bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly Divergent Genes for Methanopterin-Linked C
1
Transfer Reactions in Lake Washington, Assessed via Metagenomic Analysis and mRNA Detection
Authors: Kalyuzhnaya Marina G. , Bowerman Sarah , Nercessian Olivier , Lidstrom Mary E. , Chistoserdova Ludmila 
Published: December 2005

ABSTRACT

The origins and the evolutionary history of tetrahydromethanopterin-linked C
1
transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. In previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated
Proteobacteria
,
Planctomycetes
, or
Archaea
(M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova, Microb. Ecol. 48:463-472, 2004; M. G. Kalyuzhnaya, O. Nercessian, M. E. Lidstrom, and L. Chistoserdova, Environ. Microbiol. 7:1269-1274, 2005). Here we used a metagenomic approach to demonstrate that these divergent genes are present with high abundance in the microbial community inhabiting Lake Washington sediment. We also gained preliminary insights into the genomic composition of the organisms possessing these genes by sequencing genomic fragments from three uncultured microbes possessing the genes of interest. Phylogenetic analyses suggested that, although distantly related to each other, these organisms deeply diverge from known
Bacteria
and
Archaea
, with more relation to the former, suggesting their affiliation with a new bacterial phylum. We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling.
Comparison of Genome Sequences of Single-Stranded RNA Viruses Infecting the Bivalve-Killing Dinoflagellate
Heterocapsa circularisquama
Authors: Nagasaki Keizo , Shirai Yoko , Takao Yoshitake , Mizumoto Hiroyuki , Nishida Kensho , Tomaru Yuji 
Published: December 2005

ABSTRACT

Heterocapsa circularisquama
RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.
Cooccurrence of Aerobic and Anaerobic Methane Oxidation in the Water Column of Lake Plußsee
Authors: Eller Gundula , Känel Layla , Krüger Martin 
Published: December 2005

ABSTRACT

Dissolved methane was investigated in the water column of eutrophic Lake Plußsee and compared to temperature, oxygen, and sulfide profiles. Methane concentrations and δ-
13
C signatures indicated a zone of aerobic methane oxidation and additionally a zone of anaerobic methane oxidation in the anoxic water body. The latter coincided with a peak in hydrogen sulfide concentration. High cell numbers of aerobic and anaerobic methane-oxidizing microorganisms were detected by fluorescence in situ hybridization (FISH) or the more sensitive catalyst-amplified reporter deposition-FISH, respectively, in these layers.
Two Tsetse Fly Species,
Glossina palpalis gambiensis
and
Glossina morsitans morsitans
, Carry Genetically Distinct Populations of the Secondary Symbiont
Sodalis glossinidius
Authors: Geiger Anne , Cuny Gérard , Frutos Roger 
Published: December 2005

ABSTRACT

Genetic diversity among
Sodalis glossinidius
populations was investigated using amplified fragment length polymorphism markers. Strains collected from
Glossina palpalis gambiensis
and
Glossina morsitans morsitans
flies group into separate clusters, being differentially structured. This differential structuring may reflect different host-related selection pressures and may be related to the different vector competences of
Glossina
spp.
An Aflatoxin Biosynthesis Cluster Gene Encodes a Novel Oxidase Required for Conversion of Versicolorin A to Sterigmatocystin
Authors: Ehrlich Kenneth C. , Montalbano Beverly , Boué Stephen M. , Bhatnagar Deepak 
Published: December 2005

ABSTRACT

Disruption of the aflatoxin biosynthesis cluster gene
aflY
(
hypA
) gave
Aspergillus parasiticus
transformants that accumulated versicolorin A. This gene is predicted to encode the Baeyer-Villiger oxidase necessary for formation of the xanthone ring of the aflatoxin precursor demethylsterigmatocystin.
Phage Tail-Like (High-Molecular-Weight) Bacteriocins of
Budvicia aquatica
and
Pragia fontium
(
Enterobacteriaceae
)
Authors: Šmarda Jan , Benada Oldřich 
Published: December 2005

