bluuebunny/crossref_metadata_2025_split huggingface dataset:
Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments
Authors: Mincer Tracy J. , Jensen Paul R. , Kauffman Christopher A. , Fenical William 
Published: September 2002

ABSTRACT

A major taxon of obligate marine bacteria within the order
Actinomycetales
has been discovered from ocean sediments. Populations of these bacteria (designated MAR 1) are persistent and widespread, spanning at least three distinct ocean systems. In this study, 212 actinomycete isolates possessing MAR 1 morphologies were examined and all but two displayed an obligate requirement of seawater for growth. Forty-five of these isolates, representing all observed seawater-requiring morphotypes, were partially sequenced and found to share characteristic small-subunit rRNA signature nucleotides between positions 207 and 468 (
Escherichia coli
numbering). Phylogenetic characterization of seven representative isolates based on almost complete sequences of genes encoding 16S rRNA (16S ribosomal DNA) yielded a monophyletic clade within the family
Micromonosporaceae
and suggests novelty at the genus level. This is the first evidence for the existence of widespread populations of obligate marine actinomycetes. Organic extracts from cultured members of this new group exhibit remarkable biological activity, suggesting that they represent a prolific resource for biotechnological applications.
Differential Inhibition of Mollicute Growth: an Approach to Development of Selective Media for Specific Mollicutes
Authors: Keçeli S. A. , Miles R. J. 
Published: September 2002

ABSTRACT

The energy-generating pathways of
Mycoplasma
spp. are diverse. Thus, it was predicted that the ability of inhibitors of these pathways to block growth would vary among species. This prediction was tested with 14
Mycoplasma
species and potential inhibitors. The greatest differentiation among test species was obtained using fluoride, iodoacetate (IAA), β-fluoropyruvate (FP), cibacron blue (CB),
l
-citrulline, and carbonyl cyanide
m
-chlorophenylhydrazone. A range of other potential inhibitors, including
l
-arginine analogues, had little inhibitory effect on growth, and
d
-arginine was shown to be a growth substrate for arginine-hydrolyzing species. Fluoride selectively inhibited the growth of mycoplasmas that were able only to ferment sugars to lactate and/or to hydrolyze arginine. In contrast, IAA was most effective against organic acid-oxidizing species, and
l
-citrulline inhibited arginine-hydrolyzing species.
Mycoplasma verecundum
, a species for which energy sources have not been identified, was relatively resistant to FP. Similarly,
Acholeplasma laidlawii
was distinguished by its CB resistance.
Novel Cyanobacterial Biosensor for Detection of Herbicides
Authors: Shao C. Y. , Howe C. J. , Porter A. J. R. , Glover L. A. 
Published: September 2002

ABSTRACTThe aim of this work was to generate a cyanobacterial biosensor that could be used to detect herbicides and other environmental pollutants. A representative freshwater cyanobacterium,Synechocystissp. strain PCC6803, was chromosomally marked with the luciferase geneluc(from the fireflyPhotinus pyralis) to create a novel bioluminescent cyanobacterial strain. Successful expression of thelucgene during growth ofSynechocystissp. strain PCC6803 cultures was characterized by measuring optical density and bioluminescence. Bioluminescence was optimized with regard to uptake of the luciferase substrate, luciferin, and the physiology of the cyanobacterium. Bioassays demonstrated that a novel luminescent cyanobacterial biosensor has been developed which responded to a range of compounds including different herbicide types and other toxins. This biosensor is expected to provide new opportunities for the rapid screening of environmental samples or for the investigation of potential environmental damage.
Improvement of Recombinant Protein Yield by a Combination of Transcriptional Amplification and Stabilization of Gene Expression
Authors: Cebolla A. , Royo J. L. , de Lorenzo V. , Santero E. 
Published: September 2002

ABSTRACT

We explored the use of a cascade circuit for heterologous gene expression that consists of a regulatory module with a salicylate-inducible system that controls the expression of a second regulator,
xylS2
, whose product is activated by common inducers. Activation and increasing the concentration of the second regulator synergistically induced heterologous genes downstream of the
Pm
promoter in the expression module. This module can be placed in multicopy vectors or in the chromosome of a host strain by means of minitransposons. Using reporter genes, we evaluated gene regulation capacity and gross production of the system with different configurations. The highest yield was obtained when the expression module was in a multicopy plasmid after a 6-h induction. However, expression modules in plasmids showed low stability after induction even with selective pressure. The chromosomal configuration had the lowest basal levels and induced levels comparable to those of plasmid configurations, resulting in accumulation of more than 10% of the total protein. Unlike the configurations in plasmids, the yield was maintained for at least 3 days even without selective pressure. In conclusion, the cascade system in the chromosome configuration is more efficient for long-term fermentation because of the great stability of the overexpressing phenotype in spite of the high levels of expression.
Molecular Analysis of a Bacterial Chitinolytic Community in an Upland Pasture
Authors: Metcalfe A. C. , Krsek M. , Gooday G. W. , Prosser J. I. , Wellington E. M. H. 
Published: September 2002

