bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minireplicon from pBtoxis of
Bacillus thuringiensis
subsp.
israelensis
Authors: Tang Mujin , Bideshi Dennis K. , Park Hyun-Woo , Federici Brian A. 
Published: November 2006

ABSTRACT

A 2.2-kb fragment containing a replicon from pBtoxis, the large plasmid that encodes the insecticidal endotoxins of
Bacillus thuringiensis
subsp.
israelensis
, was identified, cloned, and sequenced. This fragment contains
cis
elements, including iterons, found in replication origins of other large plasmids and suggests that pBtoxis replicates by a type A theta mechanism. Two genes, pBt156 and pBt157, encoding proteins of 54.4 kDa and 11.8 kDa, respectively, were present in an operon within this minireplicon, and each was shown by deletion analysis to be essential for replication. The deduced amino acid sequences of the 54.4-kDa and 11.8-kDa proteins showed no substantial homology with known replication (Rep) proteins. However, the 54.4-kDa protein contained a conserved FtsZ domain, and the 11.8 kDa protein contained a helix-turn-helix motif. As FtsZ proteins have known functions in bacterial cell division and the helix-turn-helix motif is present in Rep proteins, it is likely that these proteins function in plasmid replication and partitioning. The minireplicon had a copy number of two or three per chromosome equivalent in
B. thuringiensis
subsp.
israelensis
but did not replicate in
B. cereus
,
B. megaterium
, or
B. subtilis
. A plasmid constructed to synthesize large quantities of the Cry11A and Cyt1A endotoxins demonstrated that this minireplicon can be used to engineer vectors for
cry
and
cyt
gene expression.
c
-Type Cytochromes in
Pelobacter carbinolicus
Authors: Haveman Shelley A. , Holmes Dawn E. , Ding Yan-Huai R. , Ward Joy E. , DiDonato Raymond J. , Lovley Derek R. 
Published: November 2006

ABSTRACT

Previous studies failed to detect
c
-type cytochromes in
Pelobacter
species despite the fact that other close relatives in the
Geobacteraceae
, such as
Geobacter
and
Desulfuromonas
species, have abundant
c-
type cytochromes. Analysis of the recently completed genome sequence of
Pelobacter carbinolicus
revealed 14 open reading frames that could encode
c
-type cytochromes. Transcripts for all but one of these open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. Three putative
c
-type cytochrome genes were expressed specifically during Fe(III) reduction, suggesting that the encoded proteins may participate in electron transfer to Fe(III). One of these proteins was a periplasmic triheme cytochrome with a high level of similarity to PpcA, which has a role in Fe(III) reduction in
Geobacter sulfurreducens
. Genes for heme biosynthesis and system II cytochrome
c
biogenesis were identified in the genome and shown to be expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of protein extracted from acetoin-fermenting
P. carbinolicus
cells contained three heme-staining bands which were confirmed by mass spectrometry to be among the 14 predicted
c
-type cytochromes. The number of cytochrome genes, the predicted amount of heme
c
per protein, and the ratio of heme-stained protein to total protein were much smaller in
P. carbinolicus
than in
G. sulfurreducens
. Furthermore, many of the
c
-type cytochromes that genetic studies have indicated are required for optimal Fe(III) reduction in
G. sulfurreducens
were not present in the
P. carbinolicus
genome. These results suggest that further evaluation of the functions of
c
-type cytochromes in the
Geobacteraceae
is warranted.
Genetic Differences between Blight-Causing
Erwinia
Species with Differing Host Specificities, Identified by Suppression Subtractive Hybridization
Authors: Triplett Lindsay R. , Zhao Youfu , Sundin George W. 
Published: November 2006

ABSTRACT

PCR-based subtractive hybridization was used to isolate sequences from
Erwinia amylovora
strain Ea110, which is pathogenic on apples and pears, that were not present in three closely related strains with differing host specificities:
E. amylovora
MR1, which is pathogenic only on
Rubus
spp.;
Erwinia pyrifoliae
Ep1/96, the causal agent of shoot blight of Asian pears; and
Erwinia
sp. strain Ejp556, the causal agent of bacterial shoot blight of pear in Japan. In total, six subtractive libraries were constructed and analyzed. Recovered sequences included type III secretion components, hypothetical membrane proteins, and ATP-binding proteins. In addition, we identified an Ea110-specific sequence with homology to a type III secretion apparatus component of the insect endosymbiont
Sodalis glossinidius
, as well as an Ep1/96-specific sequence with homology to the
Yersinia pestis
effector protein tyrosine phosphatase YopH.
Role ofptsP,orfT, andsssRecombinase Genes in Root Colonization byPseudomonas fluorescensQ8r1-96
Authors: Mavrodi Olga V. , Mavrodi Dmitri V. , Weller David M. , Thomashow Linda S. 
Published: November 2006

