bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MarR‐type repressor MhqR (YkvE) regulates multiple dioxygenases/glyoxalases and an azoreductase which confer resistance to 2‐methylhydroquinone and catechol in Bacillus subtilis
Authors: Töwe Stefanie , Leelakriangsak Montira , Kobayashi Kazuo , Van Duy Nguyen , Hecker Michael , Zuber Peter , Antelmann Haike 
Published: August 2007

SummaryCatechol and 2‐methylhydroquinone (2‐MHQ) cause the induction of the thiol‐specific stress response and four dioxygenases/glyoxalases in Bacillus subtilis. Using transcription factor arrays, the MarR‐type regulator YkvE was identified as a repressor of the dioxygenase/glyoxalase‐encoding mhqE gene. Transcriptional and proteome analyses of the ΔykvE mutant revealed the upregulation of ykcA (mhqA), ydfNOP (mhqNOP), yodED (mhqED) and yvaB (azoR2) encoding multiple dioxygenases/glyoxalases, oxidoreductases and an azoreductase. Primer extension experiments identified σA‐type promoter sequences upstream of mhqA, mhqNOP, mhqED and azoR2 from which transcription is elevated after thiol stress. DNase I footprinting analysis showed that YkvE protects a primary imperfect inverted repeat with the consensus sequence of tATCTcgaAtTCgAGATaaaa in the azoR2, mhqE and mhqN promoter regions. Analysis of mhqE‐promoter–bgaB fusions confirmed the significance of YkvE binding to this operator in vivo. Adjacent secondary repeats were protected by YkvE in the azoR2 and mhqN promoter regions consistent with multiple DNA–protein binding complexes. DNA‐binding activity of YkvE was not directly affected by thiol‐reactive compounds in vitro. Mutational analyses showed that MhqA, MhqO and AzoR2 confer resistance to 2‐MHQ. Moreover, the ΔykvE mutant displayed a 2‐MHQ and catechol resistant phenotype. YkvE was renamed as MhqR controlling a 2‐MHQ and catechol‐resistance regulon of B. subtilis.
Lateral rectus resection versus medial rectus re‐recession for residual esotropia: early results of a randomized clinical trial
Authors: Rajavi Zhale , Ghadim Hashem M , Ramezani Alireza , Azemati Mansoor , Daneshvar Faride 
Published: August 2007

AbstractPurpose:  To compare lateral rectus muscle resection with medial rectus muscle re‐recession for patients with residual esotropia.Methods:  This randomized controlled clinical trial included 25 patients (mean age, 18.8 ± 8.7 years) with residual esotropia who were candidates for reoperation. They were randomly assigned into two groups: re‐recession group (n = 12), in which the medial rectus muscle was recessed again, and the resection group (n = 13), in which lateral rectus muscle resection was performed. Postoperative deviation ≤10 prism dioptres was considered to be treatment success.Results:  The success rate of the re‐recession group and the resection group was 67% and 54%, respectively; this difference was not statistically significant. Each 1 mm of medial rectus re‐recession and lateral rectus resection corrected 7.5 ± 1.2 and 2.5 ± 0.5 prism dioptres of residual esotropia, respectively. In 50% of the re‐recession group, mild medial rectus muscle underaction occurred; however, only 16.5% developed an increase in the near point of convergence. Major intraoperative and postoperative complications, including overcorrection and slippage or a lost muscle, did not occur in any of the patients.Conclusions:  Medial rectus muscle re‐recession can be a substitute for lateral rectus muscle resection in patients with residual esotropia. The resultant underaction of the medial rectus muscle after re‐recession is relatively mild and causes no major problems.
TRANSFER OF PRODUCTS BETWEEN EPIPHYTIC MARINE ALGAE AND HOST PLANTS1,2
Authors: Harlin Marilyn M. 
Published: August 2007

