bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity and Fitness of
Fusarium graminearum
Populations from Rice in Korea
Authors: Lee Jungkwan , Chang In-Young , Kim Hun , Yun Sung-Hwan , Leslie John F. , Lee Yin-Won 
Published: March 2009

ABSTRACT

Fusarium graminearum
is an important fungal pathogen of cereal crops and produces mycotoxins, such as the trichothecenes nivalenol and deoxynivalenol. This species may be subdivided into a series of genetic lineages or phylogenetic species. We identified strains of
F. graminearum
from the Republic of Korea to lineage, tested their ability to produce nivalenol and deoxynivalenol, and determined the genetic composition and structure of the populations from which they were recovered. Based on amplified fragment length polymorphism (AFLP), PCR genotyping, and chemical analyses of trichothecenes, all 249 isolates from southern provinces belonged to lineage 6, with 241 having the nivalenol genotype and 8 having the deoxynivalenol genotype. In the eastern Korea province, we recovered 84 lineage 6 isolates with the nivalenol genotype and 23 lineage 7 isolates with the deoxynivalenol genotype. Among 333 lineage 6 isolates, 36% of the AFLP bands were polymorphic, and there were 270 multilocus haplotypes. Genetic identity among populations was high (>0.972), and genotype diversity was low (30 to 58%). To test the adaptation of lineage 6 to rice, conidial mixtures of strains from lineages 3, 6, and 7 were inoculated onto rice plants and then recovered from the rice grains produced. Strains representing lineages 6 and 7 were recovered from inoculated spikelets at similar frequencies that were much higher than those for the strain representing lineage 3. Abundant perithecia were produced on rice straw, and 247 single-ascospore isolates were recovered from 247 perithecia. Perithecia representing lineage 6 (87%) were the most common, followed by those representing lineage 7 (13%), with perithecia representing lineage 3 not detected. These results suggest that
F. graminearum
lineage 6 may have a host preference for rice and that it may be more fit in a rice agroecosystem than are the other lineages present in Korea.
Cultivation of Fastidious Bacteria by Viability Staining and Micromanipulation in a Soil Substrate Membrane System
Authors: Ferrari B. C. , Gillings M. R. 
Published: March 2009

ABSTRACT

Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of diverse, novel isolates, including the recalcitrant bacterium
Leifsonia xyli
, a plant pathogen that has never been isolated outside the host.
Development and Application of a
upp
-Based Counterselective Gene Replacement System for the Study of the S-Layer Protein SlpX of
Lactobacillus acidophilus
NCFM
Authors: Goh Yong Jun , Azcárate-Peril M. Andrea , O'Flaherty Sarah , Durmaz Evelyn , Valence Florence , Jardin Julien , Lortal Sylvie , Klaenhammer Todd R. 
Published: March 2009

ABSTRACT

In silico genome analysis of
Lactobacillus acidophilus
NCFM coupled with gene expression studies have identified putative genes and regulatory networks that are potentially important to this organism's survival, persistence, and activities in the gastrointestinal tract. Correlation of key genotypes to phenotypes requires an efficient gene replacement system. In this study, use of the
upp
-encoded uracil phosphoribosyltransferase (UPRTase) of
L. acidophilus
NCFM was explored as a counterselection marker to positively select for recombinants that have resolved from chromosomal integration of pORI-based plasmids. An isogenic mutant carrying a
upp
gene deletion was constructed and was resistant to 5-fluorouracil (5-FU), a toxic uracil analog that is also a substrate for UPRTase. A 3.0-kb pORI-based counterselectable integration vector bearing a
upp
expression cassette, pTRK935, was constructed and introduced into the Δ
upp
host harboring the pTRK669 helper plasmid. Extrachromosomal replication of pTRK935 complemented the mutated chromosomal
upp
allele and restored sensitivity to 5-FU. This host background provides a platform for a two-step plasmid integration and excision strategy that can select for plasmid-free recombinants with either the wild-type or mutated allele of the targeted gene in the presence of 5-FU. The efficacy of the system was demonstrated by in-frame deletion of the
slpX
gene (LBA0512) encoding a novel 51-kDa secreted protein associated with the S-layer complex of
L. acidophilus
. The resulting Δ
slpX
mutant exhibited lower growth rates, increased sensitivity to sodium dodecyl sulfate, and greater resistance to bile. Overall, this improved gene replacement system represents a valuable tool for investigating the mechanisms underlying the probiotic functionality of
L. acidophilus
.
Changes in Benthic Denitrification, Nitrate Ammonification, and Anammox Process Rates and Nitrate and Nitrite Reductase Gene Abundances along an Estuarine Nutrient Gradient (the Colne Estuary, United Kingdom)
Authors: Dong Liang F. , Smith Cindy J. , Papaspyrou Sokratis , Stott Andrew , Osborn A. Mark , Nedwell David B. 
Published: March 2009

