bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of a New Source of Rifamycin Antibiotics in Marine Sponge Actinobacteria by Phylogenetic Prediction
Authors: Kim Tae Kyung , Hewavitharana Amitha K. , Shaw P. Nicholas , Fuerst John A. 
Published: March 2006

ABSTRACTPhylogenetic analysis of the ketosynthase (KS) gene sequences of marine sponge-derivedSalinisporastrains of actinobacteria indicated that the polyketide synthase (PKS) gene sequence most closely related to that ofSalinisporawas the rifamycin B synthase ofAmycolatopsis mediterranei. This result was not expected from taxonomic species tree phylogenetics using 16S rRNA sequences. From the PKS sequence data generated from our sponge-derivedSalinisporastrains, we predicted that such strains might synthesize rifamycin-like compounds. Liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis was applied to one sponge-derivedSalinisporastrain to test the hypothesis of rifamycin synthesis. The analysis reported here demonstrates that thisSalinisporaisolate does produce compounds of the rifamycin class, including rifamycin B and rifamycin SV. A rifamycin-specific KS primer set was designed, and that primer set increased the number of rifamycin-positive strains detected by PCR screening relative to the number detectable using a conserved KS-specific set. Thus, theSalinisporagroup of actinobacteria represents a potential new source of rifamycins outside the genusAmycolatopsisand the first recorded source of rifamycins from marine bacteria.
Global Carbon Utilization Profiles of Wild-Type, Mutant, and Transformant Strains of
Hypocrea jecorina
Authors: Druzhinina Irina S. , Schmoll Monika , Seiboth Bernhard , Kubicek Christian P. 
Published: March 2006

ABSTRACT

The ascomycete
Hypocrea jecorina
(
Trichoderma reesei
), an industrial producer of cellulases and hemicellulases, can efficiently degrade plant polysaccharides. However, the catabolic pathways for the resulting monomers and their relationship to enzyme induction are not well known. Here we used the Biolog Phenotype MicroArrays technique to evaluate the growth of
H. jecorina
on 95 carbon sources. For this purpose, we compared several wild-type isolates, mutants producing different amounts of cellulases, and strains transformed with a heterologous antibiotic resistance marker gene. The wild-type isolates and transformed strains had the highest variation in growth patterns on individual carbon sources. The cellulase mutants were relatively similar to their parental strains. Both in the mutant and in the transformed strains, the most significant changes occurred in utilization of xylitol, erythritol,
d
-sorbitol,
d
-ribose,
d
-galactose,
l
-arabinose,
N
-acetyl-
d
-glucosamine, maltotriose, and β-methyl-glucoside. Increased production of cellulases was negatively correlated with the ability to grow on γ-aminobutyrate, adonitol, and 2-ketogluconate; and positively correlated with that on
d
-sorbitol and saccharic acid. The reproducibility, relative simplicity, and high resolution (±10% of increase in mycelial density) of the phenotypic microarrays make them a useful tool for the characterization of mutant and transformed strains and for a global analysis of gene function.
Minimization of Glycerol Production during the High-Performance Fed-Batch Ethanolic Fermentation Process in
Saccharomyces cerevisiae
, Using a Metabolic Model as a Prediction Tool
Authors: Bideaux Carine , Alfenore Sandrine , Cameleyre Xavier , Molina-Jouve Carole , Uribelarrea Jean-Louis , Guillouet Stéphane E. 
Published: March 2006

