bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro
Activity of Fosfomycin Alone and in Combination with Ceftriaxone or Azithromycin against Clinical Neisseria gonorrhoeae Isolates
Authors: Hauser Christoph , Hirzberger Lea , Unemo Magnus , Furrer Hansjakob , Endimiani Andrea 
Published: December 2014

ABSTRACT

New therapeutic strategies are needed to combat the emergence of infections due to multidrug-resistant
Neisseria gonorrhoeae
. In this study, fosfomycin (FOS) was tested against 89
N. gonorrhoeae
isolates using the Etest method, showing MIC
50
/MIC
90
s of only 8/16 μg/ml (range, ≤1 to 32 μg/ml). FOS in combination with ceftriaxone (CRO) or azithromycin (AZT) was then evaluated using the checkerboard method for eight strains, including
N. gonorrhoeae
F89 (CRO-resistant) and AZT-HLR (high-level AZT-resistant). All combinations that included FOS gave indifferent effects (fractional inhibitory concentration [FIC] index values, 1.2 to 2.3 for FOS plus CRO, 1.8 to 3.2 for FOS plus AZT). Time-kill experiments for FOS, CRO, AZT, and their combinations (at 0.5×, 1×, 2×, and 4× the MIC) were performed against
N. gonorrhoeae
strain ATCC 49226, one
N. gonorrhoeae
multiantigen sequence typing (NG-MAST) sequence type 1407 (ST1407) strain, F89, and AZT-HLR. For all strains, at 24 h, the results indicated that (i) FOS was bactericidal at 2× the MIC, but after >24 h, there was regrowth of bacteria; (ii) CRO was bactericidal at 0.5× the MIC; (iii) AZT was bactericidal at 4× the MIC; (iv) CRO plus AZT was less bactericidal than was CRO alone; (v) FOS plus AZT was bactericidal at 2× the MIC; and (vi) CRO plus AZT and FOS plus CRO were both bactericidal at 0.5× the MIC, but FOS plus CRO had more rapid effects. FOS is appealing for use in the management of
N. gonorrhoeae
infections because of its single and oral formulation. However, our results suggest it be used in combination with CRO. After the appropriate clinical trials are conducted, this strategy could be implemented for the treatment of infections due to isolates possessing resistance to CRO and/or AZT.
Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year
Authors: Korlević M. , Pop Ristova P. , Garić R. , Amann R. , Orlić S. 
Published: December 2014

ABSTRACT

The South Adriatic Sea is the deepest part of the Adriatic Sea and represents a key area for both the Adriatic Sea and the deep eastern Mediterranean. It has a role in dense water formation for the eastern Mediterranean deep circulation cell, and it represents an entry point for water masses originating from the Ionian Sea. The biodiversity and seasonality of bacterial picoplankton before, during, and after deep winter convection in the oligotrophic South Adriatic waters were assessed by combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition-fluorescence
in situ
hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the spring euphotic zone when the maximum value of the chlorophyll
a
in response to deep winter convection was recorded. The communities were dominated by
Bacteria
, while
Archaea
were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values occurring during the winter convection and spring postconvection periods and maximum values occurring under summer stratified conditions. The SAR11 clade was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode.
Cyanobacteria
were the second most abundant group, and their abundance strongly depended on the convection event, when minimal cyanobacterial abundance was observed. In spring and autumn, the euphotic zone was characterized by
Bacteroidetes
and
Gammaproteobacteria
.
Bacteroidetes
clades NS2b, NS4, and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. The SAR324, SAR202, and SAR406 clades were present in the deep layer, exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are greatly impacted by strong winter convection.
Evaluating the Occurrence of Escherichia albertii in Chicken Carcass Rinses by PCR, Vitek Analysis, and Sequencing of the
rpoB
Gene
Authors: Lindsey Rebecca L. , Fedorka-Cray Paula J. , Abley Melanie , Turpin Jennifer B. , Meinersmann Richard J. 
Published: December 2014

