bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclooxygenase‐2 Inhibitor Nimesulide Blocks Ultraviolet B‐induced Photocarcinogenesis in SKH‐1 Hairless Mice†
Authors: Tang Xiuwei , Kim Arianna L. , Kopelovich Levy , Bickers David R. , Athar Mohammad 
Published: February 2008

AbstractCyclooxygenase‐2 (COX‐2) inhibition can inhibit UVB‐induced carcinogenesis in the skin. We have shown that COX‐2 is overexpressed in UVB‐induced squamous cell carcinomas (SCCs). Celecoxib, a specific inhibitor of COX‐2, blocks UVB‐induced papillomas and carcinomas in murine skin. However, as COX‐2 inhibitors of this type are associated with an increased risk of adverse cardiovascular events, we decided to study nimesulide, a different class of COX‐2 inhibitor, an N‐arylmethanesulfonamide derivative not known to have these untoward effects. To assess the antitumor‐promoting effects of nimesulide, 90 mice were equally divided into three groups. Group I animals received no test agent or UVB and served as age‐matched controls; group II animals were irradiated with UVB (180 mJ cm−2, twice weekly for 35 weeks) and group III animals received 300 p.p.m. nimesulide in drinking water and were irradiated with UVB as described for group‐II. Nimesulide treatment reduced the growth of UVB‐induced tumors both in terms of tumor number and tumor volume. By weeks 25, 30 and 35, the tumor numbers in the nimesulide‐treated group were 79%, 49% and 53% less than the number occurring in UVB‐treated animals whereas tumor volume was reduced 69%, 54% and 53%, respectively, compared to the UVB‐irradiated control group. Nimesulide also inhibited the malignant progression of SCCs. The reduction in tumorigenesis was paralleled by a decrease in cell cycle regulatory proteins (cyclins A, B1, D1, E, CDK2/4/6) and the antiapoptotic protein (Bcl2); concomitantly there was an increase in proapoptotic markers, poly (ADP‐ribose) polymerase (PARP) and caspase‐3. Nimesulide also decreased ornithine decarboxylase expression and the nuclear accumulation of nuclear factor kappa B transcriptionally active protein complexes. These results show that alternative classes of COX‐2 inhibitors may likely be efficacious as cancer chemopreventive agents and may have an improved therapeutic index.
Estimating space‐use and habitat preference from wildlife telemetry data
Authors: Aarts Geert , MacKenzie Monique , McConnell Bernie , Fedak Mike , Matthiopoulos Jason 
Published: February 2008

Management and conservation of populations of animals requires information on where they are, why they are there, and where else they could be. These objectives are typically approached by collecting data on the animals' use of space, relating these positional data to prevailing environmental conditions and employing the resulting statistical models to predict usage at other geographical regions. Technical advances in wildlife telemetry have accomplished manifold increases in the amount and quality of available data, creating the need for a statistical framework that can use them to make population‐level inferences for habitat preference and space‐use. This has been slow‐in‐coming because wildlife telemetry data are spatio‐temporally autocorrelated, often unbalanced, presence‐only observations of behaviourally complex animals, responding to a multitude of cross‐correlated environmental variables.We review the evolution of regression models for the analysis of space‐use and habitat preference and outline the essential features of a framework that emerges naturally from these foundations. This allows us to derive a relationship between usage of points in geographical space and preference of habitats in environmental space. Within this framework, we discuss eight challenges, inherent in the spatial analysis of telemetry data and, for each, we propose solutions that can work in tandem. Specifically, we propose a logistic, mixed‐effects approach that uses generalized additive transformations of the environmental covariates and is fitted to a response data‐set comprising the telemetry and simulated observations, under a case‐control design.We apply this framework to a non‐trivial case‐study using satellite‐tagged grey seals Halichoerus grypus from the east coast of Scotland. We perform model selection by cross‐validation and confront our final model's predictions with telemetry data from the same, as well as different, geographical regions. We conclude that, despite the complex behaviour of the study species, flexible empirical models can capture the environmental relationships that shape population distributions.
Real-Time PCR Assays for Quantification and Differentiation of
Vibrio vulnificus
Strains in Oysters and Water
Authors: Gordon Katrina V. , Vickery Michael C. , DePaola Angelo , Staley Christopher , Harwood Valerie J. 
Published: February 2008

