bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Lantibiotic Mersacidin Is an Autoinducing Peptide
Authors: Schmitz Stephanie , Hoffmann Anja , Szekat Christiane , Rudd Brian , Bierbaum Gabriele 
Published: November 2006

ABSTRACT

The lantibiotic (lanthionine-containing antibiotic) mersacidin is an antimicrobial peptide consisting of 20 amino acids and is produced by
Bacillus
sp. strain HIL Y-85,54728. The structural gene (
mrsA
) and the genes for producer self-protection, modification enzymes, transport proteins, and regulator proteins are organized in a 12.3-kb biosynthetic gene cluster on the chromosome of the producer strain. Mersacidin is produced in stationary phase in a synthetic medium (K. Altena, A. Guder, C. Cramer, and G. Bierbaum, Appl. Environ. Microbiol. 66:2565-2571, 2000). To investigate the influence of the alternative sigma factor H on mersacidin biosynthesis, a SigH knockout was constructed. The knockout mutant was asporogenous, and a comparison to the wild-type strain indicated no significant differences concerning mersacidin production and immunity. Characterization of the
mrsA
promoter showed that the gene is transcribed by the housekeeping sigma factor A. The biosynthesis of some lantibiotic peptides like nisin or subtilin is regulated in a cell-density-dependent manner (M. Kleerebezem, Peptides 25:1405-1414, 2004). When mersacidin was added at a concentration of 2 mg/liter to an exponentially growing culture, an earlier production of antibacterial activity against
Micrococcus luteus
ATCC 4698 in comparison to that of the control culture was observed, suggesting that mersacidin itself functions as an autoinducer. In real-time PCR experiments, the expression of
mrsA
was remarkably increased in the induced culture compared to the control. In conclusion, mersacidin is yet another lantibiotic peptide whose biosynthesis can be regulated by an autoinducing mechanism.
Antimicrobial Susceptibilities of
Aeromonas
spp. Isolated from Environmental Sources
Authors: Huddleston Jennifer R. , Zak John C. , Jeter Randall M. 
Published: November 2006

ABSTRACT

Aeromonas
spp. are ubiquitous aquatic bacteria that cause serious infections in both poikilothermic and endothermic animals, including humans. Clinical isolates have shown an increasing incidence of antibiotic and antimicrobial drug resistance since the widespread use of antibiotics began. A total of 282
Aeromonas
pure cultures were isolated from both urban and rural playa lakes in the vicinity of Lubbock, Texas, and several rivers in West Texas and New Mexico. Of these, at least 104 were subsequently confirmed to be independent isolates. The 104 isolates were identified by Biolog and belonged to 11 different species. The MICs of six metals, one metalloid, five antibiotics, and two antimicrobial drugs were determined. All aeromonads were sensitive to chromate, cobalt, copper, nickel, zinc, cefuroxime, kanamycin, nalidixic acid, ofloxacin, tetracycline, and sulfamethoxazole. Low incidences of trimethoprim resistance, mercury resistance, and arsenite resistance were found. Dual resistances were found in 5 of the 104
Aeromonas
isolates. Greater numbers of resistant isolates were obtained from samples taken in March versus July 2002 and from sediment versus water. Plasmids were isolated from selected strains of the arsenite- and mercury-resistant organisms and were transformed into
Escherichia coli
XL1-Blue MRF′. Acquisition of the resistance phenotypes by the new host showed that these resistance genes were carried on the plasmids. Mercury resistance was found to be encoded on a conjugative plasmid. Despite the low incidence of resistant isolates, the six playa lakes and three rivers that were sampled in this study can be considered a reservoir for antimicrobial resistance genes.
Diversity of Basidiomycetes in Michigan Agricultural Soils
Authors: Lynch Michael D. J. , Thorn R. Greg 
Published: November 2006

ABSTRACT
We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With “species” defined as organisms yielding PCR products with ≥99% identity in the 5′ 650 bases of the nuclear large-subunit ribosomal DNA, 241 “species” were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 “species” had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple “species” could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated “species” richness for this 11.2-ha site was 367 “species” of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure.
Rapid In Situ Evolution of Nodulating Strains for
Biserrula pelecinus
L. through Lateral Transfer of a Symbiosis Island from the Original Mesorhizobial Inoculant
Authors: Nandasena Kemanthi G. , O'Hara Graham W. , Tiwari Ravi P. , Howieson John G. 
Published: November 2006

