bluuebunny/crossref_metadata_2025_split huggingface dataset:
UDP-
N
-Acetylmuramic Acid
l
-Alanine Ligase (MurC) Inhibition in a
tolC
Mutant Escherichia coli Strain Leads to Cell Death
Authors: Humnabadkar Vaishali , Prabhakar K. R. , Narayan Ashwini , Sharma Sreevalli , Guptha Supreeth , Manjrekar Praveena , Chinnapattu Murugan , Ramachandran Vasanthi , Hameed Shahul P. , Ravishankar Sudha , Chatterji Monalisa 
Published: August 2014

ABSTRACT

The Mur ligases play an essential role in the biosynthesis of bacterial peptidoglycan and hence are attractive antibacterial targets. A screen of the AstraZeneca compound library led to the identification of compound A, a pyrazolopyrimidine, as a potent inhibitor of
Escherichia coli
and
Pseudomonas aeruginosa
MurC. However, cellular activity against
E. coli
or
P. aeruginosa
was not observed. Compound A was active against efflux pump mutants of both strains. Experiments using an
E. coli
tolC
mutant revealed accumulation of the MurC substrate and a decrease in the level of product upon treatment with compound A
,
indicating inhibition of MurC enzyme in these cells. Such a modulation was not observed in the
E. coli
wild-type cells. Further, overexpression of MurC in the
E. coli
tolC
mutant led to an increase in the compound A MIC by ≥16-fold, establishing a correlation between MurC inhibition and cellular activity. In addition, estimation of the intracellular compound A level showed an accumulation of the compound over time in the
tolC
mutant strain. A significant compound A level was not detected in the wild-type
E. coli
strain even upon treatment with high concentrations of the compound. Therefore, the lack of MIC and absence of MurC inhibition in wild-type
E. coli
were possibly due to suboptimal compound concentration as a consequence of a high efflux level and/or poor permeativity of compound A.
Whole-Animal Chemical Screen Identifies Colistin as a New Immunomodulator That Targets Conserved Pathways
Authors: Cai Yun , Cao Xiou , Aballay Alejandro 
Published: August 2014

ABSTRACT

The purpose of this study was to take advantage of the nematode
Caenorhabditis elegans
to perform a whole-animal chemical screen to identify potential immune activators that may confer protection against bacterial infections. We identified 45 marketed drugs, out of 1,120 studied compounds, that are capable of activating a conserved p38/PMK-1 mitogen-activated protein kinase pathway required for innate immunity. One of these drugs, the last-resort antibiotic colistin, protected against infections by the Gram-negative pathogens
Yersinia pestis
and
Pseudomonas aeruginosa
but not by the Gram-positive pathogens
Enterococcus faecalis
and
Staphylococcus aureus
. Protection was independent of the antibacterial activity of colistin, since the drug was administered prophylactically prior to the infections and it was also effective against antibiotic-resistant bacteria. Immune activation by colistin is mediated not only by the p38/PMK-1 pathway but also by the conserved FOXO transcription factor DAF-16 and the transcription factor SKN-1. Furthermore, p38/PMK-1 was found to be required in the intestine for immune activation by colistin. Enhanced p38/PMK-1-mediated immune responses by colistin did not reduce the bacterial burden, indicating that the pathway plays a role in the development of host tolerance to infections by Gram-negative bacteria.

IMPORTANCE
The innate immune system represents the front line of our defenses against invading microorganisms. Given the ever-increasing resistance to antibiotics developed by bacterial pathogens, the possibility of boosting immune defenses represents an interesting, complementary approach to conventional antibiotic treatments. Here we report that the antibiotic colistin can protect against infections by a mechanism that is independent of its microbicidal activity. Prophylactic treatment with colistin activates a conserved p38/PMK-1 pathway in the intestine that helps the host better tolerate a bacterial infection. Since p38/PMK-1-mediated immune responses appear to be conserved from plants to mammals, colistin may also activate immunity in higher organisms, including humans. Antibiotics with immunomodulatory properties have the potential of improving the long-term outcome of patients with chronic infectious diseases.
Influenza Virus A/Anhui/1/2013 (H7N9) Replicates Efficiently in the Upper and Lower Respiratory Tracts of Cynomolgus Macaques
Authors: de Wit Emmie , Rasmussen Angela L. , Feldmann Friederike , Bushmaker Trenton , Martellaro Cynthia , Haddock Elaine , Okumura Atsushi , Proll Sean C. , Chang Jean , Gardner Don , Katze Michael G. , Munster Vincent J. , Feldmann Heinz 
Published: August 2014

