bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gprA and gprB genes encode putative G protein‐coupled receptors required for self‐fertilization in Aspergillus nidulans
Authors: Seo Jeong‐Ah , Han Kap‐Hoon , Yu Jae‐Hyuk 
Published: September 2004

SummaryThe filamentous fungus Aspergillus nidulans possesses both asexual and sexual reproductive cycles. Sexual fruiting bodies (cleistothecia) can be formed in both homothallic (self) and heterothallic (outcross) conditions. In this study, we characterized two genes, gprA and gprB, that are predicted to encode putative G protein‐coupled receptors (GPCRs) similar to fungal pheromone receptors. Deletion (Δ) of gprA or gprB resulted in the production of a few small cleistothecia carrying a reduced number of ascospores, whereas ΔgprAΔgprB eliminated fruiting body formation in homothallic conditions. However, nullifying gprA and/or gprB did not affect vegetative growth, asexual sporulation, Hülle cell formation or even cleistothecia formation in outcross, indicating that GprA and GprB are specifically required for self‐fertilization. The gprA and gprB genes encode two transcripts and, for both genes, larger transcripts are detectable during vegetative growth and asexual development whereas smaller transcripts accumulate during sexual development. Upregulation of nsdD encoding a key sexual developmental activator resulted in the production of barren cleistothecia in the ΔgprAΔgprB mutant, suggesting that NsdD can partially rescue the developmental defects caused by deletion of GPCRs and that GprA/B‐mediated signalling may activate other genes necessary for maturation of cleistothecia and ascosporogenesis. Deletion of gprA and/or gprB suppressed growth defects caused by ΔgprD, implying that GprA/B function downstream of GprD‐mediated negative control of sexual development.
Quorum sensing and signal interference: diverse implications
Authors: Zhang Lian‐Hui , Dong Yi‐Hu 
Published: September 2004

SummaryQuorum sensing (QS) is a community genetic regulation mechanism that controls microbiological functions of medical, agricultural and industrial importance. Discovery of microbial QS signals and the signalling mechanisms led to identification of numerous enzymatic and non‐enzymatic signal interference mechanisms that quench microbial QS signalling. Evidence is accumulating that such signal interference mechanisms can be developed as promising approaches to control microbial infection and biofilm formation. In addition, these mechanisms exist not only in microorganisms but also in the host organisms of bacterial pathogens, highlighting their potential implications in microbial ecology and in host–pathogen interactions. Investigation of QS and signal interference mechanisms might significantly broaden the scope of research in microbiology.
Identification of QTLs affecting adaptive traits in Castanea sativa Mill
Authors: CASASOLI M , POT D. , PLOMION C. , MONTEVERDI M. C. , BARRENECHE T. , LAUTERI M. , VILLANI F. 
Published: September 2004

ABSTRACTA QTL analysis for three different adaptive traits was performed in an F1 progeny of Castanea sativa Mill. The female and male parents originated from two Turkish chestnut populations adapted to a drought and humid environment, respectively. QTLs for bud flush, growth and carbon isotope discrimination were detected over a 3‐year period. Bud set was also recorded in the last year of measurement. Thirty‐five individual QTLs were detected for phenology, 28 for growth and 17 for carbon isotope discrimination, most of them explaining a low to moderate proportion of the total phenotypic variance. QTLs were distributed throughout the whole genome. Temporally stable QTLs were identified for all the traits analysed, with phenology showing the higher proportion of stable QTLs. Interesting phenotypic correlations and co‐localizations among QTLs for different adaptive traits were observed, allowing the formulation of an hypothesis about the genetic adaptation of the female parent to drought.
Reactive oxygen species‐mediated enzymatic systems involved in the oxidative action of 2,4‐dichlorophenoxyacetic acid*
Authors: ROMERO‐PUERTAS M. C. , MCCARTHY I. , GÓMEZ M. , SANDALIO L. M. , CORPAS F. J. , DEL RÍO L. A. , PALMA J. M. 
Published: September 2004

