bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and Spectral Features of Selenium Nanospheres Produced by Se-Respiring Bacteria
Authors: Oremland Ronald S. , Herbel Mitchell J. , Blum Jodi Switzer , Langley Sean , Beveridge Terry J. , Ajayan Pulickel M. , Sutto Thomas , Ellis Amanda V. , Curran Seamus 
Published: January 2004

ABSTRACTCertain anaerobic bacteria respire toxic selenium oxyanions and in doing so produce extracellular accumulations of elemental selenium [Se(0)]. We examined three physiologically and phylogenetically diverse species of selenate- and selenite-respiring bacteria,Sulfurospirillum barnesii,Bacillus selenitireducens, andSelenihalanaerobacter shriftii, for the occurrence of this phenomenon. When grown with selenium oxyanions as the electron acceptor, all of these organisms formed extracellular granules consisting of stable, uniform nanospheres (diameter, ∼300 nm) of Se(0) having monoclinic crystalline structures. Intracellular packets of Se(0) were also noted. The number of intracellular Se(0) packets could be reduced by first growing cells with nitrate as the electron acceptor and then adding selenite ions to washed suspensions of the nitrate-grown cells. This resulted in the formation of primarily extracellular Se nanospheres. After harvesting and cleansing of cellular debris, we observed large differences in the optical properties (UV-visible absorption and Raman spectra) of purified extracellular nanospheres produced in this manner by the three different bacterial species. The spectral properties in turn differed substantially from those of amorphous Se(0) formed by chemical oxidation of H2Se and of black, vitreous Se(0) formed chemically by reduction of selenite with ascorbate. The microbial synthesis of Se(0) nanospheres results in unique, complex, compacted nanostructural arrangements of Se atoms. These arrangements probably reflect a diversity of enzymes involved in the dissimilatory reduction that are subtly different in different microbes. Remarkably, these conditions cannot be achieved by current methods of chemical synthesis.
Rapid Detection of
Escherichia coli
O157:H7 by Using Green Fluorescent Protein-Labeled PP01 Bacteriophage
Authors: Oda Masahito , Morita Masatomo , Unno Hajime , Tanji Yasunori 
Published: January 2004

ABSTRACT

A previously isolated T-even-type PP01 bacteriophage was used to detect its host cell,
Escherichia coli
O157:H7. The phage small outer capsid (SOC) protein was used as a platform to present a marker protein, green fluorescent protein (GFP), on the phage capsid. The DNA fragment around
soc
was amplified by PCR and sequenced. The gene alignment of
soc
and its upstream region was
g56-soc.2-soc.1-soc
, which is the same as that for T2 phage. GFP was introduced into the C- and N-terminal regions of SOC to produce recombinant phages PP01-GFP/SOC and PP01-SOC/GFP, respectively. Fusion of GFP to SOC did not change the host range of PP01. On the contrary, the binding affinity of the recombinant phages to the host cell increased. However, the stability of the recombinant phages in alkaline solution decreased. Adsorption of the GFP-labeled PP01 phages to the
E. coli
cell surface enabled visualization of cells under a fluorescence microscope. GFP-labeled PP01 phage was not only adsorbed on culturable
E. coli
cells but also on viable but nonculturable or pasteurized cells. The coexistence of insensitive
E. coli
K-12 (W3110) cells did not influence the specificity and affinity of GFP-labeled PP01 adsorption on
E. coli
O157:H7. After a 10-min incubation with GFP-labeled PP01 phage at a multiplicity of infection of 1,000 at 4°C,
E. coli
O157:H7 cells could be visualized by fluorescence microscopy. The GFP-labeled PP01 phage could be a rapid and sensitive tool for
E. coli
O157:H7 detection.
Bradyrhizobium elkanii rtxC
Gene Is Required for Expression of Symbiotic Phenotypes in the Final Step of Rhizobitoxine Biosynthesis
Authors: Okazaki Shin , Sugawara Masayuki , Minamisawa Kiwamu 
Published: January 2004

