bluuebunny/crossref_metadata_2025_split huggingface dataset:
UPC2A
Is Required for High-Level Azole Antifungal Resistance in Candida glabrata
Authors: Whaley Sarah G. , Caudle Kelly E. , Vermitsky John-Paul , Chadwick Sean G. , Toner Geoffrey , Barker Katherine S. , Gygax Scott E. , Rogers P. David 
Published: May 2014

ABSTRACT

Candida glabrata
, the second most common cause of
Candida
infections, is associated with high rates of mortality and often exhibits resistance to the azole class of antifungal agents. Upc2 and Ecm22 in
Saccharomyces cerevisiae
and Upc2 in
Candida albicans
are the transcriptional regulators of
ERG11
, the gene encoding the target of azoles in the ergosterol biosynthesis pathway. Recently two homologs for these transcription factors,
UPC2A
and
UPC2B
, were identified in
C. glabrata
. One of these,
UPC2A
, was shown to influence azole susceptibility. We hypothesized that due to the global role for Upc2 in sterol biosynthesis in
S. cerevisiae
and
C. albicans
, disruption of
UPC2A
would enhance the activity of fluconazole in both azole-susceptible dose-dependent (SDD) and -resistant
C. glabrata
clinical isolates. To test this hypothesis, we constructed mutants with disruptions in
UPC2A
and
UPC2B
alone and in combination in a matched pair of clinical azole-SDD and -resistant isolates. Disruption of
UPC2A
in both the SDD and resistant isolates resulted in increased susceptibility to sterol biosynthesis inhibitors, including a reduction in fluconazole MIC and minimum fungicidal concentration, enhanced azole activity by time-kill analysis, a decrease in ergosterol content, and downregulation of baseline and inducible expression of several sterol biosynthesis genes. Our results indicate that Upc2A is a key regulator of ergosterol biosynthesis and is essential for resistance to sterol biosynthesis inhibitors in
C. glabrata
. Therefore, the
UPC2A
pathway may represent a potential cotherapeutic target for enhancing azole activity against this organism.
In Vitro
and
In Vivo
Evaluation of 28DAP010, a Novel Diamidine for Treatment of Second-Stage African Sleeping Sickness
Authors: Wenzler Tanja , Yang Sihyung , Patrick Donald A. , Braissant Olivier , Ismail Mohamed A. , Tidwell Richard R. , Boykin David W. , Wang Michael Zhuo , Brun Reto 
Published: May 2014

ABSTRACT

African sleeping sickness is a neglected tropical disease transmitted by tsetse flies. New and better drugs are still needed especially for its second stage, which is fatal if untreated. 28DAP010, a dipyridylbenzene analogue of DB829, is the second simple diamidine found to cure mice with central nervous system infections by a parenteral route of administration. 28DAP010 showed efficacy similar to that of DB829 in dose-response studies in mouse models of first- and second-stage African sleeping sickness. The
in vitro
time to kill, determined by microcalorimetry, and the parasite clearance time in mice were shorter for 28DAP010 than for DB829. No cross-resistance was observed between 28DAP010 and pentamidine on the tested
Trypanosoma brucei gambiense
isolates from melarsoprol-refractory patients. 28DAP010 is the second promising preclinical candidate among the diamidines for the treatment of second-stage African sleeping sickness.
Association between
pncA
Gene Mutations, Pyrazinamidase Activity, and Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis
Authors: Aono Akio , Chikamatsu Kinuyo , Yamada Hiroyuki , Kato Tomoko , Mitarai Satoshi 
Published: May 2014

ABSTRACT

We determined MICs for, confirmed the presence of
pncA
mutations in, and performed pyrazinamidase testing on colonies (subclones) obtained from seven isolates that exhibited differential pyrazinamide (PZA) susceptibility. Six of the seven strains were found to exhibit characteristics resulting from the mixture of strains possessing different properties. In addition, our analysis revealed large
pncA
-spanning deletions (1,565 bp, 4,475 bp, and 6,258 bp) in three strains that showed high PZA resistance.
Antagonism between Bacteriostatic and Bactericidal Antibiotics Is Prevalent
Authors: Ocampo Paolo S. , Lázár Viktória , Papp Balázs , Arnoldini Markus , Abel zur Wiesch Pia , Busa-Fekete Róbert , Fekete Gergely , Pál Csaba , Ackermann Martin , Bonhoeffer Sebastian 
Published: May 2014

