bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Integrative Method To Generate
Bacillus subtilis
Recombinant Strains Free of Selection Markers
Authors: Brans Alain , Filée Patrice , Chevigné Andy , Claessens Aurore , Joris Bernard 
Published: December 2004

ABSTRACT

The novel method described in this paper combines the use of
blaI
, which encodes a repressor involved in
Bacillus licheniformis
BlaP β-lactamase regulation, an antibiotic resistance gene, and a
B. subtilis
strain (BS1541) that is conditionally auxotrophic for lysine. We constructed a BlaI cassette containing
blaI
and the spectinomycin resistance genes and two short direct repeat DNA sequences, one at each extremity of the cassette. The BS1541 strain was obtained by replacing the
B. subtilis
P

lysA

promoter with that of the P

blaP

β-lactamase promoter. In the resulting strain, the cloning of the
blaI
repressor gene confers lysine auxotrophy to BS1541. After integration of the BlaI cassette into the chromosome of a conditionally
lys
-auxotrophic (BS1541) strain by homologous recombination and positive selection for spectinomycin resistance, the eviction of the BlaI cassette was achieved by single crossover between the two short direct repeat sequences. This strategy was successfully used to inactivate a single gene and to introduce a gene of interest in the
Bacillus
chromosome. In both cases the resulting strains are free of selection marker. This allows the use of the BlaI cassette to repeatedly further modify the
Bacillus
chromosome.
In Situ Expression of
nifD
in
Geobacteraceae
in Subsurface Sediments
Authors: Holmes Dawn E. , Nevin Kelly P. , Lovley Derek R. 
Published: December 2004

ABSTRACT

In order to determine whether the metabolic state of
Geobacteraceae
involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of
nifD
, a highly conserved gene involved in nitrogen fixation, was investigated. When
Geobacter sulfurreducens
was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of
nifD
transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of
recA
and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of
Geobacteraceae
and Fe(III) reduction, as well as the expression of
nifD
in
Geobacteraceae
. Levels of
nifD
transcripts in
Geobacteraceae
decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of
recA
and total bacterial 16S rRNA in
Geobacteraceae
remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that
Geobacteraceae
could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of
Geobacteraceae
species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by
Geobacteraceae
.
Detection and Quantification ofWallemia sebiin Aerosols by Real-Time PCR, Conventional PCR, and Cultivation
Authors: Zeng Qing-Yin , Westermark Sven-Olof , Rasmuson-Lestander Åsa , Wang Xiao-Ru 
Published: December 2004

ABSTRACTWallemia sebiis a deuteromycete fungus commonly found in agricultural environments in many parts of the world and is suspected to be a causative agent of farmer's lung disease. The fungus grows slowly on commonly used culture media and is often obscured by the fast-growing fungi. Thus, its occurrence in different environments has often been underestimated. In this study, we developed two sets of PCR primers specific toW. sebithat can be applied in either conventional PCR or real-time PCR for rapid detection and quantification of the fungus in environmental samples. Both PCR systems proved to be highly specific and sensitive forW. sebidetection even in a high background of other fungal DNAs. These methods were employed to investigate the presence ofW. sebiin the aerosols of a farm. The results revealed a high concentration ofW. sebispores, 107m−3by real-time PCR and 106m−3by cultivation, which indicates the prevalence ofW. sebiin farms handling hay and grain and in cow barns. The methods developed in this study could serve as rapid, specific, and sensitive means of detectingW. sebiin aerosol and surface samples and could thus facilitate investigations of its distribution, ecology, clinical diagnosis, and exposure risk assessment.
Quantification of Tetracycline Resistance Genes in Feedlot Lagoons by Real-Time PCR
Authors: Smith Marilyn S. , Yang Richard K. , Knapp Charles W. , Niu Yafen , Peak Nicholas , Hanfelt Margery M. , Galland John C. , Graham David W. 
Published: December 2004