ABSTRACT

We disrupted the
rtxC
gene on the chromosome of
Bradyrhizobium elkanii
USDA94 by insertion of a nonpolar
aph
cartridge. The
rtxC
mutant, designated Δ
rtxC
, produced serinol and dihydrorhizobitoxine but no rhizobitoxine, both in culture and in planta. The introduction of cosmids harboring the
rtxC
gene into the Δ
rtxC
mutant complemented rhizobitoxine production, suggesting that
rtxC
is involved in the final step of rhizobitoxine biosynthesis in
B. elkanii
USDA94.
Glycine max
cv. Lee inoculated with Δ
rtxC
or with a null mutant, Δ
rtx
::Ω1, showed no foliar chlorosis, whereas the wild-type strain USDA94 caused severe foliar chlorosis. The two mutants showed significantly less nodulation competitiveness than the wild-type strain on
Macroptilium atropurpureum
. These results indicate that dihydrorhizobitoxine, the immediate precursor of the oxidative form of rhizobitoxine, has no distinct effect on nodulation phenotype in these legumes. Thus, desaturation of dihydrorhizobitoxine by
rtxC
-encoded protein is essential for the bacterium to show rhizobitoxine phenotypes in planta. In addition, complementation analysis of
rtxC
by cosmids differing in
rtxC
transcription levels suggested that rhizobitoxine production correlates with the amount of
rtxC
transcript.
Role of Two G-Protein Alpha Subunits, TgaA and TgaB, in the Antagonism of Plant Pathogens by
Trichoderma virens
Authors: Mukherjee Prasun K. , Latha Jagannathan , Hadar Ruthi , Horwitz Benjamin A. 
Published: January 2004

ABSTRACT

G-protein α subunits are involved in transmission of signals for development, pathogenicity, and secondary metabolism in plant pathogenic and saprophytic fungi. We cloned two G-protein α subunit genes,
tgaA
and
tgaB
, from the biocontrol fungus
Trichoderma virens. tgaA
belongs to the fungal Gαi class, while
tgaB
belongs to the class defined by
gna-2
of
Neurospora crassa
. We compared loss-of-function mutants of
tgaA
and
tgaB
with the wild type for radial growth, conidiation, germination of conidia, the ability to overgrow colonies of
Rhizoctonia solani
and
Sclerotium rolfsii
in confrontation assays, and the ability to colonize the sclerotia of these pathogens in soil. Both mutants grew as well as the wild type, sporulated normally, did not sporulate in the dark, and responded to blue light by forming a conidial ring. The
tgaA
mutants germinated by straight unbranched germ tubes, while
tgaB
mutants, like the wild type, germinated by wavy and highly branched germ tubes. In confrontation assays, both
tgaA
and
tgaB
mutants and the wild type overgrew, coiled, and lysed the mycelia of
R. solani
, but
tgaA
mutants had reduced ability to colonize
S. rolfsii
colonies. In the soil plate assay, both mutants parasitized the sclerotia of
R. solani
, but
tgaA
mutants were unable to parasitize the sclerotia of
S. rolfsii
. Thus,
tgaA
is involved in antagonism against
S. rolfsii
, but neither G protein subunit is involved in antagonism against
R. solani. T. virens
, which has a wide host range, thus employs a G-protein pathway in a host-specific manner.
Bacterial Activity at −2 to −20°C in Arctic Wintertime Sea Ice
Authors: Junge Karen , Eicken Hajo , Deming Jody W. 
Published: January 2004

ABSTRACT

Arctic wintertime sea-ice cores, characterized by a temperature gradient of −2 to −20°C, were investigated to better understand constraints on bacterial abundance, activity, and diversity at subzero temperatures. With the fluorescent stains 4′,6′-diamidino-2-phenylindole 2HCl (DAPI) (for DNA) and 5-cyano-2,3-ditoyl tetrazolium chloride (CTC) (for O
2
-based respiration), the abundances of total, particle-associated (>3-μm), free-living, and actively respiring bacteria were determined for ice-core samples melted at their in situ temperatures (−2 to −20°C) and at the corresponding salinities of their brine inclusions (38 to 209 ppt). Fluorescence in situ hybridization was applied to determine the proportions of
Bacteria
,
Cytophaga
-
Flavobacteria
-
Bacteroides
(CFB), and
Archaea
. Microtome-prepared ice sections also were examined microscopically under in situ conditions to evaluate bacterial abundance (by DAPI staining) and particle associations within the brine-inclusion network of the ice. For both melted and intact ice sections, more than 50% of cells were found to be associated with particles or surfaces (sediment grains, detritus, and ice-crystal boundaries). CTC-active bacteria (0.5 to 4% of the total) and cells detectable by rRNA probes (18 to 86% of the total) were found in all ice samples, including the coldest (−20°C), where virtually all active cells were particle associated. The percentage of active bacteria associated with particles increased with decreasing temperature, as did the percentages of CFB (16 to 82% of
Bacteria
) and
Archaea
(0.0 to 3.4% of total cells). These results, combined with correlation analyses between bacterial variables and measures of particulate matter in the ice as well as the increase in CFB at lower temperatures, confirm the importance of particle or surface association to bacterial activity at subzero temperatures. Measuring activity down to −20°C adds to the concept that liquid inclusions in frozen environments provide an adequate habitat for active microbial populations on Earth and possibly elsewhere.
Genotypic and Phenotypic Studies of Murine Intestinal Lactobacilli: Species Differences in Mice with and without Colitis
Authors: Peña J. A. , Li S. Y. , Wilson P. H. , Thibodeau S. A. , Szary A. J. , Versalovic J. 
Published: January 2004