ABSTRACTPseudomonas fluorescensQ8r1-96 produces 2,4-diacetylphloroglucinol (2,4-DAPG), a polyketide antibiotic that suppresses a wide variety of soilborne fungal pathogens, includingGaeumannomyces graminisvar.tritici, which causes take-all disease of wheat. Strain Q8r1-96 is representative of the D-genotype of 2,4-DAPG producers, which are exceptional because of their ability to aggressively colonize and maintain large populations on the roots of host plants, including wheat, pea, and sugar beet. In this study, three genes, ansssrecombinase gene,ptsP, andorfT, which are important in the interaction ofPseudomonasspp. with various hosts, were investigated to determine their contributions to the unusual colonization properties of strain Q8r1-96. Thesssrecombinase andptsPgenes influence global processes, including phenotypic plasticity and organic nitrogen utilization, respectively. TheorfTgene contributes to the pathogenicity ofPseudomonas aeruginosain plants and animals and is conserved among saprophytic rhizosphere pseudomonads, but its function is unknown. Clones containing these genes were identified in a Q8r1-96 genomic library, sequenced, and used to construct gene replacement mutants of Q8r1-96. Mutants were characterized to determine their 2,4-DAPG production, motility, fluorescence, colony morphology, exoprotease and hydrogen cyanide (HCN) production, carbon and nitrogen utilization, and ability to colonize the rhizosphere of wheat grown in natural soil. TheptsPmutant was impaired in wheat root colonization, whereas mutants with mutations in thesssrecombinase gene andorfTwere not. However, all three mutants were less competitive than wild-typeP. fluorescensQ8r1-96 in the wheat rhizosphere when they were introduced into the soil by paired inoculation with the parental strain.
Quantitative Detection of
Corynebacterium casei
in Cheese by Real-Time PCR
Authors: Monnet Christophe , Correia Karine , Sarthou Anne-Sophie , Irlinger Françoise 
Published: November 2006

ABSTRACT

The flora on the surface of smear-ripened cheeses is composed of numerous species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. Due to the absence of selective media, it is very difficult to quantify cheese surface bacteria, and, consequently, the ecology of the cheese surface microflora has not been extensively investigated. We developed a SYBR green I real-time PCR method to quantify
Corynebacterium casei
, a major species of smear-ripened cheeses, using primers designed to target the 16S rRNA gene. It was possible to recover
C. casei
genomic DNA from the cheese matrix with nearly the same yield that
C. casei
genomic DNA is recovered from cells recovered by centrifugation from liquid cultures. Quantification was linear over a range from 10
5
to 10
10
CFU per g of cheese. The specificity of the assay was demonstrated with DNA from species related to
C. casei
and from other bacteria and yeasts belonging to the cheese flora. Nine commercial cheeses were analyzed by real-time PCR, and six of them were found to contain more than 10
5
CFU equivalents of
C. casei
per g. In two of them, the proportion of
C. casei
in the total bacterial flora was nearly 40%. The presence of
C. casei
in these samples was further confirmed by single-strand conformation polymorphism analysis and by a combined approach consisting of plate counting and 16S rRNA gene sequencing. We concluded that SYBR green I real-time PCR may be used as a reliable species-specific method for quantification of bacteria from the surface of cheeses.
Identification of Specific Gene Sequences Conserved in Contemporary Epidemic Strains ofSalmonella enterica
Authors: Kang Min-Su , Besser Thomas E. , Hancock Dale D. , Porwollik Steffen , McClelland Michael , Call Douglas R. 
Published: November 2006

ABSTRACTGenetic elements specific to recent and contemporary epidemic strains ofSalmonella entericawere identified using comparative genomic analysis. Two epidemic multidrug-resistant (MDR) strains, MDRSalmonella entericaserovar Typhimurium definitive phage type 104 (DT104) and cephalosporin-resistant MDRSalmonella entericaserovar Newport, and an epidemic pansusceptible strain,Salmonellaserovar Typhimurium DT160, were subjected toSalmonellagene microarray and suppression subtractive hybridization analyses. Their genome contents were compared with those of coexisting sporadic strains matched by serotype, geographic and temporal distribution, and host species origin. These paired comparisons revealed that epidemic strains ofS. entericahad specific genes and gene regions that were shared by isolates of the same subtype. Most of these gene sequences are related to mobile genetic elements, including phages, plasmids, and plasmid-like and transposable elements, and some genes may encode proteins conferring growth or survival advantages. The emergence of epidemic MDR strains may therefore be associated with the presence of fitness-associated genetic factors in addition to their antimicrobial resistance genes.
Temporal and Spatial Dispersal of
Cladobotryum
Conidia in the Controlled Environment of a Mushroom Growing Room
Authors: Adie Bruce , Grogan Helen , Archer Simon , Mills Peter 
Published: November 2006

