bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer of Genetic Material between Pathogenic and Food-Borne Yeasts
Authors: Mentel Marek , Špírek Mário , Jørck-Ramberg Dorte , Piškur Jure 
Published: July 2006

ABSTRACT
Many pathogenic yeast species are asexual and therefore not involved in intra- or interspecies mating. However, high-frequency transfer of plasmid DNA was observed when pathogenic and food-borne yeasts were grown together. This property could play a crucial role in the spread of virulence and drug resistance factors among yeasts.
Assessment of Factors Influencing Direct Enumeration of Viruses within Estuarine Sediments
Authors: Helton Rebekah R. , Liu Ling , Wommack K. Eric 
Published: July 2006

ABSTRACT
Accurate enumeration of viruses within environmental samples is critical for investigations of the ecological role of viruses and viral infection within microbial communities. This report evaluates differences in viral and bacterial direct counts between estuarine sediment samples which were either immediately processed onboard ship or frozen at −20°C and later processed. Viral and bacterial abundances were recorded at three stations spanning the length of the Chesapeake Bay in April and June 2003 within three sediment fractions: pore water (PW), whole sediment (WS), and sediment after pore water removal (AP). No significant difference in viral abundance was apparent between extracts from fresh or frozen sediments. In contrast, bacterial abundance was significantly lower in the samples subjected to freezing. Both bacterial and viral abundance showed significant differences between sediment fractions (PW, WS, or AP) regardless of the fresh or frozen status. Although pore water viral abundance has been used in the past as a measurement of viral abundance in sediments, this fraction accounted for only ca. 5% of the total sediment viral abundance across all samples. The effect of refrigerated storage of sediment viral extracts was also examined and showed that, within the first 2 h, viral abundance decreased ca. 30% in formalin-fixed extracts and 66% in unfixed extracts. Finally, the reliability of direct viral enumeration via epifluorescence microscopy was tested by using DNase treatment of WS extractions. These tests indicated that a large fraction (>86%) of the small SYBR gold fluorescing particles are likely viruses.
Marine and Freshwater Cyanophages in a Laurentian Great Lake: Evidence from Infectivity Assays and Molecular Analyses of g20 Genes
Authors: Wilhelm Steven W. , Carberry Matthew J. , Eldridge Melanie L. , Poorvin Leo , Saxton Matthew A. , Doblin Martina A. 
Published: July 2006

ABSTRACTWhile it is well established that viruses play an important role in the structure of marine microbial food webs, few studies have directly addressed their role in large lake systems. As part of an ongoing study of the microbial ecology of Lake Erie, we have examined the distribution and diversity of viruses in this system. One surprising result has been the pervasive distribution of cyanophages that infect the marine cyanobacterial isolateSynechococcussp. strain WH7803. Viruses that lytically infect this cyanobacterium were identified throughout the western basin of Lake Erie, as well as in locations within the central and eastern basins. Analyses of the gene encoding the g20 viral capsid assembly protein (a conservative phylogenetic marker for the cyanophage) indicate that these viruses, as well as amplicons from natural populations and the ballast of commercial ships, are related to marine cyanophages but in some cases form a unique clade, leaving questions concerning the native hosts of these viruses. The results suggest that cyanophages may be as important in freshwater systems as they are known to be in marine systems.
Structure, Organization, and Transcriptional Regulation of a Family of Copper Radical Oxidase Genes in the Lignin-Degrading Basidiomycete
Phanerochaete chrysosporium
Authors: Vanden Wymelenberg Amber , Sabat Grzegorz , Mozuch Michael , Kersten Philip J. , Cullen Dan , Blanchette Robert A. 
Published: July 2006