ABSTRACT

Electron microscopic analysis of contractile phage tail-like bacteriocins of three
Pragia fontium
strains and one
Budvicia aquatica
strain was performed. Fonticin and aquaticin are remarkably heat sensitive but trypsin resistant. Simultaneous production of contractile and flexible phage tail-like bacteriocins in the
P. fontium
64613 strain is shown for the first time.
Genetic Characterization of the
Bifidobacterium breve
UCC 2003
hrcA
Locus
Authors: Ventura Marco , Canchaya Carlos , Bernini Valentina , Del Casale Antonio , Dellaglio Franco , Neviani Erasmo , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: December 2005

ABSTRACT

The bacterial heat shock response is characterized by the elevated expression of a number of chaperone complexes and transcriptional regulators, including the DnaJ and the HrcA proteins. Genome analysis of
Bifidobacterium breve
UCC 2003 revealed a second copy of a
dnaJ
gene, named
dnaJ
2
, which is flanked by the
hrcA
gene in a genetic constellation that appears to be unique to the actinobacteria. Phylogenetic analysis using 53 bacterial
dnaJ
sequences, including both
dnaJ
1
and
dnaJ
2
sequences, suggests that these genes have followed a different evolutionary development. Furthermore, the
B. breve
UCC 2003
dnaJ
2
gene seems to be regulated in a manner that is different from that of the previously characterized
dnaJ
1
gene. The
dnaJ
2
gene, which was shown to be part of a 2.3-kb bicistronic operon with
hrcA
, was induced by osmotic shock but not significantly by heat stress. This induction pattern is unlike those of other characterized
dnaJ
genes and may be indicative of a unique stress adaptation strategy by this commensal microorganism.
A Novel Real-Time PCR for
Listeria monocytogenes
That Monitors Analytical Performance via an Internal Amplification Control
Authors: Rodríguez-Lázaro David , Pla Maria , Scortti Mariela , Monzó Héctor J. , Vázquez-Boland José A. 
Published: December 2005

ABSTRACT

We describe a novel quantitative real-time (Q)-PCR assay for
Listeria monocytogenes
based on the coamplification of a target
hly
gene fragment and an internal amplification control (IAC). The IAC is a chimeric double-stranded DNA containing a fragment of the rapeseed
BnACCg8
gene flanked by the
hly
-specific target sequences. This IAC is detected using a second TaqMan probe labeled with a different fluorophore, enabling the simultaneous monitoring of the
hly
and IAC signals. The
hly
-IAC assay had a specificity and sensitivity of 100%, as assessed using 49
L. monocytogenes
isolates of different serotypes and 96 strains of nontarget bacteria, including 51
Listeria
isolates. The detection and quantification limits were 8 and 30 genome equivalents, and the coefficients for PCR linearity (
R
2
) and efficiency (
E
) were 0.997 and 0.80, respectively. We tested the performance of the
hly
-IAC Q-PCR assay using various broth media and food matrices. Fraser and half-Fraser media, raw pork, and raw or cold-smoked salmon were strongly PCR-inhibitory. This Q-PCR assay for
L. monocytogenes
, the first incorporating an IAC to be described for quantitative detection of a food-borne pathogen, is a simple and robust tool facilitating the identification of false negatives or underestimations of contamination loads due to PCR failure.
Clonal Nature of
Campylobacter fetus
as Defined by Multilocus Sequence Typing
Authors: van Bergen Marcel A. P. , Dingle Kate E. , Maiden Martin C. J. , Newell Diane G. , van der Graaf-Van Bloois Linda , van Putten Jos P. M. , Wagenaar Jaap A. 
Published: December 2005