ABSTRACT

Diverse rhizobia able to nodulate
Biserrula pelecinus
evolved following in situ transfer of
nodA
and
nifH
from an inoculant to soil bacteria. Transfer of these chromosomal genes and the presence of an identical integrase gene adjacent to a Phe tRNA gene in both the inoculant and recipients indicate that there was lateral transfer of a symbiosis island.
Role of the
ptsN
Gene Product in Catabolite Repression of the
Pseudomonas putida
TOL Toluene Degradation Pathway in Chemostat Cultures
▿
Authors: Aranda-Olmedo Isabel , Marín Patricia , Ramos Juan L. , Marqués Silvia 
Published: November 2006

ABSTRACT

The
Pseudomonas putida
KT2440 TOL upper pathway is repressed under nonlimiting conditions in cells growing in chemostat with succinate as a carbon source. We show that the
ptsN
gene product IIA
Ntr
participates in this repression. Crc, involved in yeast extract-dependent repression in batch cultures, did not influence expression when cells were growing in a chemostat with succinate at maximum rate.
Global Gene Expression Analysis of Yeast Cells during Sake Brewing
Authors: Wu Hong , Zheng Xiaohong , Araki Yoshio , Sahara Hiroshi , Takagi Hiroshi , Shimoi Hitoshi 
Published: November 2006

ABSTRACT

During the brewing of Japanese sake,
Saccharomyces cerevisiae
cells produce a high concentration of ethanol compared with other ethanol fermentation methods. We analyzed the gene expression profiles of yeast cells during sake brewing using DNA microarray analysis. This analysis revealed some characteristics of yeast gene expression during sake brewing and provided a scaffold for a molecular level understanding of the sake brewing process.
System for Determining the Relative Fitness of Multiple Bacterial Populations without Using Selective Markers
Authors: Ahn Hyo-Jin , La Hyun-Joon , Forney Larry J. 
Published: November 2006

ABSTRACT
A device for simultaneously measuring the relative fitness of multiple bacterial populations was developed and evaluated. The new device eliminates the need to construct strains with selectively neutral markers so that strains can be readily distinguished, and it provides a means to perform multispecies competition experiments.
Rapid Chromatic Detection of Bacteria by Use of a New Biomimetic Polymer Sensor
Authors: Silbert Liron , Ben Shlush Izek , Israel Elena , Porgador Angel , Kolusheva Sofiya , Jelinek Raz 
Published: November 2006

ABSTRACT
We present a new platform for visual and spectroscopic detection of bacteria. The detection scheme is based on the interaction of membrane-active compounds secreted by bacteria with agar-embedded nanoparticles comprising phospholipids and the chromatic polymer polydiacetylene (PDA). We demonstrate that PDA undergoes dramatic visible blue-to-red transformations together with an intense fluorescence emission that are induced by molecules released by multiplying bacteria. The chromatic transitions are easily identified by the naked eye and can also be recorded by conventional high-throughput screening instruments. Furthermore, the color and fluorescence changes generally occur in shorter times than the visual appearance of bacterial colonies on the agar. The chromatic technology is generic and simple, does not require identification a priori of specific bacterial recognition elements, and can be applied for detection of both gram-negative and gram-positive bacteria. We demonstrate applications of the new platform for reporting on bacterial contaminations in foods and for screening for bacterial antibiotic resistance.
Lactobacillus rhamnosus
Strain GG Modulates Intestinal Absorption, Fecal Excretion, and Toxicity of Aflatoxin B
1
in Rats
Authors: Gratz S. , Täubel M. , Juvonen R. O. , Viluksela M. , Turner P. C. , Mykkänen H. , El-Nezami H. 
Published: November 2006

ABSTRACT

In this study, the modulation of aflatoxin B
1
(AFB
1
) uptake in rats by administration of the probiotic
Lactobacillus rhamnosus
GG was demonstrated. Fecal AFB
1
excretion in GG-treated rats was increased via bacterial AFB
1
binding. Furthermore, AFB
1
-associated growth faltering and liver injury were alleviated with GG treatment.
Toward a More Robust Assessment of IntraspeciesDiversity, Using Fewer GeneticMarkers
Authors: Konstantinidis Konstantinos T. , Ramette Alban , Tiedje James M. 
Published: November 2006