ABSTRACT

A new real-time PCR method is presented that detects and quantifies three tetracycline resistance (Tc
r
) genes [
tet
(O),
tet
(W), and
tet
(Q)] in mixed microbial communities resident in feedlot lagoon wastewater. Tc
r
gene real-time TaqMan primer-probe sets were developed and optimized to quantify the Tc
r
genes present in seven different cattle feedlot lagoons, to validate the method, and to assess whether resistance gene concentrations correlate with free-tetracycline levels in lagoon waters. The method proved to be sensitive across a wide range of gene concentrations and provided consistent and reproducible results from complex lagoon water samples. The log
10
of the sum of the three resistance gene concentrations was correlated with free-tetracycline levels (
r
2
= 0.50,
P
< 0.001;
n
= 18), with the geometric means of individual resistance concentrations ranging from 4- to 8.3-fold greater in lagoon samples with above-median tetracycline levels (>1.95 μg/liter by enzyme-linked immunosorbent assay techniques) than in below-median lagoon samples. Of the three Tc
r
genes tested,
tet
(W) and
tet
(Q) were more commonly found in lagoon water samples. Successful development of this real-time PCR assay will permit other studies quantifying Tc
r
gene numbers in environmental and other samples.
Hypothesis for the Role of Nutrient Starvation in Biofilm Detachment
Authors: Hunt Stephen M. , Werner Erin M. , Huang Baochuan , Hamilton Martin A. , Stewart Philip S. 
Published: December 2004

ABSTRACT

A combination of experimental and theoretical approaches was used to investigate the role of nutrient starvation as a potential trigger for biofilm detachment. Experimental observations of detachment in a variety of biofilm systems were made with pure cultures of
Pseudomonas aeruginosa
. These observations indicated that biofilms grown under continuous-flow conditions detached after flow was stopped, that hollow cell clusters were sometimes observed in biofilms grown in flow cells, and that lysed cells were apparent in the internal strata of colony biofilms. When biofilms were nutrient starved under continuous-flow conditions, detachment still occurred, suggesting that starvation and not the accumulation of a metabolic product was responsible for triggering detachment in this particular system. A cellular automata computer model of biofilm dynamics was used to explore the starvation-dependent detachment mechanism. The model predicted biofilm structures and dynamics that were qualitatively similar to those observed experimentally. The predicted features included centrally located voids appearing in sufficiently large cell clusters, gradients in growth rate within these clusters, and the release of most of the biofilm with simulated stopped-flow conditions. The model was also able to predict biofilm sloughing resulting solely from this detachment mechanism. These results support the conjecture that nutrient starvation is an environmental cue for the release of microbes from a biofilm.
Characterization of C
1
-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing
pmoA
,
mmoX
,
mxaF
,
mcrA
, and 16S rRNA Genes
Authors: Inagaki Fumio , Tsunogai Urumu , Suzuki Masae , Kosaka Ayako , Machiyama Hideaki , Takai Ken , Nunoura Takuro , Nealson Kenneth H. , Horikoshi Koki 
Published: December 2004

ABSTRACT

Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (∼34% of the total prokaryotes), including both mesophilic methanogens related to the genus
Methanolobus
and ANME-2 members of the
Methanosarcinales
, as well as members of the δ-
Proteobacteria
, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (
pmoA
), soluble methane monooxygenase (
mmoX
), methanol dehydrogenese (
mxaF
), and methyl coenzyme M reductase (
mcrA
). In the MC core sediments, the most abundant gene was
mcrA
(2.5 × 10
6
copies/g [wet weight]), while the
pmoA
gene of the type I methanotrophs (5.9 × 10
6
copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in γ-
Proteobacteria
and had a high copy number of
mxaF
(7.1 × 10
6
copies/g [wet weight]) and a much lower copy number of the
pmoA
gene (3.2 × 10
2
copies/g [wet weight]). The
mmoX
gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C
1
metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.
Viable but Nonculturable
Vibrio cholerae
O1 in the Aquatic Environment of Argentina
Authors: Binsztein Norma , Costagliola Marcela C. , Pichel Mariana , Jurquiza Verónica , Ramírez Fernando C. , Akselman Rut , Vacchino Marta , Huq Anwarul , Colwell Rita 
Published: December 2004

