bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antagonistic Interactions among Marine Bacteria Impede the Proliferation of
Vibrio cholerae
Authors: Long Richard A. , Rowley David C. , Zamora Eric , Liu Jiayuan , Bartlett Douglas H. , Azam Farooq 
Published: December 2005

ABSTRACT

Changes in global climate have raised concerns about the emergence and resurgence of infectious diseases.
Vibrio cholerae
is a reemerging pathogen that proliferates and is transported on marine particles. Patterns of cholera outbreaks correlate with sea surface temperature increases, but the underlying mechanisms for rapid proliferation of
V. cholerae
during ocean warming events have yet to be fully elucidated. In this study, we tested the hypothesis that autochthonous marine bacteria impede the spread of
V. cholerae
in the marine environment. It was found that some marine bacteria are capable of inhibiting the growth of
V. cholerae
on surfaces and that bacterial isolates derived from pelagic particles show a greater frequency of
V. cholerae
inhibition than free-living bacteria.
Vibrio cholerae
was less susceptible to antagonism at higher temperatures, such as those measured during El Niño-Southern Oscilliation and monsoonal events. Using a model system employing green fluorescent protein-labeled bacteria, we found that marine bacteria can directly inhibit
V. cholerae
colonization of particles. The mechanism of inhibition in our model system was linked to the biosynthesis of andrimid, an antibacterial agent. Antibiotic production by the model antagonistic strain decreased at higher temperatures, thereby explaining the increased competitiveness of
V. cholerae
under warmer conditions. These findings suggest that bacterium-bacterium antagonism is a contributing mechanism in regulating the proliferation of
V. cholerae
on marine particles.
Two Novel Bacterial Biosensors for Detection of Nitrate Availability in the Rhizosphere
Authors: DeAngelis Kristen M. , Ji Pingsheng , Firestone Mary K. , Lindow Steven E. 
Published: December 2005

ABSTRACT

The nitrate-regulated promoter of
narG
in
Escherichia coli
was fused to promoterless ice nucleation (
inaZ
) and green fluorescent protein (GFP) reporter genes to yield the nitrate-responsive gene fusions in plasmids pNice and pNgfp, respectively. While the promoter of
narG
is normally nitrate responsive only under anaerobic conditions, the L28H-
fnr
gene was provided in
trans
to enable nitrate-dependent expression of these reporter gene fusions even under aerobic conditions in both
E. coli
DH5α and
Enterobacter cloacae
EcCT501R.
E. cloacae
and
E. coli
cells containing the fusion plasmid pNice exhibited more than 100-fold-higher ice nucleation activity in cultures amended with 10 mM sodium nitrate than in nitrate-free media. The GFP fluorescence of
E. cloacae
cells harboring pNgfp was uniform at a given concentration of nitrate and increased about 1,000-fold when nitrate increased from 0 to 1 mM. Measurable induction of ice nucleation in
E. cloacae
EcCT501R harboring pNice occurred at nitrate concentrations of as low as 0.1 μM, while GFP fluorescence was detected in cells harboring pNgfp at about 10 μM. In the rhizosphere of wild oat (
Avena fatua
), the whole-cell bioreporter
E
.
cloacae
(pNgfp) or
E. cloacae
(pNice) expressed significantly higher GFP fluorescence or ice nucleation activity when the plants were grown in natural soils amended with nitrate than in unamended natural soils. Significantly lower nitrate abundance was detected by the
E. cloacae
(pNgfp) reporter in the
A. fatua
rhizosphere compared to in bulk soil, indicating plant competition for nitrate. Ice- and GFP-based bacterial sensors thus are useful for estimating nitrate availability in relevant microbial niches in natural environments.
Cell Surface Display of Lipase in
Pseudomonas putida
KT2442 Using OprF as an Anchoring Motif and Its Biocatalytic Applications
Authors: Lee Seung Hwan , Lee Sang Yup , Park Byoung Chul 
Published: December 2005