SUMMARYThe red alga Smithora naiadum is normally found only as an epiphyle on the sea grasses Phyllospadix scouleri and Zostera marina. I used 32P and 14CO2 to examine the chemical communication between host and alga. Both 32P and the product of 14CO2 light fixation moved from the host to the alga. Reverse movement between host and epiphyte was also demonstrated. Part of this transfer occurred through the plant and part occurred by leakage from the host into the medium and subsequent uptake by the alga. Although plants were initially labeled in the light, transfer of 14C was light independent.Transfer of 14C‐labeled products between host and epiphyte was also shown for Punctaria orbiculata and Z. marina; for Microdadia coulteri on Grateloupia doryphora, and between Gonimophyllum skottsbergii and Botryoglossum ruprechtiana. Epiphyte‐host associations do not require a penetrating rhizoid for an exchange of the isotopes tested. By their proximity alone, epiphytic flora are apparently capable l exchanging products before these are diluted by the sea.
Tricyclic antidepressants in the treatment of depressions
Authors: Kampman R. , Nummikko‐Pelkonen A. , Kuha S. 
Published: August 2007

The clinical efficacy of oral clomipramine and amitriptyline treatment (50–125 mg/day) was compared over a period of 2 months in 72 depressive patients visiting a psychiatric out‐patient clinic. Both drugs were equally effective as measured by the Hamilton Rating Scale for Depression. According to a nurse's independent evaluation of 13 items the two drugs were equipotent in relieving depressive symptoms and no statistically significant differences between the treatment groups were found in the global evaluation by the investigator and the patient. A trend in favour of clomipramine was, however, seen in several parameters.The declines in the Hamilton Rating Scale scores and the nurse's evaluation scores were highly significant during the first 2 weeks of treatment (P < 0.001) in both groups and the scores continued to decrease during the 2nd month of the study.The most common unwanted effects were dryness of the mouth and fatigue. The frequency of side effects was 51% in the clomipramine group and 43% in the amitriptyline group. The side effects were generally mild and transient and called for discontinuation of treatment in only one case in each group.
Multi-UAV Cooperative Search Using an Opportunistic Learning
Method
Authors: Yang Yanli , Polycarpou Marios M. , Minai Ali A. 
Published: August 2007

Abstract
The control of networked multivehicle systems designed to perform complex coordinated tasks is currently an important and challenging field of research. This paper addresses a cooperative search problem where a team of uninhabited aerial vehicles (UAVs) seeks to find targets of interest in an uncertain environment. We present a practical framework for online planning and control of a group of UAVs for cooperative search based on two interdependent tasks: (i) incrementally updating “cognitive maps” used as the representation of the environment through new sensor readings; (ii) continuously planning the path for each vehicle based on the information obtained through the search. We formulate the cooperative search problem and develop a decentralized strategy based on an opportunistic cooperative learning method, where the emergent coordination among vehicles is enabled by letting each vehicle consider other vehicles’ actions in its path planning procedure. By using the developed strategy, physically feasible paths for the vehicles to follow are generated, where constraints on aerial vehicles, including physical maneuverabilities, are considered and the dynamic nature of the environment is taken into account. We also present some mathematical analysis of the developed search strategy. Our analysis shows that this strategy guarantees a complete search of the environment and is robust to a partial loss of UAVs. A lower bound on the search time for any strategy and a relaxed upper bound for the proposed strategy are given. Simulation results are used to illustrate the effectiveness of the proposed strategy.
vanD
and
vanG
-Like Gene Clusters in a
Ruminococcus
Species Isolated from Human Bowel Flora
Authors: Domingo M.-C. , Huletsky A. , Giroux R. , Picard F. J. , Bergeron M. G. 
Published: August 2007