ABSTRACT

Estuarine sediments are the location for significant bacterial removal of anthropogenically derived inorganic nitrogen, in particular nitrate, from the aquatic environment. In this study, rates of benthic denitrification (DN), dissimilatory nitrate reduction to ammonium (DNRA), and anammox (AN) at three sites along a nitrate concentration gradient in the Colne estuary, United Kingdom, were determined, and the numbers of functional genes (
narG
,
napA
,
nirS
, and
nrfA
) and corresponding transcripts encoding enzymes mediating nitrate reduction were determined by reverse transcription-quantitative PCR. In situ rates of DN and DNRA decreased toward the estuary mouth, with the findings from slurry experiments suggesting that the potential for DNRA increased while the DN potential decreased as nitrate concentrations declined. AN was detected only at the estuary head, accounting for ∼30% of N
2
formation, with 16S rRNA genes from anammox-related bacteria also detected only at this site. Numbers of
narG
genes declined along the estuary, while
napA
gene numbers were stable, suggesting that NAP-mediated nitrate reduction remained important at low nitrate concentrations.
nirS
gene numbers (as indicators of DN) also decreased along the estuary, whereas
nrfA
(an indicator for DNRA) was detected only at the two uppermost sites. Similarly, nitrate and nitrite reductase gene transcripts were detected only at the top two sites. A regression analysis of log(
n
+ 1) process rate data and log(
n
+ 1) mean gene abundances showed significant relationships between DN and
nirS
and between DNRA and
nrfA
. Although these log-log relationships indicate an underlying relationship between the genetic potential for nitrate reduction and the corresponding process activity, fine-scale environmentally induced changes in rates of nitrate reduction are likely to be controlled at cellular and protein levels.
Application of a Newly Identified and Characterized 18-
O
-Acyltransferase in Chemoenzymatic Synthesis of Selected Natural and Nonnatural Bioactive Derivatives of Phoslactomycins
Authors: Ghatge Mohini S. , Palaniappan Nadaraj , Alhamadsheh Ma'moun M. , DiBari Jessica , Reynolds Kevin A. 
Published: March 2009

ABSTRACT

Phoslactomycins (PLMs) and related leustroducsins (LSNs) have been isolated from a variety of bacteria based on antifungal, anticancer, and other biological assays.
Streptomyces
sp. strain HK 803 produces five PLM analogs (PLM A and PLMs C to F) in which the C-18 hydroxyl substituent is esterified with a range of branched, short-alkyl-chain carboxylic acids. The proposed pathway intermediate, PLM G, in which the hydroxyl residue is not esterified has not been observed at any significant level in fermentation, and the only route to this potentially useful intermediate has been an enzymatic deacylation of other PLMs and LSNs. We report that deletion of
plmS
3
from the PLM biosynthetic cluster gives rise to a mutant which accumulates the PLM G intermediate. The 921-bp
plmS
3
open reading frame was cloned and expressed as an N-terminally polyhistidine-tagged protein in
Escherichia coli
and shown to be an 18-
O
acyltransferase, catalyzing conversion of PLM G to PLM A, PLM C, and PLM E using isobutyryl coenzyme A (CoA), 3-methylbutyryl-CoA, and cyclohexylcarbonyl-CoA, respectively. The efficiency of this process (
k
cat
of 28 ± 3 min
−1
and

K
m

of 88 ± 16 μM) represents a one-step chemoenzymatic alternative to a multistep synthetic process for selective chemical esterification of the C-18 hydroxy residue of PLM G. PlmS
3
was shown to catalyze esterification of PLM G with CoA and
N
-acetylcysteamine thioesters of various saturated, unsaturated, and aromatic carboxylic acids and thus also to provide an efficient chemoenzymatic route to new PLM analogs.
Metabolic Engineering of
Escherichia coli
for Enhanced Production of (
R
)- and (
S
)-3-Hydroxybutyrate
Authors: Tseng Hsien-Chung , Martin Collin H. , Nielsen David R. , Prather Kristala L. Jones 
Published: March 2009