ABSTRACT

Vibrio vulnificus
is an autochthonous estuarine bacterium and a pathogen that is frequently transmitted via raw shellfish. Septicemia can occur within 24 h; however, isolation and confirmation from water and oysters require days. Real-time PCR assays were developed to detect and differentiate two 16S rRNA variants, types A and B, which were previously associated with environmental sources and clinical fatalities, respectively. Both assays could detect 10
2
to 10
3
V. vulnificus
total cells in seeded estuarine water and in oyster homogenates. PCR assays on 11 reference
V. vulnificus
strains and 22 nontarget species gave expected results (type A or B for
V. vulnificus
and negative for nontarget species). The relationship between cell number and cycle threshold for the assays was linear (
R
2
= >0.93). The type A/B ratio of Florida clinical isolates was compared to that of isolates from oysters harvested in Florida waters. This ratio was 19:17 in clinical isolates and 5:8 (
n
= 26) in oysters harvested from restricted sites with poor water quality but was 10:1 (
n
= 22) in oysters from permitted sites with good water quality. A substantial percentage of isolates from oysters (19.4%) were type AB (both primer sets amplified), but no isolates from overlying waters were type AB. The real-time PCR assays were sensitive, specific, and quantitative in water samples and could also differentiate the strains in oysters without requiring isolation of
V. vulnificus
and may therefore be useful for rapid detection of the pathogen in shellfish and water, as well as further investigation of its population dynamics.
Rapid Growth of Planktonic
Vibrio cholerae
Non-O1/Non-O139 Strains in a Large Alkaline Lake in Austria: Dependence on Temperature and Dissolved Organic Carbon Quality
Authors: Kirschner Alexander K. T. , Schlesinger Jane , Farnleitner Andreas H. , Hornek Romana , Süß Beate , Golda Beate , Herzig Alois , Reitner Bettina 
Published: February 2008

ABSTRACT

Vibrio cholerae
non-O1/non-O139 strains have caused several cases of ear, wound, and blood infections, including one lethal case of septicemia in Austria, during recent years. All of these cases had a history of local recreational activities in the large eastern Austrian lake Neusiedler See. Thus, a monitoring program was started to investigate the prevalence of
V. cholerae
strains in the lake over several years. Genetic analyses of isolated strains revealed the presence of a variety of pathogenic genes, but in no case did we detect the cholera toxin gene or the toxin-coregulated pilus gene, both of which are prerequisites for the pathogen to be able to cause cholera. In addition, experiments were performed to elucidate the preferred ecological niche of this pathogen. As size filtration experiments indicated and laboratory microcosms showed, endemic
V. cholerae
could rapidly grow in a free-living state in natural lake water at growth rates similar to those of the bulk natural bacterial population. Temperature and the quality of dissolved organic carbon had a highly significant influence on
V. cholerae
growth. Specific growth rates, growth yield, and enzyme activity decreased markedly with increasing concentrations of high-molecular-weight substances, indicating that the humic substances originating from the extensive reed belt in the lake can inhibit
V. cholerae
growth.
In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water
Authors: Miller Sarah M. , Tourlousse Dieter M. , Stedtfeld Robert D. , Baushke Samuel W. , Herzog Amanda B. , Wick Lukas M. , Rouillard Jean Marie , Gulari Erdogan , Tiedje James M. , Hashsham Syed A. 
Published: February 2008

ABSTRACT
Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence/absence calls, probes were designed for multiple virulence and marker genes (VMGs) of each pathogen, and each VMG was targeted by an average of 17 probes. Hybridization of the biochip with amplicon mixtures demonstrated that 95% of the initially designed probes behaved as predicted in terms of positive/negative signals. The probes were further validated using DNA obtained from three different types of water samples and spiked with pathogen genomic DNA at decreasing relative abundance. Excellent specificity for making presence/absence calls was observed by using a cutoff of 0.5 for the positive fraction (i.e., the fraction of probes yielding a positive signal for a given VMG). A split multiplex PCR design for simultaneous amplification of the VMGs resulted in a detection limit of between 0.1 and 0.01% relative abundance, depending on the type of pathogen and the VMG. Thermodynamic analysis of the hybridization patterns obtained with DNA from the different water samples demonstrated that probes with a hybridization Gibbs free energy of approximately −19.3 kcal/mol provided the best trade-off between sensitivity and specificity. The developed biochip may be used to detect the described bacterial pathogens in water samples when parallel and specific detection is required.
Role of Migratory Birds in Introduction and Range Expansion of
Ixodes scapularis
Ticks and of
Borrelia burgdorferi
and
Anaplasma phagocytophilum
in Canada
Authors: Ogden N. H. , Lindsay L. R. , Hanincová K. , Barker I. K. , Bigras-Poulin M. , Charron D. F. , Heagy A. , Francis C. M. , O'Callaghan C. J. , Schwartz I. , Thompson R. A. 
Published: February 2008

