bluuebunny/crossref_metadata_2025_split huggingface dataset:
The membrane‐associated monooxygenase in the butane‐oxidizing Gram‐positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family
Authors: Sayavedra‐Soto Luis A. , Hamamura Natsuko , Liu Chih‐Wen , Kimbrel Jeffrey A. , Chang Jeff H. , Arp Daniel J. 
Published: January 2011

SummaryThe Gram‐positive bacterium Nocardioides sp. strain CF8 uses a membrane‐associated monooxygenase (pBMO) to grow on butane. The nucleotide sequences of the genes encoding this novel monooxygenase were revealed through analysis of a de novo assembled draft genome sequence determined by high‐throughput sequencing of the whole genome. The pBMO genes were in a similar arrangement to the genes for ammonia monooxygenase (AMO) from the ammonia‐oxidizing bacteria and for particulate methane monooxygenase (pMMO) from the methane‐oxidizing bacteria. The pBMO genes likely constitute an operon in the order bmoC, bmoA and bmoB. The nucleotide sequence was less than 50% similar to the genes for AMO and pMMO. The operon for pBMO was confirmed to be a single copy in the genome by Southern and computational analyses. In an incubation on butane the increase of transcriptional activity of the pBmoA gene was congruent with the increase of pBMO activity and suggested correspondence between gene expression and the utilization of butane. Phylogenetic comparison revealed distant but significant similarity of all three pBMO subunits to homologous members of the AMO/pMMO family and indicated that the pBMO represents a deeply branching third lineage of this group of particulate monooxygenases. No other bmoCAB‐like genes were found to cluster with pBMO lineage in phylogenetic analysis by database searches including genomic and metagenomic sequence databases. pBMO is the first example of the AMO/pMMO‐like monooxygenase from Gram‐positive bacteria showing similarities to proteobacterial pMMO and AMO sequences.
Spiroplasma as a model insect endosymbiont
Authors: Anbutsu Hisashi , Fukatsu Takema 
Published: January 2011

SummaryMembers of the genus Spiroplasma are actively motile and helical bacteria of the class Mollicutes, which are associated with a variety of arthropods and plants. Some spiroplasmas cause female‐biased sex ratios of their host insects as a result of selective death of the male offspring during embryogenesis. Several strains of male‐killing spiroplasmas have been successfully transfected into Drosophila melanogaster by haemolymph injection and maintained in laboratory fly stocks. Spiroplasma–Drosophila endosymbiosis represents an ideal model system for analysing the molecular mechanisms underlying host–symbiont interactions. The infection dynamics exhibited by the symbiont within the host, the effects of external and environmental factors on the symbiotic association and symbiont interactions with the host's immune system have been investigated using this system. Comparisons between a male‐killing Spiroplasma strain and its non‐male‐killing variant revealed that, in addition to different male‐killing abilities, they also differed in infection dynamics and resistance to host innate immunity. It is currently unclear whether these different phenotypes are interconnected to each other. However, if so, such pleiotropy could facilitate our understanding of the genetic and molecular mechanisms of the endosymbiotic system.
Characterization of elevated alanine aminotransferase levels during pegylated‐interferon α‐2b plus ribavirin treatment for chronic hepatitis C
Authors: Aoki Yo‐hei , Ohkoshi Shogo , Yamagiwa Satoshi , Yano Masahiko , Takahashi Hiromichi , Waguri Nobuo , Igarashi Kentaro , Sugitani Soh‐ichi , Takahashi Toru , Ishikawa Toru , Kamimura Tomoteru , Wakabayashi Hiroto , Watanabe Toshiaki , Matsuda Yasunobu , Nomoto Minoru , Aoyagi Yutaka 
Published: January 2011

