bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Ammonia Production by
Colletotrichum gloeosporioides
on
pelB
Activation, Pectate Lyase Secretion, and Fruit Pathogenicity
Authors: Kramer-Haimovich H. , Servi E. , Katan T. , Rollins J. , Okon Y. , Prusky D. 
Published: February 2006

ABSTRACT

The accumulation of ammonia and associated tissue alkalinization predispose avocado fruit to attack by
Colletotrichum gloeosporioides
. Secretion of ammonia by
C. gloeosporioides
in the presence of KNO
3
was induced by decreasing the pH from 7.0 to 4.0. When the fungus was grown at pH 4.0 or 6.0 in the absence of a nitrogen source, ammonia did not accumulate, and neither
pelB
(encoding pectate lyase) transcription nor pectate lyase secretion was detected. Under these nitrogen starvation conditions, only transcriptional activation of
areA
, which encodes the global nitrogen regulator, was detected.
pelB
transcription and pectate lyase secretion were both detected when
C. gloeosporioides
was grown at pH 6.0 in the presence of ammonia accumulated from different nitrogen sources. The early accumulation of ammonia induced early
pelB
expression and pectate lyase secretion. As the external pH increased from 4.0 to 6.0, transcripts of
pac1
, the
C. gloeosporioides pacC
homolog, also could be detected. Nit mutants of
C. gloeosporioides
, which cannot utilize KNO
3
as a nitrogen source, did not secrete ammonia, alkalinize the medium, or secrete pectate lyase. If Nit mutants were grown at pH 6.0 in the presence of glutamate, then pectate lyase secretion was induced. Infiltration of 0.1 M ammonium hydroxide at pH 10 into ripening avocado fruits enhanced the activation of quiescent infection and symptom development by
C. gloeosporioides
. These results suggest that ambient pH alkalinization resulting from ammonia accumulation and the availability of ammonia as a nitrogen source independently regulate
pelB
expression, pectate lyase secretion, and virulence of
C. gloeosporioides
. These data suggest that alkalinization during
C. gloeosporioides
infection is important for its transformation from the quiescent biotrophic stage to the necrotrophic stage of fungal colonization in the fruit host.
Specific Detection of
Xanthomonas axonopodis
pv. dieffenbachiae in Anthurium (
Anthurium andreanum
) Tissues by Nested PCR
Authors: Robène-Soustrade Isabelle , Laurent Philippe , Gagnevin Lionel , Jouen Emmanuel , Pruvost Olivier 
Published: February 2006

ABSTRACT

Efficient control of
Xanthomonas axonopodis
pv. dieffenbachiae, the causal agent of anthurium bacterial blight, requires a sensitive and reliable diagnostic tool. A nested PCR test was developed from a sequence-characterized amplified region marker identified by randomly amplified polymorphic DNA PCR for the detection of
X. axonopodis
pv. dieffenbachiae. Serological and pathogenicity tests were performed concurrently with the nested PCR test with a large collection of
X. axonopodis
pv. dieffenbachiae strains that were isolated worldwide and are pathogenic to anthurium and/or other aroids. The internal primer pair directed amplification of the expected product (785 bp) for all 70
X. axonopodis
pv. dieffenbachiae strains pathogenic to anthurium tested and for isolates originating from syngonium and not pathogenic to anthurium. This finding is consistent with previous studies which indicated that there is a high level of relatedness between strains from anthurium and strains from syngonium. Strains originating from the two host genera can be distinguished by restriction analysis of the amplification product. No amplification product was obtained with 98 strains of unrelated phytopathogenic bacteria or saprophytic bacteria from the anthurium phyllosphere, except for a weak signal obtained for one
X. axonopodis
pv. allii strain. Nevertheless, restriction enzyme analysis permitted the two pathovars to be distinguished. The detection threshold obtained with pure cultures or plant extracts (10
3
CFU ml
−1
) allowed detection of the pathogen from symptomless contaminated plants. This test could be a useful diagnostic tool for screening propagation stock plant material and for monitoring international movement of
X. axonopodis
pv. dieffenbachiae.
The Naphthalene Catabolic (
nag
) Genes of
Polaromonas naphthalenivorans
CJ2: Evolutionary Implications for Two Gene Clusters and Novel Regulatory Control
Authors: Jeon Che Ok , Park Minjeong , Ro Hyun-Su , Park Woojun , Madsen Eugene L. 
Published: February 2006

