bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shewanella oneidensis
MR-1 Uses Overlapping Pathways for Iron Reduction at a Distance and by Direct Contact under Conditions Relevant for Biofilms
Authors: Lies Douglas P. , Hernandez Maria E. , Kappler Andreas , Mielke Randall E. , Gralnick Jeffrey A. , Newman Dianne K. 
Published: August 2005

ABSTRACT

We developed a new method to measure iron reduction at a distance based on depositing Fe(III) (hydr)oxide within nanoporous glass beads. In this “Fe-bead” system,
Shewanella oneidensis
reduces at least 86.5% of the iron in the absence of direct contact. Biofilm formation accompanies Fe-bead reduction and is observable both macro- and microscopically. Fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. The amount of reactive ferric iron in the Fe-bead system is available in excess such that the rate of Fe-bead reduction is directly proportional to cell density; i.e., it is diffusion limited. Addition of either lysates prepared from anaerobic cells or exogenous electron shuttles stimulates Fe-bead reduction by
S. oneidensis
, but iron chelators or additional Fe(II) do not. Neither dissolved Fe(III) nor electron shuttling activity was detected in culture supernatants, implying that the mediator is retained within the biofilm matrix. Strains with mutations in
omcB
or
mtrB
show about 50% of the wild-type levels of reduction, while a
cymA
mutant shows less than 20% of the wild-type levels of reduction and a
menF
mutant shows insignificant reduction. The Fe-bead reduction defect of the
menF
mutant can be restored by addition of menaquinone, but menaquinone itself cannot stimulate Fe-bead reduction. Because the
menF
gene encodes the first committed step of menaquinone biosynthesis, no intermediates of the menaquinone biosynthetic pathway are used as diffusible mediators by this organism to promote iron reduction at a distance. CymA and menaquinone are required for both direct and indirect mineral reduction, whereas MtrB and OmcB contribute to but are not absolutely required for iron reduction at a distance.
Expression of Nitrite and Nitric Oxide Reductases in Free-Living and Plant-Associated
Agrobacterium tumefaciens
C58 Cells
Authors: Baek Seung-Hun , Shapleigh James P. 
Published: August 2005

ABSTRACT

A number of the bacteria that form associations with plants are denitrifiers. To learn more about how the association with plants affects expression of denitrification genes, the regulation of nitrite and nitric oxide reductases was investigated in
Agrobacterium tumefaciens
. Analysis of free-living cells revealed that expression of the genes encoding nitrite and nitric oxide reductases,
nirK
and
nor
, respectively, requires low-oxygen conditions, nitric oxide, and the transcriptional regulator NnrR. Expression of
nor
was monitored in plant-associated bacteria using
nor
-
gfp
fusion expression. In root association experiments, only a small percentage of the attached cells were fluorescent, even when they were incubated under a nitrogen atmosphere. Inactivation of
nirK
had no significant effect on the ability of
A. tumefaciens
to bind to plant roots regardless of the oxygen tension, but it did decrease the occurrence of root-associated fluorescent cells. When wild-type cells containing the
gfp
fusion were infiltrated into leaves, most cells eventually became fluorescent. The same result was obtained when a
nirK
mutant was used, suggesting that nitric oxide activated
nor
expression in the endophytic bacteria. Addition of a nitric oxide synthase inhibitor to block nitric oxide generation by the plant prevented
gfp
expression in infiltrated nitrite reductase mutants, demonstrating that plant-derived nitric oxide can activate
nor
expression in infiltrated cells.
Biodesulfurization of Dibenzothiophene by Microbial Cells Coated with Magnetite Nanoparticles
Authors: Shan GuoBin , Xing JianMin , Zhang HuaiYing , Liu HuiZhou 
Published: August 2005

ABSTRACT

Microbial cells of
Pseudomonas delafieldii
were coated with magnetic Fe
3
O
4
nanoparticles and then immobilized by external application of a magnetic field. Magnetic Fe
3
O
4
nanoparticles were synthesized by a coprecipitation method followed by modification with ammonium oleate. The surface-modified Fe
3
O
4
nanoparticles were monodispersed in an aqueous solution and did not precipitate in over 18 months. Using transmission electron microscopy (TEM), the average size of the magnetic particles was found to be in the range from 10 to 15 nm. TEM cross section analysis of the cells showed further that the Fe
3
O
4
nanoparticles were for the most part strongly absorbed by the surfaces of the cells and coated the cells. The coated cells had distinct superparamagnetic properties. The magnetization (δ
s
) was 8.39 emu · g
−1
. The coated cells not only had the same desulfurizing activity as free cells but could also be reused more than five times. Compared to cells immobilized on Celite, the cells coated with Fe
3
O
4
nanoparticles had greater desulfurizing activity and operational stability.
Concurrent Quantitation of Total
Campylobacter
and Total Ciprofloxacin-Resistant
Campylobacter
Loads in Rinses from Retail Raw Chicken Carcasses from 2001 to 2003 by Direct Plating at 42°C
Authors: Nannapaneni Ramakrishna , Story Robert , Wiggins Keith C. , Johnson Michael G. 
Published: August 2005

