bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of
Klebsiella pneumoniae
Coproducing KPC-2 and 16S rRNA Methylase ArmA in Poland
Authors: Zacharczuk Katarzyna , Piekarska Katarzyna , Szych Jolanta , Zawidzka Elwira , Sulikowska Agnieszka , Wardak Sebastian , Jagielski Marek , Gierczyński Rafał 
Published: October 2010

ABSTRACT

A
Klebsiella pneumoniae
epidemic strain that coproduced carbapenemase KPC-2 (
K. pneumoniae
carbapenemase 2) and 16S rRNA methylase ArmA has emerged in Poland. Four nonduplicate isolates from patients in a hospital in Warsaw, Poland, were found to carry the
bla
KPC-2
and
armA
genes on ca. 50-kb and 90-kb plasmids, respectively. Tn
4401
with a 100-bp deletion in the variable region was detected in all the isolates. XbaI pulsed-field gel electrophoresis (PFGE) revealed 93.2% similarity of the isolates. All the isolates were resistant to carbapenems and 4,6-disubstituted 2-deoxystreptamines.
Contribution of Specific Amino Acid Changes in Penicillin Binding Protein 1 to Amoxicillin Resistance in ClinicalHelicobacter pyloriisolates
Authors: Qureshi Nadia N. , Morikis Dimitrios , Schiller Neal L. 
Published: October 2010

ABSTRACTAmoxicillin is commonly used to treatHelicobacter pylori, a major cause of peptic ulcers, stomach cancer, and B-cell mucosa-associated lymphoid tissue lymphoma. Amoxicillin resistance inH. pyloriis increasing steadily, especially in developing countries, leading to treatment failures. In this study, we characterize the mechanism of amoxicillin resistance in the U.S. clinical isolate B258. Transformation of amoxicillin-susceptible strain 26695 with the penicillin binding protein 1 gene (pbp1) from B258 increased the amoxicillin resistance of 26695 to equal that of B258, while studies using biotinylated amoxicillin showed a decrease in the binding of amoxicillin to the PBP1 of B258. Transformation with 4pbp1fragments, each encompassing several amino acid substitutions, combined with site-directed mutagenesis studies, identified 3 amino acid substitutions in PBP1 of B258 which affected amoxicillin susceptibility (Val 469 Met, Phe 473 Leu, and Ser 543 Arg). Homology modeling showed the spatial orientation of these specific amino acid changes in PBP1 from 26695 and B258. The results of these studies demonstrate that amoxicillin resistance in the clinical U.S. isolate B258 is due solely to an altered PBP1 protein with a lower binding affinity for amoxicillin. Homology modeling analyses using previously identified amino acid substitutions of amoxicillin-resistant PBP1s demonstrate the importance of specific amino acid substitutions in PBP1 that affect the binding of amoxicillin in the putative binding cleft, defining those substitutions deemed most important in amoxicillin resistance.
Recombinant Anthrax Toxin Receptor-Fc Fusion Proteins Produced in Plants Protect Rabbits against Inhalational Anthrax
Authors: Wycoff Keith L. , Belle Archana , Deppe Dorothée , Schaefer Leah , Maclean James M. , Haase Simone , Trilling Anke K. , Liu Shihui , Leppla Stephen H. , Geren Isin N. , Pawlik Jennifer , Peterson Johnny W. 
Published: October 2010