ABSTRACT
Combination therapy is rarely used to counter the evolution of resistance in bacterial infections. Expansion of the use of combination therapy requires knowledge of how drugs interact at inhibitory concentrations. More than 50 years ago, it was noted that, if bactericidal drugs are most potent with actively dividing cells, then the inhibition of growth induced by a bacteriostatic drug should result in an overall reduction of efficacy when the drug is used in combination with a bactericidal drug. Our goal here was to investigate this hypothesis systematically. We first constructed time-kill curves using five different antibiotics at clinically relevant concentrations, and we observed antagonism between bactericidal and bacteriostatic drugs. We extended our investigation by performing a screen of pairwise combinations of 21 different antibiotics at subinhibitory concentrations, and we found that strong antagonistic interactions were enriched significantly among combinations of bacteriostatic and bactericidal drugs. Finally, since our hypothesis relies on phenotypic effects produced by different drug classes, we recreated these experiments in a microfluidic device and performed time-lapse microscopy to directly observe and quantify the growth and division of individual cells with controlled antibiotic concentrations. While our single-cell observations supported the antagonism between bacteriostatic and bactericidal drugs, they revealed an unexpected variety of cellular responses to antagonistic drug combinations, suggesting that multiple mechanisms underlie the interactions.
Gastrointestinal Colonization with a Cephalosporinase-Producing Bacteroides Species Preserves Colonization Resistance against Vancomycin-Resistant Enterococcus and Clostridium difficile in Cephalosporin-Treated Mice
Authors: Stiefel Usha , Nerandzic Michelle M. , Pultz Michael J. , Donskey Curtis J. 
Published: May 2014

ABSTRACT

Antibiotics that are excreted into the intestinal tract may disrupt the indigenous intestinal microbiota and promote colonization by health care-associated pathogens. β-Lactam, or penicillin-type, antibiotics are among the most widely utilized antibiotics worldwide and may also adversely affect the microbiota. Many bacteria are capable, however, of producing β-lactamase enzymes that inactivate β-lactam antibiotics. We hypothesized that prior establishment of intestinal colonization with a β-lactamase-producing anaerobe might prevent these adverse effects of β-lactam antibiotics, by inactivating the portion of antibiotic that is excreted into the intestinal tract. Here, mice with a previously abolished microbiota received either oral normal saline or an oral cephalosporinase-producing strain of
Bacteroides thetaiotaomicron
for 3 days. Mice then received 3 days of subcutaneous ceftriaxone, followed by either oral administration of vancomycin-resistant
Enterococcus
(VRE) or sacrifice and assessment of
in vitro
growth of epidemic and nonepidemic strains of
Clostridium difficile
in murine cecal contents. Stool concentrations of VRE and ceftriaxone were measured, cecal levels of
C. difficile
24 h after incubation were quantified, and denaturing gradient gel electrophoresis (DGGE) of microbial 16S rRNA genes was performed to evaluate the antibiotic effect on the microbiota. The results demonstrated that establishment of prior colonization with a β-lactamase-producing intestinal anaerobe inactivated intraintestinal ceftriaxone during treatment with this antibiotic, allowed recovery of the normal microbiota despite systemic ceftriaxone, and prevented overgrowth with VRE and epidemic and nonepidemic strains of
C. difficile
in mice. These findings describe a novel probiotic strategy to potentially prevent pathogen colonization in hospitalized patients.
A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131
Authors: Banerjee Ritu , Johnson James R. 
Published: May 2014