ABSTRACT

On the basis of knowledge of the biological role of glycerol in the redox balance of
Saccharomyces cerevisiae
, a fermentation strategy was defined to reduce the surplus formation of NADH, responsible for glycerol synthesis. A metabolic model was used to predict the operating conditions that would reduce glycerol production during ethanol fermentation. Experimental validation of the simulation results was done by monitoring the inlet substrate feeding during fed-batch
S. cerevisiae
cultivation in order to maintain the respiratory quotient (RQ) (defined as the CO
2
production to O
2
consumption ratio) value between 4 and 5. Compared to previous fermentations without glucose monitoring, the final glycerol concentration was successfully decreased. Although RQ-controlled fermentation led to a lower maximum specific ethanol production rate, it was possible to reach a high level of ethanol production: 85 g · liter
−1
with 1.7 g · liter
−1
glycerol in 30 h. We showed here that by using a metabolic model as a tool in prediction, it was possible to reduce glycerol production in a very high-performance ethanolic fermentation process.
Influence of Freeze-Thaw Stress on the Structure and Function of Microbial Communities and Denitrifying Populations in Soil
Authors: Sharma Shilpi , Szele Zsofia , Schilling Rolf , Munch Jean Charles , Schloter Michael 
Published: March 2006

ABSTRACT

Microbial N
2
O release during the course of thawing of soil was investigated in model experiment focusing on denitrification, since freeze-thaw has been shown to cause significant physical and biological changes in soil, including a surge of N
2
O and CO
2
. The origin of these is still controversially discussed. The increase in denitrification after thawing may be attributed to the diffusion of organic substrates newly available to denitrifiers from disrupted soil aggregates, leading to an increase in microbial activity. Laboratory experiments with upper soil layer of a grassland were conducted in microcosms for real-time gas measurements during the entire phase of freeze and thaw. Shifts in microbial communities were evident on resolution of 16S and 18S rRNA genes and transcripts by denaturing gradient gel electrophoresis (DGGE). Microbial expression profiles were compared by RNA-arbitrarily primed PCR technique and subsequent resolution of amplified products on acrylamide gels. Differences in expression levels of periplasmic nitrate reductase gene (
napA
) and cytochrome
cd
1
nitrite reductase (
nirS
) were observed by most-probable-number-reverse transcription-PCR, with higher levels of expression occurring just after thawing began, followed by a decrease.
napA
and
nirS
DGGE profiles showed no change in banding patterns with fingerprints derived from DNA, whereas those derived from cDNA showed a clear succession of denitrifying bacteria, with the most complex pattern being observed at the end of the N
2
O surge. This study provides insight into the structural community changes and expression dynamics of denitrifiers as a result of freeze-thaw stress. Also, the results presented here support the belief that the gas fluxes observed during thawing is a result of freezing initiated high microbial activity.
Identification and Characterization of a Novel Intracellular Alkaline α-Amylase from the Hyperthermophilic Bacterium
Thermotoga maritima
MSB8
Authors: Ballschmiter Meike , Fütterer Ole , Liebl Wolfgang 
Published: March 2006

ABSTRACT

The gene for a novel α-amylase, designated AmyC, from the hyperthermophilic bacterium
Thermotoga maritima
was cloned and heterologously overexpressed in
Escherichia coli
. The putative intracellular enzyme had no amino acid sequence similarity to glycoside hydrolase family (GHF) 13 α-amylases, yet the range of substrate hydrolysis and the product profile clearly define the protein as an α-amylase. Based on sequence similarity AmyC belongs to a subgroup within GHF 57. On the basis of amino acid sequence similarity, Glu185 and Asp349 could be identified as the catalytic residues of AmyC. Using a 60-min assay, the maximum hydrolytic activity of the purified enzyme, which was dithiothreitol dependent, was found to be at 90°C. AmyC displayed a remarkably high pH optimum of pH 8.5 and an unusual sensitivity towards both ATP and EDTA.
Application of Genotyping during an Extensive Outbreak of Waterborne Giardiasis in Bergen, Norway, during Autumn and Winter 2004
Authors: Robertson L. J. , Hermansen L. , Gjerde B. K. , Strand E. , Alvsvåg J. O. , Langeland N. 
Published: March 2006

