bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Tylosin Use on Erythromycin Resistance in Enterococci Isolated from Swine
Authors: Jackson Charlene R. , Fedorka-Cray Paula J. , Barrett John B. , Ladely Scott R. 
Published: July 2004

ABSTRACT

The effect of tylosin on erythromycin-resistant enterococci was examined on three farms; farm A used tylosin for growth promotion, farm B used tylosin for treatment of disease, and farm C did not use tylosin for either growth promotion or disease treatment. A total of 1,187 enterococci were isolated from gestation, farrowing, suckling, nursery, and finishing swine from the farms. From a subset of those isolates (
n
= 662), 59% (124 out of 208), 28% (80 out of 281), and 2% (4 out of 170) were resistant to erythromycin (MIC ≥ 8 μg/ml) from farms A, B, and C, respectively. PCR analysis and Southern blotting revealed that 95% (65 out of 68) of isolates chosen from all three farms for further study were positive for
ermB
, but all were negative for
ermA
and
ermC
. By using Southern blotting,
ermB
was localized to the chromosome in 56 of the isolates while 9 isolates from farms A and B contained
ermB
on two similar-sized plasmid bands (12 to 16 kb). Pulsed-field gel electrophoresis revealed that the isolates were genetically diverse and represented a heterogeneous population of enterococci. This study suggests that although there was resistance to a greater number of enterococcal isolates on a farm where tylosin was used as a growth promotant, resistant enterococci also existed on a farm where no antimicrobial agents were used.
Simultaneous Discrimination between 15 Fish Pathogens by Using 16S Ribosomal DNA PCR and DNA Microarrays
Authors: Warsen Adelaide E. , Krug Melissa J. , LaFrentz Stacey , Stanek Danielle R. , Loge Frank J. , Call Douglas R. 
Published: July 2004

ABSTRACT

We developed a DNA microarray suitable for simultaneous detection and discrimination between multiple bacterial species based on 16S ribosomal DNA (rDNA) polymorphisms using glass slides. Microarray probes (22- to 31-mer oligonucleotides) were spotted onto Teflon-masked, epoxy-silane-derivatized glass slides using a robotic arrayer. PCR products (ca. 199 bp) were generated using biotinylated, universal primer sequences, and these products were hybridized overnight (55°C) to the microarray. Targets that annealed to microarray probes were detected using a combination of Tyramide Signal Amplification and Alexa Fluor 546. This methodology permitted 100% specificity for detection of 18 microbes, 15 of which were fish pathogens. With universal 16S rDNA PCR (limited to 28 cycles), detection sensitivity for purified control DNA was equivalent to <150 genomes (675 fg), and this sensitivity was not adversely impacted either by the presence of competing bacterial DNA (1.1 × 10
6
genomes; 5 ng) or by the addition of up to 500 ng of fish DNA. Consequently, coupling 16S rDNA PCR with a microarray detector appears suitable for diagnostic detection and surveillance for commercially important fish pathogens.
Osmotic Stress Response: Quantification of Cell Maintenance and Metabolic Fluxes in a Lysine-Overproducing Strain of
Corynebacterium glutamicum
Authors: Varela Cristian A. , Baez Mauricio E. , Agosin Eduardo 
Published: July 2004

ABSTRACT

Osmotic
stress diminishes cell productivity and may cause cell
inactivation in industrial fermentations. The quantification of
metabolic changes under such conditions is fundamental for
understanding and describing microbial behavior during bioprocesses. We
quantified the gradual changes that take place when a
lysine-overproducing strain of
Corynebacterium glutamicum
is
grown in continuous culture with saline gradients at different dilution
rates. The use of compatible solutes depended on environmental
conditions; certain osmolites predominated at different dilution rates
and extracellular osmolalities. A metabolic flux analysis showed that
at high dilution rates
C. glutamicum
redistributed its
metabolic fluxes, favoring energy formation over growth. At low
dilution rates, cell metabolism accelerated as the osmolality was
steadily increased. Flexibility in the oxaloacetate node
proved to be key for the energetic redistribution that occurred when
cells were grown at high dilution rates. Substrate and ATP maintenance
coefficients increased 30- and 5-fold, respectively, when
the osmolality increased, which demonstrates that
energy pool management is fundamental for sustaining
viability.
Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State
Authors: Fredrickson James K. , Zachara John M. , Balkwill David L. , Kennedy David , Li Shu-mei W. , Kostandarithes Heather M. , Daly Michael J. , Romine Margaret F. , Brockman Fred J. 
Published: July 2004