ABSTRACT

Polaromonas naphthalenivorans
CJ2, found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (C.-O. Jeon et al., Proc. Natl. Acad. Sci. USA 100:13591-13596, 2003), is able to grow on mineral salts agar media with naphthalene as the sole carbon source. Beginning from a 484-bp
nagAc
-like region, we used a genome walking strategy to sequence genes encoding the entire naphthalene degradation pathway andadditional flanking regions. We found that the naphthalene catabolic genes in
P. naphthalenivorans
CJ2 were divided into one large and one small gene cluster, separated by an unknown distance. The large gene cluster (
nagRAaGHAbAcAdBFCQEDJI′ORF1tnpA
) is bounded by a LysR-type regulator (
nagR
). The small cluster (
nagR2ORF2I"KL
) is bounded by a MarR-type regulator (
nagR2
). The catabolic genes of
P. naphthalenivorans
CJ2 were homologous to many of those of
Ralstonia
U2, which uses the gentisate pathway to convert naphthalene to central metabolites. However, three open reading frames (
nagY
,
nagM
, and
nagN
), present in
Ralstonia
U2, were absent. Also,
P. naphthalenivorans
carries two copies of gentisate dioxygenase (
nagI
) with 77.4% DNA sequence identity to one another and 82% amino acid identity to their homologue in
Ralstonia
sp. strain U2. Investigation of the operons using reverse transcription PCR showed that each cluster was controlled independently by its respective promoter. Insertional inactivation and lacZ reporter assays showed that
nagR2
is a negative regulator and that expression of the small cluster is not induced by naphthalene, salicylate, or gentisate. Association of two putative
Azoarcus
-related transposases with the large cluster and one
Azoarcus
-related putative salicylate 5-hydroxylase gene (
ORF2
) in the small cluster suggests that mobile genetic elements were likely involved in creating the novel arrangement of catabolic and regulatory genes in
P. naphthalenivorans
.
Novel Genetic Variants of
Anaplasma phagocytophilum
,
Anaplasma bovis
,
Anaplasma centrale
, and a Novel
Ehrlichia
sp. in Wild Deer and Ticks on Two Major Islands in Japan
Authors: Kawahara Makoto , Rikihisa Yasuko , Lin Quan , Isogai Emiko , Tahara Kenji , Itagaki Asao , Hiramitsu Yoshimichi , Tajima Tomoko 
Published: February 2006

ABSTRACT

Wild deer are one of the important natural reservoir hosts of several species of
Ehrlichia
and
Anaplasma
that cause human ehrlichiosis or anaplasmosis in the United States and Europe. The primary aim of the present study was to determine whether and what species of
Ehrlichia
and
Anaplasma
naturally infect deer in Japan. Blood samples obtained from wild deer on two major Japanese islands, Hokkaido and Honshu, were tested for the presence of
Ehrlichia
and
Anaplasma
by PCR assays and sequencing of the 16S rRNA genes, major outer membrane protein
p44
genes, and
groESL
. DNA representing four species and two genera of
Ehrlichia
and
Anaplasma
was identified in 33 of 126 wild deer (26%). DNA sequence analysis revealed novel strains of
Anaplasma phagocytophilum
, a novel
Ehrlichia
sp.,
Anaplasma centrale
, and
Anaplasma bovis
in the blood samples from deer. None of these have been found previously in deer. The new
Ehrlichia
sp.,
A. bovis
, and
A. centrale
were also detected in
Hemaphysalis longicornis
ticks from Honshu Island. These results suggest that enzootic cycles of
Ehrlichia
and
Anaplasma
species distinct from those found in the United States or Europe have been established in wild deer and ticks in Japan.
Isolation and Expression of the Lysis Genes of
Actinomyces naeslundii
Phage Av-1
Authors: Delisle Allan L. , Barcak Gerard J. , Guo Ming 
Published: February 2006

