bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multidrug-Resistant Transporter Mdr1p-Mediated Uptake of a Novel Antifungal Compound
Authors: Sun Nuo , Li Dongmei , Fonzi William , Li Xin , Zhang Lixin , Calderone Richard 
Published: September 2013

ABSTRACT

The activity of many anti-infectious drugs has been compromised by the evolution of multidrug-resistant (MDR) pathogens. For life-threatening fungal infections, such as those caused by
Candida albicans
, overexpression of
MDR1
, which encodes an MDR efflux pump of the major facilitator superfamily (MFS), often confers resistance to chemically unrelated substances, including the most commonly used azole antifungals. As the development of new and efficacious antifungals has lagged far behind the growing emergence of resistant strains, it is imperative to develop strategies to overcome multidrug resistance. Previous advances have been mainly to deploy combinational therapy to restore azole susceptibility, which, however, requires coordination of two or more compounds. We observed a unique phenotype in which Mdr1p facilitates the uptake of a specific class of compounds. Among them, we describe a novel antifungal small molecule, bis[1,6-a:5′,6′-g]quinolizinium 8-methyl-salt (BQM) (U.S. patent application no. 61/793,090,2013), that has potent and broad antifungal activity. Notably, BQM exploits the MDR phenotype in
C. albicans
to promote the inhibitory effect. Rather than causing an antagonism of MDR strains, it exhibits a highly potentiated activity against a collection of clinical isolates and lab strains that overexpress
MDR1
. The activity of BQM against
MDR1
-overexpressing isolates is due to its facilitated intracellular accumulation. Microarray comparisons showed an extensive upregulation of
MDR1
as well as polyamine transporter genes in a fluconazole-resistant strain. We then demonstrated that the polyamine transporters augment the accumulation of BQM. Importantly, BQM had greater activity than fluconazole and itraconazole against various fungal pathogens, including MDR
Aspergillus fumigatus
. Thus, our findings offer a paradigm shift to overcome MDR and the promise of improving antifungal treatment, especially in MDR pathogens.
Discovery of Inhibitors of 4′-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy
Authors: de Jonge Boudewijn L. M. , Walkup Grant K. , Lahiri Sushmita D. , Huynh Hoan , Neckermann Georg , Utley Luke , Nash Tory J. , Brock Jesse , San Martin Maryann , Kutschke Amy , Johnstone Michele , Laganas Valerie , Hajec Laurel , Gu Rong-Fang , Ni Haihong , Chen Brendan , Hutchings Kim , Holt Elise , McKinney David , Gao Ning , Livchak Stephania , Thresher Jason 
Published: September 2013

ABSTRACT

Inhibitors of 4′-phosphopantetheine adenylyltransferase (PPAT) were identified through high-throughput screening of the AstraZeneca compound library. One series, cycloalkyl pyrimidines, showed inhibition of PPAT isozymes from several species, with the most potent inhibition of enzymes from Gram-positive species. Mode-of-inhibition studies with
Streptococcus pneumoniae
and
Staphylococcus aureus
PPAT demonstrated representatives of this series to be reversible inhibitors competitive with phosphopantetheine and uncompetitive with ATP, binding to the enzyme-ATP complex. The potency of this series was optimized using structure-based design, and inhibition of cell growth of Gram-positive species was achieved. Mode-of-action studies, using generation of resistant mutants with targeted sequencing as well as constructs that overexpress PPAT, demonstrated that growth suppression was due to inhibition of PPAT. An effect on bacterial burden was demonstrated in mouse lung and thigh infection models, but further optimization of dosing requirements and compound properties is needed before these compounds can be considered for progress into clinical development. These studies validated PPAT as a novel target for antibacterial therapy.
Tools for Characterizing Bacterial Protein Synthesis Inhibitors
Authors: Orelle Cédric , Carlson Skylar , Kaushal Bindiya , Almutairi Mashal M. , Liu Haipeng , Ochabowicz Anna , Quan Selwyn , Pham Van Cuong , Squires Catherine L. , Murphy Brian T. , Mankin Alexander S. 
Published: September 2013

