bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Retinoblastoma Orthologue Is Required for the Sensing of a Chalone in Dictyostelium discoideum
Authors: Bakthavatsalam Deenadayalan , White Michael J. V. , Herlihy Sarah E. , Phillips Jonathan E. , Gomer Richard H. 
Published: January 2014

ABSTRACT

Retinoblastoma-like proteins regulate cell differentiation and inhibit cell proliferation. The
Dictyostelium discoideum
retinoblastoma orthologue RblA affects the differentiation of cells during multicellular development, but it is unclear whether RblA has a significant effect on
Dictyostelium
cell proliferation, which is inhibited by the secreted proteins AprA and CfaD. We found that
rblA
−
cells in shaking culture proliferate to a higher density, die faster after reaching stationary density, and, after starvation, have a lower spore viability than wild-type cells, possibly because in shaking culture,
rblA
−
cells have both increased cytokinesis and lower extracellular accumulation of CfaD. However,
rblA
−
cells have abnormally slow proliferation on bacterial lawns. Recombinant AprA inhibits the proliferation of wild-type cells but not that of
rblA
−
cells, whereas CfaD inhibits the proliferation of both wild-type cells and
rblA
−
cells. Similar to
aprA
−
cells,
rblA
−
cells have a normal mass and protein accumulation rate on a per-nucleus basis, indicating that RblA affects cell proliferation but not cell growth. AprA also functions as a chemorepellent, and RblA is required for proper AprA chemorepellent activity despite the fact that RblA does not affect cell speed. Together, our data indicate that an autocrine proliferation-inhibiting factor acts through RblA to regulate cell density in
Dictyostelium
, suggesting that such factors may signal through retinoblastoma-like proteins to control the sizes of structures such as developing organs or tumors.
A Visual Screen of Protein Localization during Sporulation Identifies New Components of Prospore Membrane-Associated Complexes in Budding Yeast
Authors: Lam Chien , Santore Ethan , Lavoie Elizabeth , Needleman Leor , Fiacco Nicholas , Kim Carey , Neiman Aaron M. 
Published: January 2014

ABSTRACT

During ascospore formation in
Saccharomyces cerevisiae
, the secretory pathway is reorganized to create new intracellular compartments, termed prospore membranes. Prospore membranes engulf the nuclei produced by the meiotic divisions, giving rise to individual spores. The shape and growth of prospore membranes are constrained by cytoskeletal structures, such as septin proteins, that associate with the membranes. Green fluorescent protein (GFP) fusions to various proteins that associate with septins at the bud neck during vegetative growth as well as to proteins encoded by genes that are transcriptionally induced during sporulation were examined for their cellular localization during prospore membrane growth. We report localizations for over 100 different GFP fusions, including over 30 proteins localized to the prospore membrane compartment. In particular, the screen identified
IRC10
as a new component of the leading-edge protein complex (LEP), a ring structure localized to the lip of the prospore membrane. Localization of Irc10 to the leading edge is dependent on
SSP1
, but not
ADY3
. Loss of
IRC10
caused no obvious phenotype, but an
ady3 irc10
mutant was completely defective in sporulation and displayed prospore membrane morphologies similar to those of an
ssp1
strain. These results reveal the architecture of the LEP and provide insight into the evolution of this membrane-organizing complex.
CodY-Mediated Regulation of the Staphylococcus aureus Agr System Integrates Nutritional and Population Density Signals
Authors: Roux Agnès , Todd Daniel A. , Velázquez Jose V. , Cech Nadja B. , Sonenshein Abraham L. 
Published: January 2014

