bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Homologue of the
Aspergillus velvet
Gene Regulates both Cephalosporin C Biosynthesis and Hyphal Fragmentation in
Acremonium chrysogenum
Authors: Dreyer Jacqueline , Eichhorn Heiko , Friedlin Ernst , Kürnsteiner Hubert , Kück Ulrich 
Published: March 2007

ABSTRACT

The
Aspergillus nidulans velvet
(
veA
) gene encodes a global regulator of gene expression controlling sexual development as well as secondary metabolism. We have identified the
veA
homologue Ac
veA
from
Acremonium chrysogenum
, the major producer of the β-lactam antibiotic cephalosporin C. Two different disruption strains as well as the corresponding complements were generated as a prelude to detailed functional analysis. Northern hybridization and quantitative real-time PCR clearly indicate that the nucleus-localized AcVEA polypeptide controls the transcriptional expression of six cephalosporin C biosynthesis genes. The most drastic reduction in expression is seen for
cefEF
, encoding the deacetoxycephalosporine/deacetylcephalosporine synthetase. After 120 h of growth, the
cefEF
transcript level is below 15% in both disruption strains compared to the wild type. These transcriptional expression data are consistent with results from a comparative and time-dependent high-performance liquid chromatography analysis of cephalosporin C production. Compared to the recipient, both disruption strains have a cephalosporin C titer that is reduced by 80%. In addition to its role in cephalosporin C biosynthesis, Ac
veA
is involved in the developmentally dependent hyphal fragmentation. In both disruption strains, hyphal fragmentation is already observed after 48 h of growth, whereas in the recipient strain, arthrospores are not even detected before 96 h of growth. Finally, the two mutant strains show hyperbranching of hyphal tips on osmotically nonstabilized media. Our findings will be significant for biotechnical processes that require a defined stage of cellular differentiation for optimal production of secondary metabolites.
Sensitive Whole-Cell Biosensor Suitable for Detecting a Variety of
N
-Acyl Homoserine Lactones in Intact Rhizosphere Microbial Communities
Authors: DeAngelis Kristen M. , Firestone Mary K. , Lindow Steven E. 
Published: March 2007

ABSTRACT

To investigate quorum sensing in rhizosphere soil, a whole-cell biosensor,
Agrobacterium tumefaciens
(pAHL-Ice), was constructed. The biosensor responded to all
N
-acyl homoserine lactones (AHLs) tested, except C
4
homoserine lactone, with a minimum detection limit of 10
−12
M, as well as to both exogenously added AHLs and AHL-producing bacterial strains in soil. This highly sensitive biosensor reveals for the first time the increased AHL availability in intact rhizosphere microbial communities compared to that in bulk soil.
Development of High-Throughput Phenotyping of Metagenomic Clones from the Human Gut Microbiome for Modulation of Eukaryotic Cell Growth
Authors: Gloux Karine , Leclerc Marion , Iliozer Harout , L'Haridon René , Manichanh Chaysavanh , Corthier Gérard , Nalin Renaud , Blottière Hervé M. , Doré Joël 
Published: March 2007

ABSTRACTMetagenomic libraries derived from human intestinal microbiota (20,725 clones) were screened for epithelial cell growth modulation. Modulatory clones belonging to the four phyla represented among the metagenomic libraries were identified (hit rate, 0.04 to 8.7% depending on the screening cutoff). Several candidate loci were identified by transposon mutagenesis and subcloning.
Differentiation of
Bacillus anthracis
,
B. cereus
, and
B. thuringiensis
by Using Pulsed-Field Gel Electrophoresis
Authors: Zhong Wenwan , Shou Yulin , Yoshida Thomas M. , Marrone Babetta L. 
Published: March 2007

ABSTRACT

A pulsed-field gel electrophoresis (PFGE) method was developed for discriminating
Bacillus anthracis
from
B. cereus
and
B. thuringiensis
. A worldwide collection of 25
B. anthracis
isolates showed high-profile homology, and these isolates were unambiguously distinguished from
B. cereus
and
B. thuringiensis
isolates by cluster analysis of the whole-genome macrorestriction enzyme digestion patterns generated by NotI.
High-Resolution DNA Melt Curve Analysis of the Clustered, Regularly Interspaced Short-Palindromic-Repeat Locus of
Campylobacter jejuni
Authors: Price Erin P. , Smith Helen , Huygens Flavia , Giffard Philip M. 
Published: March 2007