ABSTRACT

Many antibiotics inhibit the growth of sensitive bacteria by interfering with ribosome function. However, discovery of new protein synthesis inhibitors is curbed by the lack of facile techniques capable of readily identifying antibiotic target sites and modes of action. Furthermore, the frequent rediscovery of known antibiotic scaffolds, especially in natural product extracts, is time-consuming and expensive and diverts resources that could be used toward the isolation of novel lead molecules. In order to avoid these pitfalls and improve the process of dereplication of chemically complex extracts, we designed a two-pronged approach for the
ch
aracterization of
i
nhibitors of
p
rotein
s
ynthesis (ChIPS) that is suitable for the rapid identification of the site and mode of action on the bacterial ribosome. First, we engineered antibiotic-hypersensitive
Escherichia coli
strains that contain only one rRNA operon. These strains are used for the rapid isolation of resistance mutants in which rRNA mutations identify the site of the antibiotic action. Second, we show that patterns of drug-induced ribosome stalling on mRNA, monitored by primer extension, can be used to elucidate the mode of antibiotic action. These analyses can be performed within a few days and provide a rapid and efficient approach for identifying the site and mode of action of translation inhibitors targeting the bacterial ribosome. Both techniques were validated using a bacterial strain whose culture extract, composed of unknown metabolites, exhibited protein synthesis inhibitory activity; we were able to rapidly detect the presence of the antibiotic chloramphenicol.
Hollow-Fiber Pharmacodynamic Studies and Mathematical Modeling To Predict the Efficacy of Amoxicillin for Anthrax Postexposure Prophylaxis in Pregnant Women and Children
Authors: Louie Arnold , VanScoy Brian , Liu Weiguo , Kulawy Robert , Drusano G. L. 
Published: September 2013

ABSTRACT

Amoxicillin is considered an option for postexposure prophylaxis of
Bacillus anthracis
in pregnant and postpartum women who are breastfeeding and in children because of the potential toxicities of ciprofloxacin and doxycycline to the fetus and child. The amoxicillin regimen that effectively kills
B. anthracis
and prevents resistance is unknown. Fourteen-day dose range and dose fractionation studies were conducted in
in vitro
pharmacodynamic models to identify the exposure intensity and pharmacodynamic index of amoxicillin that are linked with optimized killing of
B. anthracis
and resistance prevention. Studies with dicloxacillin, a drug resistant to
B. anthracis
beta-lactamase, evaluated the role of beta-lactamase production in the pharmacodynamic indices for
B. anthracis
killing and resistance prevention. Dose fractionation studies showed that trough/MIC and not time above MIC was the index for amoxicillin that was linked to successful outcome through resistance prevention. Failure of amoxicillin regimens was due to inducible or stable high level expression of beta-lactamases. Studies with dicloxacillin demonstrated that a time above MIC of ≥94% was linked with treatment success when
B. anthracis
beta-lactamase activity was negated. Recursive partitioning analysis showed that amoxicillin regimens that produced peak concentrations of <10.99 μg/ml and troughs of >1.75 μg/ml provided a 100% success rate. Other amoxicillin peak and trough values produced success rates of 28 to 67%. For postpartum and pregnant women and children, Monte Carlo simulations predicted success rates for amoxicillin at 1 g every 8 h (q8h) of 53, 33, and 44% (30 mg/kg q8h), respectively. We conclude that amoxicillin is suboptimal for postexposure prophylaxis of
B. anthracis
in pregnant and postpartum women and in children.
Bacillus anthracis Has Two Independent Bottlenecks That Are Dependent on the Portal of Entry in an Intranasal Model of Inhalational Infection
Authors: Lowe David E. , Ernst Stephen M. C. , Zito Christine , Ya Jason , Glomski Ian J. 
Published: September 2013

ABSTRACT

Bacillus anthracis
can cause inhalational anthrax. Murine inhalational
B. anthracis
infections have two portals of entry, the nasal mucosa-associated lymphoid tissue (NALT) and the lumen of the lungs. Analysis of the dissemination from these sites is hindered because infections are asynchronous and asymptomatic until the hosts near death. To further understand and compare how
B. anthracis
disseminates from these two different environments, clonal analysis was employed using a library of equally virulent DNA-tagged clones of a luminescent Sterne strain. Luminescence was used to determine the origin of the infection and monitor the dissemination
in vivo
. The number of clones and their proportions in the portals of entry, lymph nodes draining the portals, and kidneys were analyzed. Clonal analysis indicated a bottleneck for both portals of entry, yet the extent and location of the reduction in represented clones differed between the routes. In NALT-based infections, all clones were found to germinate in the NALT, but they underwent a bottleneck as the infection spread to the cervical lymph node. However, lung-based infections underwent a bottleneck in a focal region of growth within the lung lumen and did not need to spread through the mediastinal lymph nodes to cause a systemic infection. Further, the average number of clones found in the kidney and the rate at which genetic drift was affecting the disseminated populations were significantly higher in lung-based infections. Collectively, the data suggested that differences in the host environment alter dissemination of
B. anthracis
depending on the site of initial colonization and growth.
FimY Does Not Interfere with FimZ-FimW Interaction during Type 1 Fimbria Production by Salmonella enterica Serovar Typhimurium
Authors: Zeiner Sarah A. , Dwyer Brett E. , Clegg Steven 
Published: September 2013