ABSTRACT

A vancomycin-resistant, anaerobic, gram-positive coccus containing the
vanD
and
vanG
-like genes (strain CCRI-16110) was isolated from a human fecal specimen during a hospital surveillance program to detect carriers of vancomycin-resistant enterococci. Comparison of the 16S rRNA gene sequence of strain CCRI-16110 with databases revealed a potentially novel
Ruminococcus
species that was most similar (<94% identity) to
Clostridium
and
Ruminococcus
species. Strain CCRI-16110 was highly resistant to vancomycin and teicoplanin (MICs of >256 μg/ml). The complete DNA sequence of the
vanD
cluster was most similar (98.2% identity) to that of
Enterococcus faecium
BM4339, containing the
vanD1
allele. An
intD
gene with 99% identity with that of this
E. faecium
strain was found to be associated with the
vanD
gene cluster of this novel anaerobic bacterium. Strain CCRI-16110 also harbors genes encoding putative VanS
G
, VanG, and VanT
G
proteins displaying 56, 73.6, and 55% amino acid sequence identity, respectively, compared to the corresponding proteins encoded by the
vanG1
and
vanG2
operons of
Enterococcus faecalis
BM4518 and N03-0233. This study reports for the first time an anaerobic bacterium containing the
vanD
gene cluster. This strain also harbors a partial
vanG
-like gene cluster. The presence of
vanD
- and
vanG
-containing anaerobic bacteria in the human bowel flora suggests that these bacteria may serve as a reservoir for the
vanD
and
vanG
vancomycin resistance genes.
Molecular Subtyping and Genetic Analysis of the Enterohemolysin Gene (
ehxA
) from Shiga Toxin-Producing
Escherichia coli
and Atypical Enteropathogenic
E. coli
Authors: Cookson Adrian L. , Bennett Jenny , Thomson-Carter Fiona , Attwood Graeme T. 
Published: August 2007

ABSTRACT

Analyses of the distribution of virulence factors among different
Escherichia coli
pathotypes, including Shiga toxin-producing
E. coli
(STEC), may provide some insight into the mechanisms by which different
E. coli
strains cause disease and the evolution of distinct
E. coli
types. The aim of this study was to examine the DNA sequence of the gene for enterohemolysin, a plasmid-encoded toxin that readily causes the hemolysis of washed sheep erythrocytes, and to assess the distribution of enterohemolysin subtypes among
E. coli
isolates from various human and animal sources. The 2,997-bp
ehxA
gene was amplified from 227 (63.8%) of 356
stx
- and/or
eae
-positive
E. coli
strains isolated from cattle and sheep and from 24 (96.0%) of 25 STEC strains isolated from humans with diarrheal disease. By using PCR and restriction fragment length polymorphism (RFLP) analysis of
ehxA
, six distinct PCR-RFLP types (A to F) were observed, with strains of subtypes A and C constituting 91.6% of all the
ehxA
-positive strains. Subtype A was associated mainly with ovine strains with
stx
only (
P
< 0.001), and subtype C was associated with bovine
eae
-positive strains (
P
< 0.001). Eleven
ehxA
alleles were fully sequenced, and the phylogenetic analysis indicated the presence of three closely related (>95.0%)
ehxA
sequence groups, one including
eae
-positive strains (subtypes B, C, E, and F) and the other two including mainly
eae
-negative STEC strains (subtypes A and D). In addition to being widespread among STEC strains,
stx
-negative,
eae
-positive strains (atypical enteropathogenic
E. coli
strains) isolated from cattle and sheep have similar
ehxA
subtypes and hemolytic activities.
Membrane-Bound, 2-Keto-
d
-Gluconate-Yielding
d
-Gluconate Dehydrogenase from “
Gluconobacter dioxyacetonicus
” IFO 3271: Molecular Properties and Gene Disruption
Authors: Toyama Hirohide , Furuya Naoko , Saichana Ittipon , Ano Yoshitaka , Adachi Osao , Matsushita Kazunobu 
Published: August 2007