ABSTRACT

During the autumn and winter of 2004 and 2005, an extensive outbreak of waterborne giardiasis occurred in Bergen, Norway. Over 1,500 patients were diagnosed with giardiasis. Analysis of water from the implicated source revealed low numbers of
Giardia
cysts, but the initial contamination event probably occurred up to 10 weeks previously. While sewage leakage from a residential area is now considered to be the probable source of contamination, during the episode waste from one particular septic tank was thought to be a possible source. Genotyping of cysts from the septic tank demonstrated that they were assemblage A cysts, although the sequences were not identical to any previously published sequences. For the β-giardin gene, the closest published subgenotype was subgenotype A3; for the
gdh
gene, the closest published subgenotype was subgenotype A2. Genotyping of cysts from 21 patient samples revealed that they were assemblage B cysts; thus, the septic tank was unlikely to be the contamination source. Sequencing of the β-giardin and
gdh
genes from patient samples and a comparison of the sequences gave complex results. For the β-giardin gene, three isolates had sequences identical to subgenotype B3 sequences. However, other isolates had between one and four single-nucleotide polymorphisms (SNPs). For the
gdh
gene, none of the sequences were identical to the sequence published for subgenotype B3, and the sequences had between one and three SNPs. One isolate, which was identical to subgenotype B3 at the β-giardin gene, was more similar to subgenotype B2 at the
gdh
gene. Grouping the isolates on the basis of SNPs resulted in different groups for the two genes. The results are discussed in relation to giardiasis in Norway and to other
Giardia
genotyping studies.
Cryptosporidium parvum
Infections in Bergen, Norway, during an Extensive Outbreak of Waterborne Giardiasis in Autumn and Winter 2004
Authors: Robertson L. J. , Forberg T. , Hermansen L. , Gjerde B. K. , Alvsvåg J. O. , Langeland N. 
Published: March 2006

ABSTRACT

During a large waterborne giardiasis outbreak in Norway, many diarrheic patients were found to have
Cryptosporidium
infections. Gene sequencing identified these infections as
Cryptosporidium parvum
infections, although they were not identical. Whether these infections were due to a simultaneous outbreak of waterborne cryptosporidiosis or reflected background levels not normally detected is discussed.
Selective Biodegradation of S and N Heterocycles by a Recombinant
Rhodococcus erythropolis
Strain Containing Carbazole Dioxygenase
Authors: Yu Bo , Xu Ping , Zhu Shanshan , Cai Xiaofeng , Wang Ying , Li Li , Li Fuli , Liu Xiaoyong , Ma Cuiqing 
Published: March 2006

ABSTRACT

The carbazole dioxygenase genes were introduced into a dibenzothiophene degrader. The recombinant
Rhodococcus erythropolis
SN8 was capable of efficiently degrading dibenzothiophene and carbazole simultaneously. SN8 could also degrade various alkylated derivatives of carbazole and dibenzothiophene in FS4800 crude oil by just a one-step bioprocess.
Diverse and Unique Picocyanobacteria in Chesapeake Bay, Revealed by 16S-23S rRNA Internal Transcribed Spacer Sequences
Authors: Chen Feng , Wang Kui , Kan Jinjun , Suzuki Marcelino T. , Wommack K. Eric 
Published: March 2006

ABSTRACT

rRNA internal transcribed spacer phylogeny showed that Chesapeake Bay is populated with diverse
Synechococcus
strains, including members of the poorly studied marine cluster B. Marine cluster B prevailed in the upper bay, while marine cluster A was common in the lower bay. Interestingly, marine cluster B
Synechococcus
included phycocyanin- and phycoerythrin-rich strains.
Analysis of the Clonal Relationship of Shiga Toxin-Producing
Escherichia coli
Serogroup O165:H25 Isolated from Cattle
Authors: Geue Lutz , Selhorst Thomas , Schnick Christina , Mintel Birgit , Conraths Franz J. 
Published: March 2006