ABSTRACT2,4‐dichlorophenoxyacetic acid (2,4‐D) is an analogue compound to the plant hormone indole‐3‐acetic acid (IAA), which is used either as a growth‐promoting substance or as a herbicide, depending on its concentration. In this work, the effect of 2,4‐D on the growth and ROS metabolism of pea (Pisum sativum L.) leaves is reported. The herbicide considerably reduced the plant growth and negatively influenced several physiological parameters in a dose‐dependent manner. At structural level, damage of the mesophyll cells and the enlargement and dilation of thylakoids were observed in 2,4‐D‐treated plants. 2,4‐D notably affected xanthine oxidase and superoxide dismutase activities, as well as the activity and transcript levels of the ascorbate–glutathione cycle enzymes, ascorbate peroxidase, monodehydroascorbate reductase, and glutathione reductase. Furthermore, in herbicide‐treated plants, an increase in the H2O2 production, levels of lipid peroxidation, endopeptidase activity and oxidatively modified proteins took place. Results obtained showed that an overproduction of superoxide radicals (O2−) and hydrogen peroxide (H2O2) could take place in plants treated with 2,4‐D, thus contributing to the generation of oxidative stress, with the concomitant degradation of proteins. A model of the role of ROS‐mediated enzymatic systems in the oxidative mode of action of 2,4‐D and other auxinic herbicides is proposed.
Vinblastine‐Induced Formation of Tubulin Polymers is Electrostatically Regulated and Nucleated
Authors: Rai Sadananda S. , Wolff J. 
Published: September 2004

Vinblastine promotes tubulin polymerization as measured by turbidity at 400 nm. Unlike microtubule assembly, this mode of polymerization does not require GTP and, in fact, GTP inhibits polymerization, as do other G nucleotides in the potency order: GtetraP≥ GTP > GDP > GMP > no nucleotide. Inhibition is not nucleoside‐specific as ATP, ADP, and CTP also inhibit, and inorganic oligophosphates are as inhibitory as nucleotides in the order tetraphosphate ≈ triphosphate > pyrophosphate ≥ phosphate. Inhibition of polymerization is a rough function of the number of anionic charges and can be mimicked by suramin or tartrate. It is not due to sequestration of magnesium or to debinding of vinblastine. The anion‐induced decrease in turbidity generation is reflected in the amount of tubulin that is pelletable, but even in the absence of turbidity significant pelletable tubulin persists which can be assessed by 90° light scattering. Formation of this polymer is less sensitive to anions.Shearing of GTP‐inhibited and vinblastine‐induced samples promotes turbidity and addition of seeds made from vinblastine polymers leads to rapid increases in turbidity in a concentration‐dependent manner. Adjustment of the vinblastine concentration permits the demonstration of a latent period for polymerization that can be shortened by polymer seeds. Vinblastine‐induced polymerization shows a critical concentration, and, in the presence of GTP, two distinct critical concentrations can be identified. We conclude that charge–charge interactions play a significant role in the formation of vinblastine‐induced polymers, and that their formation is a two‐step process resembling a nucleation/elongation mechanism.
Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay, Australia
Authors: Burns Brendan P. , Goh Falicia , Allen Michelle , Neilan Brett A. 
Published: September 2004

SummaryStromatolites have been present on Earth, at various levels of distribution and diversity, for more than 3 billion years. Today, the best examples of stromatolites forming in hypersaline marine environments are in Hamelin Pool at Shark Bay, Western Australia. Despite their evolutionary significance, little is known about their associated microbial communities. Using a polyphasic approach of culture‐dependent and culture‐independent methods, we report the discovery of a wide range of microorganisms associated with these biosedimentary structures. There are no comparable reports combining these methodologies in the survey of cyanobacteria, bacteria, and archaea in marine stromatolites. The community was characterized by organisms of the cyanobacterial genera Synechococcus, Xenococcus, Microcoleus, Leptolyngbya, Plectonema, Symploca, Cyanothece, Pleurocapsa and Nostoc. We also report the discovery of potentially free‐living Prochloron. The other eubacterial isolates and clones clustered into seven phylogenetic groups: OP9, OP10, Marine A group, Proteobacteria, Low G+C Gram‐positive, Planctomycetes and Acidobacteria. We also demonstrate the presence of sequences corresponding to members of halophilic archaea of the divisions Euryarchaeota and Crenarchaeota and methanogenic archaea of the order Methanosarcinales. This is the first report of such archaeal diversity from this environment. This study provides a better understanding of the microbial community associated with these living rocks.
A New ‘Biased Coin Design’ for the Sequential Allocation of Two Treatments
Authors: Antognini Alessandro Baldi , Giovagnoli Alessandra 
Published: September 2004

