bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eight‐week oral administration of meloxicam, a non‐steroidal anti‐inflammatory drug, prevents dose reduction of pegylated interferon α‐2a in the treatment of chronic hepatitis C
Authors: Kagawa Tatehiro , Shiozawa Hirokazu , Kojima Sei‐ichiro , Takashimizu Shinji , Nagata Naruhiko , Numata Makoto , Morino Fumitoshi , Nishizaki Yasuhiro , Mochizuki Kaori , Watanabe Norihito , Watanabe Tetsu , Matsuzaki Shohei , Mine Tetsuya 
Published: September 2007

Aim:  We conducted a trial to evaluate whether eight‐week oral administration of meloxicam, a non‐steroidal anti‐inflammatory drug, would decrease the rate of the patients who required dose reduction of pegylated interferon α‐2a in the treatment of chronic hepatitis C.Methods:  Sixty patients given weekly subcutaneous administration of pegylated interferon α‐2a at a dose of 180 μg for 48 weeks were allocated into the meloxicam group (n = 22) and the control group (n = 38) before interferon treatment. Meloxicam was given orally at a dose of 10 mg once a day for eight weeks from the start of interferon treatment.Results:  The cumulative rate of dose‐reduction‐free patients was significantly higher in the meloxicam group (P < 0.05). Until week eight, 44.7% of the control group and 9.1% of the meloxicam group required dose reduction. Dose was modified by neutropenia in 31.6% and 18.2% of the control and meloxicam groups, respectively. Meloxicam relieved a declineof neutrophil count within the first eight weeks from 54.2% to 44.2% (P < 0.05). Multivariate analysis revealed that greater pretreatment neutrophil count and the use of meloxicam were independent factors associated with avoiding dose reduction. Sustained virological response was obtained in 52.6% of the patients. The multivariate logistic analysis revealed that viral serotype and viral load were the only independent factors associated with sustained virological response.Conclusion:  Eight‐week administration of meloxicam prevented dose reduction of pegylated interferon by relieving a decline of neutrophil count in the treatment of chronic hepatitis C.
Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil
Authors: Fierer Noah , Breitbart Mya , Nulton James , Salamon Peter , Lozupone Catherine , Jones Ryan , Robeson Michael , Edwards Robert A. , Felts Ben , Rayhawk Steve , Knight Rob , Rohwer Forest , Jackson Robert B. 
Published: September 2007

ABSTRACT
Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.
High Temporal but Low Spatial Heterogeneity of Bacterioplankton in the Chesapeake Bay
Authors: Kan Jinjun , Suzuki Marcelino T. , Wang Kui , Evans Sarah E. , Chen Feng 
Published: September 2007

ABSTRACT

Compared to freshwater and the open ocean, less is known about bacterioplankton community structure and spatiotemporal dynamics in estuaries, particularly those with long residence times. The Chesapeake Bay is the largest estuary in the United States, but despite its ecological and economic significance, little is known about its microbial community composition. A rapid screening approach, ITS (internal transcribed spacer)-LH (length heterogeneity)-PCR, was used to screen six rRNA operon (16S rRNA-ITS-23S rRNA) clone libraries constructed from bacterioplankton collected in three distinct regions of the Chesapeake Bay over two seasons. The natural length variation of the 16S-23S rRNA gene ITS region, as well as the presence and location of tRNA-alanine coding regions within the ITS, was determined for 576 clones. Clones representing unique ITS-LH-PCR sizes were sequenced and identified. Dramatic shifts in bacterial composition (changes within subgroups or clades) were observed for the
Alphaproteobacteria
(
Roseobacter
clade, SAR11),
Cyanobacteria
(
Synechococcus
), and
Actinobacteria
, suggesting strong seasonal variation within these taxonomic groups. Despite large gradients in salinity and phytoplankton parameters, a remarkably homogeneous bacterioplankton community was observed in the bay in each season. Stronger seasonal, rather than spatial, variation of the bacterioplankton population was also supported by denaturing gradient gel electrophoresis and LH-PCR analyses, indicating that environmental parameters with stronger seasonal, rather than regional, dynamics, such as temperature, might determine bacterioplankton community composition in the Chesapeake Bay.
Adaptation and Response of
Bifidobacterium animalis
subsp.
lactis
to Bile: a Proteomic and Physiological Approach
Authors: Sánchez Borja , Champomier-Vergès Marie-Christine , Stuer-Lauridsen Birgitte , Ruas-Madiedo Patricia , Anglade Patricia , Baraige Fabienne , de los Reyes-Gavilán Clara G. , Johansen Eric , Zagorec Monique , Margolles Abelardo 
Published: September 2007