Aim:  Elevation of alanine aminotransferase (ALT) levels during pegylated‐interferon (peg‐IFN) plus ribavirin therapy in patients with chronic hepatitis C [CHC] is a problem that cannot be disregarded. The aim of this study is to assess the frequency and to characterize clinical parameters of this phenomenon.Methods:  Two hundred and thirty‐five (235) CHC patients with genotype 1b receiving peg‐IFN α‐2b plus ribavirin therapy were analyzed. Clinical parameters that may be associated with abnormal ALT values during treatment and therapy outcomes were evaluated statistically. One hundred and sixteen (116) patients treated with peg‐IFN α‐2a plus ribavirin were also included for partial analysis.Results:  Abnormal ALT values during treatment were observed in 23.0% of patients. It was observed in 14.5% of those with sustained virological response (SVR) and 17.8% of those with relapse, in whom viral clearance was observed during therapy. Multivariate logistic regression analysis revealed that pretreatment ALT values, therapy outcome, and body mass index (BMI) were significant factors related to abnormal ALT values during treatment. Abnormal ALT values during treatment became normal in SVR patients at 6 months after the completion of treatment, but not in NR (non‐response) patients. Mean ALT values were significantly higher at some time points during treatment in patients treated with α‐2a when compared to those treated with α‐2b.Conclusion:  Abnormal ALT values during peg‐IFN plus ribavirin treatment are observed relatively frequently, even in patients without detectable HCV RNA. Direct or indirect involvement of drugs is considered as one possible cause.
Clinical evaluation of liver injury in patients with acute ischemic brain stroke treated with edaravone
Authors: Hirano Masanori 
Published: January 2011

Aim:  To elucidate the etiologic factors and features of liver injury in patients with acute ischemic brain stroke who were treated with edaravone and reported by their attending physicians to have developed serious liver injury.Methods:  The present study investigated 123 patients with a verified episode of liver injury among 132 patients with serious liver injury that had been reported attributable to edaravone.Results:  Ischemic and/or congestive liver (70.7%) were most predominant among the etiologic factors for liver injury, and edaravone‐related liver injury accounted for 20.3% (25 patients). Evident liver injury (defined in the text) was found in 104 among 123 evaluated patients; 54 patients (51.9%) of the former subset showed severe liver injury (defined increases in serum aspartate and/or alanine aminotransferase levels of ≥1000 IU/L and/or serum total bilirubin levels of ≥5 mg/dL). Among 104 patients with evident liver injury, 65 showed recovery. Furthermore, 53 patients (51.0%) were complicated by renal disorders; all of these patients had ischemic and/or congestive liver, or severe infections.Conclusions:  Edaravone was considered to be etiologic for liver injury in approximately 20% of evaluated patients. When a patient treated with edaravone developed liver injury therefore an investigation not only on edaravone but also on other potential etiologic factors (e.g. ischemic liver, congestive liver, and infection) and the quick implementation of appropriate treatments, especially for infections, revealed possible reductions in the incidences of severe liver injury and of complications by renal disorders.
Expression profiles of miRNAs in human embryonic stem cells during hepatocyte differentiation
Authors: Kim Nury , Kim Hyemin , Jung Inkyung , Kim Yeji , Kim Dongsup , Han Yong‐Mahn 
Published: January 2011

Aim:  Human embryonic stem cells (hESCs) are able to self‐renew and differentiate into a variety of cell types. Although miRNAs have emerged as key regulators in the cellular process, a few studies have been reported about behaviors of miRNAs during differentiation of hESCs into a specialized cell type. Here, we demonstrate that different kinds of miRNAs may function in a lineage‐specific manner during the differentiation of human embryonic stem cells (hESCs).Methods:  hESCs were induced to definitive endoderm (DE) cells and further differentiated to hepatocytes. The expression levels of miRNAs were examined in hESCs, DE cells, and hepatocytes by miRNA array using 799 human miRNA probes.Results:  Among 387 miRNAs significantly detected, 13 and 56 miRNAs were downregulated and upregulated during transition of hESCs to DE cells, respectively, while 30 and 92 miRNAs were downregulated and upregulated during differentiation of DE cells to hepatocytes, respectively. In particular, 5, 4, and 86 miRNAs were enriched in hESCs, DE cells, and hepatocytes, respectively. Quantitative RT‐PCR represented that miR‐512‐3p, miR‐512‐5p and miR‐520c‐3p were enriched in hESCs, miR‐9*, miR‐205 and miR‐375 in hESC‐derived DE cells, and miR‐10a, miR‐122 and miR‐21 in hESC‐derived hepatocytes. Expression patterns of lineage‐specific miRNAs in the liver tissue were similar to those of hESC‐derived hepatocytes.Conclusion:  The results indicate that different kinds of miRNAs may function in a lineage‐specific manner during differentiation of hESCs into a specialized cell type.
The natural thermoluminescence of Antarctic meteorites and their terrestrial ages and orbits: A 2010 update
Authors: SEARS Derek W. G. , YOZZO Jordan , RAGLAND Christina 
Published: January 2011