ABSTRACT

Escherichia coli
sequence type 131 (ST131) is an extensively antimicrobial-resistant
E. coli
clonal group that has spread explosively throughout the world. Recent molecular epidemiologic and whole-genome phylogenetic studies have elucidated the fine clonal structure of ST131, which comprises multiple ST131 subclones with distinctive resistance profiles, including the (nested) H30, H30-R, and H30-Rx subclones. The most prevalent ST131 subclone, H30, arose from a single common fluoroquinolone (FQ)-susceptible ancestor containing allele 30 of
fimH
(type 1 fimbrial adhesin gene). An early H30 subclone member acquired FQ resistance and launched the rapid expansion of the resulting FQ-resistant subclone, H30-R. Subsequently, a member of H30-R acquired the CTX-M-15 extended-spectrum beta-lactamase and launched the rapid expansion of the CTX-M-15-containing subclone within H30-R, H30-Rx. Clonal expansion clearly is now the dominant mechanism for the rising prevalence of both FQ resistance and CTX-M-15 production in ST131 and in
E. coli
generally. Reasons for the successful dissemination and expansion of the key ST131 subclones remain undefined but may include increased transmissibility, greater ability to colonize and/or persist in the intestine or urinary tract, enhanced virulence, and more-extensive antimicrobial resistance compared to other
E. coli
. Here we discuss the epidemiology and molecular phylogeny of ST131 and its key subclones, possible mechanisms for their ecological success, implications of their widespread dissemination, and future research needs.
The
psm
α Locus Regulates Production of Staphylococcus aureus Alpha-Toxin during Infection
Authors: Berube Bryan J. , Sampedro Georgia R. , Otto Michael , Bubeck Wardenburg Juliane 
Published: May 2014

ABSTRACT

Staphylococcus aureus
is a leading cause of human bacterial infection, causing a wide spectrum of disease ranging from skin and soft tissue infections to life-threatening pneumonia and sepsis.
S. aureus
toxins play an essential role in disease pathogenesis, contributing to both immunomodulation and host tissue injury. Prominent among these toxins are the membrane-active pore-forming cytolysin alpha-toxin (Hla) and the amphipathic α-helical phenol-soluble modulin (PSM) peptides. As deletion of either the
hla
or
psm
locus leads to a phenotypically similar virulence defect in skin and soft tissue infection, we sought to determine the relative contribution of each locus to disease pathogenesis. Here we show that production of Hla can be modulated by PSM expression. An
S. aureus
mutant lacking PSM expression exhibits a transcriptional delay in
hla
mRNA production and therefore fails to secrete normal levels of Hla at early phases of growth. This leads to attenuation of virulence
in vitro
and in murine skin and lung models of infection, correlating with reduced recovery of Hla from host tissues. Production of Hla and restoration of staphylococcal virulence can be achieved in the
psm
mutant by plasmid-driven overexpression of
hla
. Our study suggests the coordinated action of Hla and PSMs in host tissue during early pathogenesis, confirming a major role for Hla in epithelial injury during
S. aureus
infection. These findings highlight the possibility that therapeutics targeting PSM production may simultaneously prevent Hla-mediated tissue injury.
Gastric
De Novo
Muc13 Expression and Spasmolytic Polypeptide-Expressing Metaplasia during Helicobacter heilmannii Infection
Authors: Liu Cheng , Smet Annemieke , Blaecher Caroline , Flahou Bram , Ducatelle Richard , Linden Sara , Haesebrouck Freddy 
Published: May 2014

ABSTRACT

Helicobacter heilmannii
is a zoonotic bacterium that has been associated with gastric disease in humans. In this study, the mRNA expression of mucins in the stomach of BALB/c mice was analyzed at several time points during a 1-year infection with this bacterium, during which gastric disease progressed in severity. Markers for acid production by parietal cells and mucous metaplasia were also examined. In the first 9 weeks postinfection, the mRNA expression of Muc6 was clearly upregulated in both the antrum and fundus of the stomach of
H. heilmannii
-infected mice. Interestingly, Muc13 was upregulated already at 1 day postinfection in the fundus of the stomach. Its expression level remained high in the stomach over the course of the infection. This mucin is, however, not expressed in a healthy stomach, and high expression of this mucin has so far only been described in gastric cancer. In the later stages of infection, mRNA expression of H
+
/K
+
-ATPase α/β and KCNQ1 decreased, whereas the expression of Muc4, Tff2, Dmbt1, and polymeric immunoglobulin receptor (pIgR) increased starting at 16 weeks postinfection onwards, suggesting the existence of spasmolytic polypeptide-expressing metaplasia in the fundus of the stomach. Mucous metaplasia present in the mucosa surrounding low-grade mucosa-associated lymphoid tissue (MALT) lymphoma-like lesions was also histologically confirmed. Our findings indicate that
H. heilmannii
infection causes severe gastric pathologies and alterations in the expression pattern of gastric mucins, such as Muc6 and Muc13, as well as disrupting gastric homeostasis by inducing the loss of parietal cells, resulting in the development of mucous metaplasia.
The Periodontal Pathogen Porphyromonas gingivalis Induces Expression of Transposases and Cell Death of Streptococcus mitis in a Biofilm Model
Authors: Duran-Pinedo Ana E. , Baker Vinesha D. , Frias-Lopez Jorge 
Published: May 2014