ABSTRACT

Inhalational anthrax, a zoonotic disease caused by the inhalation of
Bacillus anthracis
spores, has a ∼50% fatality rate even when treated with antibiotics. Pathogenesis is dependent on the activity of two toxic noncovalent complexes: edema toxin (EdTx) and lethal toxin (LeTx). Protective antigen (PA), an essential component of both complexes, binds with high affinity to the major receptor mediating the lethality of anthrax toxin
in vivo
, capillary morphogenesis protein 2 (CMG2). Certain antibodies against PA have been shown to protect against anthrax
in vivo
. As an alternative to anti-PA antibodies, we produced a fusion of the extracellular domain of human CMG2 and human IgG Fc, using both transient and stable tobacco plant expression systems. Optimized expression led to the CMG2-Fc fusion protein being produced at high levels: 730 mg/kg fresh leaf weight in
Nicotiana benthamiana
and 65 mg/kg in
N. tabacum
. CMG2-Fc, purified from tobacco plants, fully protected rabbits against a lethal challenge with
B. anthracis
spores at a dose of 2 mg/kg body weight administered at the time of challenge. Treatment with CMG2-Fc did not interfere with the development of the animals' own immunity to anthrax, as treated animals that survived an initial challenge also survived a rechallenge 30 days later. The glycosylation of the Fc (or lack thereof) had no significant effect on the protective potency of CMG2-Fc in rabbits or on its serum half-life, which was about 5 days. Significantly, CMG2-Fc effectively neutralized,
in vitro
, LeTx-containing mutant forms of PA that were not neutralized by anti-PA monoclonal antibodies.
In Vitro
Antibiotic Synergy in Extensively Drug-Resistant
Acinetobacter baumannii
: the Effect of Testing by Time-Kill, Checkerboard, and Etest Methods
Authors: Tan Thean Yen , Lim Tze Peng , Lee Winnie Hui Ling , Sasikala Suranthran , Hsu Li Yang , Kwa Andrea Lay-Hoon 
Published: October 2010

ABSTRACT

This study examined the
in vitro
effects of polymyxin B, tigecycline, and rifampin combinations on 16 isolates of extensively drug-resistant
Acinetobacter baumannii
, including four polymyxin-resistant strains.
In vitro
synergy was demonstrated in 19 (40%) of a possible 48 isolate-antibiotic combinations by time-kill methods, 8 (17%) by checkerboard methods, and only 1 (2%) by Etest methods. There was only slight agreement between Etest and checkerboard methods and no agreement between results obtained by other methods.
Spontaneous Mutations in the
Plasmodium falciparum
Sarcoplasmic/ Endoplasmic Reticulum Ca
2+
-ATPase (PfATP6) Gene among Geographically Widespread Parasite Populations Unexposed to Artemisinin-Based Combination Therapies
Authors: Tanabe Kazuyuki , Zakeri Sedigheh , Palacpac Nirianne Marie Q. , Afsharpad Manada , Randrianarivelojosia Milijaona , Kaneko Akira , Marma Aung Swi Prue , Horii Toshihiro , Mita Toshihiro 
Published: October 2010

ABSTRACT

Recent reports on the decline of the efficacy of artemisinin-based combination therapies (ACTs) indicate a serious threat to malaria control. The endoplasmic/sarcoplasmic reticulum Ca
2+
-ATPase ortholog of
Plasmodium falciparum
(PfSERCA) has been suggested to be the target of artemisinin and its derivatives. It is assumed that continuous artemisinin pressure will affect polymorphism of the PfSERCA gene (
serca
) if the protein is the target. Here, we investigated the polymorphism of
serca
in parasite populations unexposed to ACTs to obtain baseline information for the study of potential artemisinin-driven selection of resistant parasites. Analysis of 656 full-length sequences from 13 parasite populations in Africa, Asia, Oceania, and South America revealed 64 single nucleotide polymorphisms (SNPs), of which 43 were newly identified and 38 resulted in amino acid substitutions. No isolates showed L263E and S769N substitutions, which were reportedly associated with artemisinin resistance. Among the four continents, the number of SNPs was highest in Africa. In Africa, Asia, and Oceania, common SNPs, or those with a minor allele frequency of ≥0.05, were less prevalent, with most SNPs noted to be continent specific, whereas in South America, common SNPs were highly prevalent and often shared with those in Africa. Of 50 amino acid haplotypes observed, only one haplotype (3D7 sequence) was seen in all four continents (64%). Forty-eight haplotypes had frequencies of less than 5%, and 40 haplotypes were continent specific. The geographical difference in the diversity and distribution of
serca
SNPs and haplotypes lays the groundwork for assessing whether some artemisinin resistance-associated mutations and haplotypes are selected by ACTs.
Effects of Engineered Cerium Oxide Nanoparticles on Bacterial Growth and Viability
Authors: Pelletier Dale A. , Suresh Anil K. , Holton Gregory A. , McKeown Catherine K. , Wang Wei , Gu Baohua , Mortensen Ninell P. , Allison David P. , Joy David C. , Allison Martin R. , Brown Steven D. , Phelps Tommy J. , Doktycz Mitchel J. 
Published: October 2010