ABSTRACT

Most
Gluconobacter
species produce and accumulate 2-keto-
d
-gluconate (2KGA) and 5KGA simultaneously from
d
-glucose via GA in culture medium. 2KGA is produced by membrane-bound flavin adenine dinucleotide-containing GA 2-dehydrogenase (FAD-GADH). FAD-GADH was purified from “
Gluconobacter dioxyacetonicus
” IFO 3271, and N-terminal sequences of the three subunits were analyzed. PCR primers were designed from the N-terminal sequences, and part of the FAD-GADH genes was cloned as a PCR product. Using this PCR product, gene fragments containing whole FAD-GADH genes were obtained, and finally the nucleotide sequence of 9,696 bp was determined. The cloned sequence had three open reading frames (ORFs),
gndS
,
gndL
, and
gndC
, corresponding to small, large, and cytochrome
c
subunits of FAD-GADH, respectively. Seven other ORFs were also found, one of which showed identity to glucono-δ-lactonase, which might be involved directly in 2KGA production. Three mutant strains defective in either
gndL
or
sldA
(the gene responsible for 5KGA production) or both were constructed. Ferricyanide-reductase activity with GA in the membrane fraction of the
gndL
-defective strain decreased by about 60% of that of the wild-type strain, while in the
sldA
-defective strain, activity with GA did not decrease and activities with glycerol,
d
-arabitol, and
d
-sorbitol disappeared. Unexpectedly, the strain defective in both
gndL
and
sldA
(double mutant) still showed activity with GA. Moreover, 2KGA production was still observed in
gndL
and double mutant strains. 5KGA production was not observed at all in
sldA
and double mutant strains. Thus, it seems that “
G. dioxyacetonicus
” IFO 3271 has another membrane-bound enzyme that reacts with GA, producing 2KGA.
Localization and Visualization of aCoxiella-Type Symbiont within the Lone Star Tick,Amblyomma americanum
Authors: Klyachko Olga , Stein Barry D. , Grindle Nathan , Clay Keith , Fuqua Clay 
Published: August 2007

ABSTRACTACoxiella-type microbe occurs at 100% frequency in allAmblyomma americanumticks thus far tested. Using laboratory-reared ticks free of other microbes, we identified theAmblyomma-associatedCoxiellamicrobe in several types of tissue and at various stages of the life cycle ofA. americanumby 16S rRNA gene sequencing and diagnostic PCR. We visualizedAmblyomma-associatedCoxiellathrough the use of a diagnostic fluorescence in situ hybridization (FISH) assay supplemented with PCR-based detection, nucleic acid fluorescent staining, wide-field epifluorescence and confocal microscopy, and transmission electron microscopy (TEM). Specific fluorescent foci were observed in several tick tissues, including the midgut and the Malpighian tubules, but particularly bright signals were observed in the granular acini of salivary gland clusters and in both small and large oocytes. TEM confirmed intracellular bacterial structures in the same tissues. The presence ofAmblyomma-associatedCoxiellawithin oocytes is consistent with the vertical transmission of these endosymbionts. Further, the presence of theAmblyomma-associatedCoxiellasymbiont in other tissues such as salivary glands could potentially lead to interactions with horizontally acquired pathogens.
Novel Whole-Cell Antibiotic Biosensors for Compound Discovery
Authors: Urban Andreas , Eckermann Stefan , Fast Beate , Metzger Susanne , Gehling Matthias , Ziegelbauer Karl , Rübsamen-Waigmann Helga , Freiberg Christoph 
Published: August 2007