ABSTRACT

The
Staphylococcus aureus
Agr system regulates virulence gene expression by responding to cell population density (quorum sensing). When an extracellular peptide signal (AIP-III in strain UAMS-1, used for these experiments) reaches a concentration threshold, the AgrC-AgrA two-component regulatory system is activated through a cascade of phosphorylation events, leading to induction of the divergently transcribed
agrBDCA
operon and the RNAIII gene. RNAIII is a posttranscriptional regulator of numerous metabolic and pathogenesis genes. CodY, a global regulatory protein, is known to repress
agrBDCA
and RNAIII transcription during exponential growth in rich medium, but the mechanism of this regulation has remained elusive. Here we report that phosphorylation of AgrA by the AgrC protein kinase is required for the overexpression of the
agrBDCA
operon and the RNAIII gene in a
codY
mutant during the exponential-growth phase, suggesting that the quorum-sensing system, which normally controls AgrC activation, is active even in exponential-phase cells in the absence of CodY. In part, such premature expression of RNAIII was attributable to higher-than-normal accumulation of AIP-III in a
codY
mutant strain, as determined using ultrahigh-performance liquid chromatography coupled to mass spectrometry. Although CodY is a strong repressor of the
agr
locus, CodY bound only weakly to the
agrBDCA
-RNAIII promoter region, suggesting that direct regulation by CodY is unlikely to be the principal mechanism by which CodY regulates
agr
and RNAIII expression. Taken together, these results strongly suggest that cell population density signals inducing virulence gene expression can be overridden by nutrient availability, a condition monitored by CodY.
Myxobacteria Produce Outer Membrane-Enclosed Tubes in Unstructured Environments
Authors: Wei Xueming , Vassallo Christopher N. , Pathak Darshankumar T. , Wall Daniel 
Published: January 2014

ABSTRACT

Myxobacteria are social microbes that exhibit complex multicellular behaviors. By use of fluorescent reporters, we show that
Myxococcus xanthus
isolates produce long narrow filaments that are enclosed by the outer membrane (OM) and contain proteins. We show that these OM tube (OMT) structures are produced at surprisingly high levels when cells are placed in liquid medium or buffer without agitation. OMTs can be long and easily exceed multiple cell lengths. When viewed by transmission electron microscopy, their morphology varies between tubes and chain-like structures. Intermediate-like structures are also found, suggesting that OMTs may transition between these two morphotypes. In support of this, video epifluorescence microscopy found that OMTs in solution dynamically twist and jiggle. On hard surfaces, myxobacteria glide, and upon cell-cell contact, they can efficiently exchange their OM proteins and lipids by a TraAB-dependent mechanism. Although the structure of OMTs hints at a possible role as conduits for exchange, evidence is presented to the contrary. For example, abundant OMT production occurs in
traA
or
traB
mutants and when cells are grown in liquid medium, yet transfer cannot occur under these conditions. Thus, genetic and environmental conditions that promote OMT production are incongruent with OM exchange.
YfbA, a Yersinia pestis Regulator Required for Colonization and Biofilm Formation in the Gut of Cat Fleas
Authors: Tam Christina , Demke Owen , Hermanas Timothy , Mitchell Anthony , Hendrickx Antoni P. A. , Schneewind Olaf 
Published: January 2014

ABSTRACTFor transmission to new hosts,Yersinia pestis, the causative agent of plague, replicates as biofilm in the foregut of fleas that feed on plague-infected animals or humans.Y. pestisbiofilm formation has been studied in the rat flea; however, little is known about the cat flea, a species that may bridge zoonotic and anthroponotic plague cycles. Here, we show thatY. pestisinfects and replicates as a biofilm in the foregut of cat fleas in a manner requiringhmsFR, two determinants for extracellular biofilm matrix. Examining a library of transposon insertion mutants, we identified the LysR-type transcriptional regulator YfbA, which is essential forY. pestiscolonization and biofilm formation in cat fleas.
Genetic Redundancy, Proximity, and Functionality of
lspA
, the Target of Antibiotic TA, in the Myxococcus xanthus Producer Strain
Authors: Xiao Yao , Wall Daniel 
Published: January 2014

ABSTRACT

We recently showed that type II signal peptidase (SPaseII) encoded by
lspA
is the target of an antibiotic called TA (myxovirescin), which is made by
Myxococcus xanthus
. SPaseII cleaves the signal peptide during bacterial lipoprotein processing. Bacteria typically contain one
lspA
gene; however, strikingly, the
M. xanthus
DK1622 genome contains four (
lspA1
to
lspA4
). Since two of these genes,
lspA3
and
lspA4
, are located in the giant TA biosynthetic gene cluster, we hypothesized they may play a role in TA resistance. To investigate the functions of the four
M. xanthus
lspA
(
lspA

Mx

) genes, we conducted sequence comparisons and found that they contained nearly all the conserved residues characteristic of SPaseII family members. Genetic studies found that an
Escherichia coli
Δ
lspA
mutation could be complemented by any of the
lspA

Mx

genes in an
lpp
mutant background, but not in an
E. coli lpp

+

background. Because Lpp is the most abundant
E. coli
lipoprotein, these results suggest the
M. xanthus
proteins do not function as efficiently as the host enzyme. In
E. coli
, overexpression of each of the LspA