ABSTRACT

Phylogenetic
sequence analysis of single or multiple genes has dominated the study
and census of the genetic diversity among closely related bacteria. It
remains unclear, however, how the results based on a few genes in the
genome correlate with whole-genome-based relatedness and what genes (if
any) best reflect whole-genome-level relatedness and hence should be
preferentially used to economize on cost and to improve accuracy. We
show here that phylogenies of closely related organisms based on the
average nucleotide identity (ANI) of their shared genes correspond
accurately to phylogenies based on state-of-the-art analysis of their
whole-genome sequences. We use ANI to evaluate the phylogenetic
robustness of every gene in the genome and show that almost all core
genes, regardless of their functions and positions in the genome, offer
robust phylogenetic reconstruction among strains that show 80 to 95%
ANI (16S rRNA identity, >98.5%). Lack of elapsed time and, to a
lesser extent, horizontal transfer and recombination make the selection
of genes more critical for applications that target the intraspecies
level, i.e., strains that show >95% ANI according to current
standards. A much more accurate phylogeny for the
Escherichia
coli
group was obtained based on just three best-performing genes
according to our analysis compared to the concatenated alignment of
eight genes that are commonly employed for phylogenetic purposes in
this group. Our results are reproducible within the
Salmonella
,
Burkholderia
, and
Shewanella
groups and therefore are expected to have general applicability for
microevolution studies, including metagenomic
surveys.
Application of Pseudomurein Endoisopeptidase to Fluorescence In Situ Hybridization of Methanogens within the Family
Methanobacteriaceae
Authors: Nakamura Kohei , Terada Takeshi , Sekiguchi Yuji , Shinzato Naoya , Meng Xian-Ying , Enoki Miho , Kamagata Yoichi 
Published: November 2006

ABSTRACT

In situ detection of methanogens within the family
Methanobacteriaceae
is sometimes known to be unsuccessful due to the difficulty in permeability of oligonucleotide probes. Pseudomurein endoisopeptidase (Pei), a lytic enzyme that specifically acts on their cell walls, was applied prior to 16S rRNA-targeting fluorescence in situ hybridization (FISH). For this purpose, pure cultured methanogens within this family,
Methanobacterium bryantii
,
Methanobrevibacter ruminantium
,
Methanosphaera stadtmanae
, and
Methanothermobacter thermautotrophicus
together with a
Methanothermobacter thermautotrophicus
-containing syntrophic acetate-oxidizing coculture, endosymbiotic
Methanobrevibacter
methanogens within an anaerobic ciliate, and an upflow anaerobic sludge blanket (UASB) granule were examined. Even without the Pei treatment,
Methanobacterium bryantii
and
Methanothermobacter thermautotrophicus
cells are relatively well hybridized with oligonucleotide probes. However, almost none of the cells of
Methanobrevibacter ruminantium
,
Methanosphaera stadtmanae
, cocultured
Methanothermobacter thermautotrophicus
, and the endosymbiotic methanogens and the cells within UASB granule were hybridized. Pei treatment was able to increase the probe hybridization ratio in every specimen, particularly in the specimen that had shown little hybridization. Interestingly, the hybridizing signal intensity of
Methanothermobacter thermautotrophicus
cells in coculture with an acetate-oxidizing H
2
-producing syntroph was significantly improved by Pei pretreatment, whereas the probe was well hybridized with the cells of pure culture of the same strain. We found that the difference is attributed to the differences in cell wall thicknesses between the two culture conditions. These results indicate that Pei treatment is effective for FISH analysis of methanogens that show impermeability to the probe.
Complete Nucleotide Sequence of an Exogenously Isolated Plasmid, pLB1, Involved in γ-Hexachlorocyclohexane Degradation
Authors: Miyazaki Ryo , Sato Yukari , Ito Michihiro , Ohtsubo Yoshiyuki , Nagata Yuji , Tsuda Masataka 
Published: November 2006