SummaryEfron’s biased coin design is a well-known randomization technique that helps to neutralize selection bias in sequential clinical trials for comparing treatments, while keeping the experiment fairly balanced. Extensions of the biased coin design have been proposed by several researchers who have focused mainly on the large sample properties of their designs. We modify Efron’s procedure by introducing an adjustable biased coin design, which is more flexible than his. We compare it with other existing coin designs; in terms of balance and lack of predictability, its performance for small samples appears in many cases to be an improvement with respect to the other sequential randomized allocation procedures.
Regression-Based Estimation of the False Negative Fraction When Multiple Negatives are Unverified
Authors: Lloyd Chris J. , Frommer Donald J. 
Published: September 2004

Summary
The paper describes a method of estimating the false negative fraction of a multiple-screening test when individuals who test negatively on all K tests do not have their true disease status verified. The method proposed makes no explicit assumptions about the underlying heterogeneity of the population or about serial correlation of test results within an individual. Rather, it is based on estimating false negative fractions conditionally on observed diagnostic histories and extrapolating the observed patterns in these empirical frequencies by using logistic regression. The method is illustrated on, and motivated by, data on a multiple-screening test for bowel cancer.
Risk‐Neutral Parameter Shifts and Derivatives Pricing in Discrete Time
Authors: SCHRODER MARK 
Published: September 2004

ABSTRACTWe obtain a large class of discrete‐time risk‐neutral valuation relationships, or “preference‐free” derivatives pricing models, by imposing a simple restriction on the state‐price density process. The risk‐neutral stock‐return and forward‐rate dynamics are obtained by changing only a location parameter, which can be determined independent of the preference and true location parameters. The Gaussian models of Rubinstein (1976), Brennan (1979), and Câmera (2003), and the gamma model of Heston (1993) are all special cases. The model provides simple relationships between expected returns and state‐price density parameters analogous to the diffusion case.
Competition and Coalition among Underwriters: The Decision to Join a Syndicate
Authors: SONG WEI‐LING 
Published: September 2004

ABSTRACTThis paper studies the decision of lead investment banks to organize hybrid syndicates (commercial banks participating as co‐managers) versus pure investment bank syndicates. The findings show that hybrid underwriting issues are more challenging to float. Compared to pure investment bank syndicates, hybrid syndicates serve clients that are smaller, have lower common stock rankings and less prior access to the capital markets, rely more on bank loans, and invest less capital but issue larger amounts, which indicates that commercial banks' participation enhances hybrid services. Moreover, lead investment banks tend to invite banks' participation when clients exhibit higher loyalty in reusing their services.
A Survey of IRB Process in 68 U.S. Hospitals
Authors: Larson Elaine , Bratts Tiffany , Zwanziger Jack , Stone Patricia 
Published: September 2004

Purpose

: To compare IRB processes in 68 U.S. hospitals for the same multicenter study.
Design

: Survey of IRB processes in 68 U.S. hospitals during 2001‐2002.
Methods

: Requirements of IRB submission including type and duration of review and qualifications of principal investigator were compared by hospital bed size, region, and academic affiliation.
Findings

: The majority of hospitals (63.2%) were on the East coast, and mean bed size was 465 (range: 77‐2,112). About one‐third (33.8%) required that the principal investigator listed on the application be from within the institution, 26.5% required evidence of human subjects research training, 10.3% required a conflict of interest statement. Mean number of pages for the application was 5.24 (1‐31) and up to eight copies were requested. Time from submission of the IRB application to approval averaged 45.4 days (range, 1‐303 days), and the majority of reviews were “expedited” (61.8%). Expedited reviews required more time (mean, 54.8 days) than did either exempt (mean, 10.8 days) or full (mean, 47.1 days) reviews.
Conclusions

: Current IRB review processes are cumbersome and nonstandardized, and review time varies widely. The absence of efficient and streamlined review might unnecessarily impede national clinical research projects without improving participant safety.
Requirement of a Relatively High Threshold Level of Mg
2+
for Cell Growth of a Rhizoplane Bacterium,
Sphingomonas yanoikuyae
EC-S001
Authors: Hoo Henny , Hashidoko Yasuyuki , Islam Md. Tofazzal , Tahara Satoshi 
Published: September 2004