ABSTRACT

This is the first report on the use of a normally lethal dose of ciprofloxacin in a
Campylobacter
agar medium to kill all ciprofloxacin-sensitive
Campylobacter
spp. but allow the selective isolation and quantitation of naturally occurring presumptive ciprofloxacin-resistant
Campylobacter
CFU in rinses from retail raw chicken carcasses (RTCC). Thermophilic-group total
Campylobacter
CFU and total ciprofloxacin-resistant
Campylobacter
CFU (irrespective of species) were concurrently quantified in rinses from RTCC by direct plating of centrifuged pellets from 10 or 50 ml out of 400-ml rinse subsamples concurrently on
Campylobacter
agar and ciprofloxacin-containing
Campylobacter
agar at 42°C (detection limit = 0.90 log
10
CFU/carcass). For 2001, 2002, and 2003, countable
Campylobacter
CFU were recovered from 85%, 96%, and 57% of RTCC, while countable ciprofloxacin-resistant
Campylobacter
CFU were recovered from 60%, 59%, and 17.5% of RTCC, respectively. Total
Campylobacter
CFU loads in RTCC rinses ranged from 0.90 to 4.52, 0.90 to 4.58, and 0.90 to 4.48 log
10
CFU/carcass in 2001, 2002, and 2003, respectively. Total ciprofloxacin-resistant
Campylobacter
CFU loads in RTCC rinses ranged from 0.90 to 4.06, 0.90 to 3.95, and 0.90 to 3.04 log
10
CFU/carcass in 2001, 2002, and 2003, respectively. Overall, total
Campylobacter
loads of 0.90 to 2.0, 2 to 3, 3 to 4, 4 to 5 log
10
CFU/carcass, respectively, were recovered from 16%, 32%, 26%, and 5% of RTCC tested over the 2-year sampling period. For the same period, total ciprofloxacin-resistant
Campylobacter
loads of 0.90 to 2.0, 2 to 3, 3 to 4, and 4 to 5 log
10
CFU/carcass, respectively, were recovered from 24%, 11%, 7%, and 0.2% of RTCC tested. There was a steady decline in total
Campylobacter
and total ciprofloxacin-resistant
Campylobacter
loads in RTCC rinses from 2001/2002 to 2003.
Characterization of Carbohydrate-Binding Cytochromeb562from the White-Rot FungusPhanerochaete chrysosporium
Authors: Yoshida Makoto , Igarashi Kiyohiko , Wada Masahisa , Kaneko Satoshi , Suzuki Norio , Matsumura Hirotoshi , Nakamura Nobuhumi , Ohno Hiroyuki , Samejima Masahiro 
Published: August 2005

ABSTRACTcDNA encoding a hemoprotein similar to the cytochrome domain of extracellular flavocytochrome cellobiose dehydrogenase (CDH) was cloned from the white-rot fungusPhanerochaete chrysosporium. The deduced amino acid sequence implies that there is a two-domain structure consisting of an N-terminal cytochrome domain and a C-terminal family 1 carbohydrate-binding module (CBM1) but that the flavin-containing domain of CDH is not present. The gene transcripts were observed in cultures in cellulose medium but not in cultures in glucose medium, suggesting that there is regulation by carbon catabolite repression. The gene was successfully overexpressed inPichia pastoris, and the recombinant protein was designated carbohydrate-binding cytochromeb562(CBCyt.b562). The resonance Raman spectrum suggested that the heme of CBCyt.b562is 6-coordinated in both the ferric and ferrous states. Moreover, the redox potential measured by cyclic voltammetry was similar to that of the cytochrome domain of CDH. These results suggest that the redox characteristics may be similar to those of the cytochrome domain of CDH, and so CBCyt.b562may have an electron transfer function. In a binding study with various carbohydrates, CBCyt.b562was adsorbed with high affinity on both cellulose and chitin. As far as we know, this is the first example of a CBM1 connected to a domain without apparent catalytic activity for carbohydrate; this CBM1 may play a role in localization of the redox protein on the surface of cellulose or on the fungal sheath in vivo.
Methanogen Diversity Evidenced by Molecular Characterization of Methyl Coenzyme M Reductase A (
mcrA
) Genes in Hydrothermal Sediments of the Guaymas Basin
Authors: Dhillon Ashita , Lever Mark , Lloyd Karen G. , Albert Daniel B. , Sogin Mitchell L. , Teske Andreas 
Published: August 2005

