bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of pH on an In Vitro Model of Gastric Microbiota in Enteral Nutrition Patients
Authors: O'May Graeme A. , Reynolds Nigel , Macfarlane George T. 
Published: August 2005

ABSTRACT

Patients with dysphagia due to oropharyngeal disease or cerebrovascular accident require long-term nutritional support via enteral feeding, which often results in microbial overgrowth in the upper gastrointestinal (GI) tract. Gastric acid is the primary innate defense mechanism in the stomach and has been assumed to provide an effective barrier to microbial colonization at pH values of <4. To evaluate the efficacy of gastric acid as a barrier to overgrowth, the microbiota of gastric and duodenal aspirates was assessed by culturing methods. Additionally, a fermentor-based model incorporating enteral nutrition tubing of the gastric microbiota of enteral nutrition (EN) patients was constructed to assess the effect of pH on the microbiota. Results showed that gastric acidity had a relatively small effect on the numbers of microorganisms recovered from intestinal aspirates but did influence microbiota composition. Similarly, at pH 3 in the fermentor, a complex microbiota developed in the planktonic phase and in biofilms. The effect of pH on microbiota composition was similar in aspirates and in the fermentors. Candidas and lactobacilli were aciduric, while recoveries of
Escherichia coli
and
Klebsiella pneumoniae
decreased as pH was reduced, although both were still present in significant numbers at pH 3. Only
Staphylococcus aureus
and
Bifidobacterium adolescentis
persisted at higher pH values both in vitro and in vivo. Lactate and acetate were the main organic acids detected in both aspirates and fermentors. These data show that the simulator used in this investigation was capable of modeling the effects of environmental influences on the upper GI microbiota of EN patients and that gastric pH of <4 is not sufficient to prevent microbial overgrowth in these individuals.
Composition and Structure of Microbial Communities from Stromatolites of Hamelin Pool in Shark Bay, Western Australia
Authors: Papineau Dominic , Walker Jeffrey J. , Mojzsis Stephen J. , Pace Norman R. 
Published: August 2005

ABSTRACT
Stromatolites, organosedimentary structures formed by microbial activity, are found throughout the geological record and are important markers of biological history. More conspicuous in the past, stromatolites occur today in a few shallow marine environments, including Hamelin Pool in Shark Bay, Western Australia. Hamelin Pool stromatolites often have been considered contemporary analogs to ancient stromatolites, yet little is known about the microbial communities that build them. We used DNA-based molecular phylogenetic methods that do not require cultivation to study the microbial diversity of an irregular stromatolite and of the surface and interior of a domal stromatolite. To identify the constituents of the stromatolite communities, small subunit rRNA genes were amplified by PCR from community genomic DNA with universal primers, cloned, sequenced, and compared to known rRNA genes. The communities were highly diverse and novel. The average sequence identity of Hamelin Pool sequences compared to the >200,000 known rRNA sequences was only ∼92%. Clone libraries were ∼90% bacterial and ∼10% archaeal, and eucaryotic rRNA genes were not detected in the libraries. The most abundant sequences were representative of novel proteobacteria (∼28%), planctomycetes (∼17%), and actinobacteria (∼14%). Sequences representative of cyanobacteria, long considered to dominate these communities, comprised <5% of clones. Approximately 10% of the sequences were most closely related to those of α-proteobacterial anoxygenic phototrophs. These results provide a framework for understanding the kinds of organisms that build contemporary stromatolites, their ecology, and their relevance to stromatolites preserved in the geological record.
Aphid-Symbiotic Bacteria Cultured in Insect Cell Lines
Authors: Darby A. C. , Chandler S. M. , Welburn S. C. , Douglas A. E. 
Published: August 2005

ABSTRACT

The cells and tissues of many aphids contain bacteria known as “secondary symbionts,” which under specific environmental circumstances may be beneficial to the host insect. Such symbiotic bacteria are traditionally described as intractable to cultivation in vitro. Here we show that two types of aphid secondary symbionts, known informally as T type and U type, can be cultured and maintained in three insect cell lines. The identities of the cultured bacteria were confirmed by PCR with sequencing of 16S rRNA gene fragments and fluorescence in situ hybridization. In cell lines infected with bacteria derived from aphids harboring both T type and U type, the U type persisted, while the T type was lost. We suggest that the two bacteria persist in aphids because competition between them is limited by differences in tropism for insect tissues or cell types. The culture of these bacteria in insect cell lines provides a new and unique research opportunity, offering a source of unibacterial material for genomic studies and a model system to investigate the interactions between animal cells and bacteria. We propose the provisional taxon names “
Candidatus
Consessoris aphidicola” for T type and “
Candidatus
Adiaceo aphidicola” for U type.
Escherichia coli
K1's Capsule Is a Barrier to Bacteriophage T7
Authors: Scholl Dean , Adhya Sankar , Merril Carl 
Published: August 2005