Mx

proteins conferred TA and globomycin resistance, although LspA3 conferred the highest degree of resistance. In
M. xanthus
, each
lspA

Mx

gene could be deleted and was therefore dispensable for growth. However,
lspA3
or
lspA4
deletion mutants each exhibited a tan phase variation bias, which likely accounts for their reduced-swarming and delayed-development phenotypes. In summary, we propose that all four LspA

Mx

proteins function as SPaseIIs and that LspA3 and LspA4 might also have roles in TA resistance and regulation, respectively.
Comparison of the BD Veritor System for Flu A+B with the Alere BinaxNOW Influenza A&B Card for Detection of Influenza A and B Viruses in Respiratory Specimens from Pediatric Patients
Authors: Hassan Ferdaus , Nguyen Ashley , Formanek Ashley , Bell James J. , Selvarangan Rangaraj 
Published: January 2014

ABSTRACT
The performance characteristics of two commercially available rapid tests for influenza, the BD Veritor System for Flu A+B (BD) and the Alere BinaxNOW influenza A&B card (BN), were evaluated using 200 frozen clinical specimens collected from January 2011 to June 2012 from pediatric patients. Real-time reverse transcriptase PCR (RT-PCR) was used as the gold standard to evaluate the results obtained by the two different assays. Of the 200 specimens tested, real-time RT-PCR assay detected influenza A or B virus in 116 samples, while BD detected 104 samples and BN detected 84 samples as positive. The overall sensitivity and specificity for detection of both influenza A and B virus in comparison to those of real-time RT-PCR were 89.6% (95% confidence interval [CI], 82.2 to 94.3) and 98.8% (95% CI, 92.6 to 99.9) for BD Veritor and 72.4% (95% CI, 63.2 to 80.0) and 100% (95% CI, 94.5 to 100.0) for BinaxNOW. Workflow analysis indicated that overall processing times for a batch size of 10 specimens were virtually identical between both systems. Overall, these results indicate that the BD Veritor assay was more sensitive than the BinaxNOW assay in detection of influenza A and B viruses in respiratory specimens from pediatric patients.
Three Cases of Postoperative Septic Arthritis Caused by Mycobacterium conceptionense in the Shoulder Joints of Immunocompetent Patients
Authors: Lee Keun Hwa , Heo Sang Taek , Choi Sung-Wook , Park Da Hee , Kim Young Ree , Yoo Seung Jin 
Published: January 2014

ABSTRACT

Mycobacterium conceptionense
is a species member of
Mycobacterium fortuitum
complex, a potential pathogen of increasing clinical importance among opportunistic infections. This species causes a wide spectrum of cutaneous and extracutaneous diseases. In this report, we describe three patients who underwent shoulder surgery with postoperative joint infection by
M. conceptionense
.
Fluoroquinolone Susceptibility Testing of Salmonella enterica: Detection of Acquired Resistance and Selection of Zone Diameter Breakpoints for Levofloxacin and Ofloxacin
Authors: Sjölund-Karlsson Maria , Howie Rebecca L. , Crump John A. , Whichard Jean M. 
Published: January 2014

ABSTRACT

Fluoroquinolones (e.g., ciprofloxacin) have become a mainstay for treating severe
Salmonella
infections in adults. Fluoroquinolone resistance in
Salmonella
is mostly due to mutations in the topoisomerase genes, but plasmid-mediated quinolone resistance (PMQR) mechanisms have also been described. In 2012, the Clinical and Laboratory Standards Institute (CLSI) revised the ciprofloxacin interpretive criteria (breakpoints) for disk diffusion and MIC test methods for
Salmonella
. In 2013, the CLSI published MIC breakpoints for
Salmonella
to levofloxacin and ofloxacin, but breakpoints for assigning disk diffusion results to susceptible (S), intermediate (I), and resistant (R) categories are still needed. In this study, the MICs and inhibition zone diameters for nalidixic acid, ciprofloxacin, levofloxacin, and ofloxacin were determined for 100 clinical isolates of nontyphi
Salmonella
with or without resistance mechanisms. We confirmed that the new levofloxacin MIC breakpoints resulted in the highest category agreement (94%) when plotted against the ciprofloxacin MICs and that the new ofloxacin MIC breakpoints resulted in 92% category agreement between ofloxacin and ciprofloxacin. By applying the new MIC breakpoints in the MIC zone scattergrams for levofloxacin and ofloxacin, the following disk diffusion breakpoints generated the least number of errors: ≥28 mm (S), 19 to 27 mm (I), and ≤18 mm (R) for levofloxacin and ≥25 mm (S), 16 to 24 mm (I), and ≤15 mm (R) for ofloxacin. Neither the levofloxacin nor the ofloxacin disk yielded good separation of isolates with and without resistance mechanisms. Further studies will be needed to develop a disk diffusion assay that efficiently detects all isolates with acquired resistance to fluoroquinolones.
Effect of the Initial Specimen Diversion Technique on Blood Culture Contamination Rates
Authors: Binkhamis Khalifa , Forward Kevin 
Published: January 2014