ABSTRACT

The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (
mcrA
) and 16S rRNA genes. Members of the
Methanomicrobiales
and
Methanosarcinales
dominated the
mcrA
and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H
2
/CO
2
- and formate-utilizing family
Methanomicrobiales
, two
mcrA
and 16S rRNA lineages were closely affiliated with cultured species of the genera
Methanoculleus
and
Methanocorpusculum
. The most frequently recovered
mcrA
PCR amplicons within the
Methanomicrobiales
did not branch with any cultured genera. Within the nutritionally versatile family
Methanosarcinales
, one 16S rRNA amplicon and most of the
mcrA
PCR amplicons were affiliated with the obligately acetate utilizing species
Methanosaeta concilii
. The
mcrA
clone libraries also included phylotypes related to the methyl-disproportionating genus
Methanococcoides
. However, two
mcrA
and two 16S rRNA lineages within the
Methanosarcinales
were unrelated to any cultured genus. Overall, the clone libraries indicate a diversified methanogen community that uses H
2
/CO
2
, formate, acetate, and methylated substrates. Phylogenetic affiliations of
mcrA
and 16S rRNA clones with thermophilic and nonthermophilic cultured isolates indicate a mixed mesophilic and thermophilic methanogen community in the surficial Guaymas sediments.
Elevated Temperature Enhances Virulence ofErwinia carotovorasubsp.carotovoraStrain EC153 to Plants and Stimulates Production of the Quorum Sensing Signal,N-Acyl Homoserine Lactone, and Extracellular Proteins
Authors: Hasegawa H. , Chatterjee A. , Cui Y. , Chatterjee A. K. 
Published: August 2005

ABSTRACTErwinia carotovorasubsp.atroseptica,E. carotovorasubsp.betavasculorum, andE. carotovorasubsp.carotovoraproduce high levels of extracellular enzymes, such as pectate lyase (Pel), polygalacturonase (Peh), cellulase (Cel), and protease (Prt), and the quorum-sensing signalN-acyl-homoserine lactone (AHL) at 28°C. However, the production of these enzymes and AHL by these bacteria is severely inhibited during growth at elevated temperatures (31.2°C forE. carotovorasubsp.atrosepticaand 34.5°C forE. carotovorasubsp.betavasculorumand mostE. carotovorasubsp.carotovorastrains). At elevated temperatures these bacteria produce high levels of RsmA, an RNA binding protein that promotes RNA decay.E. carotovorasubsp.carotovorastrain EC153 is an exception in that it produces higher levels of Pel, Peh, Cel, and Prt at 34.5°C than at 28°C. EC153 also causes extensive maceration of celery petioles and Chinese cabbage leaves at 34.5°C, which correlates with a higher growth rate and higher levels of rRNA and AHL. The lack of pectinase production byE. carotovorasubsp.carotovorastrain Ecc71 at 34.5°C limits the growth of this organism in plant tissues and consequently impairs its ability to cause tissue maceration. Comparative studies withahlI(the gene encoding a putative AHL synthase),pel-1, andpeh-1transcripts documented that at 34.5°C the RNAs are more stable in EC153 than in Ecc71. Our data reveal that overall metabolic activity, AHL levels, and mRNA stability are responsible for the higher levels of extracellular protein production and the enhanced virulence of EC153 at 34.5°C compared to 28°C.
Mutation of Glutamic Acid 103 of Toluene
o
-Xylene Monooxygenase as a Means To Control the Catabolic Efficiency of a Recombinant Upper Pathway for Degradation of Methylated Aromatic Compounds
Authors: Cafaro Valeria , Notomista Eugenio , Capasso Paola , Di Donato Alberto 
Published: August 2005