ABSTRACT

The production of type 1 fimbriae in
Salmonella enterica
serovar Typhimurium is controlled, in part, by three proteins, FimZ, FimY, and FimW. Amino acid sequence analysis indicates that FimZ belongs to the family of bacterial response regulators of two-component systems. In these studies, we have demonstrated that introducing a mutation mimicking phosphorylation of FimZ is necessary for activation of its target gene,
fimA
. In addition, the interaction of FimZ with FimW, a repressor of
fimA
expression, occurs only when FimZ is phosphorylated. Consequently, the negative regulatory effect of FimW is most likely due to downmodulation of the active FimZ protein. FimY does not appear to function as a response regulator, and its activity can be lost by mimicking the phosphorylation of FimY. Overproduction of FimY cannot alleviate the nonfimbriate phenotype in a FimZ mutant, whereas high levels of FimZ can overcome the nonfimbriate phenotype of a FimY mutant. It appears that FimY acts upstream of FimZ to activate
fimA
expression.
Global Transcriptome Analysis of Staphylococcus aureus Biofilms in Response to Innate Immune Cells
Authors: Scherr Tyler D. , Roux Christelle M. , Hanke Mark L. , Angle Amanda , Dunman Paul M. , Kielian Tammy 
Published: September 2013

ABSTRACT

The potent phagocytic and microbicidal activities of neutrophils and macrophages are among the first lines of defense against bacterial infections. Yet
Staphylococcus aureus
is often resistant to innate immune defense mechanisms, especially when organized as a biofilm. To investigate how
S. aureus
biofilms respond to macrophages and neutrophils, gene expression patterns were profiled using Affymetrix microarrays. The addition of macrophages to
S. aureus
static biofilms led to a global suppression of the biofilm transcriptome with a wide variety of genes downregulated. Notably, genes involved in metabolism, cell wall synthesis/structure, and transcription/translation/replication were among the most highly downregulated, which was most dramatic at 1 h compared to 24 h following macrophage addition to biofilms. Unexpectedly, few genes were enhanced in biofilms after macrophage challenge. Unlike coculture with macrophages, coculture of
S. aureus
static biofilms with neutrophils did not greatly influence the biofilm transcriptome. Collectively, these experiments demonstrate that
S. aureus
biofilms differentially modify their gene expression patterns depending on the leukocyte subset encountered.
Periodontal Treatment Downregulates Protease-Activated Receptor 2 in Human Gingival Crevicular Fluid Cells
Authors: Euzebio Alves Vanessa Tubero , Bueno da Silva Henrique Aparecido , de França Bruno Nunes , Eichler Rosangela Santos , Saraiva Luciana , de Carvalho Maria Helena Catelli , Holzhausen Marinella 
Published: September 2013

ABSTRACT

Protease-activated receptor 2 (PAR2) is implicated in the pathogenesis of chronic inflammatory diseases, including periodontitis; it can be activated by gingipain and produced by
Porphyromonas gingivalis
and by neutrophil protease 3 (P3). PAR2 activation plays a relevant role in inflammatory processes by inducing the release of important inflammatory mediators associated with periodontal breakdown. The effects of periodontal treatment on PAR2 expression and its association with levels of proinflammatory mediators and activating proteases were investigated in chronic periodontitis patients. Positive staining for PAR2 was observed in gingival crevicular fluid cells and was reflective of tissue destruction. Overexpression of PAR2 was positively associated with inflammatory clinical parameters and with the levels of interleukin-6 (IL-6), IL-8, tumor necrosis factor alpha, matrix metalloprotease 2 (MMP-2), MMP-8, hepatocyte growth factor, and vascular endothelial growth factor. Elevated levels of gingipain and P3 and decreased levels of dentilisin and the protease inhibitors secretory leukocyte protease inhibitor and elafin were also associated with PAR2 overexpression. Healthy periodontal sites from individuals with chronic periodontitis showed diminished expression of PAR2 mRNA and the PAR2 protein (
P
< 0.05). Furthermore, periodontal treatment resulted in decreased PAR2 expression and correlated with decreased expression of inflammatory mediators and activating proteases. We concluded that periodontal treatment resulted in decreased levels of proteases and that proinflammatory mediators are associated with decreased PAR2 expression, suggesting that PAR2 expression is influenced by the presence of periodontal infection and is not a constitutive characteristic favoring periodontal inflammation.
Influence of midsole hardness of standard cushioned shoes on running-related injury risk
Authors: Theisen Daniel , Malisoux Laurent , Genin Joakim , Delattre Nicolas , Seil Romain , Urhausen Axel 
Published: September 2013