ABSTRACT
The effects of agricultural-improvement treatments on the chitinolytic activity and diversity of a microbial community were investigated within an upland pasture. The treatments of interest were lime and treated sewage sludge, both commonly applied to pasture land to improve fertility. Burial of chitin-containing litter bags at the field site resulted in enrichment of bacteria according to 16S rRNA fingerprinting. Chitinolytic-activity measurements showed that the highest activity occurred in those bags recovered from sludge-amended plots, which correlated well with increased counts of actinobacteria in samples from these chitin bags. Our findings suggest that sewage sludge increases the fertility of the soil in terms of chitinase activity. Ten clone libraries were constructed from family 18 subgroup A chitinases, PCR amplified from litter bags buried in soil in July 2000 or in September 2000, in a separate study. Analysis of these libraries by restriction fragment length polymorphism and sequencing showed that they were dominated by actinobacterium-like chitinase sequences. This suggests that actinobacteria have an important chitinolytic function in this soil ecosystem. Our findings showed that sludge application increased chitinolytic activity but decreased the diversity of chitinases present.
A Plasmid Selection System in
Lactococcus lactis
and Its Use for Gene Expression in
L. lactis
and Human Kidney Fibroblasts
Authors: Glenting Jacob , Madsen Søren M. , Vrang Astrid , Fomsgaard Anders , Israelsen Hans 
Published: September 2002

ABSTRACT

We report the development of a nonantibiotic and nonpathogenic host-plasmid selection system based on lactococcal genes and threonine complementation. We constructed an auxotrophic
Lactococcus lactis
MG1363Δthr strain which carries deletions in two genes encoding threonine biosynthetic enzymes. To achieve plasmid-borne complementation, we then constructed the minimal cloning vector, pJAG5, based on the genes encoding homoserine dehydrogenase-homoserine kinase (the
hom
-
thrB
operon) as a selective marker. Using strain MG1363Δthr, selection and maintenance of cells carrying pJAG5 were obtained in threonine-free defined media. Compared to the commonly used selection system based on erythromycin resistance, the designed complementation system offers a competitive and stable plasmid selection system for the production of heterologous proteins in
L. lactis
. The potential of pJAG5 to deliver genes for expression in eukaryotes was evaluated by insertion of a mammalian expression unit encoding a modified green fluorescent protein. The successful delivery and expression of genes in human kidney fibroblasts indicated the potential of the designed nonantibiotic host-plasmid system for use in genetic immunization.
Rapid and Sensitive Enumeration of Viable Diluted Cells of Members of the Family
Enterobacteriaceae
in Freshwater and Drinking Water
Authors: Baudart Julia , Coallier Josée , Laurent Patrick , Prévost Michèle 
Published: September 2002

ABSTRACT

Water quality assessment involves the specific, sensitive, and rapid detection of bacterial indicators and pathogens in water samples, including viable but nonculturable (VBNC) cells. This work evaluates the specificity and sensitivity of a new method which combines a fluorescent in situ hybridization (FISH) approach with a physiological assay (direct viable count [DVC]) for the direct enumeration, at the single-cell level, of highly diluted viable cells of members of the family
Enterobacteriaceae
in freshwater and drinking water after membrane filtration. The approach (DVC-FISH) uses a new direct detection device, the laser scanning cytometer (Scan RDI). Combining the DVC-FISH method on a membrane with Scan RDI detection makes it possible to detect as few as one targeted cell in approximately 10
8
nontargeted cells spread over the membrane. The ability of this new approach to detect and enumerate VBNC enterobacterial cells in freshwater and drinking water distribution systems was investigated and is discussed.
Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment
Authors: Loy Alexander , Lehner Angelika , Lee Natuschka , Adamczyk Justyna , Meier Harald , Ernst Jens , Schleifer Karl-Heinz , Wagner Michael 
Published: September 2002

ABSTRACT

For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of
Desulfomicrobium
spp. in the tooth pockets and the presence of
Desulfonema
- and
Desulfomonile
-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (
dsrAB
).
Complete Sequence and Organization of pBtoxis, the Toxin-Coding Plasmid ofBacillus thuringiensissubsp.israelensis
Authors: Berry Colin , O'Neil Susan , Ben-Dov Eitan , Jones Andrew F. , Murphy Lee , Quail Michael A. , Holden Mathew T. G. , Harris David , Zaritsky Arieh , Parkhill Julian 
Published: September 2002