ABSTRACT
In March 2013, three fatal human cases of infection with influenza A virus (H7N9) were reported in China. Since then, human cases have been accumulating. Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. Cynomolgus macaques developed transient, mild to severe disease with radiographic evidence of pulmonary infiltration. Virus replicated in the upper as well as lower respiratory tract, with sustained replication in the upper respiratory tract until the end of the experiment at 6 days after inoculation. Virus shedding occurred mainly via the throat. Histopathological changes in the lungs were similar to those observed in humans, albeit less severe, with diffuse alveolar damage, infiltration of polymorphonuclear cells, formation of hyaline membranes, pneumocyte hyperplasia, and fibroproliferative changes. Analysis of gene expression profiles in lung lesions identified pathways involved in tissue damage during H7N9 infection as well as leads for development of therapeutics targeting host responses rather than virus replication. Overall, H7N9 infection was not as severe in cynomolgus macaques as in humans, supporting the possible role of underlying medical complications in disease severity as discussed for human H7N9 infection (H. N. Gao et al., N. Engl. J. Med. 368:2277–2285, 2013, doi:10.1056/NEJMoa1305584).

IMPORTANCE
Influenza A virus H7N9 emerged early in 2013, and human cases have continued to emerge since then. Although H7N9 virus-induced disease in humans is often very severe and even lethal, the majority of reported H7N9 cases occurred in older people and people with underlying medical conditions. To better understand the pathogenicity of this virus, healthy cynomolgus macaques were inoculated with influenza A virus H7N9. Cynomolgus macaques were used as a model because the receptor distribution for H7N9 virus in macaques was recently shown to be more similar to that in humans than that of other frequently used animal models. From comparison with previous studies, we conclude that the emerging H7N9 influenza virus was more pathogenic in cynomolgus macaques than seasonal influenza A viruses and most isolates of the pandemic H1N1 virus but less pathogenic than the 1918 Spanish influenza virus or highly pathogenic avian influenza (HPAI) H5N1 virus.
Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids
Authors: Lukovac Sabina , Belzer Clara , Pellis Linette , Keijser Bart J. , de Vos Willem M. , Montijn Roy C. , Roeselers Guus 
Published: August 2014

ABSTRACT

The gut microbiota is essential for numerous aspects of human health. However, the underlying mechanisms of many host-microbiota interactions remain unclear. The aim of this study was to characterize effects of the microbiota on host epithelium using a novel
ex vivo
model based on mouse ileal organoids. We have explored the transcriptional response of organoids upon exposure to short-chain fatty acids (SCFAs) and products generated by two abundant microbiota constituents,
Akkermansia muciniphila
and
Faecalibacterium prausnitzii
. We observed that
A. muciniphila
metabolites affect various transcription factors and genes involved in cellular lipid metabolism and growth, supporting previous
in vivo
findings. Contrastingly,
F. prausnitzii
products exerted only weak effects on host transcription. Additionally,
A. muciniphila
and its metabolite propionate modulated expression of Fiaf, Gpr43, histone deacetylases (HDACs), and peroxisome proliferator-activated receptor gamma (Pparγ), important regulators of transcription factor regulation, cell cycle control, lipolysis, and satiety. This work illustrates that specific bacteria and their metabolites differentially modulate epithelial transcription in mouse organoids. We demonstrate that intestinal organoids provide a novel and powerful
ex vivo
model for host-microbiome interaction studies.

IMPORTANCE
We investigated the influence of the gut microbiota and microbially produced short-chain fatty acids (SCFAs) on gut functioning. Many commensal bacteria in the gut produce SCFAs, particularly butyrate, acetate, and propionate, which have been demonstrated to reduce the risk of gastrointestinal disorders. Organoids—small crypt-villus structures grown from ileal intestinal stem cells—were exposed to SCFAs and two specific gut bacteria.
Akkermansia muciniphila
, found in the intestinal mucus, was recently shown to have a favorable effect on the disrupted metabolism associated with obesity.
Faecalibacterium prausnitzii
is a commensal gut bacterium, the absence of which may be associated with Crohn’s disease. We showed that in our model,
A. muciniphila
induces stronger effects on the host than
F. prausnitzii
. We observed that
A. muciniphila
and propionate affect the expression of genes involved in host lipid metabolism and epigenetic activation or silencing of gene expression. We demonstrated that organoids provide a powerful tool for host-microbe interaction studies.
Fur Is the Master Regulator of the Extraintestinal Pathogenic Escherichia coli Response to Serum
Authors: Huja Sagi , Oren Yaara , Biran Dvora , Meyer Susann , Dobrindt Ulrich , Bernhard Joerg , Becher Doerte , Hecker Michael , Sorek Rotem , Ron Eliora Z. 
Published: August 2014