ABSTRACT

Like most gram-positive oral bacteria,
Actinomyces naeslundii
is resistant to salivary lysozyme and to most other lytic enzymes. We are interested in studying the lysins of phages of this important oral bacterium as potential diagnostic and therapeutic agents. To identify the
Actinomyces
phage genes encoding these species-specific enzymes in
Escherichia coli
, we constructed a new cloning vector, pAD330, that can be used to enrich for and isolate phage holin genes, which are located adjacent to the lysin genes in most phage genomes. Cloned holin insert sequences were used to design sequencing primers to identify nearby lysin genes by using whole phage DNA as the template. From partial digestions of
A. naeslundii
phage Av-1 genomic DNA we were able to clone, in independent experiments, inserts that complemented the defective λ holin in pAD330, as evidenced by extensive lysis after thermal induction. The DNA sequence of the inserts in these plasmids revealed that both contained the complete lysis region of Av-1, which is comprised of two holin-like genes, designated
holA
and
holB
, and an endolysin gene, designated
lysA
. We were able to subclone and express these genes and determine some of the functional properties of their gene products.
Engineering Plant-Microbe Symbiosis for Rhizoremediation of Heavy Metals
Authors: Wu Cindy H. , Wood Thomas K. , Mulchandani Ashok , Chen Wilfred 
Published: February 2006

ABSTRACT

The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium,
Pseudomonas putida
06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing
P. putida
endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.
Molecular and Genetic Characterization of a Novel Nisin Variant Produced by
Streptococcus uberis
Authors: Wirawan Ruth E. , Klesse Nikolai A. , Jack Ralph W. , Tagg John R. 
Published: February 2006

ABSTRACT

Streptococcus uberis
is one of the principal causative agents of bovine mastitis. In this study, we report that
S. uberis
strain 42 produces a lantibiotic, nisin U, which is 78% identical (82% similar) to nisin A from
Lactococcus lactis
. The 15.6-kb nisin U locus comprises 11 open reading frames, similar in putative functionality but differing in arrangement from that of the nisin A biosynthetic cluster. The nisin U producer strain exhibits specific resistance (immunity) to nisin U and cross-resistance to nisin A, a finding consistent with the 55% sequence similarity of their respective immunity peptides. Homologues of the nisin U structural gene were identified in several additional
S. uberis
strains, and in each case cross-protective immunity was expressed to nisin A and to the other producers of nisin U and its variants. To our knowledge, this is the first report both of characterization of a bacteriocin by
S. uberis
, as well as of a member of the nisin family of peptides in a species other than
L. lactis
.
Differential Expression of Proteins and Genes in the Lag Phase of
Lactococcus lactis
subsp.
lactis
Grown in Synthetic Medium and Reconstituted Skim Milk
Authors: Larsen Nadja , Boye Mette , Siegumfeldt Henrik , Jakobsen Mogens 
Published: February 2006

ABSTRACT

We investigated protein and gene expression in the lag phase of
Lactococcus lactis
subsp.
lactis
CNRZ 157 and compared it to the exponential and stationary phases. By means of two-dimensional polyacrylamide gel electrophoresis, 28 highly expressed lag-phase proteins, implicated in nucleotide metabolism, glycolysis, stress response, translation, transcription, cell division, amino acid metabolism, and coenzyme synthesis, were identified. Among the identified proteins, >2-fold induction and down-regulation in the lag phase were determined for 12 proteins in respect to the exponential phase and for 18 proteins in respect to the stationary phase. Transcriptional changes of the lag-phase proteins in
L. lactis
were studied by oligonucleotide microarrays. Good correlation between protein and gene expression studies was demonstrated for several differentially expressed proteins, including nucleotide biosynthetic enzymes, adenylosuccinate synthase (PurA), IMP dehydrogenase (GuaB), and aspartate carbamoyl transferase (PyrB); heat-shock protein DnaK; serine hydroxymethyl transferase (GlyA); carbon catabolite control protein (CcpA); elongation factor G (FusA); and cell division protein (FtsZ).
Identification of QuiP, the Product of Gene PA1032, as the Second Acyl-Homoserine Lactone Acylase ofPseudomonas aeruginosaPAO1
Authors: Huang Jean J. , Petersen Ashley , Whiteley Marvin , Leadbetter Jared R. 
Published: February 2006