ABSTRACT

Interest in engineered nanostructures has risen in recent years due to their use in energy conservation strategies and biomedicine. To ensure prudent development and use of nanomaterials, the fate and effects of such engineered structures on the environment should be understood. Interactions of nanomaterials with environmental microorganisms are inevitable, but the general consequences of such interactions remain unclear, due to a lack of standard methods for assessing such interactions. Therefore, we have initiated a multianalytical approach to understand the interactions of synthesized nanoparticles with bacterial systems. These efforts are focused initially on cerium oxide nanoparticles and model bacteria in order to evaluate characterization procedures and the possible fate of such materials in the environment. The growth and viability of the Gram-negative species
Escherichia coli
and
Shewanella oneidensis
, a metal-reducing bacterium, and the Gram-positive species
Bacillus subtilis
were examined relative to cerium oxide particle size, growth media, pH, and dosage. A hydrothermal synthesis approach was used to prepare cerium oxide nanoparticles of defined sizes in order to eliminate complications originating from the use of organic solvents and surfactants. Bactericidal effects were determined from MIC and CFU measurements, disk diffusion tests, and live/dead assays. For
E. coli
and
B. subtilis
, clear strain- and size-dependent inhibition was observed, whereas
S. oneidensis
appeared to be unaffected by the particles. Transmission electron microscopy along with microarray-based transcriptional profiling was used to understand the response mechanism of the bacteria. Use of multiple analytical approaches adds confidence to toxicity assessments, while the use of different bacterial systems highlights the potential wide-ranging effects of nanomaterial interactions in the environment.
Antibiotic Manipulation of Intestinal Microbiota To Identify Microbes Associated with
Campylobacter jejuni
Exclusion in Poultry
Authors: Scupham A. J. , Jones J. A. , Rettedal E. A. , Weber T. E. 
Published: October 2010

ABSTRACT

The ability of various subsets of poultry intestinal microbiota to protect turkeys from colonization by
Campylobacter jejuni
was investigated. Community subsets were generated
in vivo
by inoculation of day-old poults with the cecal contents of a
Campylobacter
-free adult turkey, followed by treatment with one antimicrobial, either virginiamycin, enrofloxacin, neomycin, or vancomycin. The
C. jejuni
loads of the enrofloxacin-, neomycin-, and vancomycin-derived communities were decreased by 1 log, 2 logs, and 4 logs, respectively. Examination of the constituents of the derived communities via the array-based method oligonucleotide fingerprinting of rRNA genes detected a subtype of
Megamonas hypermegale
specific to the
C. jejuni
-suppressive treatments.
Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster
Authors: Bergmann Sebastian , Funk Alexander N. , Scherlach Kirstin , Schroeckh Volker , Shelest Ekaterina , Horn Uwe , Hertweck Christian , Brakhage Axel A. 
Published: October 2010

ABSTRACT

Filamentous fungi produce numerous natural products that constitute a consistent source of potential drug leads, yet it seems that the majority of natural products are overlooked since most biosynthesis gene clusters are silent under standard cultivation conditions. Screening secondary metabolite genes of the model fungus
Aspergillus nidulans
, we noted a silent gene cluster on chromosome II comprising two nonribosomal peptide synthetase (NRPS) genes,
inpA
and
inpB
, flanked by a regulatory gene that we named
scpR
for secondary metabolism cross-pathway regulator. The induced expression of the
scpR
gene using the promoter of the alcohol dehydrogenase AlcA led to the transcriptional activation of both the endogenous
scpR
gene and the NRPS genes. Surprisingly, metabolic profiling of the supernatant of mycelia overexpressing
scpR
revealed the production of the polyketide asperfuranone. Through transcriptome analysis we found that another silent secondary metabolite gene cluster located on chromosome VIII coding for asperfuranone biosynthesis was specifically induced. Quantitative reverse transcription-PCR proved the transcription not only of the corresponding polyketide synthase (PKS) biosynthesis genes,
afoE
and
afoG
, but also of their activator,
afoA
, under
alcAp
-
scpR
-inducing conditions. To exclude the possibility that the product of the
inp
cluster induced the asperfuranone gene cluster, a strain carrying a deletion of the NRPS gene
inpB
and, in addition, the
alcAp
-
scpR
overexpression cassette was generated. In this strain, under inducing conditions, transcripts of the biosynthesis genes of both the NRPS-containing gene cluster
inp
and the asperfuranone gene cluster except gene
inpB
were detected. Moreover, the existence of the polyketide product asperfuranone indicates that the transcription factor ScpR controls the expression of the asperfuranone biosynthesis gene cluster. This expression as well as the biosynthesis of asperfuranone was abolished after the deletion of the asperfuranone activator gene
afoA
, indicating that ScpR binds to the
afoA
promoter. To the best of our knowledge, this is the first report of regulatory cross talk between two biosynthesis gene clusters located on different chromosomes.
Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of
S
treptococcus
agalactiae
,
S. dysgalactiae
subsp.
dysgalactiae
, and
S. uberis
Authors: Haenni Marisa , Saras Estelle , Bertin Stéphane , Leblond Pierre , Madec Jean-Yves , Payot Sophie 
Published: October 2010