ABSTRACT

We developed a new cell surface display system in
Pseudomonas putida
KT2442 using OprF, an outer membrane protein of
Pseudomonas aeruginosa
, as an anchoring motif in a C-terminal deletion-fusion strategy. The
Pseudomonas fluorescens
SIK W1 lipase gene was fused to two different C-terminal truncated OprF genes, and the fusion genes were cloned into the broad-host-range plasmid pBBR1MCS2 to make pMO164PL and pMO188PL. Plasmid pMO188PL allowed better display of lipase and thus was chosen for further study. The display of lipase on the surface of
P. putida
KT2442 was confirmed by Western blot analysis, immunofluorescence microscopy, and measurement of whole-cell lipase activity. The whole-cell lipase activity of recombinant
P. putida
KT2442 harboring pMO188PL was more than fivefold higher than that of recombinant
Escherichia coli
displaying lipase in the same manner. Cell surface-displayed lipase exhibited the highest activity at 47°C and pH 9.0, and the whole-cell lipase activity was greater than 90% of the initial activity in organic solvents at 47°C for 1 week. In a biocatalytic application, enantioselective resolution of 1-phenyl ethanol was carried out in an organic solvent. (
R
)-Phenyl ethyl acetate was successfully produced with 41.9% conversion and an enantiomeric excess of more than 99% in a 36-h reaction. These results suggest that the OprF anchor can be used for efficient display of proteins in
P. putida
KT2442 and consequently for various biocatalytic applications.
Identification of Bacteria in Biofilm and Bulk Water Samples from a Nonchlorinated Model Drinking Water Distribution System: Detection of a Large Nitrite-Oxidizing Population Associated with
Nitrospira
spp
Authors: Martiny Adam C. , Albrechtsen Hans-Jørgen , Arvin Erik , Molin Søren 
Published: December 2005

ABSTRACT

In a model drinking water distribution system characterized by a low assimilable organic carbon content (<10 μg/liter) and no disinfection, the bacterial community was identified by a phylogenetic analysis of rRNA genes amplified from directly extracted DNA and colonies formed on R2A plates. Biofilms of defined periods of age (14 days to 3 years) and bulk water samples were investigated. Culturable bacteria were associated with
Proteobacteria
and
Bacteriodetes
, whereas independently of cultivation, bacteria from 12 phyla were detected in this system. These included
Acidobacteria
,
Nitrospirae
,
Planctomycetes
, and
Verrucomicrobia
, some of which have never been identified in drinking water previously. A cluster analysis of the population profiles from the individual samples divided biofilms and bulk water samples into separate clusters (
P
= 0.027). Bacteria associated with
Nitrospira moscoviensis
were found in all samples and encompassed 39% of the sequenced clones in the bulk water and 25% of the biofilm community. The close association with
Nitrospira
suggested that a large part of the population had an autotrophic metabolism using nitrite as an electron donor. To test this hypothesis, nitrite was added to biofilm and bulk water samples, and the utilization was monitored during 15 days. A first-order decrease in nitrite concentration was observed for all samples with a rate corresponding to 0.5 × 10
5
to 2 × 10
5
nitrifying cells/ml in the bulk water and 3 × 10
5
cells/cm
2
on the pipe surface. The finding of an abundant nitrite-oxidizing microbial population suggests that nitrite is an important substrate in this system, potentially as a result of the low assimilable organic carbon concentration. This finding implies that microbial communities in water distribution systems may control against elevated nitrite concentrations but also contain large indigenous populations that are capable of assisting the depletion of disinfection agents like chloramines.
Nickel and Cobalt Resistance Engineered inEscherichia coliby Overexpression of Serine Acetyltransferase from the Nickel Hyperaccumulator PlantThlaspi goesingense
Authors: Freeman John L. , Persans Michael W. , Nieman Ken , Salt David E. 
Published: December 2005

ABSTRACTThe overexpression of serine acetyltransferase from the Ni-hyperaccumulating plantThlaspi goesingensecauses enhanced nickel and cobalt resistance inEscherichia coli.Furthermore, overexpression ofT. goesingenseserine acetyltransferase results in enhanced sensitivity to cadmium and has no significant effect on resistance to zinc. Enhanced nickel resistance is directly related to the constitutive overactivation of sulfur assimilation and glutathione biosynthesis, driven by the overproduction ofO-acetyl-l-serine, the product of serine acetyltransferase and a positive regulator of the cysteine regulon. Nickel in the serine acetyltransferase-overexpressing strains is not detoxified by coordination or precipitation with sulfur, suggesting that glutathione is involved in reducing the oxidative damage imposed by nickel.
Outer Membranec-Type Cytochromes Required for Fe(III) and Mn(IV) Oxide Reduction inGeobacter sulfurreducens
Authors: Mehta T. , Coppi M. V. , Childers S. E. , Lovley D. R. 
Published: December 2005