ABSTRACT

Escherichia albertii
is a recently described species that has been associated with gastroenteritis in humans and with healthy and ill birds. Most recently, it has been identified as the causative agent in a food-borne outbreak in Japan. The distribution and clinical importance of
E. albertii
are not well studied because its importance is unclear. Culture methods for clinical isolation frequently miss
E. albertii
or incorrectly identify it as
Shigella
spp.,
Escherichia coli
, or
Hafnia alvei
. This study was designed to determine if
E. albertii
could be recovered from chicken carcass rinses collected at slaughter during a 1-year period from November 2009 until October 2010. Colonies were isolated from chicken carcass rinses and tested by PCR for the presence or absence of
clpX, lysP, mdh
, intimin (
eae
), Shiga toxins 1 and 2 (
stx
1
,
stx
2
, and
stx
2f
), heat-stable enterotoxin A (
staA
), and cytolethal distending toxins 1 and 2 (
cdtB
) genes. Sixty-five isolates were analyzed by sequencing a section of the
rpoB
gene. Analysis of the
rpoB
gene sequences revealed 14 fixed differences between
E. albertii
and other, closely related organisms. The fixed differences found in the
rpoB
gene could aid in future discrimination of
E. albertii
from closely related bacteria.
Genetic Tools for the Industrially Promising Methanotroph Methylomicrobium buryatense
Authors: Puri Aaron W. , Owen Sarah , Chu Frances , Chavkin Ted , Beck David A. C. , Kalyuzhnaya Marina G. , Lidstrom Mary E. 
Published: December 2014

ABSTRACT

Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for
Methylomicrobium buryatense
, a haloalkaliphilic gammaproteobacterial (type I) methanotroph.
M. buryatense
was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in
M. buryatense
by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make
M. buryatense
a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.
The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III
Authors: Padilla-Mejía Norma E. , Florencio-Martínez Luis E. , Moreno-Campos Rodrigo , Vizuet-de-Rueda Juan C. , Cevallos Ana M. , Hernández-Rivas Rosaura , Manning-Cela Rebeca , Martínez-Calvillo Santiago 
Published: December 2014

ABSTRACT

Eukaryotic tRNAs, transcribed by RNA polymerase III (Pol III), contain boxes A and B as internal promoter elements. One exception is the selenocysteine (Sec) tRNA (tRNA-Sec), whose transcription is directed by an internal box B and three extragenic sequences in vertebrates. Here we report on the transcriptional analysis of the tRNA-Sec gene in the protozoan parasite
Leishmania major
. This organism has unusual mechanisms of gene expression, including Pol II polycistronic transcription and maturation of mRNAs by
trans
splicing, a process that attaches a 39-nucleotide miniexon to the 5′ end of all the mRNAs. In
L. major
, tRNA-Sec is encoded by a single gene inserted into a Pol II polycistronic unit, in contrast to most tRNAs, which are clustered at the boundaries of polycistronic units. 5′ rapid amplification of cDNA ends and reverse transcription-PCR experiments showed that some tRNA-Sec transcripts contain the miniexon at the 5′ end and a poly(A) tail at the 3′ end, indicating that the tRNA-Sec gene is polycistronically transcribed by Pol II and processed by
trans
splicing and polyadenylation, as was recently reported for the tRNA-Sec genes in the related parasite
Trypanosoma brucei
. However, nuclear run-on assays with RNA polymerase inhibitors and with cells that were previously UV irradiated showed that the tRNA-Sec gene in
L. major
is also transcribed by Pol III. Thus, our results indicate that RNA polymerase specificity in
Leishmania
is not absolute
in vivo
, as has recently been found in other eukaryotes.
Two-Component Regulators Control
hilA
Expression by Controlling
fimZ
and
hilE
Expression within Salmonella enterica Serovar Typhimurium
Authors: Baxter M. Aaron , Jones Bradley D. 
Published: December 2014