ABSTRACT

Synthetic metabolic pathways have been constructed for the production of enantiopure (
R
)- and (
S
)-3-hydroxybutyrate (3HB) from glucose in recombinant
Escherichia coli
strains. To promote maximal activity, we profiled three thiolase homologs (BktB, Thl, and PhaA) and two coenzyme A (CoA) removal mechanisms (Ptb-Buk and TesB). Two enantioselective 3HB-CoA dehydrogenases, PhaB, producing the (
R
)-enantiomer, and Hbd, producing the (
S
)-enantiomer, were utilized to control the 3HB chirality across two
E. coli
backgrounds, BL21Star(DE3) and MG1655(DE3), representing
E. coli
B- and K-12-derived strains, respectively. MG1655(DE3) was found to be superior for the production of each 3HB stereoisomer, although the recombinant enzymes exhibited lower in vitro specific activities than BL21Star(DE3). Hbd in vitro activity was significantly higher than PhaB activity in both strains. The engineered strains achieved titers of enantiopure (
R
)-3HB and (
S
)-3HB as high as 2.92 g liter
−1
and 2.08 g liter
−1
, respectively, in shake flask cultures within 2 days. The NADPH/NADP
+
ratio was found to be two- to three-fold higher than the NADH/NAD
+
ratio under the culture conditions examined, presumably affecting in vivo activities of PhaB and Hbd and resulting in greater production of (
R
)-3HB than (
S
)-3HB. To the best of our knowledge, this study reports the highest (
S
)-3HB titer achieved in shake flask
E. coli
cultures to date.
Exopolyphosphatases PPX1 and PPX2 from
Corynebacterium glutamicum
Authors: Lindner Steffen N. , Knebel Sandra , Wesseling Hendrik , Schoberth Siegfried M. , Wendisch Volker F. 
Published: March 2009

ABSTRACT

Corynebacterium glutamicum
accumulates up to 300 mM of inorganic polyphosphate (PolyP) in the cytosol or in granules. The gene products of cg0488 (
ppx1
) and cg1115 (
ppx2
) were shown to be active as exopolyphosphatases (PPX), as overexpression of either gene resulted in higher exopolyphosphatase activities in crude extracts and deletion of either gene with lower activities than those of the wild-type strain. PPX1 and PPX2 from
C. glutamicum
share only 25% identical amino acids and belong to different protein groups, which are distinct from enterobacterial, archaeal, and yeast exopolyphosphatases. In comparison to that in the wild type, more intracellular PolyP accumulated in the Δ
ppx1
and Δ
ppx2
deletion mutations but less when either
ppx1
or
ppx2
was overexpressed. When
C. glutamicum
was shifted from phosphate-rich to phosphate-limiting conditions, a growth advantage of the deletion mutants and a growth disadvantage of the overexpression strains compared to the wild type were observed. Growth experiments, exopolyphosphatase activities, and intracellular PolyP concentrations revealed PPX2 as being a major exopolyphosphatase from
C. glutamicum
. PPX2
His
was purified to homogeneity and shown to be active as a monomer. The enzyme required Mg
2+
or Mn
2+
cations but was inhibited by millimolar concentrations of Mg
2+
, Mn
2+
, and Ca
2+
. PPX2 from
C. glutamicum
was active with short-chain polyphosphates, even accepting pyrophosphate, and was inhibited by nucleoside triphosphates.
Distribution, Diversity, and Potential Mobility of Extrachromosomal Elements Related to the
Bacillus anthracis
pXO1 and pXO2 Virulence Plasmids
Authors: Hu Xiaomin , Van der Auwera Géraldine , Timmery Sophie , Zhu Lei , Mahillon Jacques 
Published: March 2009