ABSTRACT

Campylobacter
fetus
can be divided into the subspecies
C. fetus
subsp.
fetus
and
C. fetus
subsp.
venerealis. C. fetus
subsp.
fetus
causes
sporadic infections in humans and abortion in cattle and sheep and has
been isolated from a variety of sites in different hosts.
C.
fetus
subsp.
venerealis
is host restricted, being
isolated mainly from the genital tracts of cattle, and is the causative
agent of bovine genital campylobacteriosis. Despite differences in
niche preference, microbiological subspecies differentiation has proven
difficult. Different typing methods divided
C. fetus
isolates
into different subgroups, depending on the methods used. The relative
value of these methods can be assessed by the evolutionary relationship
of isolates belonging to the genus; therefore, we developed a
multilocus sequence typing (MLST) scheme for
C. fetus
. This
scheme was applied to 140
C. fetus
isolates previously typed
by amplified fragment length polymorphism (AFLP) analysis. A total of
14 different sequence types (STs) were identified, and these exhibited
low levels of inter-ST genetic diversity, with only 22 variable sites
in 3,312 nucleotides. These MLST data indicate that
C. fetus
is genetically homogeneous compared to the homogeneity of other
Campylobacter
species. The two
C. fetus
subspecies
were extremely closely related genetically, but ST-4 was associated
only with
C. fetus
subsp.
venerealis
, which
represents a “bovine” clone. The
C. fetus
subsp.
fetus
isolates studied were more diverse in terms of
their STs, and the STs correlated with epidemiological relationships.
Congruence was observed among
C. fetus
subspecies,
sap
type, and ST; therefore, MLST confirms that mammalian
C. fetus
is genetically stable, probably as result of the
introduction of a single ancestral clone into a mammalian
niche.
Molecular Characterization of
Theileria
Species Associated with Mortality in Four Species of African Antelopes
Authors: Nijhof A. M. , Pillay V. , Steyl J. , Prozesky L. , Stoltsz W. H. , Lawrence J. A. , Penzhorn B. L. , Jongejan F. 
Published: December 2005

ABSTRACT

Pathogen DNA was isolated from roan antelope (
Hippotragus equinus
), sable antelope (
Hippotragus niger
), greater kudu (
Tragelaphus strepsiceros
), and common gray duiker (
Sylvicapra grimmia
) in South Africa whose deaths were attributed to either theileriosis or cytauxzoonosis. We developed
Theileria
species-specific probes used in combination with reverse line blot hybridization assays and identified three different species of
Theileria
in four African antelope species. The close phylogenetic relationship between members of the genera
Theileria
and
Cytauxzoon
, similarities in the morphologies of developmental stages, and confusion in the literature regarding theileriosis or cytauxzoonosis are discussed.
Use of Denaturing High-Performance Liquid Chromatography for Rapid Detection and Identification of Seven
Candida
Species
Authors: Goldenberg Oliver , Herrmann Stefanie , Adam Thomas , Marjoram Gina , Hong George , Göbel Ulf B. , Graf Barbara 
Published: December 2005

ABSTRACT

A novel denaturing high-performance liquid chromatography (DHPLC)-based technique allows rapid high-resolution analysis of PCR products. We used this technique for unequivocal molecular identification of seven
Candida
species. We show the application of this PCR/DHPLC approach for direct detection and identification of yeast species from blood cultures and for detection of
Candida
colonization in the gastrointestinal tract of allogeneic transplant patients.
Polyphasic Characterization Reveals that the Human Pathogen
Mycobacterium peregrinum
Type II Belongs to the Bovine Pathogen Species
Mycobacterium senegalense
Authors: Wallace Richard J. , Brown-Elliott Barbara A. , Brown June , Steigerwalt Arnold G. , Hall Leslie , Woods Gail , Cloud Joann , Mann Linda , Wilson Rebecca , Crist Christopher , Jost Kenneth C. , Byrer Dorothy E. , Tang Jane , Cooper Jason , Stamenova Elena , Campbell Brian , Wolfe Joyce , Turenne Christine 
Published: December 2005