ABSTRACT

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI),
137
Cs, and
99
Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ∼10
4
CFU g
−1
, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of
137
Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to
Arthrobacter
species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including
Rhodococcus
and
Nocardia
. Two isolates from the second-most radioactive sample (>20 μCi of
137
Cs g
−1
) were closely related to
Deinococcus radiodurans
and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste.
Natural Atypical
Listeria innocua
Strains with
Listeria monocytogenes
Pathogenicity Island 1 Genes
Authors: Johnson J. , Jinneman K. , Stelma G. , Smith B. G. , Lye D. , Messer J. , Ulaszek J. , Evsen L. , Gendel S. , Bennett R. W. , Swaminathan B. , Pruckler J. , Steigerwalt A. , Kathariou S. , Yildirim S. , Volokhov D. , Rasooly A. , Chizhikov V. , Wiedmann M. , Fortes E. , Duvall R. E. , Hitchins A. D. 
Published: July 2004

ABSTRACT

Identification of bona fide
Listeria
isolates into the six species of the genus normally requires only a few tests. Aberrant isolates do occur, but even then only one or two extra confirmatory tests are generally needed for identification to species level. We have discovered a hemolytic-positive, rhamnose and xylose fermentation-negative
Listeria
strain with surprising recalcitrance to identification to the species level due to contradictory results in standard confirmatory tests. The issue had to be resolved by using total DNA-DNA hybridization testing and then confirmed by further specific PCR-based tests including a
Listeria
microarray assay. The results show that this isolate is indeed a novel one. Its discovery provides the first fully documented instance of a hemolytic
Listeria innocua
strain. This species, by definition, is typically nonhemolytic. The
L. innocua
isolate contains all the members of the PrfA-regulated virulence gene cluster (
Listeria
pathogenicity island 1) of
L. monocytogenes
. It is avirulent in the mouse pathogenicity test. Avirulence is likely at least partly due to the absence of the
L. monocytogenes
-specific allele of
iap
, as well as the absence of
inlA
,
inlB
,
inlC
, and
daaA
. At least two of the virulence cluster genes,
hly
and
plcA
, which encode the
L. monocytogenes
hemolysin (listeriolysin O) and inositol-specific phospholipase C, respectively, are phenotypically expressed in this
L. innocua
strain. The detection by PCR assays of specific
L. innocua
genes (
lin0198
,
lin0372
,
lin0419
,
lin0558
,
lin1068
,
lin1073
,
lin1074
,
lin2454
, and
lin2693
) and noncoding intergenic regions (
lin0454-lin0455
and
nadA-lin2134
) in the strain is consistent with its
L. innocua
DNA-DNA hybridization identity. Additional distinctly different hemolytic
L. innocua
strains were also studied.
Solar and Temporal Effects on
Escherichia coli
Concentration at a Lake Michigan Swimming Beach
Authors: Whitman Richard L. , Nevers Meredith B. , Korinek Ginger C. , Byappanahalli Muruleedhara N. 
Published: July 2004

ABSTRACT

Studies on solar inactivation of
Escherichia coli
in freshwater and in situ have been limited. At 63rd St. Beach, Chicago, Ill., factors influencing the daily periodicity of culturable
E. coli
, particularly insolation, were examined. Water samples for
E. coli
analysis were collected twice daily between April and September 2000 three times a week along five transects in two depths of water. Hydrometeorological conditions were continuously logged: UV radiation, total insolation, wind speed and direction, wave height, and relative lake level. On 10 days, transects were sampled hourly from 0700 to 1500 h. The effect of sunlight on
E. coli
inactivation was evaluated with dark and transparent in situ mesocosms and ambient lake water. For the study, the number of
E. coli
samples collected (
n
) was 2,676. During sunny days,
E. coli
counts decreased exponentially with day length and exposure to insolation, but on cloudy days,
E. coli
inactivation was diminished; the
E. coli
decay rate was strongly influenced by initial concentration. In situ experiments confirmed that insolation primarily inactivated
E. coli
; UV radiation only marginally affected
E. coli
concentration. The relationship between insolation and
E. coli
density is complicated by relative lake level, wave height, and turbidity, all of which are often products of wind vector. Continuous importation and nighttime replenishment of
E. coli
were evident. These findings (i) suggest that solar inactivation is an important mechanism for natural reduction of indicator bacteria in large freshwater bodies and (ii) have implications for management strategies of nontidal waters and the use of
E. coli
as an indicator organism.
Metabolic Engineering of Mannitol Production inLactococcus lactis: Influence of Overexpression of Mannitol 1-Phosphate Dehydrogenase in Different Genetic Backgrounds
Authors: Wisselink H. Wouter , Mars Astrid E. , van der Meer Pieter , Eggink Gerrit , Hugenholtz Jeroen 
Published: July 2004