ABSTRACT

In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern.
Vibrio cholerae
O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC
V. cholerae
O1 in the estuarine and marine waters of the Río de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of
V. cholerae
O1 carrying the virulence-associated genes
ctxA
and
tcpA
. The VNC forms of
V. cholerae
O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods
Acartia tonsa
,
Diaptomus
sp.,
Paracalanus crassirostris
, and
Paracalanus parvus
. We found that under favorable conditions, the VNC form of
V. cholerae
can revert to the pathogenic, transmissible state. We concluded that
V. cholerae
O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world.
A Previously Unexposed Forest Soil Microbial Community Degrades High Levels of the Pollutant 2,4,6-Trichlorophenol
Authors: Sánchez M. A. , Vásquez M. , González B. 
Published: December 2004

ABSTRACT

2,4,6-Trichlorophenol (2,4,6-TCP) is a hazardous pollutant that is efficiently degraded by some aerobic soil bacterial isolates under laboratory conditions. The degradation of this pollutant in soils and its effect on the soil microbial community are poorly understood. We report here the ability of a previously unexposed forest soil microbiota to degrade high levels of 2,4,6-TCP and describe the changes in the soil microbial community found by terminal restriction fragment length polymorphism (T-RFLP) analysis. After 30 days of incubation, about 50% degradation of this pollutant was observed in soils amended with 50 to 5,000 ppm of 2,4,6-TCP. The T-RFLP analysis showed that the soil bacterial community was essentially unchanged after exposure to up to 500 ppm of 2,4,6-TCP. However, a significant decrease in richness was found with 2,000 and 5,000 ppm of 2,4,6-TCP, even though the removal of this pollutant remained high. The introduction of
Ralstonia eutropha
JMP134 or
R. eutropha
MS1, two efficient 2,4,6-TCP degraders, to this soil did not improve degradation of this pollutant, supporting the significant bioremediation potential of this previously unexposed, endogenous forest soil microbial community.
Diversity of Nontuberculoid
Mycobacterium
Species in Biofilms of Urban and Semiurban Drinking Water Distribution Systems
Authors: September S. M. , Brözel V. S. , Venter S. N. 
Published: December 2004

ABSTRACT

Nontuberculous mycobacteria (NTM) are ubiquitous and have been isolated from a variety of environmental sources, including water. Various NTM were isolated from biofilms in drinking water distribution systems in two urban and two semiurban areas in South Africa. Most of the isolates belonged to opportunistic pathogenic species of the NTM group, but none belonged to the
Mycobacterium avium
complex.
Association of
Escherichia coli
O157:H7 with Houseflies on a Cattle Farm
Authors: Alam Muhammad J. , Zurek Ludek 
Published: December 2004

ABSTRACT

The ecology of
Escherichia coli
O157:H7 is not well understood. The aims of this study were to determine the prevalence of and characterize
E. coli
O157:H7 associated with houseflies (HF).
Musca domestica
L. HF (
n
= 3,440) were collected from two sites on a cattle farm over a 4-month period and processed individually for
E. coli
O157:H7 isolation and quantification. The prevalence of
E. coli
O157:H7 was 2.9 and 1.4% in HF collected from feed bunks and a cattle feed storage shed, respectively.
E. coli
O157:H7 counts ranged from 3.0 × 10
1
to 1.5 × 10
5
CFU among the positive HF. PCR analysis of the
E. coli
O157:H7 isolates revealed that 90.4, 99.2, 99.2, and 100% of them (
n
= 125) possessed the
stx1
,
stx2
,
eaeA
, and
fliC
genes, respectively. Large populations of HF on cattle farms may play a role in the dissemination of
E. coli
O157:H7 among animals and to the surrounding environment.
Comparative Genomics of the T4-Like
Escherichia coli
Phage JS98: Implications for the Evolution of T4 Phages
Authors: Chibani-Chennoufi Sandra , Canchaya Carlos , Bruttin Anne , Brüssow Harald 
Published: December 2004