ABSTRACT

Oral microbial communities are extremely complex biofilms with high numbers of bacterial species interacting with each other (and the host) to maintain homeostasis of the system. Disturbance in the oral microbiome homeostasis can lead to either caries or periodontitis, two of the most common human diseases. Periodontitis is a polymicrobial disease caused by the coordinated action of a complex microbial community, which results in inflammation of tissues that support the teeth. It is the most common cause of tooth loss among adults in the United States, and recent studies have suggested that it may increase the risk for systemic conditions such as cardiovascular diseases. In a recent series of papers, Hajishengallis and coworkers proposed the idea of the “keystone-pathogen” where low-abundance microbial pathogens (
Porphyromonas gingivalis
) can orchestrate inflammatory disease by turning a benign microbial community into a dysbiotic one. The exact mechanisms by which these pathogens reorganize the healthy oral microbiome are still unknown. In the present manuscript, we present results demonstrating that
P. gingivalis
induces
S. mitis
death and DNA fragmentation in an
in vitro
biofilm system. Moreover, we report here the induction of expression of multiple transposases in a
Streptococcus mitis
biofilm when the periodontopathogen
P. gingivalis
is present. Based on these results, we hypothesize that
P. gingivalis
induces
S. mitis
cell death by an unknown mechanism, shaping the oral microbiome to its advantage.
Nucleoside Diphosphate Kinase and Flagellin from Pseudomonas aeruginosa Induce Interleukin 1 Expression via the Akt/NF-κB Signaling Pathways
Authors: Kim Yong-Jae , Lee Jung-Hoon , Lee Yeji , Jia Jingyue , Paek Se-Hwan , Kim Hyong-Bai , Jin Shouguang , Ha Un-Hwan 
Published: May 2014

ABSTRACT

Inflammatory responses are a first line of host defense against a range of invading pathogens, consisting of the release of proinflammatory cytokines followed by attraction of polymorphonuclear neutrophils (PMNs) to the site of inflammation. Among the many virulence factors that contribute to the pathogenesis of infections, nucleoside diphosphate kinase (Ndk) mediates bacterially induced toxicity against eukaryotic cells. However, no study has examined how Ndk affects inflammatory responses. The present study examined the mechanisms by which
Pseudomonas aeruginosa
activates inflammatory responses upon infection of cells. The results showed that bacterial Ndk, with the aid of an additional bacterial factor, flagellin, induced expression of the proinflammatory cytokines interleukin-1α (IL-1α) and IL-1β. Cytokine induction appeared to be dependent on the kinase activity of Ndk and was mediated via the NF-κB signaling pathway. Notably, Ndk activated the Akt signaling pathway, which acts upstream of NF-κB, as well as caspase-1, which is a key component of inflammasome. Thus, this study demonstrated that
P. aeruginosa
, through the combined effects of Ndk and flagellin, upregulates the expression of proinflammatory cytokines via the Akt/NF-κB signaling pathways.
Microbiota-Induced Changes in Drosophila melanogaster Host Gene Expression and Gut Morphology
Authors: Broderick Nichole A. , Buchon Nicolas , Lemaitre Bruno 
Published: May 2014