ABSTRACT

The white rot basidiomycete
Phanerochaete chrysosporium
produces an array of nonspecific extracellular enzymes thought to be involved in lignin degradation, including lignin peroxidases, manganese peroxidases, and the H
2
O
2
-generating copper radical oxidase, glyoxal oxidase (GLX). Preliminary analysis of the
P. chrysosporium
draft genome had identified six sequences with significant similarity to GLX and designated
cro1
through
cro6
. The predicted mature protein sequences diverge substantially from one another, but the residues coordinating copper and constituting the radical redox site are conserved. Transcript profiles, microscopic examination, and lignin analysis of inoculated thin wood sections are consistent with differential regulation as decay advances. The
cro2
-encoded protein was detected by liquid chromatography-tandem mass spectrometry in defined medium. The
cro2
cDNA was successfully expressed in
Aspergillus nidulans
under the control of the
A. niger
glucoamylase promoter and secretion signal. The recombinant CRO2 protein had a substantially different substrate preference than GLX. The role of structurally and functionally diverse
cro
genes in lignocellulose degradation remains to be established.
Purine Biosynthesis, Riboflavin Production, and Trophic-Phase Span Are Controlled by a Myb-Related Transcription Factor in the Fungus
Ashbya gossypii
Authors: Mateos Laura , Jiménez Alberto , Revuelta José L. , Santos María A. 
Published: July 2006

ABSTRACT

Ashbya gossypii
is a natural riboflavin overproducer used in the industrial production of the vitamin. We have isolated an insertional mutant exhibiting higher levels of riboflavin production than the wild type. DNA analysis of the targeted locus in the mutant strain revealed that a syntenic homolog of the
Saccharomyces cerevisiae BAS1
gene, a member of the Myb family of transcription factors, was inactivated. Directed gene disruption of Ag
BAS1
confirmed the phenotype observed for the insertional mutant, and the
Δbas1
mutant also showed auxotrophy for adenine and several growth defects, such as a delay in the germination of the spores and an abnormally prolonged trophic phase. Additionally, we demonstrate that the DNA-binding domain of AgBas1p is able to bind to the Bas1-binding motifs in the Ag
ADE4
promoter; we also show a clear nuclear localization of a green fluorescent protein-Bas1 fusion protein. Real-time quantitative PCR analyses comparing the wild type and the
Δbas1
mutant revealed that Ag
BAS1
was responsible for the adenine-mediated regulation of the purine and glycine pathways, since the transcription of the
ADE4
and
SHM2
genes was virtually abolished in the
Δbas1
mutant. Furthermore, the transcription of
ADE4
and
SHM2
in the
Δbas1
mutant did not diminish during the transition from the trophic to the productive phase did not diminish, in contrast to what occurred in the wild-type strain. A C-terminal deletion in the Ag
BAS1
gene, comprising a hypothetical regulatory domain, caused constitutive activation of the purine and glycine pathways, enhanced riboflavin overproduction, and prolonged the trophic phase. Taking these results together, we propose that in
A. gossypii
, Ag
BAS1
is an important transcription factor that is involved in the regulation of different physiological processes, such as purine and glycine biosynthesis, riboflavin overproduction, and growth.
Bacteriocin T8, a Novel Class IIa
sec
-Dependent Bacteriocin Produced by
Enterococcus faecium
T8, Isolated from Vaginal Secretions of Children Infected with Human Immunodeficiency Virus
Authors: De Kwaadsteniet M. , Fraser T. , Van Reenen C. A. , Dicks L. M. T. 
Published: July 2006