Abstract– We have examined the relationship between natural thermoluminescence (TL) and 26Al in 120 Antarctic meteorites in order to explore the orbital history and terrestrial ages of these meteorites. Our results confirm the observations of Hasan et al. (1987) which were based on 23 meteorites. For most meteorites there was a positive correlation between natural TL and 26Al, reflecting their similarity in decay rate under Antarctic conditions and thus in terrestrial age. For a small group with low TL and high 26Al a small perihelion was proposed. Within this group, natural TL decreases with terrestrial age as determined by 36Cl measurements, although the rate of TL decay is faster (half‐life approximately 10 ka) and the ages that can be determined are smaller (<200 ka) than for most meteorites. The faster decay rate and lower natural TL levels are a reflection of recent exposure to higher radiation doses and higher temperatures, since this history would populate less stable TL traps with smaller electron densities. We sort the 120 meteorites by perihelion and terrestrial age. The normal perihelion group range up to approximately 1000 ka and the small perihelion group range up to approximately 200 ka. An intermediate perihelion group tends to have short terrestrial ages (20–60 ka). There is acceptable agreement between most (34 out of 43) of our present terrestrial age estimates and those determined by isotopic means, the exceptions reflecting complex irradiation histories, long burial times in the Antarctic, or other issues.
Antibody Recognition of the Dengue Virus Proteome and Implications for Development of Vaccines
Authors: Fernandez Stefan , Cisney Emily D. , Tikhonov Alexander P. , Schweitzer Barry , Putnak Robert J. , Simmons Monika , Ulrich Robert G. 
Published: January 2011

ABSTRACTDengue is a mosquito-borne infection caused by four distinct serotypes of dengue virus, each appearing cyclically in the tropics and subtropics along the equator. Although vaccines are currently under development, none are available to the general population. One of the main impediments to the successful advancement of these vaccines is the lack of well-defined immune correlates of protection. Here, we describe a protein microarray approach for measuring antibody responses to the complete viral proteome comprised of the structural (capsid, membrane, and envelope) and nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) components of all four dengue virus serotypes (1 to 4). We examined rhesus macaques vaccinated with tetravalent vaccines consisting of live-attenuated virus (LAV) or purified inactivated virus (PIV), followed by boosting with LAV and challenging with wild-type dengue virus. We detected temporal increases in antibodies against envelope proteins in response to either vaccine, while only the PIV/LAV vaccination strategy resulted in anticapsid antibodies. In contrast to results from vaccination, naïve macaques challenged with wild-type viruses of each serotype demonstrated a balanced response to nonstructural and structural components, including responses against the membrane protein. Our results demonstrate discriminating details concerning the nature of antibody responses to dengue virus at the proteomic level and suggest the usefulness of this information for vaccine development.
Intranasal Vaccination with the Recombinant Listeria monocytogenes ΔactA prfA*Mutant Elicits Robust Systemic and Pulmonary Cellular Responses and Secretory Mucosal IgA
Authors: Qiu Jin , Yan Lin , Chen Jianbo , Chen Crystal Y. , Shen Ling , Letvin Norman L. , Haynes Barton F. , Freitag Nancy , Rong Lijun , Frencher James T. , Huang Dan , Wang Xunming , Chen Zheng W. 
Published: January 2011

ABSTRACTWe previously showed that recombinant (r)Listeria monocytogenescarrying ΔactAand a selectedprfA*mutation (r-ListeriaΔactA prfA*) secreted >100-fold more immunogen in broth culture than wild-type r-Listeriaor r-ListeriaΔactAand elicited much greater cellular and humoral immune responses than r-ListeriaΔactAafter intravenous vaccination of mice. Here, we conducted comparative studies evaluating vaccine-elicited immune responses in systemic and mucosal sites after intranasal, intravenous, intraperitoneal, or subcutaneous immunization of mice with r-ListeriaΔactA prfA*vaccine candidates. Intranasal vaccination of mice with r-ListeriaΔactA prfA* vaccine candidates elicited a robust gamma interferon-positive (IFN-γ+) cellular response in systemic sites, although intravenous or intraperitoneal immunization was more efficient. Surprisingly, intranasal vaccination elicited an appreciable pulmonary IFN-γ+cellular response that was nonstatistically higher than the magnitude induced by the intravenous route but was significantly greater than that elicited by subcutaneous immunization. Furthermore, although intranasal r-ListeriaΔactA prfA*delivery induced poor systemic IgG responses, intranasal vaccination elicited appreciable secretory immunogen-specific IgA titers that were similar to or higher in mucosal fluid than those induced by subcutaneous and intravenous immunizations. Thus, intranasal vaccination with r-ListeriaΔactA prfA*appears to be a useful approach for eliciting robust systemic and pulmonary cellular responses and measurable secretory mucosal IgA titers.
High Failure Rate of the ViroSeq HIV-1 Genotyping System for Drug Resistance Testing in Cameroon, a Country with Broad HIV-1 Genetic Diversity
Authors: Aghokeng Avelin F. , Mpoudi-Ngole Eitel , Chia Julius E. , Edoul Elvine M. , Delaporte Eric , Peeters Martine 
Published: January 2011