ABSTRACT

About 130 kb of sequence information was obtained from the coliphage JS98 isolated from the stool of a pediatric diarrhea patient in Bangladesh. The DNA shared up to 81% base pair identity with phage T4. The most conserved regions between JS98 and T4 were the structural genes, but their degree of conservation was not uniform. The head genes showed the highest sequence conservation, followed by the tail, baseplate, and tail fiber genes. Many tail fiber genes shared only protein sequence identity. Except for the insertion of endonuclease genes in T4 and gene
24
duplication in JS98, the structural gene maps of the two phages were colinear. The receptor-recognizing tail fiber proteins gp37 and gp38 were only distantly related to T4, but shared up to 83% amino acid identity to other T6-like phages, suggesting lateral gene transfer. A greater degree of variability was seen between JS98 and T4 over DNA replication and DNA transaction genes. While most of these genes came in the same order and shared up to 76% protein sequence identity, a few rearrangements, insertions, and replacements of genes were observed. Many putative gene insertions in the DNA replication module of T4 were flanked by intron-related endonuclease genes, suggesting mobile DNA elements. A hotspot of genome diversification was located downstream of the DNA polymerase gene
43
and the DNA binding gene
32
. Comparative genomics of 100-kb genome sequence revealed that T4-like phages diversify more by the accumulation of point mutations and occasional gene duplication events than by modular exchanges.
RpoS-Regulated Genes ofEscherichia coliIdentified by RandomlacZFusion Mutagenesis
Authors: Vijayakumar Somalinga R. V. , Kirchhof Mark G. , Patten Cheryl L. , Schellhorn Herb E. 
Published: December 2004

ABSTRACTRpoS is a conserved alternative sigma factor that regulates the expression of many stress response genes inEscherichia coli. The RpoS regulon is large but has not yet been completely characterized. In this study, we report the identification of over 100 RpoS-dependent fusions in a genetic screen based on the differential expression of an operon-lacZfusion bank inrpoSmutant and wild-type backgrounds. Forty-eight independent gene fusions were identified, including several in well-characterized RpoS-regulated genes, such asosmY,katE, andotsA. Many of the other fusions mapped to genes of unknown function or to genes that were not previously known to be under RpoS control. Based on the homology to other known bacterial genes, some of the RpoS-regulated genes of unknown functions are likely important in nutrient scavenging.
Damages in Islamic Law: Maghribī Muftīs and the Built Environment (9th-15th Centuries C.E.)
Authors: Kahera Akel , Benmira Omar 
Published: December 2004

AbstractThe Mālikī jurists of the Maghrib, or Islamic West, applied the ḥadīth, “no harm shall be inflicted [on anyone] or reciprocated [against anyone]” (lā ḍarar wa-lā ḍirār fī-l-Islām ). This axiom called for the exercise of the muftī's independent reasoning (ijtihād) in matters that were not explicitly clear from the text (naṣṣ) of the Qurʾāan or sunnah. Mālikī jurists used this axiom, which was open to various interpretations, as a basis for rendering legal opinions (fatāwā) in domestic conflicts arising from infractions relating to the socio-spatial world.
Islamic Values, Law and Expectations in Contemporary Indonesia
Authors: Federspiel Howard 
Published: December 2004

AbstractIn this essay I survey the wide variety of views manifested by Indonesians regarding Islamic values and law. Within government circles, the security conscious “guardian group” bars political Islam but regards worship as benign, while the Ministry of Religious Affairs has adopted an accommodationist stance which promotes Muslim community values outside of politics. Outside of government, non-Muslims and nominal Muslims are chary of Islamic values and attempts to institute Islamic law, while Muslim groups express a strong desire to have Islamic norms operate for the betterment of society and to fulfill Qurʿanic admonitions about such matters. Some Muslim groups call for greater attention by individuals to Islamic teachings, while others call for the establishment of sacred law in society. Most Muslim groups want the Indonesian state to identify with Islam, but, at the same time, many approve of the current national policies regarding inter-communal harmony and the emphasis on modernity.
Frizzled 9 knock-out mice have abnormal B-cell development
Authors: Ranheim Erik A. , Kwan Helen C. K. , Reya Tannishtha , Wang Yu-Ker , Weissman Irving L. , Francke Uta 
Published: December 2004