ABSTRACT

Toluene
o
-xylene monooxygenase (ToMO) and phenol hydroxylase (PH) of
Pseudomonas stutzeri
OX1 act sequentially in a recombinant upper pathway for the degradation of aromatic hydrocarbons. The catalytic efficiency and regioselectivity of these enzymes optimize the degradation of growth substrates like toluene and
o
-xylene. For example, the sequential monooxygenation of
o
-xylene by ToMO and PH leads to almost exclusive production of 3,4-dimethylcatechol (3,4-DMC), the only isomer that can be further metabolized by the
P. stutzeri meta
pathway. We investigated the possibility of producing ToMO mutants with modified regioselectivity compared with the regioselectivity of the wild-type protein in order to alter the ability of the recombinant upper pathway to produce methylcatechol isomers from toluene and to produce 3,4-DMC from
o
-xylene. The combination of mutant (E103G)-ToMO and PH increased the production of 4-methylcatechol from toluene and increased the formation of 3,4-DMC from
o
-xylene. These data strongly support the idea that the products and efficiency of the metabolic pathway can be controlled not only through mutations that increase the catalytic efficiency of the enzymes involved but also through tuning the substrate specificity and regioselectivity of the enzymes. These findings are crucial for the development of future metabolic engineering strategies.
Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots
Authors: Simon Holly M. , Jahn Courtney E. , Bergerud Luke T. , Sliwinski Marek K. , Weimer Paul J. , Willis David K. , Goodman Robert M. 
Published: August 2005

ABSTRACT

Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division
Crenarchaeota
over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of
Crenarchaeota
that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.
Nonpathogenic Strains ofColletotrichum lindemuthianumTrigger Progressive Bean Defense Responses during Appressorium-Mediated Penetration
Authors: Veneault-Fourrey Claire , Laugé Richard , Langin Thierry 
Published: August 2005

ABSTRACTThe fungal bean pathogenColletotrichum lindemuthianumdifferentiates appressoria in order to penetrate bean tissues. We showed that appressorium development inC. lindemuthianumcan be divided into three stages, and we obtained three nonpathogenic strains, including one strain blocked at each developmental stage. H18 was blocked at the appressorium differentiation stage; i.e., no genuine appressoria were formed. H191 was blocked at the appressorium maturation stage; i.e., appressoria exhibited a pigmentation defect and developed only partial internal turgor pressure. H290 was impaired in appressorium function; i.e., appressoria failed to penetrate into bean tissues. Furthermore, these strains could be further discriminated according to the bean defense responses that they induced. Surprisingly, appressorium maturation, but not appressorium function, was sufficient to induce most plant defense responses tested (superoxide ion production and strong induction of pathogenesis-related proteins). However, appressorium function (i.e., entry into the first host cell) was necessary for avirulence-mediated recognition of the fungus.
Novel AroA with High Tolerance to Glyphosate, Encoded by a Gene of
Pseudomonas putida
4G-1 Isolated from an Extremely Polluted Environment in China
Authors: Sun Yi-Cheng , Chen Yan-Cheng , Tian Zhe-Xian , Li Feng-Mei , Wang Xin-Yue , Zhang Jing , Xiao Zhen-Long , Lin Min , Gilmartin Niamh , Dowling David N. , Wang Yi-Ping 
Published: August 2005

ABSTRACT

Glyphosate has been used globally as a safe herbicide for weed control. It inhibits 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (AroA), which is a key enzyme in the aromatic amino acid biosynthetic pathway in microorganisms and plants. A
Pseudomonas putida
strain, 4G-1, was isolated from a soil heavily contaminated by glyphosate in China. Its AroA-encoding gene (
aroA
) has been cloned, sequenced, and expressed in
Escherichia coli
. Phylogenetic analysis revealed that this AroA belongs neither to class I nor to class II AroA enzymes. When compared with
E. coli
AroA, 4G-1 AroA shows similar values for

K
m

[PEP],

K
m

[S3P], and specific enzyme activity. Moreover, 4G-1 AroA exhibits high tolerance to glyphosate, which indicates a protein with a high potential for structural and functional studies of AroA in general and its potential usage for the generation of transgenic crops resistant to the herbicide.
Optically Transparent Porous Medium for Nondestructive Studies of Microbial Biofilm Architecture and Transport Dynamics
Authors: Leis Andrew P. , Schlicher Sven , Franke Hilmar , Strathmann Martin 
Published: August 2005