BackgroundIn this double-blind randomised controlled trial, we tested if leisure-time runners using shoes with less compliant midsoles have a higher running-related injury (RRI) risk.MethodWe provided 247 runners with standard running shoes having either a soft study shoes (soft-SS) or a hard study shoes (hard-SS) midsole and followed them prospectively for 5 months regarding RRI. All information about sports practice and injuries was uploaded on a dedicated internet platform and checked for consistency and completeness. RRI was defined as any first-time pain sustained during or as a result of running practice and impeding normal running activity for at least 1 day. Cox proportional hazards regressions were used to identify RRI risk factors.ResultThe type of study shoes used for running was not associated with RRIs (HR=0.92; 95% CI 0.57 to 1.48). The hard-SS had a 15% greater overall stiffness in the heel region. The two study groups were similar regarding personal and sports participation characteristics, except for years of running experience, which was higher (p<0.05) in the hard-SS group. Global RRI incidence was 12.1 RRI/1000 h of running. No between-group differences were found regarding injury location, type, severity or category. Nevertheless, the adjusted regression model revealed positive associations with RRI risk for body mass index (HR=1.126; 95% CI 1.033 to 1.227), previous injury (HR=1.735; 95% CI 1.037 to 2.902) and mean session intensity (HR=1.396; 95% CI 1.040 to 1.874). Protective factors were previous regular running activity (HR=0.422; 95% CI 0.228 to 0.779) and weekly volume of other sports activities (HR=0.702; 95% CI 0.561 to 0.879).ConclusionsMidsole hardness of modern cushioned running shoes does not seem to influence RRI risk.
Internet-based hearing screening using speech-in-noise: validation and comparisons of self-reported hearing problems, quality of life and phonological representation
Authors: Molander Peter , Nordqvist Peter , Öberg Marie , Lunner Thomas , Lyxell Björn , Andersson Gerhard 
Published: September 2013

ObjectivesFor the last decade a host of different projects have been launched to allow persons who are concerned about their hearing status to quickly and at a low cost test their hearing ability. Most often, this is carried out without collecting complementary information that could be correlated with hearing impairment. In this two-part study we first, present the development and validation of a novel Internet-based hearing test, and second, report on the associations between this test and phonological representation, quality of life and self-reported hearing difficulties.DesignCross-sectional study.SettingAn opportunity sample of participants was recruited at the Stockholm central station for the first study. All parts of the second study were conducted via the Internet, with testing and self-report forms adapted for online use.ParticipantsThe first part of the study was carried out in direct contact with the participants, and participants from the second study were recruited by means of advertisements in newspapers and on webpages. The only exclusion criterion was that participants had to be over 18 years old. Most participants were between 60 and 69 years old. There were almost an equal number of men and women (total n=316).Outcome measures48 participants failed the Internet-based hearing screening test. The group failing the test reported more problems on the Amsterdam Inventory of Auditory Disability. In addition, they were found to have diminished phonological representational skills. However, no difference in quality of life was found.ConclusionsAlmost one in five participants was in need of contacting their local hearing clinic. This group had more complaints regarding tinnitus and hyperacusis, rated their own hearing as worse than those who passed, and had a poorer capability of generating accurate phonological representations. This study suggests that it is feasible to screen for hearing status online, and obtain valid data.
Evaluation of the HER2 amplification status in oesophageal adenocarcinoma by conventional and automated FISH: a tissue microarray study
Authors: Prins M J D , Ruurda J P , van Diest P J , van Hillegersberg R , ten Kate F J W 
Published: September 2013