ABSTRACT

Lactobacilli represent components of the commensal mammalian gastrointestinal microbiota and are useful as probiotics, functional foods, and dairy products. This study includes systematic polyphasic analyses of murine intestinal
Lactobacillus
isolates and correlation of taxonomic findings with data from cytokine production assays. Lactobacilli were recovered from mice with microbiota-dependent colitis (interleukin-10 [IL-10]-deficient C57BL/6 mice) and from mice without colitis (Swiss Webster and inducible nitric oxide synthetase-deficient C57BL/6 mice). Polyphasic analyses were performed to elucidate taxonomic relationships among 88 reference and murine gastrointestinal lactobacilli. Genotypic tests included single-locus analyses (16S ribosomal DNA sequencing and 16S-23S rRNA intergenic spacer region PCR) and genomic DNA profiling (repetitive DNA element-based PCR), and phenotypic analyses encompassed more than 50 tests for carbohydrate utilization, enzyme production, and antimicrobial resistance. From 20 mice without colitis, six
Lactobacillus
species were recovered; the majority of the mice were colonized with
L. reuteri
or
L. murinus
(72% of isolates). In contrast, only,
L. johnsonii
was isolated from 14 IL-10-deficient mice. Using an in vitro assay, we screened murine isolates for their ability to inhibit tumor necrosis factor alpha (TNF-α) secretion by lipopolysaccharide-activated macrophages. Interestingly, a subpopulation of lactobacilli recovered from mice without colitis displayed TNF-α inhibitory properties, whereas none of the
L. johnsonii
isolates from IL-10-deficient mice exhibited this effect. We propose that differences among intestinal
Lactobacillus
populations in mammals, combined with host genetic susceptibilities, may account partly for variations in host mucosal responses.
Microstructural Characterization of Cyanobacterial Mats from the McMurdo Ice Shelf, Antarctica
Authors: de los Ríos Asunción , Ascaso Carmen , Wierzchos Jacek , Fernández-Valiente Eduardo , Quesada Antonio 
Published: January 2004

ABSTRACT
The three-dimensional structures of two types of cyanobacterium-dominated microbial mats from meltwater ponds on the McMurdo Ice Shelf were as determined by using a broad suite of complementary techniques, including optical and fluorescence microscopy, confocal scanning laser microscopy, scanning electron microscopy with back-scattered electron-imaging mode, low-temperature scanning electron microscopy, and microanalyitical X-ray energy dispersive spectroscopy. By using a combination of the different in situ microscopic techniques, the Antarctic microbial mats were found to be structures with vertical stratification of groups of cyanobacteria and mineral sediments, high contents of extracellular polymeric substances, and large void spaces occupied by water. In cyanobacterium-rich layers, heterocystous nostocalean and nonheterocystous oscillatorialean taxa were the most abundant taxa and appeared to be intermixed with fine-size deposits of epicellular silica and calcium carbonate. Most of the cyanobacterial filaments had similar orientations in zones without sediment particles, but thin filaments were tangled among thicker filaments. The combination of the microscopic techniques used showed the relative positions of biological and mineral entities within the microbial mats and enabled some speculation about their interactions.
Development of Genetic Techniques for the Psychrotrophic Fish Pathogen
Flavobacterium psychrophilum
Authors: Alvarez B. , Secades P. , McBride M. J. , Guijarro J. A. 
Published: January 2004