ABSTRACT

Bile salts are natural detergents that facilitate the digestion and absorption of the hydrophobic components of the diet. However, their amphiphilic nature makes them very inhibitory for bacteria and strongly influences bacterial survival in the gastrointestinal tract. Adaptation to and tolerance of bile stress is therefore crucial for the persistence of bacteria in the human colonic niche.
Bifidobacterium animalis
subsp.
lactis
, a probiotic bacterium with documented health benefits, is applied largely in fermented dairy products. In this study, the effect of bile salts on proteomes of
B. animalis
subsp.
lactis
IPLA 4549 and its bile-resistant derivative
B. animalis
subsp.
lactis
4549dOx was analyzed, leading to the identification of proteins which may represent the targets of bile salt response and adaptation in
B. animalis
subsp.
lactis
. The comparison of the wild-type and the bile-resistant strain responses allowed us to hypothesize about the resistance mechanisms acquired by the derivative resistant strain and about the bile salt response in
B. animalis
subsp.
lactis
. In addition, significant differences in the levels of metabolic end products of the bifid shunt and in the redox status of the cells were also detected, which correlate with some differences observed between the proteomes. These results indicate that adaptation and response to bile in
B. animalis
subsp.
lactis
involve several physiological mechanisms that are jointly dedicated to reduce the deleterious impact of bile on the cell's physiology.
Indirect Oxidation of Co(II) in the Presence of the Marine Mn(II)-Oxidizing Bacterium
Bacillus
sp. Strain SG-1
Authors: Murray Karen J. , Webb Samuel M. , Bargar John R. , Tebo Bradley M. 
Published: September 2007

ABSTRACT

Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium
Bacillus
sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.
Maximizing Recovery and Detection of
Cryptosporidium parvum
Oocysts from Spiked Eastern Oyster (
Crassostrea virginica
) Tissue Samples
Authors: Downey Autumn S. , Graczyk Thaddeus K. 
Published: September 2007

ABSTRACT

Numerous studies have documented the presence of
Cryptosporidium parvum
, an anthropozoonotic enteric parasite, in molluscan shellfish harvested for commercial purposes. Getting accurate estimates of
Cryptosporidium
contamination levels in molluscan shellfish is difficult because recovery efficiencies are dependent on the isolation method used. Such estimates are important for determining the human health risks posed by consumption of contaminated shellfish. In the present study, oocyst recovery was compared for multiple methods used to isolate
Cryptosporidium parvum
oocysts from oysters (
Crassostrea virginica
) after exposure to contaminated water for 24 h. The immunomagnetic separation (IMS) and immunofluorescent antibody procedures from Environmental Protection Agency method 1623 were adapted for these purposes. Recovery efficiencies for the different methods were also determined using oyster tissue homogenate and hemolymph spiked with oocysts. There were significant differences in recovery efficiency among the different treatment groups (
P
< 0.05). We observed the highest recovery efficiency (i.e., 51%) from spiked samples when hemolymph was kept separate during the homogenization of the whole oyster meat but was then added to the pellet following diethyl ether extraction of the homogenate, prior to IMS. Using this processing method, as few as 10 oocysts could be detected in a spiked homogenate sample by nested PCR. In the absence of water quality indicators that correlate with
Cryptosporidium
contamination levels, assessment of shellfish safety may rely on accurate quantification of oocyst loads, necessitating the use of processing methods that maximize oocyst recovery. The results from this study have important implications for regulatory agencies charged with determining the safety of molluscan shellfish for human consumption.
Degradation of Carbazole by Microbial Cells Immobilized in Magnetic Gellan Gum Gel Beads
Authors: Wang Xia , Gai Zhonghui , Yu Bo , Feng Jinhui , Xu Changyong , Yuan Yong , Lin Zhixin , Xu Ping 
Published: September 2007