ABSTRACTTo obtain a mannitol-producingLactococcus lactisstrain, the mannitol 1-phosphate dehydrogenase gene (mtlD) fromLactobacillus plantarumwas overexpressed in a wild-type strain, a lactate dehydrogenase(LDH)-deficient strain, and a strain with reduced phosphofructokinase activity. High-performance liquid chromatography and13C nuclear magnetic resonance analysis revealed that small amounts (<1%) of mannitol were formed by growing cells ofmtlD-overexpressing LDH-deficient and phosphofructokinase-reduced strains, whereas resting cells of the LDH-deficient transformant converted 25% of glucose into mannitol. Moreover, the formed mannitol was not reutilized upon glucose depletion. Of the metabolic-engineering strategies investigated in this work,mtlD-overexpressing LDH-deficientL. lactisseemed to be the most promising strain for mannitol production.
Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays
Authors: Rhee Sung-Keun , Liu Xueduan , Wu Liyou , Chong Song C. , Wan Xiufeng , Zhou Jizhong 
Published: July 2004

ABSTRACT

To effectively monitor biodegrading populations, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the 2,402 known genes and pathways involved in biodegradation and metal resistance. This array contained 1,662 unique and group-specific probes with <85% similarity to their nontarget sequences. Based on artificial probes, our results showed that under hybridization conditions of 50°C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. The detection limit was ∼5 to 10 ng of genomic DNA in the absence of background DNA and 50 to 100 ng of pure-culture genomic DNA in the presence of background DNA or 1.3 × 10
7
cells in the presence of background RNA. Strong linear relationships between the signal intensity and the target DNA and RNA were observed (

r
2

= 0.95 to 0.99). Application of this type of microarray to analyze naphthalene-amended enrichment and soil microcosms demonstrated that microflora changed differently depending on the incubation conditions. While the naphthalene-degrading genes from
Rhodococcus
-type microorganisms were dominant in naphthalene-degrading enrichments, the genes involved in naphthalene (and polyaromatic hydrocarbon and nitrotoluene) degradation from gram-negative microorganisms, such as
Ralstonia
,
Comamonas
, and
Burkholderia
, were most abundant in the soil microcosms. In contrast to general conceptions, naphthalene-degrading genes from
Pseudomonas
were not detected, although
Pseudomonas
is widely known as a model microorganism for studying naphthalene degradation. The real-time PCR analysis with four representative genes showed that the microarray-based quantification was very consistent with real-time PCR (

r
2

= 0.74). In addition, application of the arrays to both polyaromatic-hydrocarbon- and benzene-toluene-ethylbenzene-xylene-contaminated and uncontaminated soils indicated that the developed microarrays appeared to be useful for profiling differences in microbial community structures. Our results indicate that this technology has potential as a specific, sensitive, and quantitative tool in revealing a comprehensive picture of the compositions of biodegradation genes and the microbial community in contaminated environments, although more work is needed to improve detection sensitivity.
Use of Fluorescent Lectin Probes for Analysis of Footprints from
Pseudomonas aeruginosa
MDC on Hydrophilic and Hydrophobic Glass Substrata
Authors: Bejarano Eduardo Mora , Schneider René Peter 
Published: July 2004

ABSTRACT

Microbial footprints of
Pseudomonas aeruginosa
MDC attached for 1 h to clean or silanized glass were analyzed with fluorescently labeled lectin probes. Footprint composition varied, depending on cell physiology and substratum surface chemistry. This suggests that substratum physicochemistry affected the structure of cell surfaces of adsorbed organisms.
Genotyping of
Cryptosporidium
Isolates from
Chamelea gallina
Clams in Italy
Authors: Traversa Donato , Giangaspero Annunziata , Molini Umberto , Iorio Raffaella , Paoletti Barbara , Otranto Domenico , Giansante Carla 
Published: July 2004