ABSTRACT

To elucidate mechanisms underlying the complex relationships between a host and its microbiota, we used the genetically tractable model
Drosophila melanogaster
. Consistent with previous studies, the microbiota was simple in composition and diversity. However, analysis of single flies revealed high interfly variability that correlated with differences in feeding. To understand the effects of this simple and variable consortium, we compared the transcriptome of guts from conventionally reared flies to that for their axenically reared counterparts. Our analysis of two wild-type fly lines identified 121 up- and 31 downregulated genes. The majority of these genes were associated with immune responses, tissue homeostasis, gut physiology, and metabolism. By comparing the transcriptomes of young and old flies, we identified temporally responsive genes and showed that the overall impact of microbiota was greater in older flies. In addition, comparison of wild-type gene expression with that of an immune-deficient line revealed that 53% of upregulated genes exerted their effects through the immune deficiency (Imd) pathway. The genes included not only classic immune response genes but also those involved in signaling, gene expression, and metabolism, unveiling new and unexpected connections between immunity and other systems. Given these findings, we further characterized the effects of gut-associated microbes on gut morphology and epithelial architecture. The results showed that the microbiota affected gut morphology through their impacts on epithelial renewal rate, cellular spacing, and the composition of different cell types in the epithelium. Thus, while bacteria in the gut are highly variable, the influence of the microbiota at large has far-reaching effects on host physiology.

IMPORTANCE
The guts of animals are in constant association with microbes, and these interactions are understood to have important roles in animal development and physiology. Yet we know little about the mechanisms underlying the establishment and function of these associations. Here, we used the fruit fly to understand how the microbiota affects host function. Importantly, we found that the microbiota has far-reaching effects on host physiology, ranging from immunity to gut structure. Our results validate the notion that important insights on complex host-microbe relationships can be obtained from the use of a well-established and genetically tractable invertebrate model.
Binding Site Extraction by Similar Subgraphs Mining from Protein Molecular Surfaces and Its Application to Protein Classification
Authors: Kurumatani Natsumi , Monji Hiroyuki , Ohkawa Takenao 
Published: May 2014

Most proteins express their functions by binding with other proteins or molecular compounds (ligands). Since the characteristics of the local portion involved in binding (binding site) often determine the function of the protein, clarifying the location of the binding site of the protein helps analyze the function of proteins. Binding sites that bind to similar ligands often have common surface structures (surface motifs). Extracting the surface motifs among several proteins with similar functions improves binding site prediction. We propose a method that predicts binding sites by extracting the surface motifs that are frequently observed in only a specific set of proteins that bind to the same ligand (group). Since most binding sites have concave structures (pockets), the pockets are compared and common structures are searched for to extract the surface motifs by applying similar graph mining to the pocket data, which are represented as graphs. Common binding sites across several groups can be predicted in such a way to integrate more than one group. We also proposed a method of protein classification, in which the surface motifs extracted using the above method are evaluated on the assumption that a protein belongs to each one of the groups.
Use and Performance of the Melody Transcatheter Pulmonary Valve in Native and Postsurgical, Nonconduit Right Ventricular Outflow Tracts
Authors: Meadows Jeffery J. , Moore Phillip M. , Berman Darren P. , Cheatham John P. , Cheatham Sharon L. , Porras Diego , Gillespie Matthew J. , Rome Jonathan J. , Zahn Evan M. , McElhinney Doff B. 
Published: May 2014

Background—
Melody Transcatheter Pulmonary Valve (TPV) replacement therapy represents an important advance in congenital cardiovascular interventions. The off-label extension of the Melody TPV to patients with nonconduit outflow tracts (right ventricular outflow tract [RVOT]) has the potential to vastly expand the population of patients eligible to benefit from nonsurgical restoration of RVOT function. However, knowledge on the performance of the Melody TPV in this setting is limited.

Methods and Results—
This is a multicenter, retrospective review of the Melody TPV when placed in nonconduit RVOTs, in which at least a portion of the circumference was composed of native tissue. Five centers contributed data on 31 patients. The median age at implantation was 24 years (range, 7–66). At a median follow-up of 15 months, all patients were alive. No patient had greater than mild TPV insufficiency, and the median maximum instantaneous gradients across the RVOT was 23 mm Hg. Stent fracture occurred in 32%. Eight patients developed more than mild TPV obstruction, of whom 6 were associated with identified stent fracture. Three patients developed blood stream infections. There were 5 reinterventions in 3 patients, including 3 repeat TPV implantations and 2 TPV explantations.

Conclusions—
Melody TPV implantation is feasible in selected patients with RVOTs comprised solely or predominantly native tissue and has the potential to expand the population of patients eligible to benefit from nonsurgical restoration of RVOT function. In early follow-up, valve competency seems preserved. The dominant mechanism of valve dysfunction seems to be related to stent fracture with recurrent obstruction. Additional data are necessary to better understand how to safely expand TPV therapy to this population.