bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community of arbuscular mycorrhizal fungi in Japanese semi‐natural grassland dominated by Pleioblastus chino and Miscanthus sinensis
Authors: Kojima Tomoko , Hayashi Haruo , Saito Masanori 
Published: June 2007

AbstractFor 4 years, from 1999–2002, we studied the flora of arbuscular mycorrhizal (AM) fungi associated with vegetational change due to grazing in a semi‐natural grassland of central Japan. In this grassland in 1999, Pleioblastus chino was distributed widely and was the most dominant plant species, followed by Miscanthus sinensis, which was distributed in part of the grassland. Coverage by the tallgrass M. sinensis decreased with grazing, whereas coverage by P. chino did not change so much during the experimental period. The degrees of AM fungal colonization and spore population in the rhizosphere showed no remarkable yearly changes during the 4 years. Among spores collected from soils, Glomus rubiforme was always dominant. The AM fungal flora in plant roots was examined by polymerase chain reaction (PCR) with taxon‐specific primers. Glomus spp. was detected most frequently. Together, the results implied that the AM fungal community in the semi‐natural grassland in Japan might remain stable despite changes in the coverage of some dominant plant species over time.
Ovule development at anthesis in apricot (Prunus armeniaca) varieties in a Mediterranean climate
Authors: Ruiz D. , Egea J. 
Published: June 2007

AbstractThe stage of ovule development at anthesis has been studied in 2002 and 2003 in 35 apricot varieties and 4 new apricot cultivars grown in a Mediterranean climate. Significant differences were found among varieties as well as a high heterogeneity of the developmental stage of the ovules examined in each variety. In general, a relative delay of the ovule development was observed, the presence of mature ovules at anthesis being negligible. In the 2 years of the study, differences in the developmental stage of primary ovules at anthesis were not significant and correlation to flowering time was not observed, which emphasised the previously reported genetic determination of this trait.
Microplate Fluorescence Assay for Measurement of the Ability of Strains ofListeria monocytogenesfrom Meat and Meat-Processing Plants To Adhere to Abiotic Surfaces
Authors: Gamble Rachel , Muriana Peter M. 
Published: June 2007

ABSTRACTListeria monocytogenesis a significant food-borne pathogen that is capable of adhering to and producing biofilms on processing equipment, making it difficult to eliminate from meat-processing environments and allowing potential contamination of ready-to-eat (RTE) products. We devised a fluorescence-based microplate method for screening isolates ofL. monocytogenesfor the ability to adhere to abiotic surfaces. Strains ofL. monocytogeneswere incubated for 2 days at 30°C in 96-well microplates, and the plates were washed in a plate washer. The retained cells were incubated for 15 min at 25°C with 5,6-carboxyfluorescein diacetate and washed again, and then the fluorescence was read with a plate reader. Several enzymatic treatments (protease, lipase, and cellulase) were effective in releasing adherent cells from the microplates, and this process was used for quantitation on microbiological media. Strongly adherent strains ofL. monocytogeneswere identified that had 15,000-fold-higher levels of fluorescence and 100,000-fold-higher plate counts in attachment assays than weakly adherent strains. Strongly adherent strains ofL. monocytogenesadhered equally well to four different substrates (glass, plastic, rubber, and stainless steel); showed high-level attachment on microplates at 10, 20, 30, and 40°C; and showed significant differences from weakly adherent strains when examined by scanning electron microscopy. A greater incidence of strong adherence was observed for strains isolated from RTE meats than for those isolated from environmental surfaces. Analysis of surface adherence amongListeriaisolates from processing environments may provide a better understanding of the molecular mechanisms involved in attachment and suggest solutions to eliminate them from food-processing environments.
Development of a Swine-Specific Fecal Pollution Marker Based on Host Differences in MethanogenmcrAGenes
Authors: Ufnar Jennifer A. , Ufnar David F. , Wang Shiao Y. , Ellender R. D. 
Published: June 2007