ABSTRACT

Cladobotryum
spp. are responsible for cobweb disease of mushrooms. In two commercial and one experimental mushroom-growing room,
Cladobotryum
conidia were released into the air in direct response to physical disturbance of disease colonies during either crop watering or treatment by covering with salt to 10 mm. Conidia were detected using a Burkard spore trap or agar-based trap plates. A maximum concentration of ∼25,000 conidia m
−3
was recorded in a small (75-m
3
) experimental growing room in the hour following the salting of 16 cobweb patches (0.55 m
2
). Concentrations of 100 and 40 conidia m
−3
were recorded in the two larger commercial growing rooms in the hour following the salting of 18 and 11 patches of cobweb (diameter, approximately 50 to 200 mm), respectively. In controlled experiments, disturbed conidia were dispersed rapidly throughout a small growing room, with 91 to 97% of conidia settling out within 15 min. Eighty-five percent of conidia settled out within a 0.5-m radius when air-conditioning fans were switched off, consistent with airborne spore dispersal. Alternative methods for treating diseased areas to minimize conidial release and distribution were investigated and included covering disease colonies with damp paper tissue prior to salt application (tissue salting) and holding a dust extractor above disease colonies during salt application. Both methods resulted in no detectable airborne conidia, but the tissue paper salting technique was more convenient. Prevention of airborne conidial release and distribution is essential to avoid mushroom spotting symptoms, secondary colonies, and early crop termination.
Simultaneous Biodetoxification of S, N, and O Pollutants by Engineering of a Carbazole-Degrading Gene Cassette in a Recombinant Biocatalyst
Authors: Yu Bo , Ma Cuiqing , Zhou Wenjuan , Zhu Shanshan , Wang Ying , Qu Jingyao , Li Fuli , Xu Ping 
Published: November 2006

ABSTRACT

The gene cassette encoding enzymes responsible for degrading carbazole to anthranilic acid was introduced into a dibenzothiophene degrader. The resultant strain,
Rhodococcus erythropolis
XPDN, could simultaneously transform the model pollutants dibenzothiophene, carbazole, and dibenzofuran to nontoxic metabolites and may have an application potential for bioremediation.
An Integrated Approach to Functional Genomics: Construction of a Novel Reporter Gene Fusion Library forSinorhizobium meliloti
Authors: Cowie Alison , Cheng Jiujun , Sibley Christopher D. , Fong Ying , Zaheer Rahat , Patten Cheryl L. , Morton Richard M. , Golding G. Brian , Finan Turlough M. 
Published: November 2006

ABSTRACTAs a means of investigating gene function, we developed a robust transcription fusion reporter vector to measure gene expression in bacteria. The vector, pTH1522, was used to construct a random insert library for theSinorhizobium melilotigenome. pTH1522 replicates inEscherichia coliand can be transferred to, but cannot replicate in,S. meliloti. Homologous recombination of the DNA fragments cloned in pTH1522 into theS. melilotigenome generates transcriptional fusions to either the reporter genesgfp+andlacZorgusAandrfp, depending on the orientation of the cloned fragment. Over 12,000 fusion junctions in 6,298 clones were identified by DNA sequence analysis, and the plasmid clones were recombined intoS. meliloti. Reporter enzyme activities following growth of these recombinants in complex medium (LBmc) and in minimal medium with glucose or succinate as the sole carbon source allowed the identification of genes highly expressed under one or more growth condition and those expressed at very low to background levels. In addition to generating reporter gene fusions, the vector allows Flp recombinase-directed deletion formation and gene disruption, depending on the nature of the cloned fragment. We report the identification of genes essential for growth on complex medium as deduced from an inability to recover recombinants from pTH1522 clones that carried fragments internal to gene or operon transcripts. A database containing all the gene expression activities together with a web interface showing the precise locations of reporter fusion junctions has been constructed (www.sinorhizobium.org).
The Surfactant Tween 80 Enhances Biodesulfurization
Authors: Feng Jinhui , Zeng Yiyong , Ma Cuiqing , Cai Xiaofeng , Zhang Quan , Tong Mingyou , Yu Bo , Xu Ping 
Published: November 2006