ABSTRACT

Cells containing reporters which are specifically induced via selected promoters are used in pharmaceutical drug discovery and in environmental biology. They are used in screening for novel drug candidates and in the detection of bioactive compounds in environmental samples. In this study, we generated and validated a set of five
Bacillus subtilis
promoters fused to the firefly luciferase reporter gene suitable for cell-based screening, enabling the as yet most-comprehensive high-throughput diagnosis of antibiotic interference in the major biosynthetic pathways of bacteria: the biosynthesis of DNA by the
yorB
promoter, of RNA by the
yvgS
promoter, of proteins by the
yheI
promoter, of the cell wall by the
ypuA
promoter, and of fatty acids by the
fabHB
promoter. The reporter cells mainly represent novel antibiotic biosensors compatible with high-throughput screening. We validated the strains by developing screens with a set of 14,000 pure natural products, representing a source of highly diverse chemical entities, many of them with antibiotic activity (6% with anti-
Bacillus subtilis
activity of ≤25 μg/ml]). Our screening approach is exemplified by the discovery of classical and novel DNA synthesis and translation inhibitors. For instance, we show that the mechanistically underexplored antibiotic ferrimycin A1 selectively inhibits protein biosynthesis.
Comparison of Direct Genome Restriction Enzyme Analysis and Pulsed-Field Gel Electrophoresis for Typing of
Vibrio vulnificus
and Their Correspondence with Multilocus Sequence Typing Data
Authors: González-Escalona Narjol , Whitney Brooke , Jaykus Lee-Ann , DePaola Angelo 
Published: August 2007

ABSTRACT

We compared the potential of direct genome restriction enzyme analysis (DGREA) and pulsed-field gel electrophoresis (PFGE) for discriminating
Vibrio vulnificus
isolates from clinical (23) and environmental (17) sources. The genotypes generated by both methodologies were compared to previous multilocus sequence typing (MLST) data. DGREA established clearer relationships among
V. vulnificus
strains and was more consistent with MLST than with PFGE. DGREA is a very promising tool for epidemiological and ecological studies of
V. vulnificus
.
Development of Quantitative Real-Time PCR Assays for Detection and Quantification of Surrogate Biological Warfare Agents in Building Debris and Leachate
Authors: Saikaly Pascal E. , Barlaz Morton A. , de los Reyes Francis L. 
Published: August 2007

ABSTRACT

Evaluation of the fate and transport of biological warfare (BW) agents in landfills requires the development of specific and sensitive detection assays. The objective of the current study was to develop and validate SYBR green quantitative real-time PCR (Q-PCR) assays for the specific detection and quantification of surrogate BW agents in synthetic building debris (SBD) and leachate.
Bacillus atrophaeus
(vegetative cells and spores) and
Serratia marcescens
were used as surrogates for
Bacillus anthracis
(anthrax) and
Yersinia pestis
(plague), respectively. The targets for SYBR green Q-PCR assays were the 16S-23S rRNA intergenic transcribed spacer (ITS) region and
recA
gene for
B. atrophaeus
and the
gyrB
,
wzm
, and
recA
genes for
S. marcescens
. All assays showed high specificity when tested against 5 ng of closely related
Bacillus
and
Serratia
nontarget DNA from 21 organisms. Several spore lysis methods that include a combination of one or more of freeze-thaw cycles, chemical lysis, hot detergent treatment, bead beat homogenization, and sonication were evaluated. All methods tested showed similar threshold cycle values. The limit of detection of the developed Q-PCR assays was determined using DNA extracted from a pure bacterial culture and DNA extracted from sterile water, leachate, and SBD samples spiked with increasing quantities of surrogates. The limit of detection for
B. atrophaeus
genomic DNA using the ITS and
B. atrophaeus recA
Q-PCR assays was 7.5 fg per PCR. The limits of detection of
S. marcescens
genomic DNA using the
gyrB
,
wzm
, and
S. marcescens recA
Q-PCR assays were 7.5 fg, 75 fg, and 7.5 fg per PCR, respectively. Quantification of
B. atrophaeus
vegetative cells and spores was linear (
R
2
> 0.98) over a 7-log-unit dynamic range down to 10
1
B. atrophaeus
cells or spores. Quantification of
S. marcescens
(
R
2
> 0.98) was linear over a 6-log-unit dynamic range down to 10
2
S. marcescens
cells. The developed Q-PCR assays are highly specific and sensitive and can be used for monitoring the fate and transport of the BW surrogates
B. atrophaeus
and
S. marcescens
in building debris and leachate.
Variability of Bacterial Biofilms of the “Tina” Wood Vats Used in the Ragusano Cheese-Making Process
Authors: Licitra G. , Ogier J. C. , Parayre S. , Pediliggieri C. , Carnemolla T. M. , Falentin H. , Madec M. N. , Carpino S. , Lortal S. 
Published: August 2007