ABSTRACTThe goal of this study was to evaluate methanogen diversity in animal hosts to develop a swine-specific archaeal molecular marker for fecal source tracking in surface waters. Phylogenetic analysis of swinemcrAsequences compared tomcrAsequences from the feces of five animals (cow, deer, sheep, horse, and chicken) and sewage showed four distinct swine clusters, with three swine-specific clades. From this analysis, six sequences were chosen for molecular marker development and initial testing. Only onemcrAsequence (P23-2) showed specificity for swine and therefore was used for environmental testing. PCR primers for the P23-2 clonemcrAsequence were developed and evaluated for swine specificity. The P23-2 primers amplified products in P23-2 plasmid DNA (100%), pig feces (84%), and swine waste lagoon surface water samples (100%) but did not amplify a product in 47 bacterial and archaeal stock cultures and 477 environmental bacterial isolates and sewage and water samples from a bovine waste lagoon and a polluted creek. Amplification was observed in only one sheep sample out of 260 human and nonswine animal fecal samples. Sequencing of PCR products from pig feces demonstrated 100% similarity to pigmcrAsequence from clone P23-2. The minimal amount of DNA required for the detection was 1 pg for P23-2 plasmid, 1 ng for pig feces, 50 ng for swine waste lagoon surface water, 1 ng for sow waste influent, and 10 ng for lagoon sludge samples. Lower detection limits of 10−6g of wet pig feces in 500 ml of phosphate-buffered saline and 10−4g of lagoon waste in estuarine water were established for the P23-2 marker. This study was the first to utilize methanogens for the development of a swine-specific fecal contamination marker.
Attachment of Enteric Viruses to Bottles
Authors: Butot S. , Putallaz T. , Croquet C. , Lamothe G. , Meyer R. , Joosten H. , Sánchez G. 
Published: June 2007

ABSTRACT
Storage of water that was deliberately contaminated with enteric viruses in polyethylene terephthalate (PET) bottles led to a rapid decrease of the apparent viral load, thereby hampering the development of samples for a collaborative evaluation of viral detection methods for bottled water. To determine if this decrease was due to spontaneous inactivation or to adhesion, an elution protocol was developed and combined with a rapid and sensitive real-time reverse transcription-PCR-based method to quantify adsorbed norovirus (NV), hepatitis A virus (HAV), and rotavirus (RV) on bottle walls. The NV retention on PET bottle walls after 20 and 62 days reached an average level of 85% and 95% of the recovered inoculum, respectively. HAV and RV also showed adsorption onto PET bottles, reaching 90% and 80%, respectively, after 20 days of storage. NV and RV attachment was demonstrated to be dependent on the presence of autochthonous flora, whereas HAV adsorption was independent of it. Application of the elution and viral detection protocol to 294 commercially available water bottles obtained from 25 different countries did not give any positive result, thereby providing further evidence that the sources used for this product are free from enteric viruses and support for the theory that bottled water is not a vehicle for viral diseases.
Newly Discovered Penicillin Acylase Activity of Aculeacin A Acylase from
Actinoplanes utahensis
Authors: Torres-Bacete Jesús , Hormigo Daniel , Stuart Maribel , Arroyo Miguel , Torres Pedro , Castillón María P. , Acebal Carmen , García José L. , de la Mata Isabel 
Published: June 2007

ABSTRACT

Aculeacin A acylase from
Actinoplanes utahensis
produced by
Streptomyces lividans
revealed acylase activities that are able to hydrolyze penicillin V and several natural aliphatic penicillins. Penicillin K was the best substrate, showing a catalytic efficiency of 34.79 mM
−1
s
−1
. Furthermore, aculeacin A acylase was highly thermostable, with a midpoint transition temperature of 81.5°C.
Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Corals
Authors: Beman J.Michael , Roberts Kathryn J. , Wegley Linda , Rohwer Forest , Francis Christopher A. 
Published: June 2007

ABSTRACT

Corals are known to harbor diverse microbial communities of
Bacteria
and
Archaea
, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (
amoA
) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial
amoA
genes, and archaeal
amoA
gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal
amoA
sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial
amoA
gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal
amoA
gene in marine ecosystems, including coral reefs.
Production and Secretion Stress Caused by Overexpression of Heterologous α-Amylase Leads to Inhibition of Sporulation and a Prolonged Motile Phase in
Bacillus subtilis
Authors: Lulko Andrzej T. , Veening Jan-Willem , Buist Girbe , Smits Wiep Klaas , Blom Evert Jan , Beekman Aaron C. , Bron Sierd , Kuipers Oscar P. 
Published: June 2007

