bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photosynthetic and Phylogenetic Primers for Detection of Anoxygenic Phototrophs in Natural Environments
Authors: Achenbach Laurie A. , Carey Jennifer , Madigan Michael T. 
Published: July 2002

ABSTRACT

Primer sets were designed to target specific 16S ribosomal DNA (rDNA) sequences of photosynthetic bacteria, including the green sulfur bacteria, the green nonsulfur bacteria, and the members of the
Heliobacteriaceae
(a gram-positive phylum). Due to the phylogenetic diversity of purple sulfur and purple nonsulfur phototrophs, the 16S rDNA gene was not an appropriate target for phylogenetic rDNA primers. Thus, a primer set was designed that targets the
pufM
gene, encoding the M subunit of the photosynthetic reaction center, which is universally distributed among purple phototrophic bacteria. The
pufM
primer set amplified DNAs not only from purple sulfur and purple nonsulfur phototrophs but also from
Chloroflexus
species, which also produce a reaction center like that of the purple bacteria. Although the purple bacterial reaction center structurally resembles green plant photosystem II, the
pufM
primers did not amplify cyanobacterial DNA, further indicating their specificity for purple anoxyphototrophs. This combination of phylogenetic- and photosynthesis-specific primers covers all groups of known anoxygenic phototrophs and as such shows promise as a molecular tool for the rapid assessment of natural samples in ecological studies of these organisms.
Toxic-Metabolite-Producing Bacteria and Fungus in an Indoor Environment
Authors: Peltola J. , Andersson M. A. , Haahtela T. , Mussalo-Rauhamaa H. , Rainey F. A. , Kroppenstedt R. M. , Samson R. A. , Salkinoja-Salonen M. S. 
Published: July 2002

ABSTRACT

Toxic-metabolite-emitting microbes were isolated from the indoor environment of a building where the occupant was suffering serious building-related ill-health symptoms. Toxic substances soluble in methanol and inhibitory to spermatozoa at <10 μg (dry weight) ml
−1
were found from six bacterial isolates and one fungus. The substances from isolates of
Bacillus simplex
and from isolates belonging to the actinobacterial genera
Streptomyces
and
Nocardiopsis
were mitochondriotoxic. These substances dissipated the mitochondrial membrane potential (Δψ) of boar spermatozoa. The substances from the
Streptomyces
isolates also swelled the mitochondria. The substances from isolates of
Trichoderma harzianum
Rifai and
Bacillus pumilus
damaged the cell membrane barrier function of sperm cells.
Quantitative Comparisons of 16S rRNA Gene Sequence Libraries from Environmental Samples
Authors: Singleton David R. , Furlong Michelle A. , Rathbun Stephen L. , Whitman William B. 
Published: July 2002

ABSTRACTTo determine the significance of differences between clonal libraries of environmental rRNA gene sequences, differences between homologous coverage curves,CX(D), and heterologous coverage curves,CXY(D), were calculated by a Cramér-von Mises-type statistic and compared by a Monte Carlo test procedure. This method successfully distinguished rRNA gene sequence libraries from soil and bioreactors and correctly failed to find differences between libraries of the same composition.
Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations
Authors: Webster Gordon , Embley T. Martin , Prosser James I. 
Published: July 2002

ABSTRACT

The impact of soil management practices on ammonia oxidizer diversity and spatial heterogeneity was determined in improved (addition of N fertilizer), unimproved (no additions), and semi-improved (intermediate management) grassland pastures at the Sourhope Research Station in Scotland. Ammonia oxidizer diversity within each grassland soil was assessed by PCR amplification of microbial community DNA with both ammonia oxidizer-specific, 16S rRNA gene (rDNA) and functional,
amoA
, gene primers. PCR products were analysed by denaturing gradient gel electrophoresis, phylogenetic analysis of partial 16S rDNA and
amoA
sequences, and hybridization with ammonia oxidizer-specific oligonucleotide probes. Ammonia oxidizer populations in unimproved soils were more diverse than those in improved soils and were dominated by organisms representing
Nitrosospira
clusters 1 and 3 and
Nitrosomonas
cluster 7 (closely related phylogenetically to
Nitrosomonas europaea
). Improved soils were only dominated by
Nitrosospira
cluster 3 and
Nitrosomonas
cluster 7. These differences were also reflected in functional gene (
amoA
) diversity, with
amoA
gene sequences of both
Nitrosomonas
and
Nitrosospira
species detected. Replicate 0.5-g samples of unimproved soil demonstrated significant spatial heterogeneity in 16S rDNA-defined ammonia oxidizer clusters, which was reflected in heterogeneity in ammonium concentration and pH. Heterogeneity in soil characteristics and ammonia oxidizer diversity were lower in improved soils. The results therefore demonstrate significant effects of soil management on diversity and heterogeneity of ammonia oxidizer populations that are related to similar changes in relevant soil characteristics.
Population Dynamics of Active and Total Ciliate Populations in Arable Soil Amended with Wheat
Authors: Ekelund Flemming , Frederiksen Helle B. , Rønn Regin 
Published: July 2002