ABSTRACT

Polycyclic aromatic heterocycles, such as carbazole, are environmental contaminants suspected of posing human health risks. In this study, we investigated the degradation of carbazole by immobilized
Sphingomonas
sp. strain XLDN2-5 cells. Four kinds of polymers were evaluated as immobilization supports for
Sphingomonas
sp. strain XLDN2-5. After comparison with agar, alginate, and κ-carrageenan, gellan gum was selected as the optimal immobilization support. Furthermore, Fe
3
O
4
nanoparticles were prepared by a coprecipitation method, and the average particle size was about 20 nm with 49.65-electromagnetic-unit (emu) g
−1
saturation magnetization. When the mixture of gellan gel and the Fe
3
O
4
nanoparticles served as an immobilization support, the magnetically immobilized cells were prepared by an ionotropic method. The biodegradation experiments were carried out by employing free cells, nonmagnetically immobilized cells, and magnetically immobilized cells in aqueous phase. The results showed that the magnetically immobilized cells presented higher carbazole biodegradation activity than nonmagnetically immobilized cells and free cells. The highest biodegradation activity was obtained when the concentration of Fe
3
O
4
nanoparticles was 9 mg ml
−1
and the saturation magnetization of magnetically immobilized cells was 11.08 emu g
−1
. Additionally, the recycling experiments demonstrated that the degradation activity of magnetically immobilized cells increased gradually during the eight recycles. These results support developing efficient biocatalysts using magnetically immobilized cells and provide a promising technique for improving biocatalysts used in the biodegradation of not only carbazole, but also other hazardous organic compounds.
Antimicrobial Susceptibilities of
Vibrio parahaemolyticus
and
Vibrio vulnificus
Isolates from Louisiana Gulf and Retail Raw Oysters
Authors: Han Feifei , Walker Robert D. , Janes Marlene E. , Prinyawiwatkul Witoon , Ge Beilei 
Published: September 2007

ABSTRACT

The antimicrobial susceptibilities of 168
Vibrio parahaemolyticus
and 151
Vibrio vulnificus
isolates recovered from 82 Louisiana Gulf and retail oysters in 2005 and 2006 were determined. Overall, the two vibrios remained susceptible to the majority of antimicrobials tested; reduced susceptibility was detected only in
V. parahaemolyticus
for ampicillin (81%; MIC ≥ 16 μg/ml). Additionally,
V. parahaemolyticus
displayed significantly higher MICs for cefotaxime, ciprofloxacin, and tetracycline than
V. vulnificus
.
Identification and Expression Analyses of Putative Sesquiterpene Synthase Genes in
Phormidium
sp. and Prevalence of
geoA
-Like Genes in a Drinking Water Reservoir
Authors: Ludwig Frank , Medger Anja , Börnick Hilmar , Opitz Michael , Lang Kathrin , Göttfert Michael , Röske Isolde 
Published: September 2007