ABSTRACT

In biocatalytic conversions, substrates and products may display inhibitory or toxic effects on the biocatalyst.
Rhodococcus erythropolis
1awq could further remove sulfur from hydrodesulfurized diesel oil, and the biodesulfurization was enhanced by the surfactant Tween 80. Tween 80 was shown to decrease the product concentration associated with the cells, reducing product inhibition.
Interspecific Transfer of Bacterial Endosymbionts between Tsetse Fly Species: Infection Establishment and Effect on Host Fitness
Authors: Weiss Brian L. , Mouchotte Rosa , Rio Rita V. M. , Wu Yi-neng , Wu Zheyang , Heddi Abdelaziz , Aksoy Serap 
Published: November 2006

ABSTRACT

Tsetse flies (
Glossina
spp.) can harbor up to three distinct species of endosymbiotic bacteria that exhibit unique modes of transmission and evolutionary histories with their host. Two mutualist enterics,
Wigglesworthia
and
Sodalis
, are transmitted maternally to tsetse flies' intrauterine larvae. The third symbiont, from the genus
Wolbachia
, parasitizes developing oocytes. In this study, we determined that
Sodalis
isolates from several tsetse fly species are virtually identical based on a phylogenetic analysis of their
ftsZ
gene sequences. Furthermore, restriction fragment-length polymorphism analysis revealed little variation in the genomes of
Sodalis
isolates from tsetse fly species within different subgenera (
Glossina fuscipes fuscipes
and
Glossina morsitans morsitans
). We also examined the impact on host fitness of transinfecting
G. fuscipes fuscipes
and
G. morsitans morsitans
flies with reciprocal
Sodalis
strains. Tsetse flies cleared of their native
Sodalis
symbionts were successfully repopulated with the
Sodalis
species isolated from a different tsetse fly species. These transinfected flies effectively transmitted the novel symbionts to their offspring and experienced no detrimental fitness effects compared to their wild-type counterparts, as measured by longevity and fecundity. Quantitative PCR analysis revealed that transinfected flies maintained their
Sodalis
populations at densities comparable to those in flies harboring native symbionts. Our ability to transinfect tsetse flies is indicative of
Sodalis
' recent evolutionary history with its tsetse fly host and demonstrates that this procedure may be used as a means of streamlining future paratransgenesis experiments.
Role of Quorum Sensing and Antimicrobial Component Production by
Serratia plymuthica
in Formation of Biofilms, Including Mixed Biofilms with
Escherichia coli
Authors: Moons Pieter , Van Houdt Rob , Aertsen Abram , Vanoirbeek Kristof , Engelborghs Yves , Michiels Chris W. 
Published: November 2006

ABSTRACT

We have previously characterized the
N
-acyl-
l
-homoserine lactone-based quorum-sensing system of the biofilm isolate
Serratia plymuthica
RVH1. Here we investigated the role of quorum sensing and of quorum-sensing-dependent production of an antimicrobial compound (AC) on biofilm formation by RVH1 and on the cocultivation of RVH1 and
Escherichia coli
in planktonic cultures or in biofilms. Biofilm formation of
S. plymuthica
was not affected by the knockout of
splI
or
splR
, the
S. plymuthica
homologs of the
luxI
or
luxR
quorum-sensing gene, respectively, or by the knockout of AC production.
E. coli
grew well in mixed broth culture with RVH1 until the latter reached 8.5 to 9.5 log CFU/ml, after which the
E. coli
colony counts steeply declined. In comparison, only a very small decline occurred in cocultures with the
S. plymuthica
AC-deficient and
splI
mutants. Complementation with exogenous
N
-hexanoyl-
l
-homoserine lactone rescued the wild-type phenotype of the
splI
mutant. The
splR
knockout mutant also induced a steep decline of
E. coli
, consistent with its proposed function as a repressor of quorum-sensing-regulated genes. The numbers of
E. coli
in 3-day-old mixed biofilms followed a similar pattern, being higher with
S. plymuthica
deficient in SplI or AC production than with wild-type
S. plymuthica
, the
splR
mutant, or the
splI
mutant in the presence of
N
-hexanoyl-
l
-homoserine lactone. Confocal laser scanning microscopic analysis of mixed biofilms established with strains producing different fluorescent proteins showed that
E. coli
microcolonies were less developed in the presence of RVH1 than in the presence of the AC-deficient mutant.
Sensitivity of an Immunomagnetic-Separation-Based Test for DetectingEscherichia coliO26 in Bovine Feces
Authors: Hall L. M. , Evans J. , Smith A. W. , Pearce M. C. , Knight H. I. , Foster G. , Low J. C. , Gunn G. J. 
Published: November 2006