ABSTRACTSoil protozoa are characterized by their ability to produce cysts, which allows them to survive unfavorable conditions (e.g., desiccation) for extended periods. Under favorable conditions, they may rapidly excyst and begin feeding, but even under optimal conditions, a large proportion of the population may be encysted. The factors governing the dynamics of active and encysted cells in the soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in soil microcosms, the active and total populations of ciliates, their potential prey (bacteria and small protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable for mathematical modeling. Following the addition of fresh organic material, bacterial numbers increased more than 1,400-fold. There was a temporary increase in the number of active ciliates, followed by a rapid decline, although the size of the bacterial prey populations remained high. During this initial burst of ciliate growth, the population of cystic ciliates increased 100-fold. We suggest that internal population regulation is the major factor governing ciliate encystment and that the rate of encystment depends on ciliate density. This model provides a quantitative explanation of ciliatostasis and can explain why protozoan growth in soil is less than that in aquatic systems. Internally governed encystment may be an essential adaptation to an unpredictable environment in which individual protozoa cannot predict when the soil will dry out and will survive desiccation only if they have encysted in time.
Molecular and Culture-Based Analyses of Prokaryotic Communities from an Agricultural Soil and the Burrows and Casts of the EarthwormLumbricus rubellus
Authors: Furlong Michelle A. , Singleton David R. , Coleman David C. , Whitman William B. 
Published: July 2002

ABSTRACTThe microbial populations in no-till agricultural soil and casts of the earthwormLumbricus rubelluswere examined by culturing and molecular methods. Clone libraries of the 16S rRNA genes were prepared from DNA isolated directly from the soil and earthworm casts. Although no single phylum dominated the soil library of 95 clones, the largest numbers of clones were fromAcidobacteria(14%),Cytophagales(13%),Chloroflexi(8%), and γ-Proteobacteria(8%). While the cast clone library of 102 clones was similar to the soil library, the abundances of several taxa were different. Representatives of thePseudomonasgenus as well as theActinobacteriaandFirmicutesincreased in number, and one group of unclassified organisms found in the soil library was absent in the cast library. Likewise, soil and cast archaeal 16S rRNA gene libraries were similar, although the abundances of some groups were different. Two hundred and thirty aerobic bacteria were also isolated on general heterotrophic media from casts, burrows, and soil. The cast isolates were both phenotypically and genotypically different from the soil isolates. The cast isolates were more likely to reduce nitrate, grow on acetate and Casamino Acids, and utilize fewer sugars than the soil isolates. On the basis of their ribotypes, the cast isolates were dominated byAeromonasspp. (28%), which were not found in the soil isolates, and other γ-Proteobacteria(49%). In contrast, the soil isolates were mostlyActinobacteria(53%),Firmicutes(16%), and γ-Proteobacteria(19%). Isolates obtained from the sides of earthworm burrows were not different from the soil isolates. Diversity indices for the collections of isolates as well as rRNA gene libraries indicated that the species richness and evenness were decreased in the casts from their levels in the soil. These results were consistent with a model where a large portion of the microbial population in soil passes through the gastrointestinal tract of the earthworm unchanged while representatives of some phyla increase in abundance.
Identification of the Functionally Active Methanotroph Population in a Peat Soil Microcosm by Stable-Isotope Probing
Authors: Morris Samantha A. , Radajewski Stefan , Willison Toby W. , Murrell J. Colin 
Published: July 2002