ABSTRACT

The initial specimen diversion technique (ISDT) was first described by Patton and Schmitt (J. Clin. Microbiol.
48:
4501–4503, 2010, doi:10.1128/JCM.00910-10). This study looked at the effect of implementation of the ISDT on blood culture contamination rates at our center. We found a reduction of 30.34% in potential blood culture contaminants.
Detection of Trichomonas vaginalis DNA by Use of Self-Obtained Vaginal Swabs with the BD ProbeTec Q
x
Assay on the BD Viper System
Authors: Van Der Pol Barbara , Williams James A. , Taylor Stephanie N. , Cammarata Catherine L. , Rivers Charles A. , Body Barbara A. , Nye Melinda , Fuller Deanna , Schwebke Jane R. , Barnes Mathilda , Gaydos Charlotte A. 
Published: January 2014

ABSTRACT

Trichomonas vaginalis
is the most prevalent nonviral sexually transmitted infection worldwide, and improved diagnostic methods are critical for controlling this pathogen. Diagnostic assays that can be used in conjunction with routine chlamydia/gonorrhea nucleic acid-based screening are likely to have the most impact on disease control. Here we describe the performance of the new BD
T. vaginalis
Q
x
(TVQ) amplified DNA assay, which can be performed on the automated BD Viper system. We focus on data from vaginal swab samples, since this is the specimen type routinely used for traditional trichomonas testing and the recommended specimen type for chlamydia/gonorrhea screening. Vaginal swabs were obtained from women attending sexually transmitted disease or family planning clinics at 7 sites. Patient-collected vaginal swabs were tested by the TVQ assay, and the Aptima
T. vaginalis
(ATV) assay was performed using clinician-collected vaginal swabs. Additional clinician-collected vaginal swabs were used for the wet mount and culture methods. Analyses included comparisons versus the patient infection status (PIS) defined by positive results with the wet mount method or culture, direct comparisons assessed with κ scores, and latent class analysis (LCA) as an unbiased estimator of test accuracy. Data from 838 women, 116 of whom were infected with
T. vaginalis
, were analyzed. The TVQ assay sensitivity and specificity estimates based on the PIS were 98.3% and 99.0%, respectively. The TVQ assay was similar to the ATV assay (κ = 0.938) in direct analysis. LCA estimated the TVQ sensitivity and specificity as 98.3 and 99.6%, respectively. The TVQ assay performed well using self-collected vaginal swabs, the optimal sample type, as recommended by the CDC for chlamydia/gonorrhea screening among women.
Clinical Validation of the HPV-Risk Assay, a Novel Real-Time PCR Assay for Detection of High-Risk Human Papillomavirus DNA by Targeting the E7 Region
Authors: Hesselink A. T. , Berkhof J. , van der Salm M. L. , van Splunter A. P. , Geelen T. H. , van Kemenade F. J. , Bleeker M. G. B. , Heideman D. A. M. 
Published: January 2014