ABSTRACT

Mycobacterium peregrinum
consists of two taxa: types I and II. We evaluated 43 clinical type II strains from throughout the United States. They were responsible for soft-tissue and bone infections, catheter-related infections, and possible pneumonitis. By carbohydrate utilization, they were indistinguishable from type I strains, being
d
-mannitol and trehalose positive. However, they had a distinct susceptibility pattern that included intermediate ciprofloxacin MICs but low clarithromycin and doxycycline MICs of ≤1 μg/ml. These features were also shared by reference isolates of
Mycobacterium senegalense
from African bovine cases of “farcy.” By 16S rRNA gene sequencing, the type II isolates shared 100% sequence identity with
M. senegalense
. Partial sequencing of the type II
hsp65
gene (441 bp) revealed four sequevars showing ≥98.4% identity with each other and ≥98.6% identity with the sequence of five bovine strains of
M. senegalense
. There was ≤97.1% identity with
M. peregrinum
type I isolates and other
Mycobacterium fortuitum
group species. Sequencing of additional gene targets including the 16S-23S rDNA internal transcribed spacer region and the
rpoB
gene (partial sequence) revealed a similar phylogenetic grouping. DNA-DNA hybridization showed 76 to 99% relatedness between the bovine and human strains. These studies demonstrate that type II isolates are not isolates of
M. peregrinum
but represent human strains of
M. senegalense
. This study is the first to demonstrate this species as a human pathogen. Representative human
M. senegalense
strains include ATCC 35755 and newly submitted strains ATCC BAA-849, ATCC BAA-850, and ATCC BAA-851.
Diagnostic Accuracy of Two rK39 Antigen-Based Dipsticks and the Formol Gel Test for Rapid Diagnosis of Visceral Leishmaniasis in Northeastern Uganda
Authors: Chappuis François , Mueller Yolanda , Nguimfack Alexandre , Rwakimari John Bosco , Couffignal Sophie , Boelaert Marleen , Cavailler Philippe , Loutan Louis , Piola Patrice 
Published: December 2005

ABSTRACT
The development of an accurate, practical, and affordable diagnostic test is essential to improve the management of visceral leishmaniasis (VL) in remote health centers. We evaluated the Formol Gel test (FGT) and two rK39 antigen-based dipsticks, the DUAL-IT L/M, and the Kalazar Detect for VL diagnosis in Amudat Hospital in Uganda. The DUAL-IT L/M was also evaluated for the diagnosis of malaria. All patients clinically suspect of VL were prospectively included in the study between October 2003 and March 2004. The gold standard used to define a VL case was a positive spleen aspirate or a direct agglutination test titer of >1:12,800 with an appropriate clinical response to antileishmanial therapy. A total of 131 VL and 112 non-VL patients were included in the analysis. The DUAL IT L/M was found to be more sensitive than the Kalazar Detect: 97% (95% confidence interval [95%CI] = 92 to 99%) versus 82% (95%CI = 74 to 87%). The Kalazar Detect and the DUAL IT L/M were highly specific (99% [95%CI = 95 to 100%] and 97% [95%CI = 92 to 99%], respectively). The FGT lacked both sensitivity (66% [95%CI = 57 to 73%]) and specificity (90% [95%CI = 83 to 94%]). The sensitivity of the DUAL IT L/M for malaria was only 57% (95%CI = 37 to 76%). The two rK39 dipsticks can be used for diagnostic confirmation of VL in this region. The DUAL-IT L/M without its malaria diagnostic component (DiaMed-IT LEISH) will be adopted as first-line test for VL in Uganda.
Mistaken Identity:
Neosartorya pseudofischeri
and Its Anamorph Masquerading as
Aspergillus fumigatus
Authors: Balajee S. Arunmozhi , Gribskov Jennifer , Brandt Mary , Ito James , Fothergill Annette , Marr Kieren A. 
Published: December 2005

ABSTRACT

Invasive fungal infections caused by
Neosartorya pseudofischeri
S. W. Peterson [anamorph
Aspergillus thermomutatus
(Paden) S. W. Peterson] are extremely rare. Phenotypically, the anamorphic state of
N. pseudofischeri
resembles
Aspergillus fumigatus
, the predominant agent of invasive aspergillosis in immunocompromised hosts. We report the recovery of three clinical isolates of
N. pseudofischeri
, all initially misidentified by morphological characteristics as
A. fumigatus
. All three isolates were correctly identified by sequencing portions of the β-tubulin and the rodlet A genes. Only one of the three isolates produced the confirmatory fruiting bodies and was thus classified as
N. pseudofischeri
; the other isolates did not produce asci and were therefore identified as
A. thermomutatus
. All three isolates had higher MICs to voriconazole in vitro compared to
A. fumigatus
Af293. This report emphasizes that phenotypic identification of filamentous fungi may not identify morphologically similar, but genetically distinct, members of the genus
Aspergillus
section
Fumigati
. Accurate identification of these organisms may be clinically meaningful, given their potential differences in antifungal susceptibilities.
Isolation of Nontuberculous Mycobacteria in Zambia: Eight Case Reports
Authors: Buijtels Patricia C. A. M. , Petit Pieter L. C. , Verbrugh Henri A. , van Belkum Alex , van Soolingen Dick 
Published: December 2005