ABSTRACTWe describe a novel and noninvasive, microscopy-based method for visualizing the structure and dynamics of microbial biofilms, individual fluorescent microbial cells, and inorganic colloids within a model porous medium. Biofilms growing in flow cells packed with granules of an amorphous fluoropolymer could be visualized as a consequence of refractive index matching between the solid fluoropolymer grains and the aqueous immersion medium. In conjunction with the capabilities of confocal microscopy for nondestructive optical sectioning, the use of amorphous fluoropolymers as a solid matrix permits observation of organisms and dynamic processes to a depth of 2 to 3 mm, whereas sediment biofilms growing in sand-filled flow cells can only be visualized in the region adjacent to the flow cell wall. This method differs fundamentally from other refractive index-matching applications in that optical transparency was achieved by matching a solid phase to water (and not vice versa), thereby permitting real-time microscopic studies of particulate-containing, low-refractive-index media such as biological and chromatographic systems.
Isolation and Characterization of
Aspergillus oryzae
Vacuolar Protein Sorting Mutants
Authors: Ohneda Mamoru , Arioka Manabu , Kitamoto Katsuhiko 
Published: August 2005

ABSTRACT

The vacuolar protein sorting (
vps
) system in the filamentous fungus
Aspergillus oryzae
, which has unique cell polarity and the ability to secrete large amounts of proteins, was evaluated by using mutants that missort vacuolar proteins into the medium. Vacuolar carboxypeptidase Y (CPY) fused with enhanced green fluorescent protein (EGFP) was used as a vacuolar marker. Twenty
dfc
(
d
im EGFP
f
luorescence in
c
onidia) mutants with reduced intracellular EGFP fluorescence in conidia were isolated by fluorescence-activated cell sorting from approximately 20,000 UV-treated conidia. Similarly, 22
hfm
(
h
yper-EGFP
f
luorescence released into the
m
edium) mutants with increased extracellular EGFP fluorescence were isolated by using a fluorescence microplate reader from approximately 20,000 UV-treated conidia. The
dfc
and
hfm
mutant phenotypes were pH dependent, and missorting of CPY-EGFP could vary by 10- to 40-fold depending on the ambient pH. At pH 5.5, the dfc-14 and hfm-4 mutants had an abnormal hyphal morphology that is consistent with fragmentation of vacuoles and defects in cell polarity. In contrast, the hyphal and vacuolar morphology of the dfc-14 and hfm-4 mutants was normal at pH 8.0, although CPY-EGFP accumulated in perivacuolar dot-like structures similar to the class E compartments in
Saccharomyces cerevisiae vps
mutants. In hfm-21, CPY-EGFP localized at the Spitzenkörper when the mutant was grown at pH 8.0 but not in vacuoles, suggesting that hfm-21 may transport CPY-EGFP via a novel pathway that involves the Spitzenkörper. Correlations between vacuolar protein sorting, pH response, and cell polarity are reported for the first time for filamentous fungi.
Fluorophore-Labeled Primers Improve the Sensitivity, Versatility, and Normalization of Denaturing Gradient Gel Electrophoresis
Authors: Neufeld Josh D. , Mohn William W. 
Published: August 2005

ABSTRACTDenaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.
Identification of Acyl-Homoserine Lactone Signal Molecules Produced by
Nitrosomonas europaea
Strain Schmidt
Authors: Burton E. O. , Read H. W. , Pellitteri M. C. , Hickey W. J. 
Published: August 2005

ABSTRACT

Nitrosomonas europaea
strain Schmidt produces at least three acyl homoserine lactone (AHL) signal molecules: C
6
-homoserine lactone (HSL), C
8
-HSL, and C
10
-HSL. These compounds were identified in extracts of chemostat culture effluent by three independent methods. The concentrations of AHL in effluent were low (0.4 to 2.2 nM) but within the range known to induce AHL-responsive systems. The absence of LuxI and LuxM homologs from the genome of
N. europaea
strain Schmidt suggested that AHL synthesis occurs by an alternate pathway, possibly mediated by an HdtS homolog. To the best of our knowledge, the present report is the first to document the types and levels of AHLs produced by
N. europaea
.
Transcriptome-Based Identification of the
Sinorhizobium meliloti
NodD1 Regulon
Authors: Capela Delphine , Carrere Sébastien , Batut Jacques 
Published: August 2005

ABSTRACT

The NodD1 regulon of
Sinorhizobium meliloti
was determined through the analysis of the
S. meliloti
transcriptome in response to the plant flavone luteolin and the overexpression of
nodD1
. Nine new genes regulated by both NodD1 and luteolin were identified, demonstrating that NodD1 controls few functions behind nodulation in
S. meliloti
.