ABSTRACT

Variations in time and space of a clonal group of
Escherichia coli
O165:H25 on a cattle farm were monitored. The virulence marker pattern (
stx
genes,
eae
gene,
hly
EHEC
gene,
katP
gene,
espP
gene,
efa
gene) suggests that
E. coli
O165:H25 of bovine origin may represent a risk for human infection.
Casein-Derived Antimicrobial Peptides Generated by
Lactobacillus acidophilus
DPC6026
Authors: Hayes M. , Ross R. P. , Fitzgerald G. F. , Hill C. , Stanton C. 
Published: March 2006

ABSTRACT

Three peptides produced by a
Lactobacillus acidophilus
DPC6026 fermentation of sodium caseinate and showing antibacterial activity against pathogenic strains
Enterobacter sakazakii
ATCC 12868 and
Escherichia coli
DPC5063 were characterized. These peptides were all generated from bovine α
s1
-casein and identified as IKHQGLPQE, VLNENLLR, and SDIPNPIGSENSEK. These peptides may have bioprotective applicability and potential use in milk-based formula, which has been linked to
E. sakazakii
infection in neonates.
Analysis of Feces Samples Collected from a Wild-Bird Garden Feeding Station in Scotland for the Presence of Verocytotoxin-Producing
Escherichia coli
O157
Authors: Foster Geoffrey , Evans Judith , Knight Hazel I. , Smith Alastair W. , Gunn George J. , Allison Lesley J. , Synge Barti A. , Pennycott Tom W. 
Published: March 2006

ABSTRACT

Composite wild bird feces collected at regular intervals from a garden feeding station in southwest Scotland over a 3-year period were examined for verocytotoxin-producing
Escherichia coli
O157. One sample was positive for
Escherichia coli
O157. The isolate belonged to phage type 21/28 and possessed
vtx
2
,
eaeA
, and enterohemorrhagic
E. coli hlyA
genes.
Complementation of the
Lactococcus lactis
Secretion Machinery with
Bacillus subtilis
SecDF Improves Secretion of Staphylococcal Nuclease
Authors: Nouaille S. , Morello E. , Cortez-Peres N. , Le Loir Y. , Commissaire J. , Gratadoux J. J. , Poumerol E. , Gruss A. , Langella P. 
Published: March 2006

ABSTRACT

Unlike
Bacillus subtilis
and
Escherichia coli
, the gram-positive lactic acid bacterium
Lactococcus lactis
does not possess the SecDF protein, a component of the secretion (Sec) machinery involved in late secretion stages and required for the high-capacity protein secretion in
B. subtilis
. In this study, we complemented the
L. lactis
Sec machinery with SecDF from
B. subtilis
and evaluated the effect on the secretion of two forms of staphylococcal nuclease, NucB and NucT, which are efficiently and poorly secreted, respectively. The
B. subtilis
SecDF-encoding gene was tested in
L. lactis
at different levels. Increased quantities of the precursor and mature forms were observed only at low levels of SecDF and at high NucT production levels. This SecDF secretion enhancement was observed at the optimal growth temperature (30°C) and was even greater at 15°C. Furthermore, the introduction of
B. subtilis
SecDF into
L. lactis
was shown to have a positive effect on a secreted form of
Brucella abortus
L7/L12 antigen.
Conversion of
Sphingobium chlorophenolicum
ATCC 39723 to a Hexachlorobenzene Degrader by Metabolic Engineering
Authors: Yan Da-Zhong , Liu Hong , Zhou Ning-Yi 
Published: March 2006

ABSTRACT

The gene cassette (
camA
+
camB
+
camC
) encoding a cytochrome P-450
cam
variant was integrated into the nonessential gene
pcpM
of the pentachlorophenol degrader
Sphingobium chlorophenolicum
ATCC 39723 by homologous recombination. The recombinant strain could degrade hexachlorobenzene at a rate of 0.67 nmol · mg (dry weight)
−1
· h
−1
, and intermediate pentachlorophenol was also identified.
Prophagic DNA Fragments in
Streptococcus agalactiae
Strains and Association with Neonatal Meningitis
Authors: van der Mee-Marquet Nathalie , Domelier Anne-Sophie , Mereghetti Laurent , Lanotte Philippe , Rosenau Agnès , van Leeuwen Willem , Quentin Roland 
Published: March 2006

