bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differentiation of Strains of
Xylella fastidiosa
by a Variable Number of Tandem Repeat Analysis
Authors: Coletta-Filho Helvécio Della , Takita Marco Aurélio , de Souza Alessandra Alves , Aguilar-Vildoso Carlos Ivan , Machado Marcos Antonio 
Published: July 2002

ABSTRACT

Short sequence repeats (SSRs) with a potential variable number of tandem repeat (VNTR) loci were identified in the genome of the citrus pathogen
Xylella fastidiosa
and used for typing studies. Although mono- and dinucleotide repeats were absent, we found several intermediate-length 7-, 8-, and 9-nucleotide repeats, which we examined for allelic polymorphisms using PCR. Five genuine VNTR loci were highly polymorphic within a set of 27
X. fastidiosa
strains from different hosts. The highest average Nei's measure of genetic diversity (
H
) estimated for VNTR loci was 0.51, compared to 0.17 derived from randomly amplified polymorphic DNA (RAPD) analysis. For citrus
X. fastidiosa
strains, some specific VNTR loci had a
H
value of 0.83, while the maximum value given by specific RAPD loci was 0.12. Our approach using VNTR markers provides a high-resolution tool for epidemiological, genetic, and ecological analysis of citrus-specific
X. fastidiosa
strains.
DNA from Uncultured Organisms as a Source of 2,5-Diketo-
d
-Gluconic Acid Reductases
Authors: Eschenfeldt William H. , Stols Lucy , Rosenbaum Helga , Khambatta Zubin S. , Quaite-Randall Elsie , Wu Shan , Kilgore Donna C. , Trent Jonathan D. , Donnelly Mark I. 
Published: July 2002

ABSTRACT

Total DNA of a population of uncultured organisms was extracted from soil samples, and by using PCR methods, the genes encoding two different 2,5-diketo-
d
-gluconic acid reductases (DKGRs) were recovered. Degenerate PCR primers based on published sequence information gave internal gene fragments homologous to known DKGRs. Nested primers specific for the internal fragments were combined with random primers to amplify flanking gene fragments from the environmental DNA, and two hypothetical full-length genes were predicted from the combined sequences. Based on these predictions, specific primers were used to amplify the two complete genes in single PCRs. These genes were cloned and expressed in
Escherichia coli.
The purified gene products catalyzed the reduction of 2,5-diketo-
d
-gluconic acid to 2-keto-
l
-gulonic acid. Compared to previously described DKGRs isolated from
Corynebacterium
spp., these environmental reductases possessed some valuable properties. Both exhibited greater than 20-fold-higher
k
cat
/
K

m

values than those previously determined, primarily as a result of better binding of substrate. The
K

m

values for the two new reductases were 57 and 67 μM, versus 2 and 13 mM for the
Corynebacterium
enzymes. Both environmental DKGRs accepted NADH as well as NADPH as a cosubstrate; other DKGRs and most related aldo-keto reductases use only NADPH. In addition, one of the new reductases was more thermostable than known DKGRs.
Xylulokinase Overexpression in Two Strains ofSaccharomyces cerevisiaeAlso Expressing Xylose Reductase and Xylitol Dehydrogenase and Its Effect on Fermentation of Xylose and Lignocellulosic Hydrolysate
Authors: Johansson Björn , Christensson Camilla , Hobley Timothy , Hahn-Hägerdal Bärbel 
Published: July 2002

ABSTRACTFermentation of the pentose sugar xylose to ethanol in lignocellulosic biomass would make bioethanol production economically more competitive. Saccharomyces cerevisiae, an efficient ethanol producer, can utilize xylose only when expressing the heterologous genesXYL1(xylose reductase) andXYL2(xylitol dehydrogenase). Xylose reductase and xylitol dehydrogenase convert xylose to its isomer xylulose. The geneXKS1encodes the xylulose-phosphorylating enzyme xylulokinase. In this study, we determined the effect ofXKS1overexpression on two differentS. cerevisiaehost strains, H158 and CEN.PK, also expressingXYL1andXYL2. H158 has been previously used as a host strain for the construction of recombinant xylose-utilizingS. cerevisiaestrains. CEN.PK is a new strain specifically developed to serve as a host strain for the development of metabolic engineering strategies. Fermentation was carried out in defined and complex media containing a hexose and pentose sugar mixture or a birch wood lignocellulosic hydrolysate.XKS1overexpression increased the ethanol yield by a factor of 2 and reduced the xylitol yield by 70 to 100% and the final acetate concentrations by 50 to 100%. However,XKS1overexpression reduced the total xylose consumption by half for CEN.PK and to as little as one-fifth for H158. Yeast extract and peptone partly restored sugar consumption in hydrolysate medium. CEN.PK consumed more xylose but produced more xylitol than H158 and thus gave lower ethanol yields on consumed xylose. The results demonstrate that strain background and modulation ofXKS1expression are important for generating an efficient xylose-fermenting recombinant strain ofS. cerevisiae.
Transcriptional Regulation of
Nostoc
Hydrogenases: Effects of Oxygen, Hydrogen, and Nickel
Authors: Axelsson Rikard , Lindblad Peter 
Published: July 2002