ABSTRACT

A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of
Campylobacter jejuni
is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing
C. jejuni
genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species.
Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments
Authors: Gontang Erin A. , Fenical William , Jensen Paul R. 
Published: March 2007

ABSTRACT

Major advances in our understanding of marine bacterial diversity have been gained through studies of bacterioplankton, the vast majority of which appear to be gram negative. Less effort has been devoted to studies of bacteria inhabiting marine sediments, yet there is evidence to suggest that gram-positive bacteria comprise a relatively large proportion of these communities. To further expand our understanding of the aerobic gram-positive bacteria present in tropical marine sediments, a culture-dependent approach was applied to sediments collected in the Republic of Palau from the intertidal zone to depths of 500 m. This investigation resulted in the isolation of 1,624 diverse gram-positive bacteria spanning 22 families, including many that appear to represent new taxa. Phylogenetic analysis of 189 representative isolates, based on 16S rRNA gene sequence data, indicated that 124 (65.6%) belonged to the class
Actinobacteria
while the remaining 65 (34.4%) were members of the class
Bacilli
. Using a sequence identity value of ≥98%, the 189 isolates grouped into 78 operational taxonomic units, of which 29 (37.2%) are likely to represent new taxa. The high degree of phylogenetic novelty observed during this study highlights the fact that a great deal remains to be learned about the diversity of gram-positive bacteria in marine sediments.
Molecular Characterization of a Glucokinase with Broad Hexose Specificity from
Bacillus sphaericus
Strain C3-41
Authors: Han Bei , Liu Haizhou , Hu Xiaomin , Cai Yajun , Zheng Dasheng , Yuan Zhiming 
Published: March 2007

ABSTRACT

Bacillus sphaericus
cannot metabolize sugar since it lacks several of the enzymes necessary for glycolysis. Our results confirmed the presence of a glucokinase-encoding gene,
glcK
, and a phosphofructokinase-encoding gene,
pfk
, on the bacterial chromosome and expression of glucokinase during vegetative growth of
B. sphaericus
strains. However, no phosphoglucose isomerase gene (
pgi
) or phosphoglucose isomerase enzyme activity was detected in these strains. Furthermore, one
glcK
open reading frame was cloned from
B. sphaericus
strain C3-41 and then expressed in
Escherichia coli
. Biochemical analysis revealed that this gene encoded a protein with a molecular mass of 33 kDa and that the purified recombinant glucokinase had
K

m

values of 0.52 and 0.31 mM for ATP and glucose, respectively. It has been proved that this ATP-dependent glucokinase can also phosphorylate fructose and mannose, and sequence alignment of the
glcK
gene indicated that it belongs to the ROK protein family. It is postulated that the absence of the phosphoglucose isomerase-encoding gene
pgi
in
B. sphaericus
might be one of the reasons for the inability of this bacterium to metabolize carbohydrates. Our findings provide additional data that further elucidate the specific metabolic pathway and could be used for genetic improvement of
B. sphaericus
.
Diversity and Abundance of Nitrate Reductase Genes (
narG
and
napA
), Nitrite Reductase Genes (
nirS
and
nrfA
), and Their Transcripts in Estuarine Sediments
Authors: Smith Cindy J. , Nedwell David B. , Dong Liang F. , Osborn A. Mark 
Published: March 2007

ABSTRACT

Estuarine systems are the major conduits for the transfer of nitrate from agricultural and other terrestrial-anthropogenic sources into marine ecosystems. Within estuarine sediments some microbially driven processes (denitrification and anammox) result in the net removal of nitrogen from the environment, while others (dissimilatory nitrate reduction to ammonium) do not. In this study, molecular approaches have been used to investigate the diversity, abundance, and activity of the nitrate-reducing communities in sediments from the hypernutrified Colne estuary, United Kingdom, via analysis of nitrate and nitrite reductase genes and transcripts. Sequence analysis of cloned PCR-amplified
narG
,
napA
, and
nrfA
gene sequences showed the indigenous nitrate-reducing communities to be both phylogenetically diverse and also divergent from previously characterized nitrate reduction sequences in soils and offshore marine sediments and from cultured nitrate reducers. In both the
narG
and
nrfA
libraries, the majority of clones (48% and 50%, respectively) were related to corresponding sequences from delta-proteobacteria. A suite of quantitative PCR primers and TaqMan probes was then developed to quantify phylotype-specific nitrate (
narG
and
napA
) and nitrite reductase (
nirS
and
nrfA
) gene and transcript numbers in sediments from three sites along the estuarine nitrate gradient. In general, both nitrate and nitrite reductase gene copy numbers were found to decline significantly (
P
< 0.05) from the estuary head towards the estuary mouth. The development and application, for the first time, of quantitative reverse transcription-PCR assays to quantify mRNA sequences in sediments revealed that transcript numbers for three of the five phylotypes quantified were greatest at the estuary head.
Experimental Infection of Neonatal Foals withRhodococcus equiTriggers Adult-Like Gamma Interferon Induction
Authors: Jacks Stephanie , Giguère Steeve , Crawford P. Cynda , Castleman William L. 
Published: April 2007