ABSTRACT

The presence of a pXO1- and/or pXO2-like plasmid(s) in clinical isolates of
Bacillus cereus
sensu stricto and in strains of the biopesticide
Bacillus thuringiensis
has been reported recently, and the pXO2-like plasmid pBT9727 and another pXO2-like plasmid, pAW63, were found to be conjugative. In this study, a total of 1,000
B. cereus
group isolates were analyzed for the presence of pXO1- and pXO2-like replicons and for the presence of pXO2-related conjugative modules. pXO1- and pXO2-like replicons were present in ca. 6.6% and 7.7% of random environmental samples, respectively, and ca. 1.54% of the strains were positive for pXO2-like transfer module genes. Only the strains harboring a pXO2-like replicon also contained the corresponding transfer genes. For the strains which contained a pXO1- and/or pXO2-like replicon(s), a large plasmid(s) whose size was similar to that of pXO1-like and/or pXO2-like plasmids was also observed, but none of these isolates were found to carry the
Bacillus anthracis
toxin or capsule virulence genes. Furthermore, 17 of 22 pXO2-like plasmids containing the transfer modules were able to self-transfer and to mobilize small plasmids. No pXO1- or pXO2-like plasmid lacking the cognate transfer modules has been found to have transfer potential. In the strains possessing the putative pXO2-like conjugative apparatus, variations in the presence of the group II introns B.th.I.1 and B.th.I.2 were observed, suggesting that there is important flexibility in the conjugation modules and their regulation. There was no consistent correlation between a pXO2-like
repA
dendrogram and the presence of the
tra
region or between a
virB4
dendrogram and transfer ability. Discrepancies between pXO2-like
repA
and
virB4
dendrograms were also observed, indicating that the evolution of pXO2 is an active process.
Light-Dependent Transcriptional Regulation of Genes of Biogeochemical Interest in the Diploid and Haploid Life Cycle Stages of
Emiliania huxleyi
Authors: Richier Sophie , Kerros Marie-Emmanuelle , de Vargas Colomban , Haramaty Liti , Falkowski Paul G. , Gattuso Jean-Pierre 
Published: March 2009

ABSTRACT

The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore
Emiliania huxleyi
was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.
Failure To Detect
Helicobacter pylori
DNA in Drinking and Environmental Water in Dhaka, Bangladesh, Using Highly Sensitive Real-Time PCR Assays
Authors: Janzon Anders , Sjöling Åsa , Lothigius Åsa , Ahmed Dilruba , Qadri Firdausi , Svennerholm Ann-Mari 
Published: March 2009

ABSTRACT

The main transmission pathway of
Helicobacter pylori
has not been determined, but several reports have described detection of
H. pylori
DNA in drinking and environmental water, suggesting that
H. pylori
may be waterborne. To address this possibility, we developed, tested, and optimized two complementary
H. pylori
-specific real-time PCR assays for quantification of
H. pylori
DNA in water. The minimum detection level of the assays including collection procedures and DNA extraction was shown to be approximately 250
H. pylori
genomes per water sample. Using our assays, we then analyzed samples of drinking and environmental water (
n
= 75) and natural water biofilms (
n
= 21) from a high-endemicity area in Bangladesh. We could not identify
H. pylori
DNA in any of the samples, even though other pathogenic bacteria have been found previously in the same water samples by using the same methodology. A series of control experiments were performed to ensure that the negative results were not falsely caused by PCR inhibition, nonspecific assays, degradation of template DNA, or low detection sensitivity. Our results suggest that it is unlikely that the predominant transmission route of
H. pylori
in this area is waterborne.
Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-Oxidizing Prokaryotes in Freshwater Sediments
Authors: Herrmann Martina , Saunders Aaron M. , Schramm Andreas 
Published: March 2009

ABSTRACT

Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species
Littorella uniflora
,
Juncus bulbosus
, and
Myriophyllum alterniflorum
were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (
amoA
) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting
amoA
, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with
M. alterniflorum
(0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of
L. uniflora
and
J. bulbosus
. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like
L. uniflora
and
J. bulbosus
, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions.
Negative Correlation between Individual-Insect-Level Virulence and Colony-Level Virulence of
Paenibacillus larvae
, the Etiological Agent of American Foulbrood of Honeybees
Authors: Rauch Sandra , Ashiralieva Ainura , Hedtke Kati , Genersch Elke 
Published: March 2009

ABSTRACT

Paenibacillus larvae
is the etiological agent of American foulbrood (AFB) in honeybees. Recently, different genotypes of
P. larvae
(ERIC I to ERIC IV) were defined, and it was shown that these genotypes differ inter alia in their virulence on the larval level. On the colony level, bees mitigate AFB through the hygienic behavior of nurse bees. Therefore, we investigated how the hygienic behavior shapes
P. larvae
virulence on the colony level. Our results indicate that
P. larvae
virulence on the larval level and that on the colony level are negatively correlated.
Influence of Stress on Single-Cell Lag Time and Growth Probability for
Listeria monocytogenes
in Half Fraser Broth
Authors: Dupont Claire , Augustin Jean-Christophe 
Published: March 2009