ABSTRACT

The transcription of structural genes encoding two hydrogenases in N
2
-fixing cultures of the cyanobacteria
Nostoc muscorum
and
Nostoc
sp. strain PCC 73102 were examined by reverse transcription-PCR. A low level of oxygen and addition of nickel induce higher transcript levels of both hydrogenases, whereas molecular hydrogen has a positive effect on the transcription of the genes encoding only the uptake hydrogenase.
Wax Ester Production from
n
-Alkanes by
Acinetobacter
sp. Strain M-1: Ultrastructure of Cellular Inclusions and Role of Acyl Coenzyme A Reductase
Authors: Ishige Takeru , Tani Akio , Takabe Keiji , Kawasaki Kazunori , Sakai Yasuyoshi , Kato Nobuo 
Published: July 2002

ABSTRACT

Acinetobacter
sp. strain M-1 accumulated a large amount of wax esters from an
n
-alkane under nitrogen-limiting conditions. Under the optimized conditions with
n
-hexadecane as the substrate, the amount of hexadecyl hexadecanoate in the cells reached 0.17 g/g of cells (dry weight). Electron microscopic analysis revealed that multilayered disk-shaped intracellular inclusions were formed concomitant with wax ester formation. The contribution of acyl-CoA reductase to wax ester synthesis was evaluated by gene disruption analysis.
Genetic Relationship among Worldwide Strains of
Xanthomonas
Causing Canker in Citrus Species and Design of New Primers for Their Identification by PCR
Authors: Cubero J. , Graham J. H. 
Published: July 2002

ABSTRACT

Partial sequence analysis of the ribosomal operon in
Xanthomonas axonopodis
allowed discrimination among strains causing the A, B, and C types of citrus bacterial canker (CBC) and quantification of the relationship of these organisms with other species and pathovars in the same genus. Sets of primers based on sequence differences in the internally transcribed spacer and on a sequence from the plasmid gene
pthA
involved in virulence were designed for specific identification of xanthomonads causing CBC diseases. The two sets were validated with a collection of
Xanthomonas
strains associated with citrus species. The primer set based on ribosomal sequences had a high level of specificity for
X. axonopodis
pv. citri, whereas the set based on the
pthA
gene was universal for all types of CBC organisms. Moreover, the relationships among worldwide
Xanthomonas
strains causing CBC were analyzed by amplification of repetitive sequences (enterobacterial repetitive intergenic consensus and BOX elements). Under specific conditions, pathotypes of these
Xanthomonas
strains could be discerned, and subgroups of the pathotypes were identified. Subgroups of strains were associated with certain geographic areas of the world, and on this basis the origin of type A strains introduced into Florida could be inferred.
Reduction of Olive Knot Disease by a Bacteriocin from
Pseudomonas syringae
pv. ciccaronei
Authors: Lavermicocca Paola , Lonigro Stella Lisa , Valerio Francesca , Evidente Antonio , Visconti Angelo 
Published: July 2002

ABSTRACT

A bacteriocin produced by
Pseudomonas syringae
pv. ciccaronei, used at different purification levels and concentrations in culture and in planta, inhibited the multiplication of
P. syringae
subsp.
savastanoi
, the causal agent of olive knot disease, and affected the epiphytic survival of the pathogen on the leaves and twigs of treated olive plants. Treatments with bacteriocin from
P. syringae
pv. ciccaronei inhibited the formation of overgrowths on olive plants caused by
P. syringae
subsp.
savastanoi
strains PVBa229 and PVBa304 inoculated on V-shaped slits and on leaf scars at concentrations of 10
5
and 10
8
CFU ml
−1
, respectively. In particular, the application of 6,000 arbitrary units (AU) of crude bacteriocin (dialyzed ammonium sulfate precipitate of culture supernatant) ml
−1
at the inoculated V-shaped slits and leaf scars resulted in the formation of knots with weight values reduced by 81 and 51%, respectively, compared to the control, depending on the strains and inoculation method used. Crude bacteriocin (6,000 AU ml
−1
) was also effective in controlling the multiplication of epiphytic populations of the pathogen. In particular, the bacterial populations recovered after 30 days were at least 350 and 20 times lower than the control populations on twigs and on leaves, respectively. These results suggest that bacteriocin from
P. syringae
pv. ciccaronei can be used effectively to control the survival of the causal agent of olive knot disease and to prevent its multiplication at inoculation sites.
Fusaric Acid-Producing Strains of
Fusarium oxysporum
Alter 2,4-Diacetylphloroglucinol Biosynthetic Gene Expression in
Pseudomonas fluorescens
CHA0 In Vitro and in the Rhizosphere of Wheat
Authors: Notz Regina , Maurhofer Monika , Dubach Helen , Haas Dieter , Défago Geneviève 
Published: July 2002