ABSTRACTThe relevance of the acyl homoserine lactone (acyl-HSL) quorum signalsN-3-oxododecanoyl-homoserine lactone (3OC12HSL) andN-butanoyl-homoserine lactone to the biology and virulence ofPseudomonas aeruginosais well investigated. Previously,P. aeruginosawas shown to degrade long-chain, but not short-chain, acyl-HSLs as sole carbon and energy sources (J. J. Huang, J.-I. Han, L.-H. Zhang, and J. R. Leadbetter, Appl. Environ. Microbiol.69:5941-5949, 2003). A gene encoding an enzyme with acyl-HSL acylase activity,pvdQ(PA2385), was identified, but it was not required for acyl-HSL utilization. This indicated thatP. aeruginosaencodes another acyl-HSL acylase, which we identify here. A comparison of total cell proteins of cultures grown with long-acyl acyl-HSLs versus other substrates implicated the involvement of a homolog of PvdQ, the product of gene PA1032, for which we propose the name QuiP. Transposon mutants ofquiPwere defective for growth whenP. aeruginosawas cultured in medium containing decanoyl-HSL as a sole carbon and energy source. Complementation with a functional copy ofquiPrescued this growth defect. WhenP. aeruginosawas grown in buffered lysogeny broth, constitutive expression of QuiP inP. aeruginosaled to decreased accumulations of the quorum signal 3OC12HSL, relative to the wild type. Heterologous expression of QuiP was sufficient to confer long-chain acyl-HSL acylase activity uponEscherichia coli. Examination of gene expression patterns during acyl-HSL-dependent growth ofP. aeruginosafurther supported the involvement ofquiPin signal decay and revealed other genes also possibly involved. It is not yet known under which “natural” conditionsquiPis expressed or howP. aeruginosabalances the expression of its quorum-sensing systems with the expression of its acyl-HSL acylase activities.
Genetic Variance in the Composition of Two Functional Groups (Diazotrophs and Cyanobacteria) from a Hypersaline Microbial Mat
Authors: Yannarell Anthony C. , Steppe Timothy F. , Paerl Hans W. 
Published: February 2006

ABSTRACT

Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and F
ST
tests of genetic differentiation of
nifH
and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).
Detection of Type A, B, E, and F
Clostridium botulinum
Neurotoxins in Foods by Using an Amplified Enzyme-Linked Immunosorbent Assay with Digoxigenin-Labeled Antibodies
Authors: Sharma Shashi K. , Ferreira Joseph. L. , Eblen Brian S. , Whiting Richard C. 
Published: February 2006

ABSTRACT

An amplified enzyme-linked immunosorbent assay (ELISA) for the detection of
Clostridium botulinum
complex neurotoxins was evaluated for its ability to detect these toxins in food. The assay was found to be suitable for detecting type A, B, E, and F botulinum neurotoxins in a variety of food matrices representing liquids, solid, and semisolid food. Specific foods included broccoli, orange juice, bottled water, cola soft drinks, vanilla extract, oregano, potato salad, apple juice, meat products, and dairy foods. The detection sensitivity of the test for these botulinum complex serotypes was found to be 60 pg/ml (1.9 50% lethal dose [LD
50
]) for botulinum neurotoxin type A (BoNT/A), 176 pg/ml (1.58 LD
50
) for BoNT/B, 163 pg/ml for BoNT/E (4.5 LD
50
), and 117 pg/ml for BoNT/F (less than 1 LD
50
) in casein buffer. The test could also readily detect 2 ng/ml of neurotoxins type A, B, E, and F in a variety of food samples. For specificity studies, the assay was also used to test a large panel of type A
C. botulinum
, a smaller panel of proteolytic and nonproteolytic type B, E, and F neurotoxin-producing
Clostridia
, and nontoxigenic organisms using an overnight incubation of toxin production medium. The assay appears to be an effective tool for large-scale screening of the food supply in the event of a botulinum neurotoxin contamination event.
New Threshold and Confidence Estimates for Terminal Restriction Fragment Length Polymorphism Analysis of Complex Bacterial Communities
Authors: Osborne Catherine A. , Rees Gavin N. , Bernstein Yaniv , Janssen Peter H. 
Published: February 2006