ABSTRACT

We identified—by randomly amplified polymorphic DNA (RAPD) analysis at the population level followed by DNA differential display, cloning, and sequencing—three prophage DNA fragments (F5, F7, and F10) in
Streptococcus agalactiae
that displayed significant sequence similarity to the DNA of
S. agalactiae
and
Streptococcus pyogenes
. The F5 sequence aligned with a prophagic gene encoding the large subunit of a terminase, F7 aligned with a phage-associated cell wall hydrolase and a phage-associated lysin, and F10 aligned with a transcriptional regulator (
ArpU
family) and a phage-associated endonuclease. We first determined the prevalence of F5, F7, and F10 by PCR in a collection of 109 strains isolated in the 1980s and divided into two populations: one with a high risk of causing meningitis (HR group) and the other with a lower risk of causing meningitis (LR group). These fragments were significantly more prevalent in the HR group than in the LR group (
P
< 0.001). Our findings suggest that lysogeny has increased the ability of some
S. agalactiae
strains to invade the neonatal brain endothelium. We then determined the prevalence of F5, F7, and F10 by PCR in a collection of 40 strains recently isolated from neonatal meningitis cases for comparison with the cerebrospinal fluid (CSF) strains isolated in the 1980s. The prevalence of the three prophage DNA fragments was similar in these two populations isolated 15 years apart. We suggest that the prophage DNA fragments identified have remained stable in many CSF
S. agalactiae
strains, possibly due to their importance in virulence or fitness.
Use of Flocked Swabs and a Universal Transport Medium To Enhance Molecular Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
Authors: Chernesky Max , Castriciano Santina , Jang Dan , Smieja Marek 
Published: March 2006

ABSTRACT

The use of new flocked swabs, compared to kit swabs, enhanced the ability of three commercial nucleic acid amplification tests to detect low levels of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
nucleic acids when the organisms were diluted in a universal transport medium as mocked specimens.
Comparison of Testing Methods for Detection of Decreased Linezolid Susceptibility Due to G2576T Mutation of the 23S rRNA Gene in
Enterococcus faecium
and
Enterococcus faecalis
Authors: Qi Chao , Zheng Xiaotian , Obias Arlene , Scheetz Marc H. , Malczynski Michael , Warren John R. 
Published: March 2006

ABSTRACT

E-test, Vitek 2, MicroScan, agar dilution, and disk diffusion were compared for detection of decreased linezolid susceptibility due to 23S rRNA gene G2576T mutation among 32 clinical
Enterococcus
strains initially reported as intermediate or resistant by E-test alone or Vitek 2 confirmed by E-test. Agar and broth dilution methods were in concordance with PCR detection of the mutation, and disk diffusion was somewhat less sensitive but equally specific.
Accuracy of Three Automated Systems (MicroScan WalkAway, VITEK, and VITEK 2) for Susceptibility Testing of
Pseudomonas aeruginosa
against Five Broad-Spectrum Beta-Lactam Agents
Authors: Sader Helio S. , Fritsche Thomas R. , Jones Ronald N. 
Published: March 2006