ABSTRACT

The isolation of nontuberculous mycobacteria (NTM) raises the question of their clinical significance, especially in an African setting. We found a high percentage of NTM isolated from various specimens, including ones that are normally sterile, among 213 patients in Zambia. Because tuberculosis can affect all parts of the body, we decided to include patients who had signs and symptoms in any part of the body for more than 2 weeks. Most patients had tractus respiratorius (80%) and tractus digestivus (10%) symptoms. During three consecutive days, sputum was collected and two separate sputum specimens were cultured for mycobacteria. Depending on the clinical picture, pleural effusion, ascites, abscess material, or enlarged lymph nodes were also cultured for mycobacteria. A specimen from one sterile body site was collected from 25 patients (60% human immunodeficiency virus [HIV] positive). NTM were isolated from 8 of these 25 specimens.
Mycobacterium lentiflavum
was isolated from four patients, and
Mycobacterium goodii
was isolated from one patient. In order to exclude the possibility of laboratory cross-contamination, a novel amplified fragment length polymorphism DNA typing method for
M. lentiflavum
was developed. Genetic variation was detected, rendering the likelihood of laboratory contamination unlikely. Clinically relevant infection due to NTM occurs in both HIV-positive and HIV-negative patients in Zambia, and their clinical impact seems to be underestimated. This is the first report of
M. lentiflavum
and
M. goodii
infections in Africa.
Presence of
Rickettsia conorii
subsp.
israelensis
, the Causative Agent of Israeli Spotted Fever, in Sicily, Italy, Ascertained in a Retrospective Study
Authors: Giammanco Giovanni M. , Vitale Giustina , Mansueto Serafino , Capra Giuseppina , Caleca Maria Pia , Ammatuna Pietro 
Published: December 2005

ABSTRACT

A retrospective analysis by molecular-sequence-based techniques was performed to correctly identify the etiological agent of 24 Mediterranean spotted fever cases occurring in Western Sicily, Italy, from 1987 to 2001. Restriction analysis of a 632-bp PCR-amplified portion of the
ompA
gene allowed presumptive identification of five clinical isolates as belonging to
Rickettsia conorii
subsp.
israelensis
, the etiological agent of Israeli spotted fever (ISF). The remaining 19 rickettsial isolates were
Rickettsia conorii
subsp.
conorii
, the only pathogenic rickettsia of the spotted fever group reported in Italy until the present. Sequence analysis of the
ompA
gene confirmed the identification of all the
R. conorii
subsp.
israelensis
isolates and demonstrated that rickettsiosis caused by
R. conorii
subsp.
israelensis
can be traced back to 1991 in Sicily. The recorded clinical data of the five ISF patients support the idea that these strains could correlate to more-severe forms of human disease. Three of five patients experienced severe disease, and one of them died.
Recognition of SCC
mec
Types According to Typing Pattern Determined by Multienzyme Multiplex PCR-Amplified Fragment Length Polymorphism Analysis of Methicillin-Resistant
Staphylococcus aureus
Authors: van der Zee Anneke , Heck Max , Sterks Marcel , Harpal Airien , Spalburg Emile , Kazobagora Leonard , Wannet Wim 
Published: December 2005

ABSTRACT

Multienzyme multiplex PCR-amplified fragment length polymorphism (ME-AFLP) typing is a reliable and simple method for typing of bacterial species. In this study we analyzed two well-documented strain collections of
Staphylococcus aureus
and compared ME-AFLP typing results with results of various other typing methods. The discriminatory power of ME-AFLP was found comparable to pulsed-field gel electrophoresis, and typing results were highly concordant. ME-AFLP typing presents a suitable method for prescreening of large strain collections. Furthermore, the obtained typing patterns were found to cluster according to the staphylococcal cassette chromosome mec types of the strains.