ABSTRACT

Escherichia coli
strains that produce the K1 polysaccharide capsule have long been associated with pathogenesis. This capsule is believed to increase the cell's invasiveness, allowing the bacteria to avoid phagocytosis and inactivation by complement. It is also recognized as a receptor by some phages, such as K1F and K1-5, which have virion-associated enzymes that degrade the polysaccharide. In this report we show that expression of the K1 capsule in
E. coli
physically blocks infection by T7, a phage that recognizes lipopolysaccharide as the primary receptor. Enzymatic removal of the K1 antigen from the cell allows T7 to adsorb and replicate. This observation suggests that the capsule plays an important role as a defense against some phages that recognize structures beneath it and that the K1-specific phages evolved to counter this physical barrier.
Novel Approach to Quantitative Detection of Specific rRNA in a Microbial Community, Using Catalytic DNA
Authors: Suenaga Hikaru , Liu Rui , Shiramasa Yuko , Kanagawa Takahiro 
Published: August 2005

ABSTRACT

We developed a novel method for the quantitative detection of the 16S rRNA of a specific bacterial species in the microbial community by using deoxyribozyme (DNAzyme), which possesses the catalytic function to cleave RNA in a sequence-specific manner. A mixture of heterogeneous 16S rRNA containing the target 16S rRNA was incubated with a species-specific DNAzyme. The cleaved target 16S rRNA was separated from the intact 16S rRNA by electrophoresis, and then their amounts were compared for the quantitative detection of target 16S rRNA. This method was used to determine the abundance of the 16S rRNA of a filamentous bacterium,
Sphaerotilus natans
, in activated sludge, which is a microbial mixture used in wastewater treatment systems. The result indicated that this DNAzyme-based approach would be applicable to actual microbial communities.
Correlation of
Campylobacter
Bacteriophage with Reduced Presence of Hosts in Broiler Chicken Ceca
Authors: Atterbury R. J. , Dillon E. , Swift C. , Connerton P. L. , Frost J. A. , Dodd C. E. R. , Rees C. E. D. , Connerton I. F. 
Published: August 2005

ABSTRACT

Campylobacter jejuni
and
Campylobacter
-specific bacteriophage were enumerated from broiler chicken ceca selected from 90 United Kingdom flocks (
n
= 205).
C. jejuni
counts in the presence of bacteriophage (mean log
10
5.1 CFU/g) were associated with a significant (
P
< 0.001) reduction compared to samples with
Campylobacter
alone (mean log
10
6.9 CFU/g).
Insertional Inactivation of Determinants for Mg
2+
and Co
2+
Transport as a Tool for Screening Recombinant
Lactococcus
Species Clones
Authors: Mills Susan , Coffey Aidan , Hill Colin , Fitzgerald Gerald F. , McAuliffe Olivia , Ross R. Paul 
Published: August 2005

ABSTRACT

Insertional inactivation of the plasmid-encoded determinants for Mg
2+
and Co
2+
transport,
orf18
/
corA
, provides a tool for screening recombinant clones in
Lactococcus
, based on the observation that overexpression of
orf18
/
corA
results in cell growth inhibition on certain concentrations of CoCl
2
. The lacticin 3147 immunity gene,
ltnI
, was used to insertionally inactivate
orf18
/
corA
. The resulting clones were capable of growth on concentrations of CoCl
2
that were inhibitory to the parent strain. Since only 3 of 17 lactococcal starters naturally harbor
corA
, the system has potential as a screen for selecting recombinant lactococcal clones.
Habits of Magnetosome Crystals in Coccoid Magnetotactic Bacteria
Authors: Lins Ulysses , McCartney Martha R. , Farina Marcos , Frankel Richard B. , Buseck Peter R. 
Published: August 2005