ABSTRACT

One hundred recent clinical
Pseudomonas aeruginosa
isolates were used to assess the quantitative (MIC) and qualitative (susceptibility category) accuracies of the MicroScan WalkAway, VITEK, and VITEK 2 automated susceptibility test systems when five-broad spectrum β-lactams, aztreonam, cefepime, ceftazidime, imipenem, and piperacillin-tazobactam, were tested. Isolates were selected so that the MICs for the isolates overrepresented the MICs near the breakpoints to assess precisely the agreement between the results obtained with the automated systems and the results obtained by the reference tests. The categorical and MIC results from the automated systems were compared to the consensus result of three reference methods: broth microdilution, agar dilution, and disk diffusion. The consensus categorical testing (susceptibility and resistance) rates were 47 and 27%, respectively, for aztreonam; 59 and 14%, respectively, for cefepime; 44 and 43%, respectively, for ceftazidime; 71 and 19%, respectively, for imipenem; and 50 and 50%, respectively, for piperacillin-tazobactam. All systems tested exhibited a high, unacceptable level of very major (false-susceptible) errors for piperacillin-tazobactam (19 to 27%). Major (false-resistant) error rates were generally acceptable (0 to 3%), but minor error rates were elevated (8 to 32%) for cefepime (VITEK 2 and VITEK) and for aztreonam (all three systems), leading to consistent trends toward false resistance. Manufacturer reevaluation of these automated systems for the testing of selected β-lactams with current clinical isolates of
P. aeruginosa
that exhibit contemporary resistance mechanisms would be prudent to minimize the potential for serious reporting errors.
Application of UL144 Molecular Typing To Determine Epidemiology of Cytomegalovirus Infections in Preterm Infants
Authors: Stranska R. , Schuurman R. , Toet M. , Verboon-Maciolek M. , de Vries L. S. , van Loon A. M. 
Published: March 2006

ABSTRACT
Sequence analysis of the UL144 gene of human cytomegalovirus (CMV) was used to investigate the epidemiology of CMV infections in preterm infants. Nosocomial transmission of CMV from congenitally infected infant to preterm twins was excluded based on distinct molecular profiles of CMV strains. Indistinguishable molecular profiles between strains from the mother and the infant indicated postnatal acquisition of CMV through breastfeeding.
Detection of Human Bocavirus in Japanese Children with Lower Respiratory Tract Infections
Authors: Ma Xiaoming , Endo Rika , Ishiguro Nobuhisa , Ebihara Takashi , Ishiko Hiroaki , Ariga Tadashi , Kikuta Hideaki 
Published: March 2006

ABSTRACT

Human bocavirus (HBoV), a newly cloned human virus of the genus
Bocavirus
, was detected by PCR from nasopharyngeal swab samples (8 of 318; 5.7%) collected from children with lower respiratory tract infections. HBoV may be one of the causative agents of lower respiratory tract infections in young children.
Distribution of the Serine-Aspartate Repeat Protein-Encoding
sdr
Genes among Nasal-Carriage and Invasive
Staphylococcus aureus
Strains
Authors: Sabat Artur , Melles Damian C. , Martirosian Gayane , Grundmann Hajo , van Belkum Alex , Hryniewicz Waleria 
Published: March 2006

ABSTRACT

The
sdr
locus was found in all 497 investigated
Staphylococcus aureus
strains, although in 29 strains it contained only the
sdrC
gene (
sdrD
negative,
sdrE
negative). The
sdrC
-positive,
sdrD
-negative,
sdrE
-negative gene profile was exclusive to methicillin-sensitive
S. aureus
(MSSA) strains (Fisher's exact test;
P
= 0.0005) and was not found in the strains collected from bone infections (
P
= 0.0019). We also found a strong association between the presence of the
sdrD
gene and methicillin-resistant
S. aureus
strains (
P
< 0.0001). Our findings suggest that MSSA strains with the newly uncovered
sdrC
-positive,
sdrD
-negative,
sdrE
-negative gene profile have a substantially decreased potential to establish bone infection.
Evaluation of a Rapid Gram Stain Interpretation Method for Diagnosis of Bacterial Vaginosis
Authors: Hilmarsdóttir I. , Hauksdóttir G. S. , Jóhannesdóttir J. D. , Daníelsdóttir T. , Thorsteinsdóttir H. , Ólafsson J. H. 
Published: March 2006

ABSTRACTA simple Gram stain evaluation for the diagnosis of bacterial vaginosis was assessed in comparison to Nugent's method. The sensitivity (90%), specificity (94%), positive and negative predictive values (90% and 94%), and good interobserver agreement obtained indicate that the test method can be performed reliably in the routine clinical microbiology laboratory.