ABSTRACT

Chamelea gallina
clams collected from the mouths of rivers along the Adriatic Sea (central Italy) were found to harbor
Cryptosporidium parvum
(genotype 2), which is the lineage involved in zoonotic transmission. The clams were collected from the mouths of rivers near whose banks ruminants are brought to graze. This paper reports the environmental spread of
C. parvum
in Italy and highlights the fact that genotyping of seaborne
Cryptosporidium
isolates is a powerful tool with which to investigate the transmission patterns and epidemiology of this microorganism.
Combined Immunomagnetic Separation-Molecular Beacon-Reverse Transcription-PCR Assay for Detection of Hepatitis A Virus from Environmental Samples
Authors: Abd El Galil Khaled H. , El Sokkary M. A. , Kheira S. M. , Salazar Andre M. , Yates Marylynn V. , Chen Wilfred , Mulchandani Ashok 
Published: July 2004

ABSTRACT
In this study, a molecular-beacon-based real-time reverse transcription (RT)-PCR assay was developed to detect the presence of hepatitis A virus (HAV) in environmental samples. A 125-bp, highly conserved 5′ noncoding region of HAV was targeted. The sensitivity of the real-time RT-PCR assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, and only HAV was positively identified. When combined with immunomagnetic separation, the real-time RT-PCR assay successfully detected as few as 20 PFU in seeded groundwater samples. Because of its simplicity and specificity, this assay has broad applications for the rapid detection of HAV in contaminated foods or water.
Evidence for Acyl Homoserine Lactone Signal Production in Bacteria Associated with Marine Sponges
Authors: Taylor Michael W. , Schupp Peter J. , Baillie Harriet J. , Charlton Timothy S. , de Nys Rocky , Kjelleberg Staffan , Steinberg Peter D. 
Published: July 2004

ABSTRACT
We report for the first time the production of acyl homoserine lactones (AHLs) by bacteria associated with marine sponges. Given the involvement of AHLs in bacterial colonization of many higher organisms, we speculate that such quorum sensing signals could play a part in interactions between sponges and the dense bacterial communities living within them.
Online Tool for Analysis of Denaturing Gradient Gel Electrophoresis Profiles
Authors: Huber Florian , Peduzzi Peter 
Published: July 2004

ABSTRACT

We
present an online tool (EquiBands,
http://www.univie.ac.at/IECB/limno/equibands/EquiBands.html
)
that quantifies the matching of two bands considered to be the same in
different samples, even when samples are applied to different
denaturing gradient gel electrophoresis gels. With an environmental
example we demonstrate the procedure for the classification of two
bands of different samples with the help of
EquiBands.
Degradation of Alkyl Ethers, Aralkyl Ethers, and Dibenzyl Ether by
Rhodococcus
sp. Strain DEE5151, Isolated from Diethyl Ether-Containing Enrichment Cultures
Authors: Kim Yong-Hak , Engesser Karl-Heinrich 
Published: July 2004

ABSTRACT

Twenty strains isolated from sewage sludge were found to degrade various ethers, including alkyl ethers, aralkyl ethers, and dibenzyl ether. In
Rhodococcus
strain DEE5151, induction of ether degradation needed substrates exhibiting at least one unsubstituted Cα-methylene moiety as the main structural prerequisite. The cleavage reaction observed with anisole, phenetole, and dibenzyl ether indicates that the initial oxidation occurs at such respective Cα positions. Diethyl ether-induced strain DEE5151 degraded dibenzyl ether via intermediately accumulated benzoic acid. Phenetole seems to be subject also to another ether-cleaving enzyme. Other strains of this group showed different enzymatic activities towards the substrate classes investigated.
Arthrobacter aurescens
TC1 Atrazine Catabolism Genes
trzN
,
atzB
, and
atzC
Are Linked on a 160-Kilobase Region and Are Functional in
Escherichia coli
Authors: Sajjaphan Kannika , Shapir Nir , Wackett Lawrence P. , Palmer Michael , Blackmon Barbara , Tomkins Jeff , Sadowsky Michael J. 
Published: July 2004