ABSTRACTThe α-proteobacterial strainSphingobium japonicumUT26 utilizes a highly chlorinated pesticide, γ-hexachlorocyclohexane (γ-HCH), as a sole source of carbon and energy, and haloalkane dehalogenase LinB catalyzes the second step of γ-HCH degradation in UT26. Functional complementation of alinBmutant of UT26, UT26DB, was performed by the exogenous plasmid isolation technique using HCH-contaminated soil, leading to our successful identification of a plasmid, pLB1, carrying thelinBgene. Complete sequencing analysis of pLB1, with a size of 65,998 bp, revealed that it carries (i) 50 totally annotated coding sequences, (ii) an IS6100composite transposon containing two copies oflinB, and (iii) potential genes for replication, maintenance, and conjugative transfer with low levels of similarity to other homologues. A minireplicon assay demonstrated that a 2-kb region containing the predictedrepAgene and its upstream region of pLB1 functions as an autonomously replicating unit in UT26. Furthermore, pLB1 was conjugally transferred from UT26DB to other α-proteobacterial strains but not to any of the β- or γ-proteobacterial strains examined to date. These results suggest that this exogenously isolated novel plasmid contributes to the dissemination of at least some genes for γ-HCH degradation in the natural environment. To the best of our knowledge, this is the first detailed report of a plasmid involved in γ-HCH degradation.
Survival of
Wolbachia pipientis
in Cell-Free Medium
Authors: Rasgon Jason L. , Gamston Courtney E. , Ren Xiaoxia 
Published: November 2006

ABSTRACT

Wolbachia pipientis
is an obligate intracellular bacterium found in a wide range of invertebrate taxa. While over ecological timescales
Wolbachia
infections are maintained by strict maternal inheritance, horizontal transfer events are common over evolutionary time. To be horizontally transferred between organisms,
Wolbachia
bacteria must pass through and survive an extracellular phase. We used BacLight live-dead staining, PCR, and fluorescence in situ hybridization to assess the ability for purified
Wolbachia
bacteria to survive in cell-free media. We found that purified
Wolbachia
bacteria were able to survive extracellularly for up to 1 week with no decrease in viability. While no replication was observed in the extracellular phase, purified
Wolbachia
bacteria were able to reinvade cells and establish stable infections at all time points. The ability of
Wolbachia
bacteria to survive outside host cells may increase the probability of successful horizontal transfer and the exploitation of new ecological niches. Our development of methods to purify and maintain viable
Wolbachia
bacteria from cultured cells will be useful for other researchers studying
Wolbachia
biology.
Use of a Multiple Restriction Fragment Length Polymorphism Method for Detecting Vaccine-Derived Polioviruses in Clinical Samples
Authors: Romanenkova Natalia I. , Guillot Sophie , Rozaeva Nadejda R. , Crainic Radu , Bichurina Maina A. , Delpeyroux Francis 
Published: November 2006

ABSTRACT
Since the announcement of the WHO program for the global eradication of poliomyelitis and the establishment of epidemiological and virological surveillance, the emergence and circulation of pathogenic vaccine-derived polioviruses (VDPV) presenting >1% nucleotide divergence from the sequence of the original vaccine strain have been demonstrated in certain regions. We developed and used a multiple restriction fragment length polymorphism (RFLP) method to investigate the frequency of these VDPV in a population with a high level of oral poliovirus vaccine coverage in northwestern Russia. Modified RFLP profiles were found to be strongly correlated with the presence of mutations and recombination events in vaccine strains. We found that a substantial proportion of vaccine strains had high percentages of nucleotide substitutions (>0.5%), including a type 3 VDPV with 1.4% nucleotide divergence. These findings indicate that VDPV or pre-VDPV strains are not rare in certain populations with high levels of vaccine coverage. The multiple RFLP method appears to be a simple and rapid tool for monitoring such strains, which could jeopardize the benefits of the eradication program.
Molecular Epidemiology of Hospital-Acquired Vancomycin-Resistant Enterococci
Authors: Abele-Horn Marianne , Vogel Ulrich , Klare Ingo , Konstabel Carola , Trabold Rene , Kurihara Risa , Witte Wolfgang , Kreth Wolfgang , Schlegel Paul-Gerhardt , Claus Heike 
Published: November 2006

ABSTRACT

Vancomycin-resistant
Enterococcus faecium
strains are a significant cause of nosocomial infections in predisposed patients. Multiple-locus variable-number tandem repeat analysis (MLVA) has been validated recently by use of a global strain collection. In this report, we applied MLVA together with multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) to type 14 isolates from three clusters of patients colonized or infected with vancomycin-resistant
Enterococcus faecium
and another 10 epidemiologically unrelated isolates from the same hospital. The clusters could be distinguished by all three typing methods, which proved to be concordant. PFGE patterns provided the highest resolution. We observed seven sequence types (ST), six MLVA types (MT), and nine distinct ST/MT combinations. The combination of MLST and MLVA may be an alternative to PFGE in hospital epidemiology, providing the benefits of high accuracy, reproducibility, and portability.
Genotyping of Varicella-Zoster Virus and the Discrimination of Oka Vaccine Strains by TaqMan Real-Time PCR
Authors: Parker S. P. , Quinlivan M. , Taha Y. , Breuer J. 
Published: November 2006