ABSTRACTRhodococcus equiis a facultative intracellular pathogen that causes pneumonia in young foals but does not induce disease in immunocompetent adult horses. Clearance ofR. equidepends mainly on gamma interferon (IFN-γ) production by T lymphocytes, whereas the predominance of interleukin 4 (IL-4) is detrimental. Young foals, like neonates of many other species, are generally deficient in the ability to produce IFN-γ. The objective of this study was to compare the cytokine profiles, as well as cell-mediated and antibody responses, of young foals to those of adult horses following intrabronchial challenge withR. equi. The lymphoproliferative responses of bronchial lymph node (BLN) cells to concanavalin A were significantly higher in foals than in adult horses. In contrast, adult horses had significantly higher lymphoproliferative responses toR. equiantigens than did foals. Infected foals had significantly lower IL-4 mRNA expression but significantly higher IFN-γ expression and IFN-γ/IL-4 ratio inR. equi-stimulated BLN lymphocytes than did infected adults. Infection withR. equiin foals resulted in a significant increase in the percentage of T lymphocytes and CD4+T lymphocytes in bronchoalveolar lavage fluid in association with a significant decrease in the percentage of these cell populations in BLNs. Infection of foals also resulted in a marked increase in serum immunoglobulin Ga (IgGa) and IgGb levels, resulting in concentrations in serum that were significantly higher than those of adult horses. This study demonstrates that the immune response toR. equiin foals is not biased toward IL-4 and is characterized by the predominant induction of IFN-γ.
Genome Sequence and Analysis of aPropionibacterium acnesBacteriophage
Authors: Farrar Mark D. , Howson Karen M. , Bojar Richard A. , West David , Towler James C. , Parry James , Pelton Katharine , Holland Keith T. 
Published: March 2007

ABSTRACTCutaneous propionibacteria are important commensals of human skin and are implicated in a wide range of opportunistic infections.Propionibacterium acnesis also associated with inflammatory acne vulgaris. Bacteriophage PA6 is the first phage ofP. acnesto be sequenced and demonstrates a high degree of similarity to many mycobacteriophages both morphologically and genetically. PA6 possesses an icosahedreal head and long noncontractile tail characteristic of theSiphoviridae. The overall genome organization of PA6 resembled that of the temperate mycobacteriophages, although the genome was much smaller, 29,739 bp (48 predicted genes), compared to, for example, 50,550 bp (86 predicted genes) for the Bxb1 genome. PA6 infected onlyP. acnesand produced clear plaques with turbid centers, but it lacked any obvious genes for lysogeny. The host range of PA6 was restricted toP. acnes, but the phage was able to infect and lyse allP. acnesisolates tested. Sequencing of the PA6 genome makes an important contribution to the study of phage evolution and propionibacterial genetics.
Membrane-Bound Nitrate Reductase Is Required for Anaerobic Growth in Cystic Fibrosis Sputum
Authors: Palmer Kelli L. , Brown Stacie A. , Whiteley Marvin 
Published: March 2007

ABSTRACT

The autosomal recessive disorder cystic fibrosis (CF) affects approximately 70,000 people worldwide and is characterized by chronic bacterial lung infections with the opportunistic pathogen
Pseudomonas aeruginosa
. To form a chronic CF lung infection,
P. aeruginosa
must grow and proliferate within the CF lung, and the highly viscous sputum within the CF lung provides a likely growth substrate. Recent evidence indicates that anaerobic microenvironments may be present in the CF lung sputum layer. Since anaerobic growth significantly enhances
P. aeruginosa
biofilm formation and antibiotic resistance, it is important to examine
P. aeruginosa
physiology and metabolism in anaerobic environments. Measurement of nitrate levels revealed that CF sputum contains sufficient nitrate to support significant
P. aeruginosa
growth anaerobically, and mutational analysis revealed that the membrane-bound nitrate reductase is essential for
P. aeruginosa
anaerobic growth in an in vitro CF sputum medium. In addition, expression of genes coding for the membrane-bound nitrate reductase complex is responsive to CF sputum nitrate levels. These findings suggest that the membrane-bound nitrate reductase is critical for
P. aeruginosa
anaerobic growth with nitrate in the CF lung.
An Extracytoplasmic Function Sigma Factor Acts as a General Stress Response Regulator inSinorhizobium meliloti
Authors: Sauviac Laurent , Philippe Heinui , Phok Kounthéa , Bruand Claude 
Published: March 2007