ABSTRACT

Salmonellae initiate disease through the invasion of host cells within the intestine. This ability to invade requires the coordinated action of numerous genes, many of which are found within
Salmonella
pathogenicity island 1 (SPI-1). The key to this process is the ability of the bacteria to respond to the environment, thereby upregulating the necessary genes under optimal conditions. Central to the control of SPI-1 is the transcriptional activator
hilA
. Work has identified at least 10 different activators and 8 different repressors responsible for the control of
hilA
. We have previously shown that
hilE
is a
Salmonella
-specific negative regulator that is able to repress
hilA
expression and invasion. Additionally,
fimZ
, a transcriptional activator responsible for the expression of type I fimbriae as well as flagellar genes, has also been implicated in this process.
fimZ
is homologous to response regulators from other two-component regulatory systems, although a sensor for the system has not been identified. The
phoPQ
and
phoBR
regulons are both two-component systems that negatively affect
hilA
expression, although the mechanism of action has not been determined. Our results show that PhoBR is capable of inducing
fimZ
expression, whereas PhoPQ does not affect
fimZ
expression but does upregulate
hilE
in an FimZ-dependent manner. Therefore, phosphate (sensed by PhoBR) and magnesium (sensed by PhoPQ) levels are important in controlling
hilA
expression levels when
Salmonella
is in the intestinal environment.
Role of BrnQ1 and BrnQ2 in Branched-Chain Amino Acid Transport and Virulence in Staphylococcus aureus
Authors: Kaiser Julienne C. , Omer Sameha , Sheldon Jessica R. , Welch Ian , Heinrichs David E. 
Published: December 2014

ABSTRACT

The branched-chain amino acids (BCAAs; Ile, Leu, and Val) not only are important nutrients for the growth of
Staphylococcus aureus
but also are corepressors for CodY, which regulates virulence gene expression, implicating BCAAs as an important link between the metabolic state of the cell and virulence. BCAAs are either synthesized intracellularly or acquired from the environment.
S. aureus
encodes three putative BCAA transporters, designated BrnQ1, BrnQ2, and BrnQ3; their functions have not yet been formally tested. In this study, we mutated all three
brnQ
paralogs so as to characterize their substrate specificities and their roles in growth
in vitro
and
in vivo
. We demonstrated that in the community-associated, methicillin-resistant
S. aureus
(CA-MRSA) strain USA300, BrnQ1 is involved in uptake of all three BCAAs, BrnQ2 transports Ile, and BrnQ3 does not have a significant role in BCAA transport under the conditions tested. Of the three, only BrnQ1 is essential for USA300 to grow in a chemically defined medium that is limited for Leu or Val. Interestingly, we observed that a
brnQ2
mutant grew better than USA300 in media limited for Leu and Val, owing to the fact that this mutation leads to overexpression of
brnQ1
. In a murine infection model, the
brnQ1
mutant was attenuated, but in contrast,
brnQ2
mutants had significantly increased virulence compared to that of USA300, a phenotype we suggest is at least partially linked to enhanced
in vivo
scavenging of Leu and Val through BrnQ1. These data uncover a hitherto-undiscovered connection between nutrient acquisition and virulence in CA-MRSA.
Role of the Nuclease of Nontypeable Haemophilus influenzae in Dispersal of Organisms from Biofilms
Authors: Cho Christine , Chande Aroon , Gakhar Lokesh , Bakaletz Lauren O. , Jurcisek Joseph A. , Ketterer Margaret , Shao Jian , Gotoh Kenji , Foster Eric , Hunt Jason , O'Brien Erin , Apicella Michael A. 
Published: December 2014

ABSTRACT

Nontypeable
Haemophilus influenzae
(NTHI) forms biofilms in the middle ear during human infection. The biofilm matrix of NTHI contains extracellular DNA. We show that NTHI possesses a potent nuclease, which is a homolog of the thermonuclease of
Staphylococcus aureus
. Using a biofilm dispersal assay, studies showed a biofilm dispersal pattern in the parent strain, no evidence of dispersal in the nuclease mutant, and a partial return of dispersion in the complemented mutant. Quantitative PCR of mRNA from biofilms from a 24-h continuous flow system demonstrated a significantly increased expression of the nuclease from planktonic organisms compared to those in the biofilm phase of growth (
P
< 0.042). Microscopic analysis of biofilms grown
in vitro
showed that in the nuclease mutant the nucleic acid matrix was increased compared to the wild-type and complemented strains. Organisms were typically found in large aggregates, unlike the wild-type and complement biofilms in which the organisms were evenly dispersed throughout the biofilm. At 48 h, the majority of the organisms in the mutant biofilm were dead. The nuclease mutant formed a biofilm in the chinchilla model of otitis media and demonstrated a propensity to also form similar large aggregates of organisms. These studies indicate that NTHI nuclease is involved in biofilm remodeling and organism dispersal.
Design of Glycoconjugate Vaccines against Invasive African Salmonella enterica Serovar Typhimurium
Authors: Rondini S. , Micoli F. , Lanzilao L. , Gavini M. , Alfini R. , Brandt C. , Clare S. , Mastroeni P. , Saul A. , MacLennan C. A. 
Published: December 2014