ABSTRACT

Single nucleotide polymorphisms (SNPs) in five genes have been used to identify four major subtypes of wild-type varicella-zoster virus (VZV) A, B, C, and J. Additional SNPs, located in the IE62 major transactivating gene can be used to differentiate the Oka vaccine strain (vOka) from wild-type VZV. Primer-probe sets for the detection of the five polymorphic loci were designed by Applied Biosystems for the ABI 7900HT platform. Probes for each allele were labeled with VIC or 6-carboxyfluorescein fluorogenic markers. Each primer-probe set was validated to establish assay sensitivity and specificity using VZV DNA of predetermined copy number and genotype. Further evaluation was carried out using DNA samples from the vesicle fluid or skin swab of the rash of adult patients with herpes zoster or rashes due to vOka. Assay sensitivity ranged from 10 and 10
8
copies/ml of VZV DNA (equivalent to 2 to 20 copies per reaction). Statistical analyses showed that for each genotype, a set of two probes clearly differentiated the nucleotide present (allele) at that locus (
P
< 0.0001). It was possible to determine the genotype of wild-type VZV using one of four SNP assays and also to differentiate wild type from vOka using a single SNP assay. The assay can be used for diagnostic and epidemiological studies of VZV, including the differentiation of vOka from wild-type strains, investigation of breakthrough infections, and varicella outbreaks following immunization.
Usefulness of Adult Bovine Serum for
Helicobacter pylori
Culture Media
Authors: Shibayama Keigo , Nagasawa Mitsuaki , Ando Takafumi , Minami Masaaki , Wachino Jun-ichi , Suzuki Satowa , Arakawa Yoshichika 
Published: November 2006

ABSTRACT

Fetal bovine serum (FBS) and adult bovine serum (BS) exhibited bactericidal activity against
Helicobacter pylori
at various levels, which were higher in BS than in FBS. The bactericidal activity was inactivated by heat treatment at 56°C for 30 min. Our results demonstrated that heat-treated BS is a useful serum source of
H. pylori
culture medium.
Lymphogranuloma Venereum Prevalence in Sweden among Men Who Have Sex with Men and Characterization ofChlamydia trachomatis ompAGenotypes
Authors: Klint Markus , Löfdahl Margareta , Ek Carolina , Airell Åsa , Berglund Torsten , Herrmann Björn 
Published: November 2006

ABSTRACTAn outbreak of lymphogranuloma venereum (LGV) infections has recently been reported from The Netherlands and other European countries. The Swedish surveillance system has identified three LGV cases since 2004, all with clinically suspected infection in men who have sex with men (MSM). In order to assess the prevalence of LGV in a high-risk group of MSM and include clinically atypical cases, retrospective analysis of 197Chlamydia trachomatis-infected men was performed. Sequencing of theompAgene showed a different serotype distribution compared to recent Swedish studies in heterosexual populations. The most common types were G (45%), D (27%), and J (26%), whereas the normally predominant type E accounted for only 4% of the chlamydia cases. Furthermore, certainompAgenotype variants of the dominant serotypes were highly prevalent among MSM, and the reason for this is discussed. No additional case of LGV was detected by retrospective analysis of the high-risk MSM population. This indicates that, thus far, LGV in Sweden is only a result of sporadic import from infected MSM clusters abroad.
Fatal Granulomatous
Acanthamoeba
Encephalitis Mimicking a Stroke, Diagnosed by Correlation of Results of Sequential Magnetic Resonance Imaging, Biopsy, In Vitro Culture, Immunofluorescence Analysis, and Molecular Analysis
Authors: McKellar Mehri S. , Mehta Lahar R. , Greenlee John E. , Hale Devon C. , Booton Gregory C. , Kelly Daryl J. , Fuerst Paul A. , Sriram Rama , Visvesvara Govinda S. 
Published: November 2006

ABSTRACT
Amebic infections involving the central nervous system are rare and difficult to diagnose. Magnetic resonance imaging (MRI) at timed intervals may be helpful, where scans reveal enhancing lesions and increased signal. We report a unique case of granulomatous amebic encephalitis that was proven pathologically with progressive radiological findings on MRI.