ABSTRACT

Mg
2+
is one of the essential elements for bacterial cell growth. The presence of the magnesium cation (Mg
2+
) in various concentrations often affects cell growth restoration in plant-associating bacteria. This study attempted to determine whether Mg
2+
levels in
Sphingomonas yanoikuyae
EC-S001 affected cell growth restoration in the host plant and what the threshold level is.
S. yanoikuyae
EC-S001, isolated from the rhizoplane of spinach seedlings grown from surface-sterilized seeds under aseptic conditions, displayed uniform dispersion and attachment throughout the rhizoplane and phylloplane of the host seedlings.
S. yanoikuyae
EC-S001 did not grow in potato-dextrose broth medium but grew well in an aqueous extract of spinach leaves. Chemical investigation of the growth factor in the spinach leaf extract led to identification of the active principle as the magnesium cation. A concentration of ca. 0.10 mM Mg
2+
or more allowed
S. yanoikuyae
EC-S001 to grow in potato-dextrose broth medium. Some saprophytic and/or diazotrophic bacteria used in our experiment were found to have diverse threshold levels for their Mg
2+
requirements. For example,
Burkholderia cepacia
EC-K014, originally isolated from the rhizoplane of a
Melastoma
sp., could grow even in Mg
2+
-free Hoagland's no. 2 medium with saccharose and glutamine (HSG medium) and requires a trace level of Mg
2+
for its growth. In contrast,
S. yanoikuyae
EC-S001, together with
Bacillus subtilis
IFO12113, showed the most drastic restoring responses to subsequent addition of 0.98 mM Mg
2+
to Mg
2+
-free HSG medium. Our studies concluded that Mg
2+
is more than just the essential trace element needed for cell growth restoration in
S. yanoikuyae
EC-S001 and that certain nonculturable bacteria may require a higher concentration of Mg
2+
or another specific essential element for their growth.
Comparative Proteomic Analysis of Extracellular Proteins of Enterohemorrhagic and Enteropathogenic
Escherichia coli
Strains and Their
ihf
and
ler
Mutants
Authors: Li M. , Rosenshine I. , Tung S. L. , Wang X. H. , Friedberg D. , Hew C. L. , Leung K. Y. 
Published: September 2004

ABSTRACT

Enterohemorrhagic and enteropathogenic
Escherichia coli
(EHEC and EPEC, respectively) strains are closely related human pathogens that are responsible for food-borne epidemics in many countries. Integration host factor (IHF) and the locus of enterocyte effacement-encoded regulator (Ler) are needed for the expression of virulence genes in EHEC and EPEC, including the elicitation of actin rearrangements for attaching and effacing lesions. We applied a proteomic approach, using two-dimensional polyacrylamide gel electrophoresis in combination with matrix-assisted laser desorption ionization-time of flight mass spectrometry and a protein database search, to analyze the extracellular protein profiles of EHEC EDL933, EPEC E2348/69, and their
ihf
and
ler
mutants. Fifty-nine major protein spots from the extracellular proteomes were identified, including six proteins of unknown function. Twenty-six of them were conserved between EHEC EDL933 and EPEC E2348/69, while some of them were strain-specific proteins. Four common extracellular proteins (EspA, EspB, EspD, and Tir) were regulated by both IHF and Ler in EHEC EDL933 and EPEC E2348/69. TagA in EHEC EDL933 and EspC and EspF in EPEC E2348/69 were present in the wild-type strains but absent from their respective
ler
and
ihf
mutants, while FliC was overexpressed in the
ihf
mutant of EPEC E2348/69. Two dominant forms of EspB were found in EHEC EDL933 and EPEC E2348/69, but the significance of this is unknown. These results show that proteomics is a powerful platform technology for accelerating the understanding of EPEC and EHEC pathogenesis and identifying markers for laboratory diagnoses of these pathogens.
Multiple Nonidentical Reductive-Dehalogenase-Homologous Genes Are Common in
Dehalococcoides
Authors: Hölscher Tina , Krajmalnik-Brown Rosa , Ritalahti Kirsti M. , von Wintzingerode Friedrich , Görisch Helmut , Löffler Frank E. , Adrian Lorenz 
Published: September 2004