ABSTRACTNontyphoidal salmonellae, particularlySalmonella entericaserovar Typhimurium, are a major cause of invasive disease in Africa, affecting mainly young children and HIV-infected individuals. Glycoconjugate vaccines provide a safe and reliable strategy against invasive polysaccharide-encapsulated pathogens, and lipopolysaccharide (LPS) is a target of protective immune responses. With the aim of designing an effective vaccine againstS. Typhimurium, we have synthesized different glycoconjugates, by linking O-antigen and core sugars (OAg) of LPS to the nontoxic mutant of diphtheria toxin (CRM197). The OAg-CRM197conjugates varied in (i) OAg source, with threeS. Typhimurium strains used for OAg extraction, producing OAg with differences in structural specificities, (ii) OAg chain length, and (iii) OAg/CRM197ratio. All glycoconjugates were compared for immunogenicity and ability to induce serum bactericidal activity in mice.In vivoenhancement of bacterial clearance was assessed for a selectedS. Typhimurium glycoconjugate by challenge with liveSalmonella. We found that the largest anti-OAg antibody responses were elicited by (i) vaccines synthesized from OAg with the highest glucosylation levels, (ii) OAg composed of mixed- or medium-molecular-weight populations, and (iii) a lower OAg/CRM197ratio. In addition, we found that bactericidal activity can be influenced byS. Typhimurium OAg strain, most likely as a result of differences in OAg O-acetylation and glucosylation. Finally, we confirmed that mice immunized with the selected OAg-conjugate were protected againstS. Typhimurium colonization of the spleen and liver. In conclusion, our findings indicate that differences in the design of OAg-based glycoconjugate vaccines against invasive AfricanS. Typhimurium can have profound effects on immunogenicity and therefore optimal vaccine design requires careful consideration.
Another Look at Mutations in Ribosomal Protein S4 Lends Strong Support to the Domain Closure Model
Authors: Fredrick Kurt 
Published: December 2014

ABSTRACT

Ribosomes employ a “kinetic discrimination” mechanism, in which correct substrates are incorporated more rapidly than incorrect ones. The structural basis of this mechanism may involve 30S domain closure, a global conformational change that coincides with codon recognition. In a direct screen for fidelity-altering mutations,
Agarwal and coworkers
(D. Agarwal, D. Kamath, S. T. Gregory, and M. O'Connor, J Bacteriol 197:1017–1025, 2015, doi:
10.1128/JB.02485-14
) isolated mutations that progressively truncate the C terminus of S4. All of these promote miscoding and undoubtedly destabilize the S4-S5 interface, consistent with the domain closure model.
Direct Serum Assay for Cell-Free Bmi-1 mRNA and Its Potential Diagnostic and Prognostic Value for Colorectal Cancer
Authors: Zhang Xin , Yang Xiaoyun , Zhang Yanli , Liu Xinfeng , Zheng Guixi , Yang Yongmei , Wang Lili , Du Lutao , Wang Chuanxin 
Published: December 2014