ABSTRACT

Transcriptome analysis was used to investigate the global stress response of the gram-positive bacterium
Bacillus subtilis
caused by overproduction of the well-secreted AmyQ α-amylase from
Bacillus amyloliquefaciens
. Analyses of the control and overproducing strains were carried out at the end of exponential growth and in stationary phase, when protein secretion from
B. subtilis
is optimal. Among the genes that showed increased expression were
htrA
and
htrB
, which are part of the CssRS regulon, which responds to high-level protein secretion and heat stress. The analysis of the transcriptome profiles of a
cssS
mutant compared to the wild type, under identical secretion stress conditions, revealed several genes with altered transcription in a CssRS-dependent manner, for example,
citM
,
ylxF
,
yloA
,
ykoJ
, and several genes of the
flgB
operon. However, high-affinity CssR binding was observed only for
htrA
,
htrB
, and, possibly,
citM
. In addition, the DNA macroarray approach revealed that several genes of the sporulation pathway are downregulated by AmyQ overexpression and that a group of motility-specific (σ
D
-dependent) transcripts were clearly upregulated. Subsequent flow-cytometric analyses demonstrate that, upon overproduction of AmyQ as well as of a nonsecretable variant of the α-amylase, the process of sporulation is severely inhibited. Similar experiments were performed to investigate the expression levels of the
hag
promoter, a well-established reporter for σ
D
-dependent gene expression. This approach confirmed the observations based on our DNA macroarray analyses and led us to conclude that expression levels of several genes involved in motility are maintained at high levels under all conditions of α-amylase overproduction.
At Least Two Origins of Fungicide Resistance in Grapevine Downy Mildew Populations
Authors: Chen Wei-Jen , Delmotte François , Cervera Sylvie Richard , Douence Lisette , Greif Charles , Corio-Costet Marie-France 
Published: June 2007

ABSTRACTQuinone outside inhibiting (QoI) fungicides represent one of the most widely used groups of fungicides used to control agriculturally important fungal pathogens. They inhibit the cytochromebc1complex of mitochondrial respiration. Soon after their introduction onto the market in 1996, QoI fungicide-resistant isolates were detected in field plant pathogen populations of a large range of species. However, there is still little understanding of the processes driving the development of QoI fungicide resistance in plant pathogens. In particular, it is unknown whether fungicide resistance occurs independently in isolated populations or if it appears once and then spreads globally by migration. Here, we provide the first case study of the evolutionary processes that lead to the emergence of QoI fungicide resistance in the plant pathogenPlasmopara viticola. Sequence analysis of the complete cytochromebgene showed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Phylogenetic analysis of a large mitochondrial DNA fragment including the cytochromebgene (2,281 bp) across a wide range of EuropeanP. viticolaisolates allowed the detection of four major haplotypes belonging to two distinct clades, each of which contains a different QoI fungicide resistance allele. This is the first demonstration that a selected substitution conferring resistance to a fungicide has occurred several times in a plant-pathogen system. Finally, a high population structure was found when the frequency of QoI fungicide resistance haplotypes was assessed in 17 French vineyards, indicating that pathogen populations might be under strong directional selection for local adaptation to fungicide pressure.
Metabolic Engineering of
Bacillus subtilis
for Ethanol Production: Lactate Dehydrogenase Plays a Key Role in Fermentative Metabolism
Authors: Romero Susana , Merino Enrique , Bolívar Francisco , Gosset Guillermo , Martinez Alfredo 
Published: June 2007

ABSTRACT

Wild-type
Bacillus subtilis
ferments 20 g/liter glucose in 48 h, producing lactate and butanediol, but not ethanol or acetate. To construct an ethanologenic
B. subtilis
strain, homologous recombination was used to disrupt the native lactate dehydrogenase (LDH) gene (
ldh
) by chromosomal insertion of the
Zymomonas mobilis
pyruvate decarboxylase gene (
pdc
) and alcohol dehydrogenase II gene (
adhB
) under the control of the
ldh
native promoter. The values of the intracellular PDC and ADHII enzymatic activities of the engineered
B. subtilis
BS35 strain were similar to those found in an ethanologenic
Escherichia coli
strain. BS35 produced ethanol and butanediol; however, the cell growth and glucose consumption rates were reduced by 70 and 65%, respectively, in comparison to those in the progenitor strain. To eliminate butanediol production, the acetolactate synthase gene (
alsS
) was inactivated. In the BS36 strain (BS35 Δ
alsS
), ethanol production was enhanced, with a high yield (89% of the theoretical); however, the cell growth and glucose consumption rates remained low. Interestingly, kinetic characterization of LDH from
B. subtilis
showed that it is able to oxidize NADH and NADPH. The expression of the transhydrogenase encoded by
udhA
from
E. coli
allowed a partial recovery of the cell growth rate and an early onset of ethanol production. Beyond pyruvate-to-lactate conversion and NADH oxidation, an additional key physiological role of LDH for glucose consumption under fermentative conditions is suggested. Long-term cultivation showed that 8.9 g/liter of ethanol can be obtained using strain BS37 (BS35 Δ
alsS udhA
+
). As far as we know, this is the highest ethanol titer and yield reported with a
B. subtilis
strain.
Recombinant Expression and Characterization of a Reducing-End Xylose-Releasing Exo-Oligoxylanase from
Bifidobacterium adolescentis
Authors: Lagaert Stijn , Van Campenhout Steven , Pollet Annick , Bourgois Tine M. , Delcour Jan A. , Courtin Christophe M. , Volckaert Guido 
Published: June 2007