ABSTRACT

The active population of low-affinity methanotrophs in a peat soil microcosm was characterized by stable-isotope probing. “Heavy”
13
C-labeled DNA, produced after microbial growth on
13
CH
4
, was separated from naturally abundant
12
C-DNA by cesium chloride density gradient centrifugation and used as a template for the PCR. Amplification products of 16S rRNA genes and
pmoA
,
mxaF
, and
mmoX
, which encode key enzymes in the CH
4
oxidation pathway, were analyzed. Sequences related to extant type I and type II methanotrophs were identified, indicating that these methanotrophs were active in peat exposed to 8% (vol/vol) CH
4
. The
13
C-DNA libraries also contained clones that were related to β-subclass
Proteobacteria
, suggesting that novel groups of bacteria may also be involved in CH
4
cycling in this soil.
Evaluation of 12 Commercial Tests for Detection of Epstein-Barr Virus-Specific and Heterophile Antibodies
Authors: Bruu Anne-Lise , Hjetland Reidar , Holter Ellen , Mortensen Liisa , Natås Olav , Petterson Wenche , Skar Anne Grete , Skarpaas Tone , Tjade Trygve , Åsjø Birgitta 
Published: July 2002

ABSTRACT
Ten microbiological departments in Norway have participated in a multicenter evaluation of the following commercial tests for detection of Epstein-Barr virus (EBV)-specific and heterophile antibodies: CAPTIA Select viral capsid antigen (VCA)-M/G/EBNA (Centocor Inc.), Enzygnost anti-EBV/immunoglobulin M (IgM) and IgG (Dade Behring), Vironostika EBV VCA IgM/IgG/EBNA enzyme-linked immunosorbent assay (ELISA) (Organon Teknika), SEROFLUOR immunofluorescence assay and EBV Combi-Test (Institute Virion Ltd.), anti-EBV recombinant IgM- and IgG-early antigen/EBNA IgG ELISA (Biotest Diagnostics), EBV IgM/IgG/EBNA ELISA (Gull Laboratories), Paul-Bunnell-Davidsohn test (Sanofi Diagnostics Pasteur), Monosticon Dri-Dot (Organon Teknika), Avitex-IM (Omega Diagnostics Ltd.), Alexon Serascan infectious mononucleosis test (Alexon Biomedical Inc.), Clearview IM (Unipath Ltd.), and Cards±OS Mono (Pacific Biotech, Inc.). The test panel included sera from patients with primary EBV infection, immunocompromised patients with recent cytomegalovirus infection, healthy persons (blood donors), and EBV-seronegative persons. Among the tests for EBV-specific antibodies the sensitivity was good, with only small differences between the different assays. However, there was a greater variation in specificity, which varied between 100% (Enzygnost) and 86% (Biotest). Tests for detection of heterophile antibodies based on purified or selected antigen (Avitex, Alexon, Clearview IM, and Cards±OS Mono) were more sensitive than the Paul-Bunnell-Davidsohn and Monosticon tests.
Antibody Response of Patients with
Helicobacter pylori
-Related Gastric Adenocarcinoma: Significance of Anti-CagA Antibodies
Authors: Vaucher Christine , Janvier Blandine , Nousbaum Jean-Baptiste , Grignon Bernadette , Pezennec Leon , Robaszkiewicz Michel , Gouerou Herve , Picard Bertrand , Fauchere Jean-Louis 
Published: July 2002

ABSTRACT

The aim of this study was to search for a specific antibody pattern in sera from patients suffering from
Helicobacter pylori
-related gastric adenocarcinoma (GAC). The serological response of 22 patients suffering from GAC, 31 patients with gastroduodenal ulcer, and 39 asymptomatic subjects was analyzed using immunoblotting performed with three
H. pylori
strains: strain ATCC 43579; strain B110, isolated from a patient with ulcers; and strain B225, isolated from a patient with GAC. In addition, the latex agglutination test Pyloriset Dry was used to analyze ambiguous sera.
H. pylori
seropositivity was 75% in the GAC group, 61.3% in the ulcer group, and 56.4% in the asymptomatic group. Anti-CagA antibodies were found more often in the GAC group (48.8%) and in the ulcer group (47.3%) than in the asymptomatic group (21.2%). These percentages depended on the strain used as an antigen: in the GAC group, the anti-CagA frequencies were 93.3, 40, and 13.3% with strains B225, B110, and ATCC 43579, respectively. Thus the presence of anti-CagA antibodies was increased in patients suffering from
H. pylori
-related GAC, in particular when the CagA antigen was from a GAC strain. These data suggest the existence of a CagA protein specifically expressed by
H. pylori
strains isolated from GAC patients.
Placental Cellular Immune Response in Women Infected with Human Parvovirus B19 during Pregnancy
Authors: Jordan Jeanne A. , Huff Dale , DeLoia Julie A. 
Published: July 2002