ABSTRACTThe ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.
Detection of Bacillus Galmette-Guérin (Mycobacterium bovis BCG) DNA in Urine and Blood Specimens after Intravesical Immunotherapy for Bladder Carcinoma
Authors: Siatelis Argyrios , Houhoula Dimitra P. , Papaparaskevas Joseph , Delakas Dimitrios , Tsakris Athanassios 
Published: January 2011

ABSTRACT

A real-time PCR targeting IS
6110
was employed for the detection of
Mycobacterium tuberculosis
DNA in specimens collected from 10 patients treated with intravesical
M. bovis
bacillus Galmette-Guérin (BCG) immunotherapy for bladder malignancy. BCG DNA was detected in all urine specimens taken 24 h after the instillations, as well as in 24% of the specimens collected 7 days after the instillations; it was also detected in a single specimen taken 6 weeks after the last instillation. BCG DNA was detected in 8.3% of the blood specimens taken 1 day after instillation, and its amplification was associated with cases of self-limiting fever. These findings give indications that this real-time PCR is helpful to recognize BCG bacteremic cases, which may lead to mycobacterial infection.
Novel Nested Direct PCR Technique for Malaria Diagnosis Using Filter Paper Samples
Authors: Fuehrer Hans-Peter , Fally Markus A. , Habler Verena E. , Starzengruber Peter , Swoboda Paul , Noedl Harald 
Published: January 2011

ABSTRACT

The use of direct nested PCR enables the detection of
Plasmodium
spp. from blood samples collected on filter papers without requiring the time-consuming procedures associated with DNA extraction. Direct PCR provides a rapid, highly sensitive, and cost-effective alternative to diagnosing malaria using filter paper samples and standard nested PCR.
Multilocus Sequence Typing Subtypes of Poultry Clostridium perfringens Isolates Demonstrate Disease Niche Partitioning
Authors: Hibberd M. C. , Neumann A. P. , Rehberger T. G. , Siragusa G. R. 
Published: January 2011

ABSTRACT

Clostridium perfringens
is a ubiquitous and versatile pathogenic bacterium and is implicated in the etiology of the poultry diseases necrotic enteritis (NE) and poultry gangrene (PG). In this study, multilocus sequence typing was used to investigate genotypic relationships among 139
C. perfringens
isolates from 74 flocks. These isolates had multiple disease, host, and environmental origins. The results indicated a polymorphic yet highly clonal population, with 79.6% of all isolates partitioning into one of six clonal complexes or two dominant sequence types, ST-9 and ST-31. The most prolific clonal complex, CC-1, contained 27.3% of all isolates and was not clearly associated with one particular disease. The subtypes CC-4 and ST-31 were highly associated with NE and represented 9.4% and 7.2% of the total isolates, respectively. No PG-associated and NE-associated
C. perfringens
isolates shared the same sequence type or clonal complex. NE-associated subtypes were more clonal and appeared more evolutionarily divergent than PG-associated subtypes, which tended to cluster in the more ancestral lineages alongside isolates from asymptomatic chickens and turkeys. Toxin gene screening identified
cpb2
throughout these isolates and correlated the presence of
netB
with NE pathology. Previous investigations into the genetic basis of
C. perfringens
pathogenicity have focused on toxins and other variable genetic elements. This study presents the first sequence-based comparison of
C. perfringens
isolates recovered in clinical cases of PG and NE and demonstrates that niche specialization is observable in the core genomes of poultry-associated
C. perfringens
isolates, a concept with both epidemiological and evolutionary significance.
Gordonia bronchialis Bacteremia and Pleural Infection: Case Report and Review of the Literature
Authors: Johnson Jennifer A. , Onderdonk Andrew B. , Cosimi Lisa A. , Yawetz Sigal , Lasker Brent A. , Bolcen Shanna J. , Brown June M. , Marty Francisco M. 
Published: January 2011