ABSTRACT
High-resolution transmission electron microscopy and electron holography were used to study the habits of exceptionally large magnetite crystals in coccoid magnetotactic bacteria. In addition to the crystal habits, the crystallographic positioning of successive crystals in the magnetosome chain appears to be under strict biological control.
Development of PCR Assays Targeting Genes in O-Antigen Gene Clusters for Detection and Identification of
Escherichia coli
O45 and O55 Serogroups
Authors: DebRoy Chitrita , Fratamico Pina M. , Roberts Elisabeth , Davis Michael A. , Liu Yanhong 
Published: August 2005

ABSTRACT

The
Escherichia coli
O45 O-antigen gene cluster of strain O45:H2 96-3285 was sequenced, and conventional (singleplex), multiplex, and real-time PCR assays were designed to amplify regions in the
wzx
(O-antigen flippase) and
wzy
(O-antigen polymerase) genes. In addition, PCR assays targeting the
E. coli
O55
wzx
and
wzy
genes were designed based on previously published sequences. PCR assays targeting
E. coli
O45 showed 100% specificity for this serogroup, whereas by PCR assays specific for
E. coli
O55, 97/102 strains serotyped as
E. coli
O55 were positive for
wzx
and 98/102 for
wzy
. Multiplex PCR assays targeting the
E. coli
O45 and the
E. coli
O55
wzx
and
wzy
genes were used to detect the organisms in fecal samples spiked at levels of 10
6
and 10
8
CFU/0.2 g feces. Thus, the PCR assays can be used to detect and identify
E. coli
serogroups O45 and O55.
Specificity of a
Bacteroides thetaiotaomicron
Marker for Human Feces
Authors: Carson C. Andrew , Christiansen Jessica M. , Yampara-Iquise Helen , Benson Verel W. , Baffaut Claire , Davis Jerri V. , Broz Robert R. , Kurtz William B. , Rogers Wendi M. , Fales William H. 
Published: August 2005

ABSTRACT

A bacterial primer set, known to produce a 542-bp amplicon specific for
Bacteroides thetaiotaomicron
, generated this product in PCR with 1 ng of extracted DNA from 92% of 25 human fecal samples, 100% of 20 sewage samples, and 16% of 31 dog fecal samples. The marker was not detected in 1 ng of fecal DNA from 61 cows, 35 horses, 44 pigs, 24 chickens, 29 turkeys, and 17 geese.
Patterns of CD8 T-Cell Epitopes within the Human Papillomavirus Type 16 (HPV 16) E6 Protein among Young Women Whose HPV 16 Infection Has Become Undetectable
Authors: Nakagawa Mayumi , Kim Kevin H. , Moscicki Anna-Barbara 
Published: August 2005

ABSTRACT
The patterns of CD8 T-cell epitopes recognized within the E6 protein in women who had cleared their human papillomavirus 16 infection were examined. T-cell lines were established using autologous dendritic cells infected with a recombinant vaccinia virus. Evidence of potential antigenic epitopes was shown in 8 of 23 (34.8%) women.
Critical Evaluation of Urine-Based PCR Assay for Diagnosis of Lyme Borreliosis
Authors: Rauter Carolin , Mueller Markus , Diterich Isabel , Zeller Sabine , Hassler Dieter , Meergans Thomas , Hartung Thomas 
Published: August 2005

ABSTRACT

Many approaches were made in recent years to establish urine PCR as a diagnostic tool for Lyme borreliosis, but results are contradictory. In the present study, a standardized protocol spiking urine from healthy donors with a defined amount of whole
Borrelia
or
Borrelia
DNA was established. The development of a nested real-time PCR targeting
ospA
enabled a highly sensitive and quantitative analysis of these samples. We show the following. (i) Storage of spiked urine samples for up to 6 months at −20°C had no negative effect on spike recovery. (ii) Centrifugation of 10 ml of urine at 40,000 ×
g
for 30 min resulted in a concentration of both spikes, i.e., whole
Borrelia
and DNA. (iii) The inhibition of DNA spike recovery in 48% (11 of 23 samples) of urine samples tested could be attributed to nuclease activity. This was abrogated by alkalizing the urine or by working with the samples on ice. Despite optimized conditions, analysis of urine samples of 12 patients with erythema migrans, the clinical stage considered to be associated with the highest bacterial load, revealed a positive result in only one sample. All 12 samples were negative by an alternative PCR targeting flagellin. The results of our study support doubts that urine is a suitable material for diagnosis of Lyme borreliosis.
Modification of Rapid Human Immunodeficiency Virus (HIV) Antibody Assay Protocols for Detecting Recent HIV Seroconversion
Authors: Soroka Stephen D. , Granade Timothy C. , Candal Debra , Parekh Bharat S. 
Published: August 2005