IntroductionThe manual fluorescence in situ hybridisation (FISH) Human Epidermal Growth Factor Receptor 2 (HER2)/CEP17 testing method is frequently used, however, it is time consuming and liable to subjectivity. Automation of FISH might increase the throughput and accuracy.AimTo evaluate the agreement between automated and conventional FISH with regard to a reference test silver-enhanced in situ hybridization (SISH) for HER2 amplification, as well as its prognostic significance.Material and methods154 oesophageal adenocarcinomas were included in a tissue microarray. HER2/CEP17 gene amplification was assessed by automated FISH and was compared with conventional HER2/CEP17 testing methods.Results46.8% of patients showed HER2 amplified tumours by automated FISH (ratio ≥1.8) compared with 18.1% by conventional FISH. A high automated HER2/CEP17 ratio (≥1.8) was significantly associated with worse survival (HR 1.731; 95% CI 1.075 to 2.786; p=0.024). However, agreement between automated and conventional FISH was only 72.2% and 71.4% between automated FISH and SISH, compared with 94.6% for conventional FISH/SISH. Therefore, thresholds for HER2/CEP17 amplification were sequentially raised from HER2/CEP17 ratio 1.8 till 5.0. A HER2/CEP17 ratio threshold of ≥3.6 had similar prognostic significance as conventional FISH (HR 1.880; 95% CI 1.060 to 3.332; p=0.031 vs HR 1.828; 95% CI 1.102 to 3.033; p=0.020), yielded comparable amplification rates as conventional FISH (14.3% vs 18.1%) and comparable agreement to SISH/Immunohistochemistry (IHC).ConclusionsAutomation of HER2 FISH analysis in oesophageal cancer has not been performed before. Automated HER2 is feasible, but it seems that the HER2/CEP17 threshold should be adjusted to ≥3.6 to arrive at best comparability with other methods and prognostic value.
A study of α5 chain of collagen IV, caldesmon, placental alkaline phosphatase and smoothelin as immunohistochemical markers of gastrointestinal smooth muscle neoplasms
Authors: Wong Newton ACS , Wingate Jenny , Colling Richard 
Published: September 2013

AimsThe histological distinction between gastrointestinal smooth muscle neoplasms (SMNs) and their differential diagnoses, especially gastrointestinal stromal tumours (GISTs), has important clinical management implications. This study aimed to investigate preliminary data suggesting that loss of the α5 chain of collagen IV (α5(IV)), placental acid phosphatase (PLAP) expression and smoothelin expression can be used diagnostically as markers of gastrointestinal SMNs. To aid this investigation, these potential markers were directly compared against caldesmon.Methods31 SMNs and 111 potential differential diagnoses (16 different neoplasm types) were immunostained for caldesmon, PLAP and smoothelin.ResultsA pilot study indicated that loss of α5(IV) positivity was neither a specific nor sensitive marker of SMN. Caldesmon, PLAP and smoothelin were expressed by all 31 SMNs though leiomyosarcomas showed some loss of staining proportion and/or intensity. Caldesmon positivity was commonly shown by GISTs, glomus tumours and angiomyolipomas. Cytoplasmic smoothelin positivity was commonly shown by glomus tumours and angiomyolipomas, whereas PLAP positivity was shown by one desmoplastic small round cell tumour studied and only infrequently shown by angiomyolipomas. Nuclear smoothelin positivity was seen among four leiomyosarcomas but also a wide range of non-SMNs.Conclusionsα5(IV) immunohistochemistry with the A7 antibody is not a diagnostically useful marker of gastrointestinal SMNs. Both PLAP and smoothelin (cytoplasmic expression only) are as sensitive as but are more specific than caldesmon as such a marker. Further, PLAP and smoothelin immunostainings are technically reliable and can be reproducibly assessed.
Meiobenthos in marine coastal sediments
Authors: Urban-Malinga Barbara 
Published: September 2013

Abstract

The term meiobenthos refers to a group of invertebrate organisms that are intermediate in size between macro- and microfauna, and inhabit all sediment types in all marine environments and in all climatic zones. They may occur at enormously high densities of millions of individuals per square metre; this means that 10 cm
3
of sediment in any given habitat may contain thousands of these organisms. Although meiobenthos in some extreme arctic habitats is uncommonly poor, the abundance and composition of the polar or subpolar meiobenthic assemblages are not essentially different from those found in boreal–tropical locations at corresponding sediments and depths.