ABSTRACT

The phytotoxic pathogenicity factor fusaric acid (FA) represses the production of 2,4-diacetylphloroglucinol (DAPG), a key factor in the antimicrobial activity of the biocontrol strain
Pseudomonas fluorescens
CHA0. FA production by 12
Fusarium oxysporum
strains varied substantially. We measured the effect of FA production on expression of the
phlACBDE
biosynthetic operon of strain CHA0 in culture media and in the wheat rhizosphere by using a translational
phlA
′-′
lacZ
fusion. Only FA-producing
F. oxysporum
strains could suppress DAPG production in strain CHA0, and the FA concentration was strongly correlated with the degree of
phlA
repression. The repressing effect of FA on
phlA
′-′
lacZ
expression was abolished in a mutant that lacked the DAPG pathway-specific repressor PhlF. One FA-producing strain (798) and one nonproducing strain (242) of
F. oxysporum
were tested for their influence on
phlA
expression in CHA0 in the rhizosphere of wheat in a gnotobiotic system containing a sand and clay mineral-based artificial soil.
F. oxysporum
strain 798 (FA
+
) repressed
phlA
expression in CHA0 significantly, whereas strain 242 (FA
−
) did not. In the
phlF
mutant CHA638,
phlA
expression was not altered by the presence of either
F. oxysporum
strain 242 or 798.
phlA
expression levels were seven to eight times higher in strain CHA638 than in the wild-type CHA0, indicating that PhlF limits
phlA
expression in the wheat rhizosphere.
Assessing the Role of
Pseudomonas aeruginosa
Surface-Active Gene Expression in Hexadecane Biodegradation in Sand
Authors: Holden P. A. , LaMontagne M. G. , Bruce A. K. , Miller W. G. , Lindow S. E. 
Published: July 2002

ABSTRACT

Low pollutant substrate bioavailability limits hydrocarbon biodegradation in soils. Bacterially produced surface-active compounds, such as rhamnolipid biosurfactant and the PA bioemulsifying protein produced by
Pseudomonas aeruginosa
, can improve bioavailability and biodegradation in liquid culture, but their production and roles in soils are unknown. In this study, we asked if the genes for surface-active compounds are expressed in unsaturated porous media contaminated with hexadecane. Furthermore, if expression does occur, is biodegradation enhanced? To detect expression of genes for surface-active compounds, we fused the
gfp
reporter gene either to the promoter region of
pra
, which encodes for the emulsifying PA protein, or to the promoter of the transcriptional activator
rhlR
. We assessed green fluorescent protein (GFP) production conferred by these gene fusions in
P. aeruginosa
PG201. GFP was produced in sand culture, indicating that the
rhlR
and
pra
genes are both transcribed in unsaturated porous media. Confocal laser scanning microscopy of liquid drops revealed that
gfp
expression was localized at the hexadecane-water interface. Wild-type PG201 and its mutants that are deficient in either PA protein, rhamnolipid synthesis, or both were studied to determine if the genetic potential to make surface-active compounds confers an advantage to
P. aeruginosa
biodegrading hexadecane in sand. Hexadecane depletion rates and carbon utilization efficiency in sand culture were the same for wild-type and mutant strains, i.e., whether PG201 was proficient or deficient in surfactant or emulsifier production. Environmental scanning electron microscopy revealed that colonization of sand grains was sparse, with cells in small monolayer clusters instead of multilayered biofilms. Our findings suggest that
P. aeruginosa
likely produces surface-active compounds in sand culture. However, the ability to produce surface-active compounds did not enhance biodegradation in sand culture because well-distributed cells and well-distributed hexadecane favored direct contact to hexadecane for most cells. In contrast, surface-active compounds enable bacteria in liquid culture to adhere to the hexadecane-water interface when they otherwise would not, and thus production of surface-active compounds is an advantage for hexadecane biodegradation in well-dispersed liquid systems.
Genetic Complementation of an Outer Membrane Cytochrome
omcB
Mutant of
Shewanella putrefaciens
MR-1 Requires
omcB
Plus Downstream DNA
Authors: Myers Judith M. , Myers Charles R. 
Published: July 2002