ABSTRACTThe potential role of outer membrane proteins in electron transfer to insoluble Fe(III) oxides byGeobacter sulfurreducenswas investigated because this organism is closely related to the Fe(III) oxide-reducing organisms that are predominant in many Fe(III)-reducing environments. Two of the most abundant proteins that were easily sheared from the outer surfaces of intact cells werec-type cytochromes. One, designated OmcS, has a molecular mass of ca. 50 kDa and is predicted to be an outer membrane hexahemec-type cytochrome. Transcripts foromcScould be detected during growth on Fe(III) oxide, but not on soluble Fe(III) citrate. TheomcSmRNA consisted primarily of a monocistronic transcript, and to a lesser extent, a longer transcript that also contained the downstream geneomcT, which is predicted to encode a second hexaheme outer membrane cytochrome with 62.6% amino acid sequence identity to OmcS. The other abundantc-type cytochrome sheared from the outer surface ofG. sulfurreducens, designated OmcE, has a molecular mass of ca. 30 kDa and is predicted to be an outer membrane tetrahemec-type cytochrome. When eitheromcSoromcEwas deleted,G. sulfurreducenscould no longer reduce Fe(III) oxide but could still reduce soluble electron acceptors, including Fe(III) citrate. The mutants could reduce Fe(III) in Fe(III) oxide medium only if the Fe(III) chelator, nitrilotriacetic acid, or the electron shuttle, anthraquinone 2,6-disulfonate, was added. ExpressingomcSoromcEintransrestored the capacity for Fe(III) oxide reduction. OmcT was not detected among the sheared proteins, and genetic studies indicated thatG. sulfurreducenscould not reduce Fe(III) oxide whenomcTwas expressed but OmcS was absent. In contrast, Fe(III) oxide was reduced whenomcSwas expressed in the absence of OmcT. These results suggest that OmcS and OmcE are involved in electron transfer to Fe(III) oxides inG. sulfurreducens. They also emphasize the importance of evaluating mechanisms for Fe(III) reduction with environmentally relevant Fe(III) oxide, rather than the more commonly utilized Fe(III) citrate, because additional electron transfer components are required for Fe(III) oxide reduction that are not required for Fe(III) citrate reduction.
Effect ofl-Proline on Sake Brewing and Ethanol Stress inSaccharomyces cerevisiae
Authors: Takagi Hiroshi , Takaoka Miki , Kawaguchi Akari , Kubo Yoshito 
Published: December 2005

ABSTRACTDuring the fermentation of sake, cells ofSaccharomyces cerevisiaeare exposed to high concentrations of ethanol, thereby damaging the cell membrane and functional proteins.l-Proline protects yeast cells from damage caused by freezing or oxidative stress. In this study, we evaluated the role of intracellularl-proline in cells ofS. cerevisiaegrown under ethanol stress. Anl-proline-accumulating laboratory strain carries a mutant allele ofPRO1,pro1D154N, which encodes the Asp154Asn mutant γ-glutamyl kinase. This mutation increases the activity of γ-glutamyl kinase and γ-glutamyl phosphate reductase, which catalyze the first two steps ofl-proline synthesis and which together may form a complex in vivo. When cultured in liquid medium in the presence of 9% and 18% ethanol under static conditions, the cell viability of thel-proline-accumulating laboratory strain is greater than the cell viability of the parent strain. This result suggests that intracellular accumulation ofl-proline may confer tolerance to ethanol stress. We constructed a novel sake yeast strain by disrupting thePUT1gene, which is required forl-proline utilization, and replacing the wild-typePRO1allele with thepro1D154Nallele. The resultant strain accumulatedl-proline and was more tolerant to ethanol stress than was the control strain. We used the strain that could accumulatel-proline to brew sake containing five times morel-proline than what is found in sake brewed with the control strain, without affecting the fermentation profiles.
Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription, Integration, Distribution, and Phylogenetic Analysis
Authors: Ventura Marco , Lee Ju-Hoon , Canchaya Carlos , Zink Ralf , Leahy S. , Moreno-Munoz J. A. , O'Connell-Motherway M. , Higgins D. , Fitzgerald Gerald F. , O'Sullivan Daniel J. , van Sinderen Douwe 
Published: December 2005