ABSTRACT

Drug-resistant extraintestinal pathogenic
Escherichia coli
(ExPEC) strains are the major cause of colisepticemia (colibacillosis), a condition that has become an increasing public health problem in recent years. ExPEC strains are characterized by high resistance to serum, which is otherwise highly toxic to most bacteria. To understand how these bacteria survive and grow in serum, we performed system-wide analyses of their response to serum, making a clear distinction between the responses to nutritional immunity and innate immunity. Thus, mild heat inactivation of serum destroys the immune complement and abolishes the bactericidal effect of serum (inactive serum), making it possible to examine nutritional immunity. We used a combination of deep RNA sequencing and proteomics in order to characterize ExPEC genes whose expression is affected by the nutritional stress of serum and by the immune complement. The major change in gene expression induced by serum—active and inactive—involved metabolic genes. In particular, the serum metabolic response is coordinated by three transcriptional regulators, Fur, BasR, and CysB. Fur alone was responsible for more than 80% of the serum-induced transcriptional response. Consistent with its role as a major serum response regulator, deletion of Fur renders the bacteria completely serum sensitive. These results highlight the role of metabolic adaptation in colisepticemia and virulence.

IMPORTANCE
Drug-resistant extraintestinal pathogenic
Escherichia coli
(ExPEC) strains have emerged as major pathogens, especially in community- and hospital-acquired infections. These bacteria cause a large spectrum of syndromes, the most serious of which is septicemia, a condition with a high mortality rate. These bacterial strains are characterized by high resistance to serum, otherwise highly toxic to most bacteria. To understand the basis of this resistance, we carried out system-wide analyses of the response of ExPEC strains to serum by using proteomics and deep RNA sequencing. The major changes in gene expression induced by exposure to serum involved metabolic genes, not necessarily implicated in relation to virulence. One metabolic regulator—Fur—involved in iron metabolism was responsible for more than 80% of the serum-induced response, and its deletion renders the bacteria completely serum sensitive. These results highlight the role of metabolic adaptation in virulence.
Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors
Authors: Williams Thomas R. , Marco Maria L. 
Published: August 2014

ABSTRACT

The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of
Betaproteobacteria
as opposed to the
Gammaproteobacteria-
enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of
Escherichia coli
O157:H7 was unchanged by microbial community transfer; however, the inoculation of
E. coli
O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety.

IMPORTANCE
The phyllosphere is a habitat for a variety of microorganisms, including bacteria with significant relevance to plant and human health. Some indigenous epiphytic bacteria might affect the persistence of human food-borne pathogens in the phyllosphere. However, studies on human pathogens are typically performed on plants grown indoors. This study compares the phyllosphere microbiota on Romaine lettuce plants grown in a Salinas Valley, CA, field to that on lettuce plants grown in environmental chambers. We show that phyllosphere microbiota from laboratory-grown plants is distinct from that colonizing plants grown in the field and that the field microbiota can be successfully transferred to plants grown indoors. The microbiota transplantation method was used to examine alterations to the phyllosphere microbiota after
Escherichia coli
O157:H7 inoculation on lettuce plants in a controlled environment. Our findings show the importance and validity of phyllosphere microbiota transplantation for future phyllosphere microbiology research.
Cross Talk between the Cell Wall Integrity and Cyclic AMP/Protein Kinase A Pathways in Cryptococcus neoformans
Authors: Donlin Maureen J. , Upadhya Rajendra , Gerik Kimberly J. , Lam Woei , VanArendonk Laura G. , Specht Charles A. , Sharma Neil K. , Lodge Jennifer K. 
Published: August 2014

ABSTRACT

Cryptococcus neoformans
is a fungal pathogen of immunocompromised people that causes fatal meningitis. The fungal cell wall is essential to viability and pathogenesis of
C. neoformans
, and biosynthesis and repair of the wall is primarily controlled by the cell wall integrity (CWI) signaling pathway. Previous work has shown that deletion of genes encoding the four major kinases in the CWI signaling pathway, namely,
PKC1
,
BCK1
,
MKK2
, and
MPK1
results in severe cell wall phenotypes, sensitivity to a variety of cell wall stressors, and for Mpk1, reduced virulence in a mouse model. Here, we examined the global transcriptional responses to gene deletions of
BCK1
,
MKK2
, and
MPK1
compared to wild-type cells. We found that over 1,000 genes were differentially expressed in one or more of the deletion strains, with 115 genes differentially expressed in all three strains, many of which have been identified as genes regulated by the cyclic AMP (cAMP)/protein kinase A (PKA) pathway. Biochemical measurements of cAMP levels in the kinase deletion strains revealed significantly less cAMP in all of the deletion strains compared to the wild-type strain. The deletion strains also produced significantly smaller capsules than the wild-type KN99 strain did under capsule-inducing conditions, although the levels of capsule they shed were similar to those shed by the wild type. Finally, addition of exogenous cAMP led to reduced sensitivity to cell wall stress and restored surface capsule to levels near those of wild type. Thus, we have direct evidence of cross talk between the CWI and cAMP/PKA pathways that may have important implications for regulation of cell wall and capsule homeostasis.