ABSTRACT

Flavobacterium psychrophilum
, a member of the
Cytophaga-Flavobacterium-Bacteroides
group, is an important pathogen of salmonid fish. Previous attempts to develop genetic techniques for this fastidious, psychrotrophic bacterium have met with failure. Here we describe the development of techniques for the genetic manipulation of
F. psychrophilum
and the identification of plasmids, selectable markers, a reporter system, and a transposon that function in several isolates of this fish pathogen. The antibiotic resistance genes
ermF
,
cfxA
, and
tetQ
function in
F. psychrophilum
. Cloning vectors based on the
F. psychrophilum
cryptic plasmid pCP1 which carried these selectable markers were introduced by conjugation from
E. coli
, resulting in antibiotic-resistant colonies of
F. psychrophilum
. Conjugative transfer of DNA into
F. psychrophilum
was strain dependent. Efficient transfer was observed for two of the seven strains tested (THC02-90 and THC04-90).
E. coli lacZY
functioned in
F. psychrophilum
when expressed from a pCP1 promoter, allowing its development as a reporter for studies of gene expression. Plasmids isolated from
F. psychrophilum
were efficiently introduced into
F. psychrophilum
by electroporation, but plasmids isolated from
E. coli
were not suitable for transfer by this route, suggesting the presence of a restriction barrier. DNA isolated from
F. psychrophilum
was resistant to digestion by
Sau
3AI and
Bam
HI, indicating that a
Sau
3AI-like restriction modification system may constitute part of this barrier. Tn
4351
was introduced into
F. psychrophilum
from
E. coli
and transposed with apparent randomness, resulting in erythromycin-resistant colonies. The techniques developed in this study allow for genetic manipulation and analysis of this important fish pathogen.
Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community
Authors: Ginige Maneesha P. , Hugenholtz Philip , Daims Holger , Wagner Michael , Keller Jürg , Blackall Linda L. 
Published: January 2004

ABSTRACT

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO
3
−
-N mg of mixed-liquor volatile suspended solids (MLVSS)
−1
h
−1
to a steady-state value of 0.06 mg of NO
3
−
-N mg of MLVSS
−1
h
−1
over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [
13
C]methanol to biomark the DNA of the denitrifiers. The extracted [
13
C]DNA and [
12
C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [
13
C]DNA clone library was closely related to those of the obligate methylotrophs
Methylobacillus
and
Methylophilus
in the order
Methylophilales
of the
Betaproteobacteria
(96 to 97% sequence identities), while the most abundant clone groups in the [
12
C]DNA clone library mostly belonged to the family
Saprospiraceae
in the
Bacteroidetes
phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and
Methylophilales
(probes DEN67 and MET1216, respectively) and the
Saprospiraceae
clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera
Hyphomicrobium
and
Paracoccus
or the
Saprospiraceae
clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [
14
C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that
Methylophilales
bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.
Quantum Dots as a Novel Immunofluorescent Detection System for
Cryptosporidium parvum
and
Giardia lamblia
Authors: Zhu Liang , Ang Simon , Liu Wen-Tso 
Published: January 2004

ABSTRACT

Semiconductor quantum dot-conjugated antibodies were successfully developed to label
Cryptosporidium parvum
and
Giardia lamblia
. This novel fluorescence system exhibited superior photostability, gave 1.5- to 9-fold-higher signal-to-noise ratios than traditional organic dyes in detecting
C. parvum
, and allowed dual-color detection for
C. parvum
and
G. lamblia
.
Analysis of the
gyrA
Gene of Clinical
Yersinia ruckeri
Isolates with Reduced Susceptibility to Quinolones
Authors: Gibello Alicia , Porrero M. Concepción , Blanco M. Mar , Vela Ana I. , Liébana Pilar , Moreno Miguel A. , Fernández-Garayzábal José F. , Domínguez Lucas 
Published: January 2004

ABSTRACT

Antimicrobial susceptibility of seven clinical strains of
Yersinia ruckeri
representative of those isolated between 1994 and 2002 from a fish farm with endemic enteric redmouth disease was studied. All isolates displayed indistinguishable pulsed-field gel electrophoresis restriction patterns, indicating that they represented a single strain. However, considering both inhibition zone diameters (IZD) and MICs, the isolates recovered in 2001-2002 formed a separate cluster with lower levels of susceptibility to all the quinolones tested, especially nalidixic acid (NA) and oxolinic acid (OA), compared with the isolates recovered between 1994 and 1998. Analysis of the PCR product of the quinolone resistance-determining region of the
gyr
A gene from clinical isolates of
Y. ruckeri
with reduced susceptibility to OA and NA revealed a single amino acid substitution, Ser-83 to Arg-83 (
Escherichia coli
numbering). Identical substitution was observed in induced OA-resistant mutant strains, which displayed IZD and MICs of quinolones similar to those of the clinical isolates of
Y. ruckeri
with reduced susceptibility to these antimicrobial agents. These data indicate in that for
Y. ruckeri
, the substitution of Ser by Arg at position 83 of the
gyr
A gene is associated with reduced susceptibility to quinolones.
Cloning and Heterologous Expression of Hematin-Dependent Catalase Produced by
Lactobacillus plantarum
CNRZ 1228
Authors: Abriouel Hikmate , Herrmann Anette , Stärke Joachim , Yousif Nuha M. K. , Wijaya Agus , Tauscher Bernhard , Holzapfel Wilhelm , Franz Charles M. A. P. 
Published: January 2004