ABSTRACT

So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus
Bifidobacterium
. In this report we analyzed three prophage-like elements that are present in the genomes of
Bifidobacterium breve
UCC 2003,
Bifidobacterium longum
NCC 2705, and
Bifidobacterium longum
DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria. All three prophage-like elements are integrated in a tRNA
Met
gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that the
attB
sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when a
B. longum
DJO10A culture was exposed to mitomycin C or hydrogen peroxide. The Bbr-1 prophage-like element appears to consist of a noninducible 28.5-kb chimeric DNA fragment composed of a composite mobile element inserted into prophage-like sequences, which do not appear to be widely distributed among
B. breve
strains. Northern blot analysis of the Bbr-1 prophage-like element showed that large parts of its genome are transcriptionally silent. Interestingly, a gene predicted to encode an extracellular beta-glucosidase carried within the Bbr-1 prophage-like element was shown to be transcribed.
Allelic Variation of Polymorphic Locus
lytB
, Encoding a Choline-Binding Protein, from Streptococci of the Mitis Group
Authors: Moscoso Miriam , Obregón Virginia , López Rubens , García José L. , García Ernesto 
Published: December 2005

ABSTRACT

The choline-binding protein LytB, an
N
-acetylglucosaminidase of
Streptococcus pneumoniae
, is the key enzyme for daughter cell separation and is believed to play a critical pathogenic role, facilitating bacterial spreading during infection. Because of these peculiarities LytB is a putative vaccine target. To determine the extent of LytB polymorphism, the
lytB
alleles from seven typical, clinical pneumococcal isolates of various serotypes and from 13 additional streptococci of the mitis group (12 atypical pneumococci and the
Streptococcus mitis
type strain) were sequenced. Sequence alignment showed that the main differences among alleles were differences in the number of repeats (range, 12 to 18) characteristic of choline-binding proteins. These differences were located in the region corresponding to repeats 11 to 17. Typical pneumococcal strains contained either 14, 16, or 18 repeats, whereas all of the atypical isolates except strains 1283 and 782 (which had 14 and 16 repeats, respectively) and the
S. mitis
type strain had only 12 repeats; atypical isolate 10546 turned out to be a Δ
lytB
mutant. We also found that there are two major types of alternating repeats in
lytB
, which encode 21 and 23 amino acids. Choline-binding proteins are linked to the choline-containing cell wall substrate through choline residues at the interface of two consecutive choline-binding repeats that create a choline-binding site. The observation that all strains contained an even number of repeats suggests that the duplication events that gave rise to the choline-binding repeats of LytB involved two repeats simultaneously, an observation that is in keeping with previous crystallographic data. Typical pneumococcal isolates usually grew as diplococci, indicating that an active LytB enzyme was present. In contrast, most atypical isolates formed long chains of cells that did not disperse after addition of purified LytB, suggesting that in these strains chains were produced through mechanisms unrelated to LytB.
Identification and Localization of Extraradicular Biofilm-Forming Bacteria Associated with Refractory Endodontic Pathogens
Authors: Noguchi Nobuo , Noiri Yuichiro , Narimatsu Masahiro , Ebisu Shigeyuki 
Published: December 2005

ABSTRACT

Bacterial biofilms have been found to develop on root surfaces outside the apical foramen and be associated with refractory periapical periodontitis. However, it is unknown which bacterial species form extraradicular biofilms. The present study aimed to investigate the identity and localization of bacteria in human extraradicular biofilms. Twenty extraradicular biofilms, used to identify bacteria using a PCR-based 16S rRNA gene assay, and seven root-tips, used to observe immunohistochemical localization of three selected bacterial species, were taken from 27 patients with refractory periapical periodontitis. Bacterial DNA was detected from 14 of the 20 samples, and 113 bacterial species were isolated.
Fusobacterium nucleatum
(14 of 14),
Porphyromonas gingivalis
(12 of 14), and
Tannellera forsythensis
(8 of 14) were frequently detected. Unidentified and uncultured bacterial DNA was also detected in 11 of the 14 samples in which DNA was detected. In the biofilms,
P. gingivalis
was immunohistochemically detected in all parts of the extraradicular biofilms. Positive reactions to anti-
F. nucleatum
and anti-
T. forsythensis
sera were found at specific portions of the biofilm. These findings suggested that
P. gingivalis
,
T. forsythensis
, and
F. nucleatum
were associated with extraradicular biofilm formation and refractory periapical periodontitis.
Culture-Independent Characterization of the Microbiota of the Ant LionMyrmeleon mobilis(Neuroptera: Myrmeleontidae)
Authors: Dunn Anne K. , Stabb Eric V. 
Published: December 2005