ABSTRACT

The impacts of 12 common food industry stresses on the single-cell growth probability and single-cell lag time distribution of
Listeria monocytogenes
were determined in half Fraser broth, the primary enrichment broth of the International Organization for Standardization detection method. First, it was determined that the ability of a cell to multiply in half Fraser broth is conditioned by its history (the probability for a cell to multiply can be decreased to 0.05), meaning that, depending on the stress in question, the risk of false-negative samples can be very high. Second, it was established that when cells are injured, the single-cell lag times increase in mean and in variability and that this increase represents a true risk of not reaching the detection threshold of the method in the enrichment broth. No relationship was observed between the impact on single-cell lag times and that on growth probabilities. These results emphasize the importance of taking into account the physiological state of the cells when evaluating the performance of methods to detect pathogens in food.
Acetobacter tropicalisIs a Major Symbiont of the Olive Fruit Fly (Bactrocera oleae)
Authors: Kounatidis Ilias , Crotti Elena , Sapountzis Panagiotis , Sacchi Luciano , Rizzi Aurora , Chouaia Bessem , Bandi Claudio , Alma Alberto , Daffonchio Daniele , Mavragani-Tsipidou Penelope , Bourtzis Kostas 
Published: March 2009

ABSTRACTFollowing cultivation-dependent and -independent techniques, we investigated the microbiota associated withBactrocera oleae, one of the major agricultural pests in olive-producing countries. Bacterial 16S rRNA gene libraries and ultrastructural analyses revealed the presence of several bacterial taxa associated with this insect, among whichAcetobacter tropicaliswas predominant. The recent increased detection of acetic acid bacteria as symbionts of other insect model organisms, such asAnopheles stephensi(G. Favia et al., Proc. Natl. Acad. Sci. USA 104:9047-9051, 2007) orDrosophila melanogaster(C. R. Cox and M. S. Gilmore, Infect. Immun. 75:1565-1576, 2007), prompted us to investigate the association established betweenA. tropicalisandB. oleae. Using anA. tropicalis-specific PCR assay, the symbiont was detected in all insects tested originating from laboratory stocks or field-collected from different locations in Greece. This acetic acid bacterium was successfully established in cell-free medium, and typing analyses, carried out on a collection of isolates, revealed that differentA. tropicalisstrains are present in fly populations. The capability to colonize and lodge in the digestive system of both larvae and adults and in Malpighian tubules of adults was demonstrated by using a strain labeled with a green fluorescent protein.
Oxidative Stress Function of the
Saccharomyces cerevisiae
Skn7 Receiver Domain
Authors: He Xin-Jian , Mulford KariAn E. , Fassler Jan S. 
Published: March 2009

ABSTRACT

The bifunctional
Saccharomyces cerevisiae
Skn7 transcription factor regulates osmotic stress response genes as well as oxidative stress response genes; however, the mechanisms involved in these two types of regulation differ. Skn7 osmotic stress activity depends on the phosphorylation of the receiver domain aspartate, D427, by the Sln1 histidine kinase. In contrast, D427 and the SLN1-SKN7 phosphorelay are dispensable for the oxidative stress response, although the receiver domain is required. The majority of oxidative stress response genes regulated by Skn7 also are regulated by the redox-responsive transcription factor Yap1. It is therefore possible that the nuclearly localized Skn7 does not itself respond to the oxidant but simply cooperates with Yap1 when it translocates to the nucleus. We report here that oxidative stress leads to a phosphatase-sensitive, slow-mobility Skn7 variant. This suggests that Skn7 undergoes a posttranslational modification by phosphorylation following exposure to oxidant. Oxidant-dependent Skn7 phosphorylation was eliminated in strains lacking the Yap1 transcription factor. This suggests that the phosphorylation of Skn7 is regulated by Yap1. Mutations in the receiver domain of Skn7 were identified that affect its oxidative stress function. These mutations were found to compromise the association of Yap1 and Skn7 at oxidative stress response gene promoters. A working model is proposed in which the association of Yap1 with Skn7 in the nucleus is a prerequisite for Skn7 phosphorylation and the activation of oxidative stress response genes.