ABSTRACT

During the spring in 2005 and 2006, 39,095 northward-migrating land birds were captured at 12 bird observatories in eastern Canada to investigate the role of migratory birds in northward range expansion of Lyme borreliosis, human granulocytic anaplasmosis, and their tick vector,
Ixodes scapularis
. The prevalence of birds carrying
I. scapularis
ticks (mostly nymphs) was 0.35% (95% confidence interval [CI] = 0.30 to 0.42), but a nested study by experienced observers suggested a more realistic infestation prevalence of 2.2% (95% CI = 1.18 to 3.73). The mean infestation intensity was 1.66 per bird. Overall, 15.4% of
I. scapularis
nymphs (95% CI = 10.7 to 20.9) were PCR positive for
Borrelia burgdorferi
, but only 8% (95% CI = 3.8 to 15.1) were positive when excluding nymphs collected at Long Point, Ontario, where
B. burgdorferi
is endemic. A wide range of
ospC
and
rrs
-
rrl
intergenic spacer alleles of
B. burgdorferi
were identified in infected ticks, including those associated with disseminated Lyme disease and alleles that are rare in the northeastern United States. Overall, 0.4% (95% CI = 0.03 to 0.41) of
I. scapularis
nymphs were PCR positive for
Anaplasma phagocytophilum
. We estimate that migratory birds disperse 50 million to 175 million
I. scapularis
ticks across Canada each spring, implicating migratory birds as possibly significant in
I. scapularis
range expansion in Canada. However, infrequent larvae and the low infection prevalence in ticks carried by the birds raise questions as to how
B. burgdorferi
and
A. phagocytophilum
become endemic in any tick populations established by bird-transported ticks.
Discovery of the Autonomously Replicating Plasmid pMF1 from
Myxococcus fulvus
and Development of a Gene Cloning System in
Myxococcus xanthus
Authors: Zhao Jing-yi , Zhong Li , Shen Mei-juan , Xia Zhi-jie , Cheng Qiu-xiang , Sun Xia , Zhao Guo-ping , Li Yue-zhong , Qin Zhong-jun 
Published: February 2008

ABSTRACT

Myxobacteria are very important due to their unique characteristics, such as multicellular social behavior and the production of diverse and novel bioactive secondary metabolites. However, the lack of autonomously replicating plasmids has hindered genetic manipulation of myxobacteria for decades. To determine whether indigenous plasmids are present, we screened about 150 myxobacterial strains, and a circular plasmid designated pMF1 was isolated from
Myxococcus fulvus
124B02. Sequence analysis showed that this plasmid was 18,634 bp long and had a G+C content of 68.7%. Twenty-three open reading frames were found in the plasmid, and 14 of them were not homologous to any known sequence. Plasmids containing the gene designated pMF1.14, which encodes a large unknown protein, were shown to transform
Myxococcus xanthus
DZ1 and DK1622 at high frequencies (∼10
5
CFU/μg DNA), suggesting that the locus is responsible for the autonomous replication of pMF1. Shuttle vectors were constructed for both
M. xanthus
and
Escherichia coli
. The
pilA
gene, which is essential for pilus formation and social motility in
M. xanthus
, was cloned into the shuttle vectors and introduced into the
pilA
-deficient mutant DK10410. The transformants subsequently exhibited the ability to form pili and social motility. Autonomously replicating plasmid pMF1 provides a new tool for genetic manipulation in
Myxococcus.
Enhanced Heterologous Production of Desosaminyl Macrolides and Their Hydroxylated Derivatives by Overexpression of the
pikD
Regulatory Gene in
Streptomyces venezuelae
Authors: Jung Won Seok , Jeong Soon Jeong , Park Sung Ryeol , Choi Cha Yong , Park Byoung Chul , Park Je Won , Yoon Yeo Joon 
Published: February 2008