ABSTRACTThe sensitivity of a test for cattle sheddingEscherichia coliserogroup O26 was estimated using several fecal pats artificially inoculated at a range of concentrations with differentE. coliO26 strains. The test involves the enrichment of fecal microflora in buffered peptone water, the selective concentration ofE. coliO26 using antibody-coated immunomagnetic-separation beads, the identification ofE. colicolonies on Chromocult tryptone bile X-glucuronide agar, and confirmation of the serogroup withE. coliserogroup O26-specific antisera using slide agglutination. The effective dose ofE. coliO26 for an 80% test sensitivity (ED80) was 1.0 × 104CFU g−1feces (95% confidence interval, 4.7 × 103to 2.4 × 104). Differences in test sensitivity between differentE. coliO26 strains and fecal pats were also observed. Individual estimates of ED80for each strain and fecal pat combination ranged from 4.2 × 102to 4.8 × 105CFU g−1. These results suggest that the test is useful for identifying individuals shedding a large number ofE. coliO26 organisms or, if an appropriate number of individuals in a herd are sampled, for identifying affected herds. The study also provides a benchmark estimate of sensitivity that can be used to compare alternative tests forE. coliO26 and a methodological approach that can be applied to tests for other pathogenic members of theEnterobacteriaceaeand other sample types.
Reverse Transcription-PCR-Enzyme-Linked Immunosorbent Assay for Rapid Detection and Differentiation of Alphavirus Infections
Authors: Wang Eryu , Paessler Slobodan , Aguilar Patricia V. , Carrara Anne-Sophie , Ni Haolin , Greene Ivorlyne P. , Weaver Scott C. 
Published: November 2006

ABSTRACT
Due to the lack of a rapid, simple, and inexpensive assay for detecting alphavirus infections, we combined a reverse transcription-PCR with an enzyme-linked immunosorbent assay (RT-PCR-ELISA) to identify human pathogenic alphaviruses that are endemic in the New World. By combining the sensitivity of PCR, the detection simplicity of ELISA, and the specificities of DNA probes, this method rapidly detected and differentiated closely related species and subtypes of several medically important alphaviruses. After an amplification using RT-PCR with primers targeting conserved sequences in the nonstructural protein 1 gene, sequence-specific, biotin-labeled probes targeted against Venezuelan, eastern, and western equine encephalitis or Mayaro virus genes were used for the detection of amplicons using ELISA. The assay is simple, fast, and easy to perform in an ordinary diagnostic laboratory or clinical setting. Nucleic acid derived from cell cultures infected with several alphaviruses, clinical specimens, and mosquito pools as well as frozen and paraffin-embedded animal tissues were detected and identified within 6 to 7 h in a sensitive and specific manner.
Variable-Number Tandem Repeats That Are Useful in Genotyping Isolates of
Salmonella enterica
subsp.
enterica
Serovars Typhimurium and Newport
Authors: Witonski D. , Stefanova R. , Ranganathan A. , Schutze G. E. , Eisenach K. D. , Cave M. D. 
Published: November 2006

ABSTRACT

The genome of
Salmonella enterica
subsp.
enterica
serovar Typhimurium strain LT2 was analyzed for direct repeats, and 54 sequences containing variable-number tandem repeat loci were identified. Ten primer pairs that anneal upstream and downstream of each selected locus were designed and used to amplify PCR targets in isolates of
S. enterica
serovars Typhimurium and Newport. Four of the 10 loci did not show polymorphism in the length of products. Six loci were selected for analysis. Isolates of
S. enterica
serovars Typhimurium and Newport that were related to specific outbreaks and showed identical pulsed-field gel electrophoresis patterns were indistinguishable by the length of the six variable-number tandem repeats. Isolates that differed in their pulsed-field gel electrophoresis patterns showed polymorphism in variable-number tandem repeat profiles. Length of the products was confirmed by DNA sequence analysis. Only 2 of the 10 loci contained exact integers of the direct repeat. Eight loci contained partial copies. The partial copies were maintained at the ends of the variable-number tandem repeat loci in all isolates. In spite of having partial copies that were maintained in all isolates, the number of direct repeats at a locus was polymorphic. Six variable-number tandem repeat loci were useful in distinguishing isolates of
S. enterica
serovars Typhimurium and Newport that had different pulsed-field gel electrophoresis patterns and in identifying outbreak-associated cases that shared a common pulsed-field gel pattern.