ABSTRACT

The occurrence of taste and odor problems in drinking water supplies is a widespread phenomenon. From a Saxonian water reservoir we isolated a cyanobacterial species which was classified as
Phormidium
sp. Under laboratory conditions it produced an earthy-musty smell due to the synthesis of geosmin. The only genes shown to be involved in geosmin biosynthesis are
cyc2
and
geoA
of
Streptomyces
. Based on the alignment of Cyc2 with a putative sesquiterpene synthase of
Nostoc punctiforme
, a degenerate primer pair was designed. By PCR, we could amplify two similar genes in
Phormidium
sp., which we named
geoA1
and
geoA2
. Their expression was studied by reverse transcription-PCR. This revealed that both genes are expressed at 20°C and a light-dark cycle of 12 h. Expression was not detectable at the end of a 24-h dark period. To analyze the prevalence of
geoA1
and
geoA2
in samples from the phytobenthos, we generated PCR fragments with the same degenerate primer pair. Fifty-five different sequences that might represent
geoA
variants were obtained. The GC content ranged from 42% to 67%, suggesting that taxonomically very different bacteria might contain such genes.
Detection and Quantification of
Geobacter lovleyi
Strain SZ: Implications for Bioremediation at Tetrachloroethene- and Uranium-Impacted Sites
Authors: Amos Benjamin K. , Sung Youlboong , Fletcher Kelly E. , Gentry Terry J. , Wu Wei-Min , Criddle Craig S. , Zhou Jizhong , Löffler Frank E. 
Published: September 2007

ABSTRACT

Geobacter lovleyi
strain SZ reduces hexavalent uranium, U(VI), to U(IV) and is the first member of the metal-reducing
Geobacter
group capable of using tetrachloroethene (PCE) as a growth-supporting electron acceptor. Direct and nested PCR with specific 16S rRNA gene-targeted primer pairs distinguished strain SZ from other known chlorinated ethene-dechlorinating bacteria and closely related
Geobacter
isolates, including its closest cultured relative,
G. thiogenes
. Detection limits for direct and nested PCR were approximately 1 × 10
6
and 1 × 10
4
16S rRNA gene copies per μl of template DNA, respectively. A quantitative real-time PCR (qPCR) approach increased the sensitivity to as few as 30 16S rRNA gene copies per μl of template DNA but was less specific. Melting curve analysis and comparison of the shapes of amplification plots identified false-positive signals and distinguished strain SZ from
G. thiogenes
when analyzed separately. These indicators were less reliable when target (strain SZ) DNA and nontarget (
G. thiogenes
) DNA with high sequence similarity were mixed, indicating that the development of qPCR protocols should not only evaluate specificity but also explore the effects of nontarget DNA on the accuracy of quantification. Application of specific tools detected strain SZ-like amplicons in PCE-dechlorinating consortia, including the bioaugmentation consortium KB-1, and two chlorinated ethene-impacted groundwater samples. Strain SZ-like amplicons were also detected in 13 of 22 groundwater samples following biostimulation at the uranium- and chlorinated solvent-contaminated Integrated Field-Scale Subsurface Research Challenge (IFC) site in Oak Ridge, TN. The numbers of strain SZ-like cells increased from below detection to 2.3 × 10
7
± 0.1 × 10
7
per liter groundwater, suggesting that strain SZ-like organisms contribute to contaminant transformation. The
G. lovleyi
strain SZ-specific tools will be useful for monitoring bioremediation efforts at uranium- and/or chlorinated solvent-impacted sites such as the Oak Ridge IFC site.
Characterization of Regulatory Pathways in
Xylella fastidiosa
: Genes and Phenotypes Controlled by
algU
Authors: Shi Xiang Yang , Dumenyo C. Korsi , Hernandez-Martinez Rufina , Azad Hamid , Cooksey Donald A. 
Published: September 2007

ABSTRACT

Many virulence genes in plant bacterial pathogens are coordinately regulated by “global” regulatory genes. Conducting DNA microarray analysis of bacterial mutants of such genes, compared with the wild type, can help to refine the list of genes that may contribute to virulence in bacterial pathogens. The regulatory gene
algU
, with roles in stress response and regulation of the biosynthesis of the exopolysaccharide alginate in
Pseudomonas aeruginosa
and many other bacteria, has been extensively studied. The role of
algU
in
Xylella fastidiosa
, the cause of Pierce's disease of grapevines, was analyzed by mutation and whole-genome microarray analysis to define its involvement in aggregation, biofilm formation, and virulence. In this study, an
algU
::
nptII
mutant had reduced cell-cell aggregation, attachment, and biofilm formation and lower virulence in grapevines. Microarray analysis showed that 42 genes had significantly lower expression in the
algU
::
nptII
mutant than in the wild type. Among these are several genes that could contribute to cell aggregation and biofilm formation, as well as other physiological processes such as virulence, competition, and survival.
Impact of Inorganic Carbon Availability on Microcystin Production by
Microcystis aeruginosa
PCC 7806
Authors: Jähnichen Sabine , Ihle Tilo , Petzoldt Thomas , Benndorf Jürgen 
Published: September 2007