ABSTRACT

Assay protocols of three rapid human immunodeficiency virus (HIV) assays, OraQuick-1/2, SeroStrip-1/2, and Determine-1/2, were modified to detect recent HIV seroconversion using a higher dilution of serum specimens. Optimal predilution of specimens resulted in negative test results during early periods of seroconversion (about 6 months), when antibody levels were low. A total of 269 seropositive specimens from routine HIV type 1 testing and from commercial sources (low-titer and seroconversion panels) were tested, and results were recorded as negative (score = 0) or positive using intensity scores from 0.5 (weak positive) to 4 (strongly positive). The same specimens were previously tested by a less sensitive (LS) enzyme immunoassay (EIA), Abbott 3A11-LS, and were classified as recent or long-term infections based on the standardized optical density (SOD) cutoff of 0.75. Overall concordance of >94% was observed between 3A11-LS and modified rapid tests (RT-LSs) for detecting and distinguishing recent HIV seroconversion from long-term HIV infection (kappa statistics = 0.894 to 0.901). Moreover, intensity scores on RT-LSs correlated well with median 3A11-LS SOD values (
R
2
> 0.98). Our results indicate that rapid HIV tests can be modified to detect recent seroconversion with results comparable to those from less sensitive EIA.
Noninfectious Virus-Like Particle Antigen for Detection of Swine Vesicular Disease Virus Antibodies in Pigs by Enzyme-Linked Immunosorbent Assay
Authors: Ko Young-Joon , Choi Kang-Seuk , Nah Jin-Ju , Paton David J. , Oem Jae-Ku , Wilsden Ginette , Kang Shien-Young , Jo Nam-In , Lee Joo-Ho , Kim Jae-Hong , Lee Hee-Woo , Park Jong-Myeong 
Published: August 2005

ABSTRACT

An inactivated SVDV antigen is used in current enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies to swine vesicular disease virus (SVDV). To develop a noninfectious recombinant alternative, we produced SVDV-like particles (VLPs) morphologically and antigenically resembling authentic SVDV particles by using a dual baculovirus recombinant, which expresses simultaneously the P1 and 3CD protein genes of SVDV under different promoters. Antigenic differences between recombinant VLPs and SVDV particles were not statistically significant in results obtained with a 5B7-ELISA kit, indicating that the VLPs could be used in the place of SVDV antigen in ELISA kits. We developed a blocking ELISA using the VLPs and SVDV-specific neutralizing monoclonal antibody 3H10 (VLP-ELISA) for detection of SVDV serum antibodies in pigs. The VLP-ELISA showed a high specificity of 99.9% when tested with pig sera that are negative for SVDV neutralization (
n
= 1,041). When tested using sera (
n
= 186) collected periodically from pigs (
n
= 19) with experimental infection with each of three different strains of SVDV, the VLP-ELISA detected SVDV serum antibodies as early as 3 days postinfection and continued to detect the antibodies from all infected pigs until termination of the experiments (up to 121 days postinfection). This test performance was similar to that of the gold standard virus neutralization test and indicates that the VLP-ELISA is a highly specific and sensitive method for the detection of SVDV serum antibodies in pigs. This is the first report of the production and diagnostic application of recombinant VLPs of SVDV. Further potential uses of the VLPs are discussed.
Naturally Acquired Antibodies against Four
Enterococcus faecalis
Capsular Polysaccharides in Healthy Human Sera
Authors: Hufnagel Markus , Kropec Andrea , Theilacker Christian , Huebner Johannes 
Published: August 2005