ABSTRACT

To elevate the production level of heterologous polyketide in
Streptomyces venezuelae
, an additional copy of the positive regulatory gene
pikD
was introduced into the pikromycin (Pik) polyketide synthase (PKS) deletion mutant of
S. venezuelae
ATCC 15439 expressing tylosin PKS genes. The resulting mutant strain showed enhanced production of both tylactone (TL) and desosaminyl tylactone (DesTL) of 2.7- and 17.1-fold, respectively. The notable increase in DesTL production strongly suggested that PikD upregulates the expression of the desosamine (
des
) biosynthetic gene cluster. In addition, two hydroxylated forms of DesTL were newly detected from the extract of this mutant. These hydroxylated forms presumably resulted from a PikD-dependent increase in expression of the
pikC
gene that encodes P450 hydroxylase. Gene expression analysis by reverse transcriptase PCR and bioconversion experiments of 10-deoxymethynolide, narbonolide, and TL into the corresponding desosaminyl macrolides indicated that PikD is a positive regulator of the
des
and
pikC
genes, as well as the Pik PKS genes. These results demonstrate the role of PikD as a pathway-specific positive regulator of the entire Pik biosynthetic pathway and its usefulness in the development of a host-vector system for efficient heterologous production of desosaminyl macrolides and novel hydroxylated compounds.
Characterization and Application of a Glucose-Repressible Promoter in
Francisella tularensis
Authors: Horzempa Joseph , Tarwacki Deanna M. , Carlson Paul E. , Robinson Cory M. , Nau Gerard J. 
Published: February 2008

ABSTRACT

Francisella tularensis
, the causative agent of tularemia, is a category A biodefense agent. The examination of gene function in this organism is limited due to the lack of available controllable promoters. Here, we identify a promoter element of
F. tularensis
LVS that is repressed by glucose (termed the
Francisella g
lucose-
r
epressible
p
romoter, or FGRp), allowing the management of downstream gene expression. In bacteria cultured in medium lacking glucose, this promoter induced the expression of a red fluorescent protein allele,
tdtomato
. FGRp activity was used to produce antisense RNA of
iglC
, an important virulence factor, which severely reduced IglC protein levels. Cultivation in glucose-containing medium restored IglC levels, indicating the usefulness of this promoter for controlling both exogenous and chromosomal gene expression. Moreover, FGRp was shown to be active during the infection of human macrophages by using the fluorescence reporter. In this environment, the FGRp-mediated expression of antisense
iglC
by
F. tularensis
LVS resulted in reduced bacterial fitness, demonstrating the applicability of this promoter. An analysis of the genomic sequence indicated that this promoter region controls a gene, FTL_0580, encoding a hypothetical protein. A deletion analysis determined the critical sites essential for FGRp activity to be located within a 44-bp region. This is the first report of a conditional promoter and the use of antisense constructs in
F. tularensis
, valuable genetic tools for studying gene function both in vitro and in vivo.
A Ferroxidase Encoded by
FOX1
Contributes to Iron Assimilation under Conditions of Poor Iron Nutrition in
Chlamydomonas
Authors: Chen Jen-Chih , Hsieh Scott I. , Kropat Janette , Merchant Sabeeha S. 
Published: February 2008

ABSTRACT

When the abundance of the
FOX1
gene product is reduced,
Chlamydomonas
cells grow poorly in iron-deficient medium, but not in iron-replete medium, suggesting that FOX1-dependent iron uptake is a high-affinity pathway. Alternative pathways for iron assimilation, such as those involving ZIP family transporters IRT1 and IRT2, may be operational.
“
Candidatus
Cloacamonas Acidaminovorans”: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division
Authors: Pelletier Eric , Kreimeyer Annett , Bocs Stéphanie , Rouy Zoé , Gyapay Gábor , Chouari Rakia , Rivière Delphine , Ganesan Akila , Daegelen Patrick , Sghir Abdelghani , Cohen Georges N. , Médigue Claudine , Weissenbach Jean , Le Paslier Denis 
Published: February 2008