ABSTRACT

Batch culture experiments with the cyanobacterium
Microcystis aeruginosa
PCC 7806 were performed in order to test the hypothesis that microcystins (MCYSTs) are produced in response to a relative deficiency of intracellular inorganic carbon (C
i,i
). In the first experiment, MCYST production was studied under increased C
i,i
deficiency conditions, achieved by restricting sodium-dependent bicarbonate uptake through replacement of sodium bicarbonate in the medium with its potassium analog. The same experimental approach was used in a second experiment to compare the response of the wild-type strain
M. aeruginosa
PCC 7806 with its
mcyB
mutant, which lacks the ability to produce MCYSTs. In a third experiment, the impact of varying the C
i,i
status on MCYST production was examined without suppressing the sodium-dependent bicarbonate transporter; instead, a detailed investigation of a dark-light cycle was performed. In all experiments, a relative C
i,i
deficiency was indicated by an elevated variable fluorescence signal and led to enhanced phycocyanin cell quotas. Higher MCYST cell quotas (in the first and third experiments) and increased total (intracellular plus extracellular) MCYST production (in the first experiment) were detected with increased C
i,i
deficiency. Furthermore, the MCYST-producing wild-type strain and its
mcyB
mutant showed basically the same response to restrained inorganic carbon uptake, with elevated variable fluorescence and phycocyanin cell quotas with increased C
i,i
deficiency. The response of the wild type, however, was distinctly stronger and also included elevated chlorophyll
a
cell quotas. These differences indicate the limited ability of the mutant to adapt to low-C
i,i
conditions. We concluded that MCYSTs may be involved in enhancing the efficiency of the adaptation of the photosynthetic apparatus to fluctuating inorganic carbon conditions in cyanobacterial cells.
Impact of Environmental and Genetic Factors on Biofilm Formation by the Probiotic Strain
Lactobacillus rhamnosus
GG
Authors: Lebeer Sarah , Verhoeven Tine L. A. , Perea Vélez Mónica , Vanderleyden Jos , De Keersmaecker Sigrid C. J. 
Published: September 2007

ABSTRACT

Lactobacillus rhamnosus
GG (ATCC 53103) is one of the clinically best-studied probiotic organisms. Moreover,
L. rhamnosus
GG displays very good in vitro adherence to epithelial cells and mucus. Here, we report that
L. rhamnosus
GG is able to form biofilms on abiotic surfaces, in contrast to other strains of the
Lactobacillus casei
group tested under the same conditions. Microtiter plate biofilm assays indicated that in vitro biofilm formation by
L. rhamnosus
GG is strongly modulated by culture medium factors and conditions related to the gastrointestinal environment, including low pH; high osmolarity; and the presence of bile, mucins, and nondigestible polysaccharides. Additionally, phenotypic analysis of mutants affected in exopolysaccharides (
wzb
), lipoteichoic acid (
dltD
), and central metabolism (
luxS
) showed their relative importance in biofilm formation by
L. rhamnosus
GG.
Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots
Authors: Flores-Mireles Ana L. , Winans Stephen C. , Holguin Gina 
Published: September 2007

ABSTRACT

An analysis of the molecular diversity of N
2
fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of
nifH
(N
2
fixation) and
nirS
and
nirK
(denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for
nifH
was higher than that for
nirK
or
nirS
at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest
nifH
diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For
nirS
, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for
nifH
. OTU defined on the basis of
nirK
were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of
nifH
,
nirK
, and
nirS
showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.