ABSTRACTThe entire 127,923-bp sequence of the toxin-encoding plasmid pBtoxis fromBacillus thuringiensissubsp.israelensisis presented and analyzed. In addition to the four known Cry and two known Cyt toxins, a third Cyt-type sequence was found with an additional C-terminal domain previously unseen in such proteins. Many plasmid-encoded genes could be involved in several functions other than toxin production. The most striking of these are several genes potentially affecting host sporulation and germination and a set of genes for the production and export of a peptide antibiotic.
Variability in
Pseudomonas aeruginosa
Lipopolysaccharide Expression during Crude Oil Degradation
Authors: Norman R. Sean , Frontera-Suau Roberto , Morris Pamela J. 
Published: September 2002

ABSTRACT

Bacterial utilization of crude oil components, such as the
n
-alkanes, requires complex cell surface adaptation to allow adherence to oil. To better understand microbial cell surface adaptation to growth on crude oil, the cell surface characteristics of two
Pseudomonas aeruginosa
strains, U1 and U3, both isolated from the same crude oil-degrading microbial community enriched on Bonny Light crude oil (BLC), were compared. Analysis of growth rates demonstrated an increased lag time for U1 cells compared to U3 cells. Amendment with EDTA inhibited U1 and U3 growth and degradation of the
n
-alkane component of BLC, suggesting a link between cell surface structure and crude oil degradation. U1 cells demonstrated a smooth-to-rough colony morphology transition when grown on BLC, while U3 cells exhibited rough colony morphology at the outset. Combining high-resolution atomic force microscopy of the cell surface and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of extracted lipopolysaccharides (LPS), we demonstrate that isolates grown on BLC have reduced O-antigen expression compared with that of glucose-grown cells. The loss of O-antigen resulted in shorter LPS molecules, increased cell surface hydrophobicity, and increased
n
-alkane degradation.
Roles ofVibrio fischeriand Nonsymbiotic Bacteria in the Dynamics of Mucus Secretion during Symbiont Colonization of theEuprymna scolopesLight Organ
Authors: Nyholm Spencer V. , Deplancke Bart , Gaskins H. Rex , Apicella Michael A. , McFall-Ngai Margaret J. 
Published: September 2002

ABSTRACTDuring light organ colonization of the squidEuprymna scolopesbyVibrio fischeri,host-derived mucus provides a surface upon which environmentalV. fischeriforms a biofilm and aggregates prior to colonization. In this study we defined the temporal and spatial characteristics of this process. Although permanent colonization is specific to certain strains ofV. fischeri, confocal microscopy analyses revealed that light organ crypt spaces took up nonspecific bacteria and particles that were less than 2 μm in diameter during the first hour after hatching. However, within 2 h after inoculation, these cells or particles were not detectable, and further entry by nonspecific bacteria or particles appeared to be blocked. Exposure to environmental gram-negative or -positive bacteria or bacterial peptidoglycan caused the cells of the organ's superficial ciliated epithelium to release dense mucin stores at 1 to 2 h after hatching that were used to form the substrate upon whichV. fischeriformed a biofilm and aggregated. Whereas the uncolonized organ surface continued to shed mucus, within 48 h of symbiont colonization mucus shedding ceased and the formation of bacterial aggregations was no longer observed. Eliminating the symbiont from the crypts with antibiotics restored the ability of the ciliated fields to secrete mucus and aggregate bacteria. While colonization byV. fischeriinhibited mucus secretion by the surface epithelium, secretion of host-derived mucus was induced in the crypt spaces. Together, these data indicate that although initiation of mucus secretion from the superficial epithelium is nonspecific, the inhibition of mucus secretion in these cells and the concomitant induction of secretion in the crypt cells are specific to natural colonization byV. fischeri.
Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park
Authors: Blank Carrine E. , Cady Sherry L. , Pace Norman R. 
Published: September 2002

ABSTRACT

The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that
Thermocrinis ruber
, a member of the order
Aquificales
, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in
Thermocrinis ruber
SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of
Thermocrinis ruber
in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.
Direct and Efficient Production of Ethanol from Cellulosic Material with a Yeast Strain Displaying Cellulolytic Enzymes
Authors: Fujita Yasuya , Takahashi Shouji , Ueda Mitsuyoshi , Tanaka Atsuo , Okada Hirofumi , Morikawa Yasushi , Kawaguchi Takashi , Arai Motoo , Fukuda Hideki , Kondo Akihiko 
Published: September 2002