ABSTRACT

Enterococcus faecium
T8, isolated from vaginal secretions of children with human immunodeficiency virus, produces a class IIa
sec
-dependent bacteriocin that is structurally different from three other class IIa
sec
-dependent bacteriocins, i.e., enterocin P and an enterocin P-like bacteriocin, produced by
Enterococcus faecium
, and bacteriocin 31, produced by
Enterococcus faecalis
, and from a class III bacteriocin produced by
E. faecalis
. The genes encoding the bacteriocin, immunity protein, mobilization protein, and relaxase nuclease are located on a 7-kb plasmid. Bacteriocin T8 has a molecular mass of 5.1 kDa based on its DNA sequence, similar to the 5.0 kDa recorded for bacteriocin 31 but larger than the 4.6 kDa reported for enterocin P. At the amino acid level, bacteriocin T8 is 69% homologous to bacteriocin 31 and 47% homologous to enterocin P. Bacteriocin T8 is active against
E. faecalis
isolated from patients diagnosed with vaginosis, against
Lactobacillus sakei
, and against a
Propionibacterium
sp. The peptide is heat stable (60 min at 100°C) and remains active in phosphate buffer from pH 4.0 to 10.0. The mode of activity is bactericidal, as determined with
E. faecalis
.
Acetate Oxidation Is the Dominant Methanogenic Pathway from Acetate in the Absence of
Methanosaetaceae
Authors: Karakashev Dimitar , Batstone Damien J. , Trably Eric , Angelidaki Irini 
Published: July 2006

ABSTRACT

The oxidation of acetate to hydrogen, and the subsequent conversion of hydrogen and carbon dioxide to methane, has been regarded largely as a niche mechanism occurring at high temperatures or under inhibitory conditions. In this study, 13 anaerobic reactors and sediment from a temperate anaerobic lake were surveyed for their dominant methanogenic population by using fluorescent in situ hybridization and for the degree of acetate oxidation relative to aceticlastic conversion by using radiolabeled [2-
14
C]acetate in batch incubations. When
Methanosaetaceae
were not present, acetate oxidation was the dominant methanogenic pathway. Aceticlastic conversion was observed only in the presence of
Methanosaetaceae
.
Generating Tetracycline-Inducible Auxotrophy in
Escherichia coli
and
Salmonella enterica
Serovar Typhimurium by Using an Insertion Element and a Hyperactive Transposase
Authors: Köstner Martin , Schmidt Britta , Bertram Ralph , Hillen Wolfgang 
Published: July 2006

ABSTRACT

We report the construction and application of a novel insertion element for transposase-mediated mutagenesis in gram-negative bacteria. Besides Km
r
as a selectable marker, the insertion element InsTet
G−
1 carries the anhydrotetracycline (atc)-regulated outward-directed P
A
promoter so that atc-dependent conditional gene knockouts or knockdowns are generated. The complex formed between the purified hyperactive transposase and InsTet
G−
1 was electroporated into
Escherichia coli
or
Salmonella enterica
serovar Typhimurium, and mutant pools were collected. We used
E. coli
strains with either TetR or the reverse variant revTetR
r2
, while only TetR was employed in
Salmonella
. Screening of the InsTet
G−
1 insertion mutant pools revealed 15 atc-regulatable auxotrophic mutants for
E. coli
and 4 atc-regulatable auxotrophic mutants for
Salmonella
. We have also screened one
Salmonella
mutant pool in murine macrophage-like J774-A.1 cells using ampicillin enrichment. Two mutants with the InsTet
G−
1 insertion in the gene
pyrE
or
argA
survived this procedure, indicating a reduced intracellular growth rate in J774-A.1 cells. The nature of the mutants and the modes of their regulation are discussed.
Stratified Communities of Active Archaea in Deep Marine Subsurface Sediments
Authors: Sørensen Ketil B. , Teske Andreas 
Published: July 2006

ABSTRACT

Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB
Archaea
are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.
Effectiveness of Enterobacterial Repetitive Intergenic Consensus PCR and Random Amplified Polymorphic DNA Fingerprinting for
Helicobacter pylori
Strain Differentiation
Authors: Finger S. Alison , Velapatiño Billie , Kosek Margaret , Santivañez Livia , Dailidiene Daiva , Quino Willi , Balqui Jacqueline , Herrera Phabiola , Berg Douglas E. , Gilman Robert H. 
Published: July 2006