ABSTRACT

Anaerobically grown cells of the metal-reducing bacterium
Shewanella putrefaciens
MR-1 contain multiple outer membrane (OM) cytochromes. A gene replacement mutant (strain OMCB1) lacking the OM cytochrome OmcB is markedly deficient in the reduction of MnO
2
and exhibits reduced rates of Fe(III) reduction. The levels of other OM cytochromes are also decreased in OMCB1. Complementation of OMCB1 with wild-type
omcB
did not restore any of these defects. However, a 21-kb genomic fragment from MR-1, which included
omcB
and 19 kb of downstream DNA, fully restored MnO
2
and Fe(III) reduction and the full complement of OM cytochromes to OMCB1. A 14.7-kb DNA fragment, including
omcB
and 12 kb of downstream DNA, provided only a modest increase in MnO
2
reduction and OM cytochrome content, but it fully restored Fe(III) citrate reduction and partially restored FeOOH reduction. While
omcB
mRNA was readily detected in this complement, the OmcB protein was not detected in any cellular compartment. The restoration of Fe(III) reduction despite the absence of OmcB suggests that OmcB itself is not required for Fe(III) reduction. Another OM cytochrome, OmcA, was mislocalized to the cytoplasmic membrane of OMCB1. Only the 21-kb genomic fragment was able to restore proper localization of OmcA to the OM. This 21-kb fragment does not contain
omcA
, but it does contain several open reading frames (ORFs) downstream from
omcB
. The most downstream of these ORFs (
altA
) encodes a putative AraC-like transcriptional regulator. However, a gene replacement mutant of
altA
resembled the wild type with respect to MnO
2
reduction, OM cytochrome content, and the localization of OmcA and OmcB to the OM. Since OMCB1 continues to express genes immediately downstream from
omcB
, the lack of expression of this downstream DNA does not explain its phenotype or the need for the large complementing fragment. The results suggest that the DNA downstream of
omcB
must be present in
cis
in order to restore Fe(III) reduction, MnO
2
reduction, OM cytochrome content, and the localization of OmcA and OmcB to the OM.
Dothistroma pini
, a Forest Pathogen, Contains Homologs of Aflatoxin Biosynthetic Pathway Genes
Authors: Bradshaw Rosie E. , Bhatnagar Deepak , Ganley Rebecca J. , Gillman Carmel J. , Monahan Brendon J. , Seconi Janet M. 
Published: July 2002

ABSTRACT

Homologs of aflatoxin biosynthetic genes have been identified in the pine needle pathogen
Dothistroma pini. D. pini
produces dothistromin, a difuranoanthraquinone toxin with structural similarity to the aflatoxin precursor versicolorin B. Previous studies with purified dothistromin suggest a possible role for this toxin in pathogenicity. By using an aflatoxin gene as a hybridization probe, a genomic
D. pini
clone was identified that contained four
dot
genes with similarity to genes in aflatoxin and sterigmatocystin gene clusters with predicted activities of a ketoreductase (
dotA
), oxidase (
dotB
), major facilitator superfamily transporter (
dotC
), and thioesterase (
dotD
). A
D. pini dotA
mutant was made by targeted gene replacement and shown to be severely impaired in dothistromin production, confirming that
dotA
is involved in dothistromin biosynthesis. Accumulation of versicolorin A (a precursor of aflatoxin) by the
dotA
mutant confirms that the
dotA
gene product is involved in an aflatoxin-like biosynthetic pathway. Since toxin genes have been found to be clustered in fungi in every case analyzed so far, it is speculated that the four
dot
genes may comprise part of a dothistromin biosynthetic gene cluster. A fifth gene,
ddhA
, is not a homolog of aflatoxin genes and could be at one end of the dothistromin cluster. These genes will allow comparative biochemical and genetic studies of the aflatoxin and dothistromin biosynthetic pathways and may also lead to new ways to control
Dothistroma
needle blight.
Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces
Authors: Harmsen Hermie J. M. , Raangs Gerwin C. , He Tao , Degener John E. , Welling Gjalt W. 
Published: July 2002