ABSTRACTAnt lions are insect larvae that feed on the liquefied internal components of insect prey. Prey capture is assisted by the injection of toxins that are reportedly derived from both the insect and bacterial symbionts. These larvae display interesting gut physiology where the midgut is not connected to the hindgut, preventing elimination of solid waste until adulthood. The presence of a discontinuous gut and the potential involvement of bacteria in prey paralyzation suggest an interesting microbial role in ant lion biology; however, the ant lion microbiota has not been described in detail. We therefore performed culture-independent 16S rRNA gene sequence analysis of the bacteria associated with tissues of an ant lion,Myrmeleon mobilis. All 222 sequences were identified asProteobacteriaand could be subdivided into two main groups, the α-Proteobacteriawith similarity toWolbachiaspp. (75 clones) and the γ-Proteobacteriawith similarity to the familyEnterobacteriaceae(144 clones). TheEnterobacteriaceae-like 16S rRNA gene sequences were most commonly isolated from gut tissue, andWolbachia-like sequences were predominant in the head and body tissue. Fluorescence in situ hybridization analyses supported the localization of enterics to gut tissue andWolbachiato nongut tissue. The diversity of sequences isolated from freshly caught, laboratory-fed, and laboratory-starved ant lions were qualitatively similar, although the libraries from each treatment were significantly different (P= 0.05). These results represent the first culture-independent analysis of the microbiota associated with a discontinuous insect gut and suggest that the ant lion microbial community is relatively simple, which may be a reflection of the diet and gut physiology of these insects.
Modification of Surface Properties of Biomaterials Influences the Ability of
Candida albicans
To Form Biofilms
Authors: Chandra Jyotsna , Patel Jasmine D. , Li Jian , Zhou Guangyin , Mukherjee Pranab K. , McCormick Thomas S. , Anderson James M. , Ghannoum Mahmoud A. 
Published: December 2005

ABSTRACT

Candida albicans
biofilms form on indwelling medical devices (e.g., denture acrylic or intravenous catheters) and are associated with both oral and invasive candidiasis. Here, we determined whether surface modifications of polyetherurethane (Elasthane 80A [E80A]), polycarbonateurethane, and poly(ethyleneterephthalate) (PET) can influence fungal biofilm formation. Polyurethanes were modified by adding 6% polyethylene oxide (6PEO), 6% fluorocarbon, or silicone, while the PET surface was modified to generate hydrophilic, hydrophobic, cationic, or anionic surfaces. Formation of biofilm was quantified by determining metabolic activity and total biomass (dry weight), while its architecture was analyzed by confocal scanning laser microscopy (CSLM). The metabolic activity of biofilm formed by
C. albicans
on 6PEO-E80A was significantly reduced (by 78%) compared to that of biofilm formed on the nonmodified E80A (optical densities of 0.054 ± 0.020 and 0.24 ± 0.10, respectively;
P
= 0.037). The total biomass of
Candida
biofilm formed on 6PEO-E80A was 74% lower than that on the nonmodified E80A surface (0.46 ± 0.15 versus 1.76 ± 0.32 mg, respectively;
P
= 0.003). Fungal cells were easily detached from the 6PEO-E80A surface, and we were unable to detect
C. albicans
biofilm on this surface by CSLM. All other surface modifications allowed formation of
C. albicans
biofilm, with some differences in thearchitecture. Correlation between contact angle and biofilm formation was observed for polyetherurethane substrates (
r
= 0.88) but not for PET biomaterials (
r
= −0.40). This study illustrates that surface modification is a viable approach for identifying surfaces that have antibiofilm characteristics. Investigations into the clinical utility of the identified surfaces are warranted.