ABSTRACT

The family 8 glycoside hydrolase (RexA) from
Bifidobacterium adolescentis
was expressed in
Escherichia coli
. The recombinant enzyme was characterized as a reducing-end xylose-releasing exo-oligoxylanase. Apart from giving insights into this new class of enzymes, knowledge of the RexA enzyme helps to postulate a mechanism for the
B. adolescentis
breakdown of prebiotic xylooligosaccharides.
Virus Attachment to Transparent Exopolymeric Particles along Trophic Gradients in the Southwestern Lagoon of New Caledonia
Authors: Mari Xavier , Kerros Marie-Emmanuelle , Weinbauer Markus G. 
Published: June 2007

ABSTRACT

Viruses on organic aggregates such as transparent exopolymeric particles (TEP) are not well investigated. The number of TEP-attached viruses was assessed along trophic gradients in the southwestern lagoon of New Caledonia by determining the fraction of viruses removed after magnetic isolation of TEP. In order to isolate TEP magnetically, TEP were formed in the presence of magnetic beads from submicrometer precursors collected along the trophic gradients. The mixed aggregates of TEP-beads-viruses were removed from solution with a magnetic field. The percentage of viruses associated with newly formed TEP averaged 8% (range, 3 to 13%) for most of the stations but was higher (ca. 30%) in one bay characterized by the low renewal rate of its water mass. The number of viruses (
N
) attached to TEP varied as a function of TEP size (
d
[in micrometers]) according to the formulas
N
= 100
d
1.60
and
N
= 230
d
1.75
, respectively, for TEP occurring in water masses with short (i.e., <40 days) and long (i.e., >40 days) residence times. These two relationships imply that viral abundance decreases with TEP size, and they indicate that water residence time influences viral density and virus-bacterium interactions within aggregates. Our data suggest that the fraction of viruses attached to TEP is highest in areas characterized by a low renewal rate of the water mass and can constitute at times a significant fraction of total virus abundance. Due to the small distance between viruses and hosts on TEP, these particles may be hot spots for viral infection.
Molecular and Biochemical Characterization of 3-Hydroxybenzoate 6-Hydroxylase from
Polaromonas naphthalenivorans
CJ2
Authors: Park Minjeong , Jeon Yeji , Jang Ho Hee , Ro Hyun-Su , Park Woojun , Madsen Eugene L. , Jeon Che Ok 
Published: June 2007