ABSTRACT

For the detection of six groups of anaerobic bacteria in human feces, we designed seven new 16S rRNA-based oligonucleotide probes. This set of probes extends the current set of probes and gives more data on the composition of the human gut flora. Probes were designed for
Phascolarctobacterium
and relatives (Phasco741),
Veillonella
(Veil223),
Eubacterium hallii
and relatives (Ehal1469),
Lachnospira
and relatives (Lach571), and
Eubacterium cylindroides
and relatives (Ecyl387), and two probes were designed for
Ruminococcus
and relatives (Rbro730 and Rfla729). The hybridization conditions for the new probes were optimized for fluorescent in situ hybridization, and the probes were validated against a set of reference organisms. The probes were applied to fecal samples of 11 volunteers to enumerate their target bacterial groups. The Phasco741 and Veil223 probes both detected average numbers below 1% of the total number of bacteria as determined with the bacterial kingdom-specific Bact338 probe. The Ecyl387 probe detected about 1.4%, the Lach571 and Ehal1469 probes detected 3.8 and 3.6%, respectively, and a combination of the Rbro730 and Rfla729 probes detected 10.3%. A set of 15 probes consisting of probes previously described and those presented here were evaluated in hybridization with the fecal samples of the same volunteers. Together, the group-specific probes detected 90% of the total bacterial cells.
Vancomycin-Resistant
Enterococcus faecium
(VREF) from Norwegian Poultry Cluster with VREF from Poultry from the United Kingdom and The Netherlands in an Amplified Fragment Length Polymorphism Genogroup
Authors: Borgen Katrine , Wasteson Yngvild , Kruse Hilde , Willems Rob J. L. 
Published: July 2002

ABSTRACT

The genetic relationship between 197 vancomycin-resistant
Enterococcus faecium
(VREF) isolates and 21 vancomycin-susceptible
E. faecium
isolates from Norwegian poultry was analyzed by amplified fragment length polymorphism (AFLP). The isolates were compared to 255 VREF isolates from various sources and countries. The Norwegian isolates constituted a relatively homogeneous population of
E. faecium
and clustered in a previously defined poultry AFLP genogroup.
Diagnosis of Tuberculosis Based on the Two Specific Antigens ESAT-6 and CFP10
Authors: van Pinxteren Laurens A. H. , Ravn Pernille , Agger Else Marie , Pollock John , Andersen Peter 
Published: July 2002

ABSTRACTTests based on tuberculin purified protein derivative (PPD) cannot distinguish between tuberculosis infection,Mycobacterium bovisBCG vaccination, or exposure to environmental mycobacteria. The present study investigated the diagnostic potential of twoMycobacterium tuberculosis-specific antigens (ESAT-6 and CFP10) in experimental animals as well as during natural infection in humans and cattle. Both antigens were frequently recognized in vivo and in vitro based on the induction of delayed-type hypersensitivity responses and the ability to induce gamma interferon production by lymphocytes, respectively. The combination of ESAT-6 and CFP10 was found to be highly sensitive and specific for both in vivo and in vitro diagnosis. In humans, the combination had a high sensitivity (73%) and a much higher specificity (93%) than PPD (7%).
Induction of Hypergammaglobulinemia and Macrophage Activation by Silicone Gels and Oils in Female A.SW Mice
Authors: Naim J. O. , Satoh M. , Buehner N. A. , Ippolito K. M. L. , Yoshida H. , Nusz D. , Kurtelawicz L. , Cramer S. F. , Reeves W. H. 
Published: July 2002

ABSTRACTAlthough most published epidemiological studies have found little evidence of systemic autoimmune disease associated with silicone breast implants, there still remains a question of whether silicones can cause local and/or systemic immune dysfunction. This study further investigates the effects of silicones on autoantibody and immunoglobulin production and macrophage activation in female A.SW mice. Sixty mice were divided among four treatment groups receiving a 0.5-ml intraperitoneal injection of either phosphate-buffered saline (PBS), pristane, silicone gel, or silicone oil. Test bleeds were taken periodically for 6 months. In contrast to pristane, neither silicone gel nor silicone oil induced lupus-associated antinuclear autoantibodies (immunoglobulin G [IgG] anti-nRNP/Sm, Su, and ribosomal P) or lupus nephritis. However, serum IgM became elevated persistently within 1 month of silicone gel or silicone oil administration. Also, the level of IgG3 was clearly elevated in silicone oil-treated mice. In contrast, IgG1, IgG2a, and IgG2b levels were not affected greatly by either silicone gel or oil. Furthermore, peritoneal macrophages from silicone- and pristane-treated mice produced higher levels of interleukin-1β (IL-1β) and IL-6 than those from PBS-treated mice after lipopolysaccharide stimulation. These results suggest that silicone gels and oils are capable of inducing hypergammaglobulinemia and activating macrophages in female A.SW mice.