ABSTRACT

Lactobacillus plantarum
CNRZ 1228 exhibited heme-dependent catalase activity under environmental conditions similar to those encountered during sausage fermentation. The 1,455-bp catalase gene (
katL
) was cloned and encoded a protein of 484 amino acids. Expression of
katL
in a heterologous host showed that
katL
encodes a functional catalase. PCR screening of selected strains of lactic acid bacteria for
katL
indicated the presence of similar genes in other strains of lactobacilli.
A Complete Library of Amino Acid Alterations at N304 in
Streptomyces clavuligerus
Deacetoxycephalosporin C Synthase Elucidates the Basis for Enhanced Penicillin Analogue Conversion
Authors: Chin Hong Soon , Goo Kian Sim , Sim T. S. 
Published: January 2004

ABSTRACT

N304 of
Streptomyces clavuligerus
deacetoxycephalosporin C synthase was mutagenized to alter its catalytic ability. Given that N304A, N304K, N304L, and N304R mutant enzymes exhibited significant improvements in penicillin analogue conversions, we advocate that replacement of N304 with residues with aliphatic or basic side chains is preferable for engineering of a hypercatalytic enzyme.
Localization of the Insertion Site and Pathotype Determination of the Locus of Enterocyte Effacement of Shiga Toxin-Producing
Escherichia coli
Strains
Authors: Bertin Yolande , Boukhors Karima , Livrelli Valerie , Martin Christine 
Published: January 2004

ABSTRACT

Of 220 Shiga toxin-producing
Escherichia coli
(STEC) strains collected in central France from healthy cattle, food samples, and asymptomatic children, 12 possessed the
eae
gene included in the locus of enterocyte effacement (LEE) pathogenicity island. Based on gene typing, we observed 7 different
eae espA espB tir
pathotypes among the 12 STEC strains and described the new
espA
βv variant. As previously observed, the O157 serogroup is associated with
eae
γ, O26 is associated with
eae
β, and O103 is associated with
eae
ε. However, the unexpected
eae
ζ allele was detected in 5 of the 12 isolates. PCR amplification and pulsed-field gel electrophoresis using the I-
Ceu
I endonuclease followed by Southern hybridization indicated that the LEE was inserted in the vicinity of the
selC
(three isolates),
pheU
(two isolates), or
pheV
(six isolates) tRNA gene. Six isolates harbored two or three of these tRNA loci altered by the insertion of integrase genes (CP4-
int
and/or
int-phe
), suggesting the insertion of additional foreign DNA fragments at these sites. In spite of great genetic diversity of LEE pathotypes and LEE insertion sites, bovine strains harbor alleles of LEE genes that are frequently found in clinical STEC strains isolated from outbreaks and sporadic cases around the world, underscoring the potential risk of the bovine strains on human health.
Simple and Reliable Method To Precipitate Proteins from Bacterial Culture Supernatant
Authors: Caldwell Randolph B. , Lattemann Claus T. 
Published: January 2004

ABSTRACT
A simple and reliable method for precipitating protein from bacterial culture supernatants based on a pyrogallol red-molybdate-methanol (PRMM) protocol has been developed and applied for the analysis of proteins secreted by a bacterial type III secretion system. PRMM-based precipitation has been shown to be more efficient and robust than are conventional protocols.
Pet Snakes as a Reservoir for
Salmonella enterica
subsp.
diarizonae
(Serogroup IIIb): a Prospective Study
Authors: Schröter Matthias , Roggentin Peter , Hofmann Jörg , Speicher Angelika , Laufs Rainer , Mack Dietrich 
Published: January 2004

ABSTRACT

Reptile-associated
Salmonella
infections are an increasing problem for humans. We have prospectively screened two breeding groups of 16 pet snakes for colonization with
Salmonella
species. Various serovars of
S. enterica
subsp.
diarizonae
were found in 81% of the snakes. To avoid transmission, strict hygienic precautions should be applied when reptiles are handled.