ABSTRACTSinorhizobium melilotigenes transcriptionally up-regulated after heat stress, as well as upon entry into stationary phase, were identified by microarray analyses. Sixty stress response genes were thus found to be up-regulated under both conditions. One of them,rpoE2(smc01506), encodes a putative extracytoplasmic function (ECF) sigma factor. We showed that this sigma factor controls its own transcription and is activated by various stress conditions, including heat and salt, as well as entry into stationary phase after either carbon or nitrogen starvation. We also present evidence that the product of the gene cotranscribed withrpoE2negatively regulates RpoE2 activity, and we therefore propose that it plays the function of anti-sigma factor. By combining transcriptomic, bioinformatic, and quantitative reverse transcription-PCR analyses, we identified 44 RpoE2-controlled genes and predicted the number of RpoE2 targets to be higher. Strikingly, more than one-third of the 60 stress response genes identified in this study are RpoE2 targets. Interestingly, two genes encoding proteins with known functions in stress responses, namely,katCandrpoH2, as well as a second ECF-encoding gene,rpoE5, were found to be RpoE2 regulated. Altogether, these data suggest that RpoE2 is a major global regulator of the general stress response inS. meliloti. Despite these observations, and although this sigma factor is well conserved among alphaproteobacteria, no in vitro nor in planta phenotypic difference from the wild-type strain could be detected forrpoE2mutants. This therefore suggests that other important actors in the general stress response have still to be identified inS. meliloti.
Re
-Citrate Synthase from
Clostridium kluyveri
Is Phylogenetically Related to Homocitrate Synthase and Isopropylmalate Synthase Rather Than to
Si
-Citrate Synthase
Authors: Li Fuli , Hagemeier Christoph H. , Seedorf Henning , Gottschalk Gerhard , Thauer Rudolf K. 
Published: March 2007

ABSTRACT

The synthesis of citrate from acetyl-coenzyme A and oxaloacetate is catalyzed in most organisms by a
Si
-citrate synthase, which is
Si
-face stereospecific with respect to C-2 of oxaloacetate. However, in
Clostridium kluyveri
and some other strictly anaerobic bacteria, the reaction is catalyzed by a
Re
-citrate synthase, whose primary structure has remained elusive. We report here that
Re
-citrate synthase from
C. kluyveri
is the product of a gene predicted to encode isopropylmalate synthase.
C. kluyveri
is also shown to contain a gene for
Si
-citrate synthase, which explains why cell extracts of the organism always exhibit some
Si
-citrate synthase activity.
ScrG, a GGDEF-EAL Protein, Participates in Regulating Swarming and Sticking inVibrio parahaemolyticus
Authors: Kim Yun-Kyeong , McCarter Linda L. 
Published: March 2007

ABSTRACTIn this work, we describe a new gene controlling lateral flagellar gene expression. The gene encodes ScrG, a protein containing GGDEF and EAL domains. This is the second GGDEF-EAL-encoding locus determined to be involved in the regulation of swarming: the first was previously characterized and namedscrABC(for “swarming and capsular polysaccharide regulation”). GGDEF and EAL domain-containing proteins participate in the synthesis and degradation of the nucleotide signal cyclic di-GMP (c-di-GMP) in many bacteria. Overexpression ofscrGwas sufficient to induce lateral flagellar gene expression in liquid, decrease biofilm formation, decreasecpsgene expression, and suppress the ΔscrABCphenotype. Removal of its EAL domain reversed ScrG activity, converting ScrG to an inhibitor of swarming and activator ofcpsexpression. Overexpression ofscrGdecreased the intensity of a32P-labeled nucleotide spot comigrating with c-di-GMP standard, whereas overexpression ofscrGΔEALenhanced the intensity of the spot. Mutants with defects inscrGshowed altered swarming and lateral flagellin production and colony morphology (but not swimming motility); furthermore, mutation of two GGDEF-EAL-encoding loci (scrGandscrABC) produced cumulative effects on swarming, lateral flagellar gene expression, lateral flagellin production and colony morphology. Mutant analysis supports the assignment of the primary in vivo activity of ScrG to acting as a phosphodiesterase. The data are consistent with a model in which multiple GGDEF-EAL proteins can influence the cellular nucleotide pool: a low concentration of c-di-GMP favors surface mobility, whereas high levels of this nucleotide promote a more adhesiveVibrio parahaemolyticuscell type.
YhdJ, a Nonessential CcrM-Like DNA Methyltransferase of
Escherichia coli
and
Salmonella enterica
Authors: Broadbent Sarah E. , Balbontin Roberto , Casadesus Josep , Marinus Martin G. , van der Woude Marjan 
Published: March 2007