ABSTRACT

The HPV-Risk assay is a novel real-time PCR assay targeting the E7 region of 15 high-risk human papillomavirus (HPV) types (i.e., HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -67, and −68), and provides additional genotype information for HPV16 and HPV18. This study evaluated the clinical performance and reproducibility of the HPV-Risk assay with cervical scraping specimens and its utility with self-collected (cervico)vaginal specimens. The clinical performance of the HPV-Risk assay for cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) with cervical scraping specimens was evaluated by a noninferiority analysis, relative to high-risk HPV GP5+/6+ PCR, following international guidelines for HPV test requirements for cervical cancer screening. The HPV-Risk assay showed clinical sensitivity for CIN2+ of 97.1% (95% confidence interval [CI], 89.1 to 99.3%; 67/69 samples) and a clinical specificity for CIN2+ of 94.3% (95% CI, 92.5 to 95.7%; 777/824 samples). The clinical sensitivity and specificity were noninferior to those of GP5+/6+ PCR (noninferiority score test,
P
= 0.006 and 0.0003, respectively). Intralaboratory reproducibility over time (99.5% [95% CI, 98.6 to 99.8%]; 544/547 samples, kappa = 0.99) and interlaboratory agreement (99.2% [95% CI, 98.6 to 99.8%]; 527/531 samples, kappa = 0.98) for the HPV-Risk assay with cervical scraping specimens were high. The agreement of the HPV-Risk assay results for self-collected (cervico)vaginal specimens and clinician-obtained cervical scraping specimens was also high, i.e., 95.9% (95% CI, 85.1 to 99.0%; 47/49 samples, kappa = 0.90) for self-collected lavage samples and 91.6% (95% CI, 84.6 to 95.6%; 98/107 samples, kappa = 0.82) for self-collected brush samples. In conclusion, the HPV-Risk assay meets the cross-sectional clinical and reproducibility criteria of the international guidelines for HPV test requirements and can be considered clinically validated for cervical screening purposes. The compatibility of the HPV-Risk assay with self-collected specimens supports its utility for HPV self-sampling.
Novel Real-Time PCR Assays Using TaqMan Minor Groove Binder Probes for Identification of Fecal Carriage of Streptococcus bovis/Streptococcus equinus Complex from Rectal Swab Specimens
Authors: Lopes Paulo Guilherme Markus , Cantarelli Vlademir Vicente , Agnes Grasiela , Costabeber Ane Micheli , d'Azevedo Pedro Alves 
Published: January 2014

ABSTRACT

Real-time PCR based on the
recN
and
gyrB
genes was developed to detect four
Streptococcus bovis
/
Streptococcus equinus
complex (SBEC) subspecies from rectal swab specimens. The overall prevalence was 35.2%:
Streptococcus gallolyticus
subsp.
gallolyticus
(11.1%),
S. gallolyticus
subsp.
pasteurianus
(13%),
Streptococcus infantarius
subsp.
coli
(20.4%), and
S. infantarius
subsp.
infantarius
(11.1%). To conclude, these real-time PCR assays provide a reliable molecular method to detect SBEC pathogenic subspecies from rectal swab specimens.
Rapid Ertapenem Susceptibility Testing and Klebsiella pneumoniae Carbapenemase Phenotype Detection in Klebsiella pneumoniae Isolates by Use of Automated Microscopy of Immobilized Live Bacterial Cells
Authors: Burnham Carey-Ann D. , Frobel Rachel A. , Herrera Monica L. , Wickes Brian L. 
Published: January 2014

ABSTRACT

We evaluated detection of ertapenem (ETP) resistance and
Klebsiella pneumoniae
carbapenemase (KPC) in 47
Klebsiella pneumoniae
isolates using a novel automated microscopy system. Automated microscopy correctly classified 22/23 isolates as ETP resistant and 24/24 as ETP susceptible and correctly classified 21/21 isolates as KPC positive and 26/26 as KPC negative.
Human Herpesvirus 7 U21 Tetramerizes To Associate with Class I Major Histocompatibility Complex Molecules
Authors: May Nathan A. , Wang Qiuhong , Balbo Andrea , Konrad Sheryl L. , Buchli Rico , Hildebrand William H. , Schuck Peter , Hudson Amy W. 
Published: January 2014

ABSTRACTThe U21 gene product from human herpesvirus 7 binds to and redirects class I major histocompatibility complex (MHC) molecules to a lysosomal compartment. The molecular mechanism by which U21 reroutes class I MHC molecules to lysosomes is not known. Here, we have reconstituted the interaction between purified soluble U21 and class I MHC molecules, suggesting that U21 does not require additional cellular proteins to interact with class I MHC molecules. Our results demonstrate that U21, itself predicted to contain an MHC class I-like protein fold, interacts tightly with class I MHC molecules as a tetramer, in a 4:2 stoichiometry. These observations have helped to elucidate a refined model describing the mechanism by which U21 escorts class I MHC molecules to the lysosomal compartment.IMPORTANCEIn this report, we show that the human herpesvirus 7 (HHV-7) immunoevasin U21, itself a class I MHC-like protein, binds with high affinity to class I MHC molecules as a tetramer and escorts them to lysosomes, where they are degraded. While many class I MHC-like molecules have been described in detail, this unusual viral class I-like protein functions as a tetramer, associating with class I MHC molecules in a 4:2 ratio, illuminating a functional significance of homooligomerization of a class I MHC-like protein.