Abstract
Purpose: Cell-free Bmi-1 mRNA is stably detectable in the serum/plasma and is associated with the development and progression of some tumors. Previous methods detecting extracellular Bmi-1 mRNA with RNA extraction are inefficient. This study developed a novel reverse transcription quantitative PCR (RT-qPCR) approach directly applied in serum (RT-qPCR-D) to quantify Bmi-1 mRNA, and assessed its diagnostic and prognostic potential in colorectal cancer.
Experimental Design: The feasibility of the RT-qPCR-D method was first analyzed in 50 serum samples. Then, using the RT-qPCR-D method, Bmi-1 mRNA expression was validated in serum from an independent cohort of patients with 87 normal colonoscopy, 76 hyperplastic polyp, 82 inflammatory bowel disease, 68 adenoma, and 158 colorectal cancer. Receiver operating characteristic (ROC) curves and Cox analyses were used to evaluate its diagnosis and prognosis value, respectively.
Results: In a pilot study, levels of Bmi-1 mRNA were increased in colorectal cancer serum samples detected by RT-qPCR-D and significantly associated with results obtained by RT-qPCR. In a validation cohort, serum Bmi-1 mRNA levels were significantly elevated in the colorectal cancer group and the adenoma group when compared with other groups. The area under ROC curve distinguishing colorectal cancer from benign colorectal diseases was 0.888, with 72.2% sensitivity and 94.9% specificity, which was superior to carcinoembryogenic antigen. Bmi-1 mRNA levels were significantly associated with survival. Cox analysis indicated Bmi-1 mRNA was an independent prognostic factor for overall survival.
Conclusions: Detection of cell-free Bmi-1 mRNA in serum by RT-qPCR-D is a simple and noninvasive approach and may be used for colorectal cancer diagnosis and prognosis. Clin Cancer Res; 21(5); 1225–33. ©2014 AACR.
Cold Extremes in North America vs. Mild Weather in Europe: The Winter of 2013–14 in the Context of a Warming World
Authors: Van Oldenborgh Geert Jan , Haarsma Rein , De Vries Hylke , Allen Myles R. 
Published: December 2014

AbstractThe winter of 2013–14 had unusual weather in many parts of the world. Here we analyze the cold extremes that were widely reported in North America and the lack of cold extremes in western Europe. We perform a statistical analysis of cold extremes at two representative stations in these areas: Chicago, Illinois, and De Bilt, the Netherlands. This shows that the lowest minimum temperature of the winter was not very unusual in Chicago, even in the current warmer climate. Around 1950 it would have been completely normal. The same holds for multiday cold periods. Only the whole winter temperature was unusual, with a return time larger than 25 years. In the Netherlands, the opposite holds: the absence of any cold waves was highly unusual even now, and would have been extremely improbable halfway through the previous century. These results are representative of other stations in the regions. The difference is due to the skewness of the temperature distribution. In both locations, cold extremes are more likely than equally large warm extremes in winter. Severe cold outbreaks and cold winters, like the winter of 2013–14 in the Great Lakes area, are therefore not evidence against global warming: they will keep on occurring, even if they become less frequent. The absence of cold weather as observed in the Netherlands is a strong signal of a warming trend, as this would have been statistically extremely improbable in the 1950s.
Potential Predictability of Malaria in Africa Using ECMWF Monthly and Seasonal Climate Forecasts
Authors: Tompkins Adrian M. , Di Giuseppe Francesca 
Published: December 2014

AbstractIdealized model experiments investigate the advance warning for malaria that may be presently possible using temperature and rainfall predictions from state-of-the-art operational monthly and seasonal weather-prediction systems. The climate forecasts drive a dynamical malaria model for all of Africa, and the predictions are evaluated using reanalysis data. The regions and months for which climate is responsible for significant interannual malaria transmission variability are first identified. In addition to epidemic-prone zones these also include hyperendemic regions subject to high variability during specific months of the year, often associated with the monsoon onset. In many of these areas, temperature anomalies are predictable from 1 to 2 months ahead, and reliable precipitation forecasts are available in eastern and southern Africa 1 month ahead. The inherent lag between the rainy seasons and malaria transmission results in potential predictability in malaria transmission 3–4 months in advance, extending the early warning available from environmental monitoring by 1–2 months, although the realizable forecast skill will be less than this because of an imperfect malaria model. A preliminary examination of the forecasts for the highlands of Uganda and Kenya shows that the system is able to predict the years during the last two decades in which documented highland outbreaks occurred, in particular the major event of 1998, but that the timing of outbreaks was often imprecise and inconsistent across lead times. In addition to country-level evaluation with district health data, issues that need addressing to integrate such a climate-based prediction system into health-decision processes are briefly discussed.