ABSTRACT

We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed
Helicobacter pylori
infection in Peruvian shantytown residents.
H. pylori
isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one
H. pylori
strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for
H. pylori
strain differentiation.
Response of
Lactobacillus helveticus
PR4 to Heat Stress during Propagation in Cheese Whey with a Gradient of Decreasing Temperatures
Authors: Di Cagno Raffaella , De Angelis Maria , Limitone Antonio , Fox Patrick F. , Gobbetti Marco 
Published: July 2006

ABSTRACT

The heat stress response was studied in
Lactobacillus helveticus
PR4 during propagation in cheese whey with a gradient of naturally decreasing temperature (55 to 20°C). Growth under a gradient of decreasing temperature was compared to growth at a constant temperature of 42°C. Proteinase, peptidase, and acidification activities of
L. helveticus
PR4 were found to be higher in cells harvested when 40°C was reached by a gradient of decreasing temperature than in cells grown at constant temperature of 42°C. When cells grown under a temperature gradient were harvested after an initial exposure of 35 min to 55°C followed by decreases in temperature to 40 (3 h), 30 (5 h 30 min), or 20°C (13 h 30 min) and were then compared with cells grown for the same time at a constant temperature of 42°C, a frequently transient induction of the levels of expression of 48 proteins was found by two-dimensional electrophoresis analysis. Expression of most of these proteins increased following cooling from 55 to 40°C (3 h). Sixteen of these proteins were subjected to N-terminal and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses. They were identified as stress proteins (e.g., DnaK and GroEL), glycolysis-related machinery (e.g., enolase and glyceraldehyde-3-phosphate dehydrogenase), and other regulatory proteins or factors (e.g., DNA-binding protein II and ATP-dependent protease). Most of these proteins have been found to play a role in the mechanisms of heat stress adaptation in other bacteria.
Microsporidian Species Known To Infect Humans Are Present in Aquatic Birds: Implications for Transmission via Water?
Authors: Slodkowicz-Kowalska Anna , Graczyk Thaddeus K. , Tamang Leena , Jedrzejewski Szymon , Nowosad Andrzej , Zduniak Piotr , Solarczyk Piotr , Girouard Autumn S. , Majewska Anna C. 
Published: July 2006

ABSTRACT

Human microsporidiosis, a serious disease of immunocompetent and immunosuppressed people, can be due to zoonotic and environmental transmission of microsporidian spores. A survey utilizing conventional and molecular techniques for examining feces from 570 free-ranging, captive, and livestock birds demonstrated that 21 animals shed microsporidian spores of species known to infect humans, including
Encephalitozoon hellem
(20 birds; 3.5%) and
Encephalitozoon intestinalis
(1 bird; 0.2%). Of 11 avian species that shed
E. hellem
and
E. intestinalis
, 8 were aquatic birds (i.e., common waterfowl). The prevalence of microsporidian infections in waterfowl (8.6%) was significantly higher than the prevalence of microsporidian infections in other birds (1.1%) (
P
< 0.03); waterfowl fecal droppings contained significantly more spores (mean, 3.6 × 10
5
spores/g) than nonaquatic bird droppings contained (mean, 4.4 × 10
4
spores/g) (
P
< 0.003); and the presence of microsporidian spores of species known to infect humans in fecal samples was statistically associated with the aquatic status of the avian host (
P
< 0.001). We demonstrated that a single visit of a waterfowl flock can introduce into the surface water approximately 9.1 × 10
8
microsporidian spores of species known to infect humans. Our findings demonstrate that waterborne microsporidian spores of species that infect people can originate from common waterfowl, which usually occur in large numbers and have unlimited access to surface waters, including waters used for production of drinking water.
Flow Cytometric Testing of Green Fluorescent Protein-TaggedLactobacillus rhamnosusGG for Response to Defensins
Authors: De Keersmaecker Sigrid C. J. , Braeken Kristien , Verhoeven Tine L. A. , Perea Vélez Mónica , Lebeer Sarah , Vanderleyden Jos , Hols Pascal 
Published: July 2006