ABSTRACT

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as “
Candidatus
Cloacamonas acidaminovorans.” “
Candidatus
Cloacamonas acidaminovorans” is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.
Control of Acetic Acid Fermentation by Quorum Sensing via
N
-Acylhomoserine Lactones in
Gluconacetobacter intermedius
Authors: Iida Aya , Ohnishi Yasuo , Horinouchi Sueharu 
Published: February 2008

ABSTRACT

A number of gram-negative bacteria regulate gene expression in a cell density-dependent manner by quorum sensing via
N
-acylhomoserine lactones (AHLs).
Gluconacetobacter intermedius
NCI1051, a gram-negative acetic acid bacterium, produces three different AHLs,
N
-decanoyl-
l
-homoserine lactone,
N
-dodecanoyl-
l
-homoserine lactone, and an
N
-dodecanoyl-
l
-homoserine lactone with a single unsaturated bond in its acyl chain, as determined by liquid chromatography-tandem mass spectrometry. Two genes encoding an AHL synthase and a cognate regulator were cloned from strain NCI1051 and designated
ginI
and
ginR
, respectively. Disruption of
ginI
or
ginR
abolished AHL production, indicating that NCI1051 contains a single set of quorum-sensing genes. Transcriptional analysis showed that
ginI
is activated by GinR, which is consistent with the finding that there is an inverted repeat whose nucleotide sequence is similar to the sequence bound by members of the LuxR family at position −45 with respect to the transcriptional start site of
ginI
. A single gene, designated
ginA
, located just downstream of
ginI
is transcribed by read-through from the GinR-inducible
ginI
promoter. A
ginA
mutant, as well as the
ginI
and
ginR
mutants, grew more rapidly in medium containing 2% (vol/vol) ethanol and accumulated acetic acid at a higher rate with a greater final yield than parental strain NCI1051. In addition, these mutants produced larger amounts of gluconic acid than the parental strain. These data demonstrate that the GinI/GinR quorum-sensing system in
G. intermedius
controls the expression of
ginA
, which in turn represses oxidative fermentation, including acetic acid and gluconic acid fermentation.
Anthrose Biosynthetic Operon of
Bacillus anthracis
Authors: Dong Shengli , McPherson Sylvia A. , Tan Li , Chesnokova Olga N. , Turnbough Charles L. , Pritchard David G. 
Published: February 2008

ABSTRACT

The exosporium of
Bacillus anthracis
spores consists of a basal layer and an external hair-like nap. The nap is composed primarily of the glycoprotein BclA, which contains a collagen-like region with multiple copies of a pentasaccharide side chain. This oligosaccharide possesses an unusual terminal sugar called anthrose, followed by three rhamnose residues and a protein-bound
N
-acetylgalactosamine. Based on the structure of anthrose, we proposed an enzymatic pathway for its biosynthesis. Examination of the
B. anthracis
genome revealed six contiguous genes that could encode the predicted anthrose biosynthetic enzymes. These genes are transcribed in the same direction and appear to form two operons. We introduced mutations into the
B. anthracis
chromosome that either delete the promoter of the putative upstream, four-gene operon or delete selected genes in both putative operons. Spores produced by strains carrying mutations in the upstream operon completely lacked or contained much less anthrose, indicating that this operon is required for anthrose biosynthesis. In contrast, inactivation of the downstream, two-gene operon did not alter anthrose content. Additional experiments confirmed the organization of the anthrose operon and indicated that it is transcribed from a σ
E
-specific promoter. Finally, we demonstrated that anthrose biosynthesis is not restricted to
B. anthracis
as previously suggested.
A General Iterative Method for Equilibrium Problems and Fixed Point Problems in Hilbert Spaces
Authors: Shang Meijuan , Su Yongfu , Qin Xiaolong 
Published: February 2008

AbstractWe introduce a general iterative scheme by the viscosity approximation method for finding a common element of the set of solutions of an equilibrium problem and the set of fixed points of a nonexpansive mapping in a Hilbert space. Our results improve and extend the corresponding ones announced by S. Takahashi and W. Takahashi in 2007, Marino and Xu in 2006, Combettes and Hirstoaga in 2005, and many others.