ABSTRACT

Arthrobacter aurescens
strain TC1 metabolizes atrazine to cyanuric acid via TrzN, AtzB, and AtzC. The complete sequence of a 160-kb bacterial artificial chromosome clone indicated that
trzN
,
atzB
, and
atzC
are linked on the
A. aurescens
genome. TrzN, AtzB, and AtzC were shown to be functional in
Escherichia coli
. Hybridization studies localized
trzN
,
atzB
, and
atzC
to a 380-kb plasmid in
A. aurescens
strain TC1.
Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean
Authors: Teira Eva , Reinthaler Thomas , Pernthaler Annelie , Pernthaler Jakob , Herndl Gerhard J. 
Published: July 2004

ABSTRACT

The recently developed CARD-FISH protocol was refined for the detection of marine
Archaea
by replacing the lysozyme permeabilization treatment with proteinase K. This modification resulted in about twofold-higher detection rates for
Archaea
in deep waters. Using this method in combination with microautoradiography, we found that
Archaea
are more abundant than
Bacteria
(42% versus 32% of 4′,6′-diamidino-2-phenylindole counts) in the deep waters of the North Atlantic and that a larger fraction of
Archaea
than of
Bacteria
takes up
l
-aspartic acid (19% versus 10%).
GPI-anchor deficiency in myeloid cells causes impaired FcγR effector functions
Authors: Hazenbos Wouter L. W. , Clausen Björn E. , Takeda Junji , Kinoshita Taroh 
Published: July 2004

AbstractSignaling by transmembrane immunoglobulin G (IgG)-Fc receptors (FcγRs) in response to ligand involves association with membrane microdomains that contain glycosyl phosphatidylinositol (GPI)-anchored proteins. Recent in vitro studies showed enhancement of FcγR signaling by forced monoclonal antibody-mediated cocrosslinking with various GPI-anchored proteins. Here, the possibility that GPI-anchored proteins are involved in normal physiologic FcγR effector functions in response to a model ligand was studied using myeloid-specific GPI-anchor-deficient mice, generated by Cre-loxP conditional targeting. GPI-anchor-deficient primary myeloid cells exhibited normal FcγR expression and binding or endocytosis of IgG-immune complexes (IgG-ICs). Strikingly, after stimulation with IgG-ICs, tumor necrosis factor-α release, dendritic cell maturation, and antigen presentation were strongly reduced by GPI-anchor deficiency. Tyrosine phosphorylation of the FcR γ-chain in response to IgG-IC was impaired in GPI-anchor-deficient cells. Myeloid GPI-anchor deficiency resulted in attenuated in vivo inflammatory processes during IgG-IC-mediated alveolitis. This study provides the first genetic evidence for an essential role of GPI-anchored proteins in physiologic FcγR effector functions in vitro and in vivo. (Blood. 2004;104:2825-2831)
KLRL1, a novel killer cell lectinlike receptor, inhibits natural killer cell cytotoxicity
Authors: Han Yanmei , Zhang Minghui , Li Nan , Chen Taoyong , Zhang Yi , Wan Tao , Cao Xuetao 
Published: July 2004

AbstractNatural killer (NK) cell inhibitory receptors play important roles in the regulation of target susceptibility to natural killing. Here, we report the molecular cloning and functional characterization of a novel NK cell receptor, KLRL1, from human and mouse dendritic cells. KLRL1 is a type II transmembrane protein with an immunoreceptor tyrosine-based inhibitory motif and a C-type lectinlike domain. The KLRL1 gene is located in the central region of the NK gene complex in both humans and mice, on human chromosome 12p13 and mouse chromosome 6F3, adjacent to the other KLR genes. KLRL1 is preferentially expressed in lymphoid tissues and immune cells, including NK cells, T cells, dendritic cells, and monocytes or macrophages. Western blot and fluorescence confocal microscopy analyses indicated that KLRL1 is a membrane-associated glycoprotein, which forms a heterodimer with an as yet unidentified partner. Human and mouse KLRL1 are both predicted to contain putative immunoreceptor tyrosine-based inhibitory motifs (ITIMs), and immunoprecipitation experiments demonstrated that KLRL1 associates with the tyrosine phosphatases SHP-1 (SH2-domain-containing protein tyrosine phosphatase 1) and SHP-2. Consistent with its potential inhibitory function, pretreatment of target cells with human KLRL1-Fc fusion protein enhances NK-mediated cytotoxicity. Taken together, our results demonstrate that KLRL1 belongs to the KLR family and is a novel inhibitory NK cell receptor.