ABSTRACT

Bovine isolates of
S
treptococcus
agalactiae
(
n
= 76),
S
treptococcus
dysgalactiae
subsp.
dysgalactiae
(
n
= 32), and
S
treptococcus
uberis
(
n
= 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for
S. agalactiae
and pulsed-field gel electrophoresis for
S. dysgalactiae
and
S. uberis
. Most of the erythromycin-resistant strains carry an
ermB
gene. Five strains of
S. uberis
that are resistant to lincomycin but susceptible to erythromycin carry the
lin
(B) gene, and one has both
linB
and
lnuD
genes. In contrast to
S. uberis
, most of the
S. agalactiae
and
S. dysgalactiae
tetracycline-resistant isolates carry a
tet
(M) gene. A
tet
(S) gene was also detected in the three species. A Tn
916
-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an
S. agalactiae
strain. Most of the isolates carry an ICE integrated in the
rplL
gene. In addition, half of the
S. agalactiae
isolates have an ICE integrated in a tRNA lysine (tRNA
Lys
) gene. Such an element is also present in 20% of the isolates of
S. dysgalactiae
and
S. uberis
. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.
Occurrence, Survival, and Persistence of Human Adenoviruses and F-Specific RNA Phages in Raw Groundwater
Authors: Ogorzaly Leslie , Bertrand Isabelle , Paris Myriam , Maul Armand , Gantzer Christophe 
Published: October 2010

ABSTRACT

Detection of specific genetic markers can rapidly identify the presence of enteric viruses in groundwater. However, comparison of stability characteristics between genetic and infectivity markers is necessary to better interpret molecular data. Human adenovirus serotype 2 (HAdV2), in conjunction with MS2 phages or GA phages, was spiked into raw groundwater microcosms. Viral stability was periodically assessed by both infectivity and real-time PCR methods. The results of this yearlong study suggest that adenoviruses have the most stable persistence profile and an ability to survive for a long time in groundwater. According to a linear regression model, infectivity reductions of HAdV2 ranged from 0.0076 log
10
/day (4°C) to 0.0279 log
10
/day (20°C) and were significantly lower than those observed for phages. No adenoviral genome degradation was observed at 4°C, and the reduction was estimated at 0.0036 log
10
/day at 20°C. Occurrence study showed that DNA of human adenoviruses could be observed in groundwater from a confined aquifer (7 of the 60 samples were positive by real-time PCR), while no fecal indicators were detected. In agreement with the persistence of genetic markers, the presence of adenoviral DNA in groundwater may be misleading in term of health risk, especially in the absence of information on the infective status.
Agrobacterium tumefaciens
-Mediated Transformation for Investigation of Somatic Recombination in the Fungal Pathogen
Armillaria mellea
Authors: Baumgartner Kendra , Fujiyoshi Phillip , Foster Gary D. , Bailey Andy M. 
Published: October 2010