ABSTRACT

Degenerate primers were used to amplify large fragments of reductive-dehalogenase-homologous (RDH) genes from genomic DNA of two
Dehalococcoides
populations, the chlorobenzene- and dioxin-dechlorinating strain CBDB1 and the trichloroethene-dechlorinating strain FL2. The amplicons (1,350 to 1,495 bp) corresponded to nearly complete open reading frames of known reductive dehalogenase genes and short fragments (approximately 90 bp) of genes encoding putative membrane-anchoring proteins. Cloning and restriction analysis revealed the presence of at least 14 different RDH genes in each strain. All amplified RDH genes showed sequence similarity with known reductive dehalogenase genes over the whole length of the sequence and shared all characteristics described for reductive dehalogenases. Deduced amino acid sequences of seven RDH genes from strain CBDB1 were 98.5 to 100% identical to seven different RDH genes from strain FL2, suggesting that both strains have an overlapping substrate range. All RDH genes identified in strains CBDB1 and FL2 were related to the RDH genes present in the genomes of
Dehalococcoides ethenogenes
strain 195 and
Dehalococcoides
sp. strain BAV1; however, sequence identity did not exceed 94.4 and 93.1%, respectively. The presence of RDH genes in strains CBDB1, FL2, and BAV1 that have no orthologs in strain 195 suggests that these strains possess dechlorination activities not present in strain 195. Comparative sequence analysis identified consensus sequences for cobalamin binding in deduced amino acid sequences of seven RDH genes. In conclusion, this study demonstrates that the presence of multiple nonidentical RDH genes is characteristic of
Dehalococcoides
strains.
Modified Serial Analysis of Gene Expression Method for Construction of Gene Expression Profiles of Microbial Eukaryotic Species
Authors: Coyne Kathryn J. , Burkholder JoAnn M. , Feldman Robert A. , Hutchins David A. , Cary S. Craig 
Published: September 2004

ABSTRACT

Serial analysis of gene expression (SAGE) is a powerful approach for the identification of differentially expressed genes, providing comprehensive and quantitative gene expression profiles in the form of short tag sequences. Each tag represents a unique transcript, and the relative frequencies of tags in the SAGE library are equal to the relative proportions of the transcripts they represent. One of the major obstacles in the preparation of SAGE libraries from microorganisms is the requirement for large amounts of starting material (i.e., mRNA). Here, we present a novel approach for the construction of SAGE libraries from small quantities of total RNA by using Y linkers to selectively amplify 3′ cDNA fragments. To validate this method, we constructed comprehensive gene expression profiles of the toxic dinoflagellate
Pfiesteria shumwayae
. SAGE libraries were constructed from an actively toxic fish-fed culture of
P. shumwayae
and from a recently toxic alga-fed culture.
P. shumwayae-
specific gene transcripts were identified by comparison of tag sequences in the two libraries. Representative tags with frequencies ranging from 0.026 to 3.3% of the total number of tags in the libraries were chosen for further analysis. Expression of each transcript was confirmed in separate control cultures of toxic
P. shumwayae
. The modified SAGE method described here produces gene expression profiles that appear to be both comprehensive and quantitative, and it is directly applicable to the study of gene expression in other environmentally relevant microbial species.
Localization and Characterization of Two Novel Genes Encoding Stereospecific Dioxygenases Catalyzing 2(2,4-Dichlorophenoxy)propionate Cleavage in
Delftia acidovorans
MC1
Authors: Schleinitz Kathleen M. , Kleinsteuber Sabine , Vallaeys Tatiana , Babel Wolfgang 
Published: September 2004

ABSTRACT

Two novel genes,
rdpA
and
sdpA
, encoding the enantiospecific α-ketoglutarate dependent dioxygenases catalyzing
R
,
S
-dichlorprop cleavage in
Delftia acidovorans
MC1 were identified. Significant similarities to other known genes were not detected, but their deduced amino acid sequences were similar to those of other α-ketoglutarate dioxygenases. RdpA showed 35% identity with TauD of
Pseudomonas aeruginosa
, and SdpA showed 37% identity with TfdA of
Ralstonia eutropha
JMP134. The functionally important amino acid sequence motif HX(D/E)X
23-26
(T/S)X
114-183
HX
10-13
R/K, which is highly conserved in group II α-ketoglutarate-dependent dioxygenases, was present in both dichlorprop-cleaving enzymes. Transposon mutagenesis of
rdpA
inactivated
R
-dichlorprop cleavage, indicating that it was a single-copy gene. Both
rdpA
and
sdpA
were located on the plasmid pMC1 that also carries the lower pathway genes. Sequencing of a 25.8-kb fragment showed that the dioxygenase genes were separated by a 13.6-kb region mainly comprising a Tn
501
-like transposon. Furthermore, two copies of a sequence similar to IS
91
-like elements were identified. Hybridization studies comparing the wild-type plasmid and that of the mutant unable to cleave dichlorprop showed that
rdpA
and
sdpA
were deleted, whereas the lower pathway genes were unaffected, and that deletion may be caused by genetic rearrangements of the IS
91
-like elements. Two other dichlorprop-degrading bacterial strains,
Rhodoferax
sp. strain P230 and
Sphingobium herbicidovorans
MH, were shown to carry
rdpA
genes of high similarity to
rdpA
from strain MC1, but
sdpA
was not detected. This suggested that
rdpA
gene products are involved in the degradation of
R
-dichlorprop in these strains.