ABSTRACT

Healthy human sera (HHS) contain naturally acquired enterococcal antibodies which promote neutrophil-mediated killing. The target antigens remain unknown. The present study used a capsular polysaccharide (CPS)-enzyme-linked immunosorbent assay (ELISA) to investigate whether the HHS antibodies of 12 healthy donors bound to the CPS of four
E. faecalis
serotypes (CPS-A to CPS-D) and then employed an opsonic-killing assay to determine if these antibodies mediated phagocyte-dependent killing. All HHS contained immunoglobulin G (IgG) and IgM antibodies directed against capsular polysaccharides of the four serotypes. Absorption of the sera with homologous and heterologous strains showed a majority of antibodies to be cross-reactive among the prototype strains. The susceptibility of the four prototype strains to opsonic killing varied. Opsonic killing of CPS-A and CPS-B strains was significantly higher than killing of CPS-C and CPS-D strains. Absorption studies revealed that the opsonic killing of HHS was only partially type specific, with cross-reactivity between CPS-A and CPS-B strains and between CPS-C and CPS-D strains. These data indicate that healthy individuals possess opsonic antibodies specific for CPS-A and CPS-B but only low titers of opsonic antibodies against CPS-C and CPS-D. Titers of opsonic antibodies did not correlate with antibody titers measured by ELISA. Whether this lack of correlation is due to the low frequency of opsonic antibodies or to increased resistance to the opsonophagocytic killing of some serotypes remains to be determined.
Borrelia burgdorferi
BmpA, BmpB, and BmpD Proteins Are Expressed in Human Infection and Contribute to P39 Immunoblot Reactivity in Patients with Lyme Disease
Authors: Bryksin Anton V. , Godfrey Henry P. , Carbonaro Carol A. , Wormser Gary P. , Aguero-Rosenfeld Maria E. , Cabello Felipe C. 
Published: August 2005

ABSTRACT

The Bmp proteins are a paralogous family of chromosomally encoded
Borrelia burgdorferi
lipoproteins. They have similar predicted immunogenicities and similar electrophoretic mobilities by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. P39 reactivity against
Borrelia burgdorferi
lysate in immunoblots of Lyme disease patients has long been identified with reactivity to BmpA, but responses to other Bmp proteins have not been examined. To determine if patients with Lyme disease developed such responses, immunoglobulin G (IgG) anti-Bmp reactivity in patient and control sera was studied by using soluble recombinant Bmp (rBmp) proteins expressed in
Escherichia coli
. Although some patient sera contained IgG immunoblot and immunodot reactivities against all four Bmp proteins, analysis of IgG anti-Bmp fine specificity by a competitive enzyme-linked immunosorbent assay with graded doses of soluble homologous and heterologous rBmp proteins showed that only the responses to BmpA, BmpB, and BmpD were specific. This suggests that at least three of the four Bmp proteins are expressed by
B. burgdorferi
in infected patients and that specific antibodies to them are likely to be present in the P39 band in some patients.
Seroreactivity to and Avidity for Recombinant Antigens in Toxoplasmosis
Authors: Pfrepper Klaus-Ingmar , Enders Gisela , Gohl Marion , Krczal Doris , Hlobil Harald , Wassenberg Doris , Soutschek Erwin 
Published: August 2005

ABSTRACTTo improve serodiagnostic methods for the diagnosis of acute toxoplasmosis during pregnancy, a new test system has been developed and evaluated based on the use of recombinant antigens. Five recombinantToxoplasma gondiiantigens (ROP1, MAG1, SAG1, GRA7, and GRA8) were cloned inEscherichia coli, purified, and applied directly onto nitrocellulose membranes in a line assay (recomLine Toxoplasma). A panel of 102 sera from 25 pregnant women with supposed recent toxoplasmosis and from two symptomatic children was compared to a panel of 71 sera from individuals with past infection. Both panels were analyzed using a recombinant line assay for immunoglobulin G (IgG), IgM, and IgA antibodies and a reference enzyme-linked immunosorbent assay. Within the IgM-positive samples, antibodies against ROP1 were predominant regardless of the infection state. In IgG analysis a characteristic antibody pattern was found for very recent infections. This pattern changed to a different one during the time course of infection: antibodies against GRA7 and GRA8 were characteristic for very early IgG, whereas antibodies against SAG1 and MAG1 appeared significantly later. These results were further confirmed by determination of the IgG antibody avidity for every single recombinant antigen. In the time course of infection, IgG antibodies against the early recognized antigens matured significantly earlier than those directed against the later antigens did. The IgA patterns did not give reliable information about the infection time points. The data revealed that the recombinant line assay provides valuable information on the actual state of infection, especially during the early infection time points.
Diagnosis and management of chronic pancreatitis
Authors: Gupta V , Toskes P P 
Published: August 2005

AbstractChronic pancreatitis represents a condition that is challenging for clinicians secondary to the difficulty in making an accurate diagnosis and the less than satisfactory means of managing chronic pain. This review emphasises the various manifestations that patients with chronic pancreatitis may have and describes recent advances in medical and surgical therapy. It is probable that many patients with chronic abdominal pain are suffering from chronic pancreatitis that is not appreciated. As the pathophysiology of this disorder is better understood it is probable that the treatment will be more successful.