosa
persist during chronic infection. In addition, this furthers our understanding of the reach of the alginate regulators AlgU and AlgR.
Contributions of the N- and C-Terminal Domains of Initiation Factor 3 to Its Functions in the Fidelity of Initiation and Antiassociation of the Ribosomal Subunits
Authors: Ayyub Shreya Ahana , Dobriyal Divya , Varshney Umesh 
Published: March 2017

ABSTRACT

Initiation factor 3 (IF3) is one of the three conserved prokaryotic translation initiation factors essential for protein synthesis and cellular survival. Bacterial IF3 is composed of a conserved architecture of globular N- and C-terminal domains (NTD and CTD) joined by a linker region. IF3 is a ribosome antiassociation factor which also modulates selection of start codon and initiator tRNA. All the functions of IF3 have been attributed to its CTD by
in vitro
studies. However, the
in vivo
relevance of these findings has not been investigated. By generating complete and partial IF3 (
infC
) knockouts in
Escherichia coli
and by complementation analyses using various deletion constructs, we show that while the CTD is essential for
E. coli
survival, the NTD is not. Polysome profiles reaffirm that CTD alone can bind to the 30S ribosomal subunit and carry out the ribosome antiassociation function. Importantly, in the absence of the NTD, bacterial growth is compromised, indicating a role for the NTD in the fitness of cellular growth. Using reporter assays for
in vivo
initiation, we show that the NTD plays a crucial role in the fidelity function of IF3 by avoiding (i) initiation from non-AUG codons and (ii) initiation by initiator tRNAs lacking the three highly conserved consecutive GC pairs (in the anticodon stem) known to function in concert with IF3.

IMPORTANCE
Initiation factor 3 regulates the fidelity of eubacterial translation initiation by ensuring the formation of an initiation complex with an mRNA bearing a canonical start codon and with an initiator tRNA at the ribosomal P site. Additionally, IF3 prevents premature association of the 50S ribosomal subunit with the 30S preinitiation complex. The significance of our work in
Escherichia coli
is in demonstrating that while the C-terminal domain alone sustains
E. coli
for its growth, the N-terminal domain adds to the fidelity of initiation of protein synthesis and to the fitness of the bacterial growth.
LptO (PG0027) Is Required for Lipid A 1-Phosphatase Activity in Porphyromonas gingivalis W50
Authors: Rangarajan Minnie , Aduse-Opoku Joseph , Hashim Ahmed , McPhail Graham , Luklinska Zofia , Haurat M. Florencia , Feldman Mario F. , Curtis Michael A. 
Published: March 2017

ABSTRACT

Porphyromonas gingivalis
produces outer membrane vesicles (OMVs) rich in virulence factors, including cysteine proteases and A-LPS, one of the two lipopolysaccharides (LPSs) produced by this organism. Previous studies had suggested that A-LPS and PG0027, an outer membrane (OM) protein, may be involved in OMV formation. Their roles in this process were examined by using W50 parent and the Δ
PG0027
mutant strains. Inactivation of
PG0027
caused a reduction in the yield of OMVs. Lipid A from cells and OMVs of
P. gingivalis
W50 and the Δ
PG0027
mutant strains were analyzed by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Lipid A from W50 cells contained bis-P-pentaacyl, mono-P-pentaacyl, mono-P-tetraacyl, non-P-pentaacyl, and non-P-tetraacyl species, whereas lipid A from Δ
PG0027
mutant cells contained only phosphorylated species; nonphosphorylated species were absent. MALDI-TOF/TOF tandem MS of mono-P-pentaacyl (
m
/
z
1,688) and mono-P-tetraacyl (
m
/
z
1,448) lipid A from Δ
PG0027
showed that both contained lipid A 1-phosphate, suggesting that the Δ
PG0027
mutant strain lacked lipid A 1-phosphatase activity. The total phosphatase activities in the W50 and the Δ
PG0027
mutant strains were similar, whereas the phosphatase activity in the periplasm of the Δ
PG0027
mutant was lower than that in W50, supporting a role for PG0027 in lipid A dephosphorylation. W50 OMVs were enriched in A-LPS, and its lipid A did not contain nonphosphorylated species, whereas lipid A from the Δ
PG0027
mutant (OMVs and cells) contained similar species. Thus, OMVs in
P. gingivalis
are apparently formed in regions of the OM enriched in A-LPS devoid of nonphosphorylated lipid A. Conversely, dephosphorylation of lipid A through a PG0027-dependent process is required for optimal formation of OMVs. Hence, the relative proportions of nonphosphorylated and phosphorylated lipid A appear to be crucial for OMV formation in this organism.

IMPORTANCE
Gram-negative bacteria produce outer membrane vesicles (OMVs) by “blebbing” of the outer membrane (OM). OMVs can be used offensively as delivery systems for virulence factors and defensively to aid in the colonization of a host and in the survival of the bacterium in hostile environments. Earlier studies using the oral anaerobe
Porphyromonas gingivalis
as a model organism to study the mechanism of OMV formation suggested that the OM protein PG0027 and one of the two lipopolysaccharides (LPSs) synthesized by this organism, namely, A-LPS, played important roles in OMV formation. We suggest a novel mechanism of OMV formation in
P. gingivalis
involving dephosphorylation of lipid A of A-LPS controlled/regulated by PG0027, which causes destabilization of the OM, resulting in blebbing and generation of OMVs.
RCT of the effect of berryfruit polyphenolic cultivar extract in mild steroid-naive asthma: a cross-over, placebo-controlled study
Authors: Power Sharon , Williams Mathew , Semprini Alex , Munro Claire , Caswell-Smith Rachel , Pilcher Janine , Holliday Mark , Fingleton James , Harper Jacquie , Hurst Roger , Weatherall Mark , Beasley Richard , Braithwaite Irene 
Published: March 2017

ObjectiveThere is preclinical evidence that consumption of berryfruit extract may reduce chronic airways inflammation and modify airway remodelling in allergen-induced models of lung inflammation. We investigated the effect of berryfruit extract on the fractional expired nitric oxide (FeNO), a biomarker of eosinophilic airways inflammation, in adults with steroid-naïve asthma.DesignRandomised placebo-controlled cross-over double-blind trial.SettingSingle-centre community-based trial.Participants28 steroid-naïve mild asthmatics with Feno>40 ppb, of whom 25 completed both study interventions.InterventionsParticipants were randomised to receive, according to the cross-over design, 100 mg berryfruit polyphenolic extract (BFPE) or placebo for 4 weeks, with a 4-week washout period between the interventions.Primary outcome measureThe primary outcome variable was FeNO at 4 weeks, analysed by a mixed linear model, with a random effect for participant and baseline FeNo as a covariate.ResultsThe mean (SD) natural logarithm transformed (ln) FeNO after 4 weeks of treatment for the BFPE and placebo groups was 4.28 (0.47) and 4.22 (0.47), respectively. The paired change from baseline mean (SD) BFPE minus placebo ln FeNO was −0.03 (0.39), N=25. The mixed linear model estimate, with baseline covariate adjustment, difference in ln FeNO, was −0.002 (95% CI −0.15 to 0.14), p=0.98. This is equivalent to a ratio of geometric mean FeNO of 1.0 (95% CI 0.86 to 1.15).ConclusionsIn steroid-naïve participants with mild asthma and elevated FeNO, there was no effect of BFPE on FeNO, a biomarker of eosinophilic airways inflammation. Caution is required in the extrapolation of apparent benefit in murine models of lung eosinophilia to clinical efficacy in patients with asthma.Trial registration numberANZCTR:12613000451707; Results.