ABSTRACT

Prior research revealed that
Polaromonas naphthalenivorans
CJ2 carries and expresses genes encoding the gentisate metabolic pathway for naphthalene. These metabolic genes are split into two clusters, comprising
nagRAaGHAbAcAdBFCQEDJI
′-
orf1
-
tnpA
and
nagR2
-
orf2I
″
KL
(C. O. Jeon, M. Park, H. Ro, W. Park, and E. L. Madsen, Appl. Environ. Microbiol. 72:1086-1095, 2006). BLAST homology searches of sequences in GenBank indicated that the
orf2
gene from the small cluster likely encoded a salicylate 5-hydroxylase, presumed to catalyze the conversion of salicylate into gentisate. Here, we report physiological and genetic evidence that
orf2
does not encode salicylate 5-hydroxylase. Instead, we have found that
orf2
encodes 3-hydroxybenzoate 6-hydroxylase, the enzyme which catalyzes the NADH-dependent conversion of 3-hydroxybenzoate into gentisate. Accordingly, we have renamed
orf2 nagX
. After expression in
Escherichia coli
, the NagX enzyme had an approximate molecular mass of 43 kDa, as estimated by gel filtration, and was probably a monomeric protein. The enzyme was able to convert 3-hydroxybenzoate into gentisate without salicylate 5-hydroxylase activity. Like other 3-hydroxybenzoate 6-hydroxylases, NagX utilized both NADH and NADPH as electron donors and exhibited a yellowish color, indicative of a bound flavin adenine dinucleotide. An engineered mutant of
P. naphthalenivorans
CJ2 defective in
nagX
failed to grow on 3-hydroxybenzoate but grew normally on naphthalene. These results indicate that the previously described small catabolic cluster in strain CJ2 may be multifunctional and is essential for the degradation of 3-hydroxybenzoate. Because
nagX
and an adjacent MarR-type regulatory gene are both closely related to homologues in
Azoarcus
species, this study raises questions about horizontal gene transfer events that contribute to operon evolution.
New Enzymatic Method of Chiral Amino Acid Synthesis by Dynamic Kinetic Resolution of Amino Acid Amides: Use of Stereoselective Amino Acid Amidases in the Presence of α-Amino-ε-Caprolactam Racemase
Authors: Yamaguchi Shigenori , Komeda Hidenobu , Asano Yasuhisa 
Published: June 2007

ABSTRACTd- andl-amino acids were produced froml- andd-amino acid amides byd-aminopeptidase fromOchrobactrum anthropiC1-38 andl-amino acid amidase fromPseudomonas azotoformansIAM 1603, respectively, in the presence of α-amino-ε-caprolactam racemase fromAchromobacter obaeas the catalyst by dynamic kinetic resolution of amino acid amides.
Use of Multilocus Sequence Typing To Investigate the Association between the Presence of
Campylobacter
spp. in Broiler Drinking Water and
Campylobacter
Colonization in Broilers
Authors: Ogden I. D. , MacRae M. , Johnston M. , Strachan N. J. C. , Cody A. J. , Dingle K. E. , Newell D. G. 
Published: June 2007

ABSTRACT

The presence of campylobacters in broiler chickens and throughout the broiler water delivery systems of 12 farms in northeastern Scotland was investigated by sensitive enrichment methods and large-volume filtration.
Campylobacter
presence was independent of the water source and whether the water was treated. The genotypes of
Campylobacter jejuni
isolates recovered from chickens and various locations within the water delivery systems were compared by multilocus sequence typing. Matching strains in shed header tanks and birds were found at 1 of the 12 farms investigated. However, the sequence of contamination or whether the source was within or outside the shed was not determined. Nevertheless, these data provide evidence that drinking water could be associated with broiler infection by campylobacters.
Identification and In Vivo Functional Analysis by Gene Disruption of
ctnA
, an Activator Gene Involved in Citrinin Biosynthesis in
Monascus purpureus
Authors: Shimizu Takeo , Kinoshita Hiroshi , Nihira Takuya 
Published: June 2007

ABSTRACT

Citrinin, a secondary fungal metabolite of polyketide origin, is moderately nephrotoxic to vertebrates, including humans. From the red-pigment producer
Monascus purpureus
, a 21-kbp region flanking
pksCT
, which encodes citrinin polyketide synthase, was cloned. Four open reading frames (ORFs) (
orf1
,
orf2
,
orf3
, and
orf4
) in the 5′-flanking region and one ORF (
orf5
) in the 3′-flanking region were identified in the vicinity of
pksCT. orf1
to
orf5
encode a homolog of a dehydrogenase (similarity, 46%), a regulator (similarity, 38%), an oxygenase (similarity, 41%), an oxidoreductase (similarity, 26%), and a transporter (similarity, 58%), respectively.
orf2
(2,006 bp with four introns) encodes a 576-amino-acid protein containing a typical Zn(II)2Cys6 DNA binding motif at the N terminus and was designated
ctnA
. Although reverse transcriptase PCR analysis revealed that all of these ORFs, except for
orf1
, were transcribed with
pksCT
under citrinin production conditions, the disruption of
ctnA
caused large decreases in the transcription of
pksCT
and
orf5
, together with reduction of citrinin production to barely detectable levels, suggesting that these two genes are under control of the
ctnA
product. Complementation of the
ctnA
disruptant with intact
ctnA
on an autonomously replicating plasmid restored both transcription and citrinin production, indicating that CtnA is a major activator of citrinin biosynthesis.