ABSTRACT

For direct and efficient ethanol production from cellulosic materials, we constructed a novel cellulose-degrading yeast strain by genetically codisplaying two cellulolytic enzymes on the cell surface of
Saccharomyces cerevisiae
. By using a cell surface engineering system based on α-agglutinin, endoglucanase II (EGII) from the filamentous fungus
Trichoderma reesei
QM9414 was displayed on the cell surface as a fusion protein containing an RGSHis6 (Arg-Gly-Ser-His
6
) peptide tag in the N-terminal region. EGII activity was detected in the cell pellet fraction but not in the culture supernatant. Localization of the RGSHis6-EGII-α-agglutinin fusion protein on the cell surface was confirmed by immunofluorescence microscopy. The yeast strain displaying EGII showed significantly elevated hydrolytic activity toward barley β-glucan, a linear polysaccharide composed of an average of 1,200 glucose residues. In a further step, EGII and β-glucosidase 1 from
Aspergillus aculeatus
No. F-50 were codisplayed on the cell surface. The resulting yeast cells could grow in synthetic medium containing β-glucan as the sole carbon source and could directly ferment 45 g of β-glucan per liter to produce 16.5 g of ethanol per liter within about 50 h. The yield in terms of grams of ethanol produced per gram of carbohydrate utilized was 0.48 g/g, which corresponds to 93.3% of the theoretical yield. This result indicates that efficient simultaneous saccharification and fermentation of cellulose to ethanol are carried out by a recombinant yeast cells displaying cellulolytic enzymes.
Succession of Bacterial Community Structure along the Changjiang River Determined by Denaturing Gradient Gel Electrophoresis and Clone Library Analysis
Authors: Sekiguchi Hiroyuki , Watanabe Masataka , Nakahara Tadaatsu , Xu Baohua , Uchiyama Hiroo 
Published: September 2002

ABSTRACT

Bacterial community structure along the Changjiang River (which is more than 2,500 km long) was studied by using denaturing gradient gel electrophoresis (DGGE) and clone library analysis of PCR-amplified 16S ribosomal DNA (rDNA) with universal bacterial primer sets. DGGE profiles and principal-component analysis (PCA) demonstrated that the bacterial community gradually changed from upstream to downstream in both 1998 and 1999. Bacterial diversity, as determined by the Shannon index (
H
′), gradually decreased from upstream to downstream. The PCA plots revealed that the differences in the bacterial communities among riverine stations were not appreciable compared with the differences in two adjacent lakes, Lake Dongting and Lake Poyang. The relative stability of the bacterial communities at the riverine stations was probably due to the buffering action of the large amount of water flowing down the river. Clone library analysis of 16S rDNA revealed that the dominant bacterial groups changed from β-proteobacteria and the
Cytophaga-Flexibacter-Bacteroides
group upstream to high-G+C-content gram-positive bacteria downstream and also that the bacterial community structure differed among the stations in the river and the lakes. The results obtained in this study should provide a reference for future changes caused by construction of the Three Gorges Dam.
Double-Staining Method for Differentiation of Morphological Changes and Membrane Integrity of
Campylobacter coli
Cells
Authors: Alonso Jose L. , Mascellaro Salvatore , Moreno Yolanda , Ferrús María A. , Hernández Javier 
Published: September 2002

ABSTRACT

We developed a double-staining procedure involving NanoOrange dye (Molecular Probes, Eugene, Oreg.) and membrane integrity stains (LIVE/DEAD
Bac
Light kit; Molecular Probes) to show the morphological and membrane integrity changes of
Campylobacter coli
cells during growth. The conversion from a spiral to a coccoid morphology via intermediary forms and the membrane integrity changes of the
C. coli
cells can be detected with the double-staining procedure. Our data indicate that young or actively growing cells are mainly spiral shaped (green-stained cells), but older cells undergo a degenerative change to coccoid forms (red-stained cells). Club-shaped transition cell forms were observed with NanoOrange stain. Chlorinated drinking water affected the viability but not the morphology of
C. coli
cells.
In Vitro Adhesion Specificity of Indigenous Lactobacilli within the Avian Intestinal Tract
Authors: Edelman Sanna , Westerlund-Wikström Benita , Leskelä Susanna , Kettunen Hannele , Rautonen Nina , Apajalahti Juha , Korhonen Timo K. 
Published: September 2002

ABSTRACT

In vitro adherence of
Lactobacillus
strains to cell and tissue types along the chicken alimentary tract and to ileal mucus were determined. Fresh isolates from chickens adhered to the epithelium of crop and, in a strain-dependent manner, to follicle-associated epithelium and the apical surfaces of mature enterocytes of intestinal villi. No adherence to the apical surfaces of undifferentiated enterocytes, the mucus-producing goblet cells, or the ileal mucus was detected.
Detection of
Helicobacter
Colonization of the Murine Lower Bowel by Genus-Specific PCR-Denaturing Gradient Gel Electrophoresis
Authors: Grehan Martin , Tamotia Gauri , Robertson Bronwyn , Mitchell Hazel 
Published: September 2002

ABSTRACT

Helicobacter
genus-specific PCR and denaturing gradient gel electrophoresis can detect and speciate the helicobacters that colonize the lower bowel of laboratory mice. The method's sensitivity is comparable to that of species-specific PCR and may detect unnamed
Helicobacter
species. This approach should prove useful for commercial and research murine facilities.