ABSTRACT

Armillaria root disease is one of the most damaging timber and fruit tree diseases in the world. Despite its economic importance, many basic questions about the biology of the causal fungi,
Armillaria
spp., are unanswered. For example,
Armillaria
undergoes matings between diploid and haploid mycelia, which can result in a recombinant diploid without meiosis. Evidence of such somatic recombination in natural populations suggests that this reproductive mode may affect the pathogen's ecology. Investigations of the mechanisms and adaptive consequences of somatic recombination are, however, hampered by the lack of a method to reliably synthesize somatic recombinants. Here we report the first genetic transformation system for the genus
Armillaria
. We transformed
A. mellea
with selective markers for use in diploid-haploid matings to reliably synthesize somatic recombinants. This was accomplished with
Agrobacterium tumefaciens
carrying pBGgHg, which carries the hygromycin phosphotransferase gene (
hph
).
hph
was integrated into transformants, as evidenced by serial transfer to selective media, PCR, reverse transcription-PCR (RT-PCR), and Southern hybridization. Nuclear and mitochondrial markers were developed to genotype synthesized mycelia. In matings between a wild-type diploid and hygromycin-resistant haploids (transgenic), we identified recombinant, hygromycin-resistant diploids and, additionally, hygromycin-resistant triploids, all with the mitochondrial haplotype of the haploid partner. Our approach created no mycelium in which the haploid nucleus was replaced by the diploid nucleus, the typical outcome of diploid-haploid matings in
Armillaria
. This genetic transformation system, in combination with new markers to track chromosomal and cytoplasmic inheritance in
A. mellea
, will advance research aimed at characterizing the significance of somatic recombination in the ecology of this important fungus.
Biodegradation of a Biocide (Cu-
N
-Cyclohexyldiazenium Dioxide) Component of a Wood Preservative by a Defined Soil Bacterial Community
Authors: Jakobs-Schönwandt Désirée , Mathies Helena , Abraham Wolf-Rainer , Pritzkow Wolfgang , Stephan Ina , Noll Matthias 
Published: October 2010

ABSTRACT

The wood protection industry has refined their products from chrome-, copper-, and arsenate-based wood preservatives toward solely copper-based preservatives in combination with organic biocides. One of these is Cu-HDO, containing the chelation product of copper and
N
-cyclohexyldiazenium dioxide (HDO). In this study, the fate of isotope-labeled (
13
C) and nonlabeled (
12
C) Cu-HDO incorporated in wood sawdust mixed with soil was investigated. HDO concentration was monitored by high-pressure liquid chromatography. The total carbon and the δ
13
C content of respired CO
2
, as well as of the soil-wood-sawdust mixture, were determined with an elemental analyzer-isotopic ratio mass spectrometer. The concentration of HDO decreased significantly after 105 days of incubation, and after 24 days the
13
CO
2
concentration respired from soil increased steadily to a maximum after 64 days of incubation. Phospholipid fatty acid-stable isotope probing (PFA-SIP) analysis revealed that the dominant PFAs C
19:0
d8,9, C
18:0
, C
18:1
ω7, C
18:2
ω6,9, C
17:1
d7,8, C
16:0
, and C
16:1
ω7 were highly enriched in their δ
13
C content. Moreover, RNA-SIP identified members of the phylum
Acidobacteria
and the genera
Phenylobacterium
and
Comamonas
that were assimilating carbon from HDO exclusively. Cu-HDO as part of a wood preservative effectively decreased fungal wood decay and overall microbial respiration from soil. In turn, a defined bacterial community was stimulated that was able to metabolize HDO completely.
Potential of the Melanophore Pigment Response for Detection of Bacterial Toxicity
Authors: Dukovcic Stephanie R. , Hutchison Janine R. , Trempy Janine E. 
Published: October 2010

ABSTRACT

Chromatophore cells have been investigated as potential biodetectors for function-based detection of chemically and biologically toxic substances.
Oncorhynchus tshawytscha
(chinook salmon) melanophores, a chromatophore cell type containing brown pigment, rapidly detect the salmonid pathogens
Aeromonas salmonicida
,
Yersinia ruckeri
, and
Flavobacterium psychrophilum
and the human pathogen
Bacillus cereus
.
Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (
Lactuca
Species) Phyllosphere
Authors: Hunter Paul J. , Hand Paul , Pink David , Whipps John M. , Bending Gary D. 
Published: October 2010

ABSTRACT

Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by
Pseudomonas
species and the
Enterobacteriaceae
family. Significant differences in the relative proportions of genera in the
Enterobacteriaceae
were detected between lettuce accessions. Two such genera (
Erwinia
and
Enterobacter
) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.