ABSTRACT

Ragusano cheese is a “protected denomination of origin” cheese made in the Hyblean region of Sicily from raw milk using traditional wooden tools, without starter. To explore the Ragusano bacterial ecosystem, molecular fingerprinting was conducted at different times during the ripening and biofilms from the wooden vats called “tinas” were investigated. Raw milks collected at two farm sites, one on the mountain and one at sea level, were processed to produce Ragusano cheese. Raw milk, curd before and after cooking, curd at stretching time (cheese 0 time), and cheese samples (4 and 7 months) were analyzed by PCR-temporal temperature gel electrophoresis (PCR-TTGE) and by classical enumeration microbiology. With the use of universal primers, PCR-TTGE revealed many differences between the raw milk profiles, but also notable common bands identified as
Streptococcus thermophilus, Lactobacillus lactis, Lactobacillus delbrueckii
, and
Enterococcus faecium
. After the stretching, TTGE profiles revealed three to five dominant species only through the entire process of ripening. In the biofilms of the two tinas used, one to five species were detected,
S. thermophilus
being predominant in both. Biofilms from five other tinas were also analyzed by PCR-TTGE, PCR-denaturating gradient gel electrophoresis, specific PCR tests, and sequencing, confirming the predominance of lactic acid bacteria (
S. thermophilus, L. lactis
, and
L. delbrueckii
subsp.
lactis
) and the presence of a few high-GC-content species, like coryneform bacteria. The spontaneous acidification of raw milks before and after contact with the five tinas was followed in two independent experiments. The lag period before acidification can be up to 5 h, depending on the raw milk and the specific tina, highlighting the complexity of this natural inoculation system.
Ralstonia solanacearum
Strains from Martinique (French West Indies) Exhibiting a New Pathogenic Potential
Authors: Wicker Emmanuel , Grassart Laurence , Coranson-Beaudu Régine , Mian Danièle , Guilbaud Caroline , Fegan Mark , Prior Philippe 
Published: August 2007

ABSTRACT

We investigated a destructive pathogenic variant of the plant pathogen
Ralstonia solanacearum
that was consistently isolated in Martinique (French West Indies). Since the 1960s, bacterial wilt of solanaceous crops in Martinique has been caused primarily by strains of
R. solanacearum
that belong to either phylotype I or phylotype II. Since 1999, anthurium shade houses have been dramatically affected by uncharacterized phylotype II strains that also affected a wide range of species, such as
Heliconia caribea
, cucurbitaceous crops, and weeds. From 1989 to 2003, a total of 224
R. solanacearum
isolates were collected and compared to 6 strains isolated in Martinique in the 1980s. The genetic diversity and phylogenetic position of selected strains from Martinique were assessed (multiplex PCRs,
mutS
and
egl
DNA sequence analysis) and compared to the genetic diversity and phylogenetic position of 32 reference strains covering the known diversity within the
R. solanacearum
species complex. Twenty-four representative isolates were tested for pathogenicity to
Musa
species (banana) and tomato, eggplant, and sweet pepper. Based upon both PCR and sequence analysis, 119 Martinique isolates from anthurium, members of the family
Cucurbitaceae, Heliconia
, and tomato, were determined to belong to a group termed phylotype II/sequevar 4 (II/4). While these strains cluster with the Moko disease-causing strains, they were not pathogenic to banana (NPB). The strains belonging to phylotype II/4NPB were highly pathogenic to tomato, eggplant, and pepper, were able to wilt the resistant tomato variety Hawaii7996, and may latently infect cooking banana. Phylotype II/4NPB constitutes a new pathogenic variant of
R. solanacearum
that has recently appeared in Martinique and may be latently prevalent throughout Caribbean and Central/South America.