ABSTRACT

The
Caulobacter crescentus
DNA adenine methyltransferase CcrM and its homologs in the α-
Proteobacteria
are essential for viability. CcrM is 34% identical to the
yhdJ
gene products of
Escherichia coli
and
Salmonella enterica
. This study provides evidence that the
E. coli yhdJ
gene encodes a DNA adenine methyltransferase. In contrast to an earlier report, however, we show that
yhdJ
is not an essential gene in either
E. coli
or
S. enterica
.
Zinc-Responsive Regulation of Alternative Ribosomal Protein Genes inStreptomyces coelicolorInvolves Zur and σR
Authors: Owen Gillian A. , Pascoe Ben , Kallifidas Dimitris , Paget Mark S. B. 
Published: March 2007

ABSTRACTStreptomyces coelicolorcontains paralogous versions of seven ribosomal proteins (S14, S18, L28, L31, L32, L33, and L36), which differ in their potential to bind structural zinc. The paralogues are termed C+or C−on the basis of the presence or absence of putative cysteine ligands. Here, mutational studies suggest that the C−version of L31 can functionally replace its C+paralogue only when expressed at an artificially elevated level. We show that the level of expression of four transcriptional units encoding C−proteins is elevated under conditions of zinc deprivation. Zur controls the expression of three transcriptional units (includingrpmG2,rpmE2,rpmB2,rpsN2,rpmF2, and possiblyrpsR2). Zur also controls the expression of theznuACBoperon, which is predicted to encode a high-affinity zinc transport system. Surprisingly, the zinc-responsive control of therpmG3-rpmJ2operon is dictated by σR, a sigma factor that was previously shown to control the response to disulfide stress inS. coelicolor. The induction of σRactivity during zinc limitation establishes an important link between thiol-disulfide metabolism and zinc homeostasis.
Evaluation of a Commercial Real-Time PCR Kit for Detection of Dengue Virus in Samples Collected during an Outbreak in Goiânia, Central Brazil, in 2005
Authors: Levi José Eduardo , Tateno Adriana Fumie , Machado Adriana Freire , Ramalho Débora Camillo , de Souza Vanda Akico Ueda Fick , Guilarde Adriana Oliveira , de Rezende Feres Valéria Christina , Martelli Celina Maria Turchi , Turchi Marília Dalva , Siqueira João Bosco , Pannuti Cláudio Sérgio 
Published: April 2007

ABSTRACT
In the past 2 decades, dengue has reemerged in Brazil as a significant public health problem. Clinicians demand a diagnostic test with high sensitivity that is applicable during the early symptomatic phase. We aimed to test two distinct molecular methods on samples from suspected dengue cases during an outbreak in Central Brazil. Acute-phase serum specimens from 254 patients suspected of having dengue were collected during 2005 in the city of Goiânia, Central Brazil. Samples were blindly evaluated by real-time and multiplex PCR in addition to routine immunoglobulin M serology and virus culture. Overall, acute dengue was confirmed by serology, multiplex PCR, or virus isolation for 80% of patients (203/254). Another four patients presented real-time PCR-positive results as the unique marker of dengue. Higher real-time PCR positivity levels and viral loads were observed in the early symptomatic phase of disease (≤5 days) than after this period. Multiplex and real-time PCR assays presented a high kappa agreement (0.85). According to multiplex PCR, 60 samples harbored dengue virus type 3 (DEN-3), 4 samples harbored DEN-2, and 1 sample displayed a pattern compatible with a double infection with DEN-2 and -3. The dengue virus real-time kit was found to be practical and adjustable for high throughput, to display the best performance in the early symptomatic phase of dengue cases, and to be valuable for confirming dengue diagnosis in a timely manner.