ABSTRACTLactobacillus rhamnosusGG is of general interest as a probiotic. AlthoughL. rhamnosusGG is often used in clinical trials, there are few genetic tools to further determine its mode of action or to develop it as a vehicle for heterologous gene expression in therapy. Therefore, we developed a reproducible, efficient electroporation procedure forL. rhamnosusGG. The best transformation efficiency obtained was 104transformants per μg of DNA. We validated this protocol by taggingL. rhamnosusGG with green fluorescent protein (GFP) using the nisin-controlled expression (NICE) system. Parameters for overexpression were optimized, which allowed expression ofgfpinL. rhamnosusGG upon induction with nisin. The GFP+strain can be used to monitor the survival and behavior ofL. rhamnosusGG in vivo. Moreover, implementation of the NICE system as a gene expression switch inL. rhamnosusGG opens up possibilities for improving and expanding the performance of this strain. The GFP-labeled strain was used to demonstrate thatL. rhamnosusGG is sensitive to human beta-defensin-2 but not to human beta-defensin-1.
Enhanced Survival of GroESL-Overproducing
Lactobacillus paracasei
NFBC 338 under Stressful Conditions Induced by Drying
Authors: Corcoran B. M. , Ross R. P. , Fitzgerald G. F. , Dockery P. , Stanton C. 
Published: July 2006

ABSTRACT

GroESL-overproducing
Lactobacillus paracasei
NFBC 338 was dried, and its viability was compared with that of controls. Spray- and freeze-dried cultures overproducing GroESL exhibited ∼10-fold and 2-fold better survival, respectively, demonstrating the importance of GroESL in stress tolerance, which can be exploited to enhance the technological performance of sensitive probiotic cultures.
Soft-Agar-Coated Filter Method for Early Detection of Viable and Thermostable Direct Hemolysin (TDH)- or TDH-Related Hemolysin-Producing
Vibrio parahaemolyticus
in Seafood
Authors: Hayashi Sachiko , Okura Masatoshi , Osawa Ro 
Published: July 2006

ABSTRACT

A novel method for detecting viable and thermostable direct hemolysin (TDH)-producing or TDH-related hemolysin (TRH)-producing
Vibrio parahaemolyticus
in seafood was developed. The method involved (i) enrichment culture, selective for viable, motile cells penetrating a soft-agar-coated filter paper, and (ii) a multiplex PCR assay targeting both the TDH gene (
tdh
) and TRH gene (
trh
) following DNase pretreatment on the test culture to eradicate any incidental DNAs that might have been released from dead cells of
tdh
- or
trh
-positive (
tdh
+
trh
+
) strains and penetrated the agar-coated filter. A set of preliminary laboratory tests performed on 190 ml of enrichment culture that had been inoculated simultaneously with ca. 100 viable cells of a strain of
tdh
+
trh
+
V. parahaemolyticus
and dense populations of a viable strain of
tdh-
and
trh-
negative
V. parahaemolyticus
or
Vibrio alginolyticus
indicated that the method detected the presence of viable
tdh
+
trh
+
strains. Another set of preliminary tests on 190 ml of enrichment culture that had been initially inoculated with a large number of dead cells of the
tdh
+
trh
+
strain together with dense populations of the
tdh-
and
trh-
negative strains confirmed that the method did not yield any false-positive results. Subsequent quasi-field tests using various seafood samples (ca. 20 g), each of which was experimentally contaminated with either or both hemolysin-producing strains at an initial density of ca. 5 to 10 viable cells per gram, demonstrated that contamination could be detected within 2 working days.
Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification
Authors: Wu Liyou , Liu Xueduan , Schadt Christopher W. , Zhou Jizhong 
Published: July 2006

ABSTRACT

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (
r
2
= 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (
r
2
= 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (
r
2
= 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.