IMPORTANCE
Cryptococcus neoformans
is a fungal pathogen of immunocompromised people that causes fatal meningitis. The fungal cell wall is essential to viability and pathogenesis of
C. neoformans
, and biosynthesis and repair of the wall are primarily controlled by the cell wall integrity (CWI) signaling pathway. In this study, we demonstrate that deletion of any of three core kinases in the CWI pathway impacts not only the cell wall but also the amount of surface capsule. Deletion of any of the kinases results in significantly reduced cellular cyclic AMP (cAMP) levels, and addition of exogenous cAMP rescues the capsule defect and some cell wall defects, supporting a direct role for the CWI pathway in regulation of capsule in conjunction with the cAMP/protein kinase A pathway.
Tackle-related injury rates and nature of injuries in South African Youth Week tournament rugby union players (under-13 to under-18): an observational cohort study
Authors: Burger Nicholas , Lambert Mike I , Viljoen Wayne , Brown James C , Readhead Clint , Hendricks Sharief 
Published: August 2014

ObjectivesThe tackle situation is most often associated with the high injury rates in rugby union. Tackle injury epidemiology in rugby union has previously been focused on senior cohorts but less is known about younger cohorts. The aim of this study was to report on the nature and rates of tackle-related injuries in South African youth rugby union players representing their provinces at national tournaments.DesignObservational cohort study.SettingFour South African Youth Week tournaments (under-13 Craven Week, under-16 Grant Khomo Week, under-18 Academy Week, under-18 Craven Week).ParticipantsInjury data were collected from 3652 youth rugby union players (population at risk) in 2011 and 2012.Outcome measuresTackle-related injury severity (‘time-loss’ and ‘medical attention’), type and location, injury rate per 1000 h (including 95% CIs). Injury rate ratios (IRR) were calculated and modelled using a Poisson regression. A χ2analysis was used to detect linear trends between injuries and increasing match quarters.ResultsThe 2012 under-13 Craven Week had a significantly greater ‘time-loss’ injury rate when compared with the 2012 under-18 Academy Week (IRR=4.43; 95% CI 2.13 to 9.21, p<0.05) and under-18 Craven Week (IRR=3.52; 95% CI 1.54 to 8.00, p<0.05). The Poisson regression also revealed a higher probability of ‘overall’ (‘time-loss’ and ‘medical attention’ combined) and ‘time-loss’ tackle-related injuries occurring at the under-13 Craven Week. The proportion of ‘overall’ and ‘time-loss’ injuries increased significantly with each quarter of the match when all four tournaments were combined (p<0.05).ConclusionsThere was a difference in the tackle-related injury rate between the under-13 tournament and the two under-18 tournaments, and the tackle-related injury rate was higher in the final quarter of matches. Ongoing injury surveillance is required to better interpret these findings. Injury prevention strategies targeting the tackle may only be effective once the rate and nature of injuries have been accurately determined.
Developing a Platform for Learning from Mistakes: changing the culture of patient safety amongst junior doctors
Authors: Millwood Sinead 
Published: August 2014

AbstractJunior doctors commonly make mistakes which may compromise patient safety. Despite the recent push by the NHS to encourage a “no blame” culture, mistakes are still viewed as shameful, embarrassing and demoralising events. The current model for learning from mistakes means that junior doctors only learn from their own errors.A survey was designed by the author for all the Foundation Year 1 doctors (FY1s) at Yeovil District Hospital to understand better the culture surrounding mistakes, and the types of mistakes that were being made. Using the results of the survey and the support of senior staff, a “Near misses” session has been introduced for FY1s once a month at which mistakes that have been made are discussed, with a consultant present to facilitate the proceedings. The aims of these sessions are to promote a culture of no blame, feedback information to clinical governance, and share learning experiences.100% of the FY1s had made a mistake that could compromise patient safety. 63% discussed their mistakes with colleagues, 44% with seniors, and only 13% with their educational supervisor. Barriers to discussing mistakes included shame, embarrassment, fear of judgement, and unapproachable seniors. 94% thought a “Near misses” session would be useful. After the third session 100% of the FY1s agreed that the sessions were useful; 53% had changed their practice as a result of something they learned at the sessions.After discussing errors as a group we have worked with the clinical governance department, enacting strategies to avoid repetition of mistakes. Feedback from the junior doctors has been overwhelmingly positive and we have found these sessions to be a simple, inexpensive, and popular solution to cultural change in our organisation.