AbstractThe binding of frizzled (Fzd) receptors by their Wnt ligands results in the inhibition of β-catenin degradation and subsequent transcription of β-catenin/LEF–inducible genes. The β-catenin pathway is known to be involved in development, tumorigenesis, and stem cell self-renewal. In humans, the FZD9 gene lies in the region of chromosome 7q11.23 deleted in the neurodevelopmental disorder, Williams-Beuren syndrome (WBS). Fzd9-/- mice show no obvious features of WBS, but reveal a role for Fzd9 in lymphoid development and maturation. Fzd9-/- mice show pronounced splenomegaly, thymic atrophy, and lymphadenopathy with age, with accumulation of plasma cells in lymph nodes. There is a depletion of developing B cells in the bone marrow (BM), particularly in the pre-B stage where immunoglobulin heavy chains are expressed and the cells are undergoing clonal expansion prior to light chain rearrangement. The pre-B defect is partially intrinsic to the hematopoietic system; as in competitive BM reconstitution studies, Fzd9-/--derived BM exhibits defective B-cell development when implanted into a wild-type host. Mature B cells are present in normal numbers in lymph node and spleen. These findings suggest a role for Fzd9 signaling in lymphoid development, particularly at points where B cells undergo self-renewal prior to further differentiation.
Downregulation of Smac/DIABLO Expression in Renal Cell Carcinoma and Its Prognostic Significance
Authors: Mizutani Yoichi , Nakanishi Hiroyuki , Yamamoto Kosuke , Li Yong Nan , Matsubara Hiroki , Mikami Kazuya , Okihara Koji , Kawauchi Akihiro , Bonavida Benjamin , Miki Tsuneharu 
Published: December 2004

Purpose Second mitochondria-derived activator of caspase/direct inhibitor of apoptosis-binding protein with low pI (Smac/DIABLO) was recently identified as a protein that is released from mitochondria in response to apoptotic stimuli and promotes apoptosis by antagonizing inhibitor of apoptosis proteins. Furthermore, Smac/DIABLO plays an important regulatory role in the sensitization of cancer cells to both immune- and drug-induced apoptosis. However, little is known about the clinical significance of Smac/DIABLO in various cancers, including renal cell carcinoma (RCC). This study examined Smac/DIABLO expression in 78 healthy kidneys and 78 RCCs. Materials and Methods The level of Smac/DIABLO expression was quantified by Western blot analysis using nonfixed fresh frozen tissues. Results The expression of Smac/DIABLO was lower in RCC compared with the autologous normal kidney. Sixty-four (82%) of 78 of RCC expressed Smac/DIABLO, and 18% were negative, whereas 100% of normal kidney tissues were positive. In stage I/II RCC, 96% expressed Smac/DIABLO, whereas only 50% expressed Smac/DIABLO in stage III/IV. Smac/DIABLO expression inversely correlated with the grade of RCC. Patients with RCC expressing Smac/DIABLO had a longer postoperative disease-specific survival than those without Smac/DIABLO expression in the 5-year follow-up. Transfection with Smac/DIABLO cDNA enhanced tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) –mediated and cisplatin-mediated cytotoxicity in RCC. Conclusion The present study demonstrates for the first time that Smac/DIABLO expression was downregulated in RCC and that no Smac/DIABLO expression in RCC predicted a worse prognosis. In addition, transfection with Smac/DIABLO sensitized RCC to TRAIL/cisplatin-induced apoptosis. These results suggest that Smac/DIABLO expression in RCC may be used as a prognostic parameter, and that enhancement of Smac/DIABLO expression in RCC may potentiate immunotherapy and chemotherapy.
First Geometrical Isomerization of [Co(d-pen-N,O,S)2]− Induced by Forming S-Bridged Structure with AuI or AgI: Crystal Structure of a CoIII3AuI3 Hexanuclear Metallacycle [Au3{Co(d-pen-N,O,S)2}3] (d-pen = d-Penicillaminate)
Authors: Konno Takumi , Hattori Masashi , Yoshimura Takashi , Hirotsu Masakazu 
Published: December 2004

Abstract
The reactions of trans(N)-[Co(d-pen-N,O,S)2]− with AuI or AgI in water led to the formation of novel S-bridged CoIII3M3 hexanuclear metallacycles [M3{Co(d-pen-N,O,S)2}3] (M = AuI (1), AgI (2)), in which [Co(d-pen-N,O,S)2]− units adopt a trans(O) geometry. The molecular structure of 1 was determined by X-ray crystallography.