ABSTRACT
Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variable percentage threshold method. We found that making conclusions about the similarities of complex bacterial communities from T-RFLP profiles generated by a single restriction enzyme (RE) may lead to erroneous conclusions. Instead, the use of multiple REs, each individually, to generate multiple data sets allowed us to determine a confidence estimate for groupings of apparently similar communities and at the same time minimized the effects of RE selection. In conjunction with the variable percentage threshold method, this allowed us to make confident conclusions about the similarities of the complex bacterial communities in the 17 different samples.
Rapid High-Throughput Assessment of Aerobic Bacteria in Complex Samples by Fluorescence-Based Oxygen Respirometry
Authors: O'Mahony Fiach C. , Papkovsky Dmitri B. 
Published: February 2006

ABSTRACT

A simple method has been developed for the analysis of aerobic bacteria in complex samples such as broth and food homogenates. It employs commercial phosphorescent oxygen-sensitive probes to monitor oxygen consumption of samples containing bacteria using standard microtiter plates and fluorescence plate readers. As bacteria grow in aqueous medium, at certain points they begin to deplete dissolved oxygen, which is seen as an increase in probe fluorescence above baseline signal. The time required to reach threshold signal is used to either enumerate bacteria based on a predetermined calibration or to assess the effects of various effectors on the growth of test bacteria by comparison with an untreated control. This method allows for the sensitive (down to a single cell), rapid (0.5 to 12 h) enumeration of aerobic bacteria without the need to conduct lengthy (48 to 72 h) and tedious colony counts on agar plates. It also allows for screening a wide range of chemical and environmental samples for their toxicity. These assays have been validated with different bacteria, including
Escherichia coli
,
Micrococcus luteus
, and
Pseudomonas fluorescens
, with the enumeration of total viable counts in broth and industrial food samples (packaged ham, chicken, and mince meat), and comparison with established agar plating and optical-density-at-600-nm assays has been given.
Strategy for Identification of
Bacillus cereus
and
Bacillus thuringiensis
Strains Closely Related to
Bacillus anthracis
Authors: Daffonchio Daniele , Raddadi Noura , Merabishvili Maya , Cherif Ameur , Carmagnola Lorenzo , Brusetti Lorenzo , Rizzi Aurora , Chanishvili Nina , Visca Paolo , Sharp Richard , Borin Sara 
Published: February 2006

ABSTRACT

Bacillus cereus
strains that are genetically closely related to
B. anthracis
can display anthrax-like virulence traits (A. R. Hoffmaster et al., Proc. Natl. Acad. Sci. USA 101:8449-8454, 2004). Hence, approaches that rapidly identify these “near neighbors” are of great interest for the study of
B. anthracis
virulence mechanisms, as well as to prevent the use of such strains for
B. anthracis
-based bioweapon development. Here, a strategy is proposed for the identification of near neighbors of
B. anthracis
based on single nucleotide polymorphisms (SNP) in the 16S-23S rRNA intergenic spacer (ITS) containing tRNA genes, characteristic of
B. anthracis
. By using restriction site insertion-PCR (RSI-PCR) the presence of two SNP typical of
B. anthracis
was screened in 126
B. cereus
group strains of different origin. Two
B. cereus
strains and one
B. thuringiensis
strain showed RSI-PCR profiles identical to that of
B. anthracis
. The sequencing of the entire ITS containing tRNA genes revealed two of the strains to be identical to
B. anthracis
. The strict relationship with
B. anthracis
was confirmed by multilocus sequence typing (MLST) of four other independent loci:
cerA
,
plcR
, AC-390, and SG-749. The relationship to
B. anthracis
of the three strains described by MLST was comparable and even higher to that of four
B. cereus
strains associated with periodontitis in humans and previously reported as the closest known strains to
B. anthracis
. SNP in ITS containing tRNA genes combined with RSI-PCR provide a very efficient tool for the identification of strains closely related to
B. anthracis
.