ABSTRACT

Gordonia
species are aerobic actinomycetes recently recognized as causing human disease, often in the setting of intravascular catheter-related infections. We describe a case of
Gordonia bronchialis
bacteremia and pleural space infection in the absence of an indwelling intravascular catheter and review the breadth of reported infections with this emerging pathogen.
Salmonella enterica Serotype Gambia with CTX-M-3 and
armA
Resistance Markers: Nosocomial Infections with a Fatal Outcome
Authors: Moissenet D. , Weill F.-X. , Arlet G. , Harrois D. , Girardet J. P. , Vu-Thien H. 
Published: January 2011

ABSTRACT

We report two cases of bacteremia caused by the
Salmonella enterica
serotype Gambia in our children's hospital, with one fatal outcome. The isolates showed indistinguishable genotypes and infrequent resistance markers: CTX-M-3 extended-spectrum β-lactamase and
armA
methyltransferase. This is the first report of
S
. Gambia exhibiting CTX-M-3 and
armA
markers involved in serious infections.
Diagnostic Accuracy Assessment of Sensititre and Agar Disk Diffusion for Determining Antimicrobial Resistance Profiles of Bovine Clinical Mastitis Pathogens
Authors: Saini V. , Riekerink R. G. M. Olde , McClure J. T. , Barkema H. W. 
Published: January 2011

ABSTRACT

Determining the accuracy and precision of a measuring instrument is pertinent in antimicrobial susceptibility testing. This study was conducted to predict the diagnostic accuracy of the Sensititre MIC mastitis panel (Sensititre) and agar disk diffusion (ADD) method with reference to the manual broth microdilution test method for antimicrobial resistance profiling of
Escherichia coli
(
n
= 156),
Staphylococcus aureus
(
n
= 154), streptococcal (
n
= 116), and enterococcal (
n
= 31) bovine clinical mastitis isolates. The activities of ampicillin, ceftiofur, cephalothin, erythromycin, oxacillin, penicillin, the penicillin-novobiocin combination, pirlimycin, and tetracycline were tested against the isolates. Diagnostic accuracy was determined by estimating the area under the receiver operating characteristic curve; intertest essential and categorical agreements were determined as well. Sensititre and the ADD method demonstrated moderate to highly accurate (71 to 99%) and moderate to perfect (71 to 100%) predictive accuracies for 74 and 76% of the isolate-antimicrobial MIC combinations, respectively. However, the diagnostic accuracy was low for
S. aureus
-ceftiofur/oxacillin combinations and other streptococcus-ampicillin combinations by either testing method. Essential agreement between Sensititre automatic MIC readings and MIC readings obtained by the broth microdilution test method was 87%. Essential agreement between Sensititre automatic and manual MIC reading methods was 97%. Furthermore, the ADD test method and Sensititre MIC method exhibited 92 and 91% categorical agreement (sensitive, intermediate, resistant) of results, respectively, compared with the reference method. However, both methods demonstrated lower agreement for
E. coli
-ampicillin/cephalothin combinations than for Gram-positive isolates. In conclusion, the Sensititre and ADD methods had moderate to high diagnostic accuracy and very good essential and categorical agreement for most udder pathogen-antimicrobial combinations and can be readily employed in veterinary diagnostic laboratories.
Isolation and Characterization of “Pseudomonas andersonii” from Four Cases of Pulmonary Granulomas and Emended Species Description
Authors: Simmon Keith E. , Fang Deanna C. , Tesic Vera , Khot Prasanna D. , Giangeruso Enrico , Bolesta E. Stephen , Wagner-Reiss Katherine M. , Fisher Mark A. , Petti Cathy A. , Han Xiang Y. , She Rosemary C. 
Published: January 2011

ABSTRACT

“
Pseudomonas andersonii
” is a Gram-negative bacillus initially isolated from a granulomatous lung lesion. Novel species status has not been validated for this single strain. We report four additional cases of pulmonary granuloma involving
P. andersonii
and further characterize the organism. These patients had pulmonary nodules that were surgically resected and which grew
P. andersonii
on routine culture.
Mycobacterium avium
complex was concomitantly isolated in two cases, and fungal structures were identified histopathologically in two other cases. The five
P. andersonii
strains described to date were similar in growth characteristics, biochemical reactions, matrix-assisted laser desorption ionization–time of flight mass spectrometry protein profiles, and susceptibility to antimicrobial agents. Their 16S rRNA genes were 99.9 to 100% identical but less than 95.0% similar to those of all other known bacteria. The
gyrA
genes of these strains were 99.5 to 100% identical. These shared features illustrate
P. andersonii
as a unique and distinct bacterium and support the novel species status of the organism.