ABSTRACT

Human parvovirus B19 can cause congenital infection with variable morbidity and mortality in the fetus and neonate. Although much information exists on the B19-specific antibody response in pregnant women, little information is available describing the cell-mediated immune (CMI) response at the maternal-fetal interface. The focus of this study was to characterize the CMI response within placentas from women who seroconverted to B19 during their pregnancies and compare it to controls. Immunohistochemical techniques were used to identify the various immune cells and the inflammatory cytokine present within placental tissue sections. Group 1 consisted of placentas from 25 women whose pregnancies were complicated by B19 infection; 6 women with good outcome (near-term or term delivery), and 19 with poor outcome (spontaneous abortion, nonimmune hydrops fetalis, or fetal death). Group 2 consisted of placentas from 20 women whose pregnancies were complicated with nonimmune hydrops fetalis of known, noninfectious etiology. Group 3 consisted of placentas from eight women whose pregnancies ended in either term delivery or elective abortion. The results of the study revealed a statistically significant increase in the number of CD3-positive T cells present within placentas from group 1 compared to group 2 or 3 (13.3 versus 2 and 1, respectively) (
P
< 0.001). In addition, the inflammatory cytokine interleukin 2 was detected in every placenta within group 1 but was absent from all placentas evaluated from groups 2 and 3. Together, these findings demonstrate evidence for an inflammation-mediated cellular immune response within placentas from women whose pregnancies are complicated with B19 infection.
Immunoglobulin G1 Antibody Response toHelicobacter pyloriHeat Shock Protein 60 Is Closely Associated with Low-Grade Gastric Mucosa-Associated Lymphoid Tissue Lymphoma
Authors: Ishii E. , Yokota K. , Sugiyama T. , Fujinaga Y. , Ayada K. , Hokari I. , Hayashi S. , Hirai Y. , Asaka M. , Oguma K. 
Published: July 2002

ABSTRACTGastric mucosa-associated lymphoid tissue (MALT) lymphoma is related toHelicobacter pyloriinfection. Specifically, it has been pointed out that pathogenesis of MALT lymphoma involves the 60-kDa heat shock protein (hsp60). To investigate humoral immune responses to theH. pylorihsp60 in patients with gastroduodenal diseases and patients with MALT lymphoma, the hsp60 ofH. pyloriwas expressed with a glutathioneS-transferase fusion protein and was purified (recombinant hsp60). Sera were obtained fromH. pylori-positive patients with gastroduodenal diseases (MALT lymphoma,n= 13; gastric ulcer,n= 20; duodenal ulcer,n= 20; gastritis,n= 20) and fromH. pylori-negative healthy volunteers (n= 9). Sera from patients with MALT lymphoma were also obtained at two times: before and after eradication therapy. Antibodies to hsp60 andH. pyloriwere assessed by enzyme-linked immunosorbent assay. The levels of immunoglobulin G (IgG) antibodies to the hsp60 ofH. pylori-positive patients with gastroduodenal diseases were significantly elevated compared to those in the controls. The levels of IgG1 antibodies to hsp60 were elevated and correlated with the levels of anti-H. pyloriantibodies in patients with MALT lymphoma. Humarol immunity against hsp60 may be important and relevant to gastroduodenal diseases induced byH. pyloriinfection.
Emergence of DiverseHelicobacterSpecies in the Pathogenesis of Gastric and Enterohepatic Diseases
Authors: Solnick Jay V. , Schauer David B. 
Published: July 2002

SUMMARYSince Helicobacter pylori was first cultivated from human gastric biopsy specimens in 1982, it has become apparent that many related species can often be found colonizing the mucosal surfaces of humans and other animals. These other Helicobacter species can be broadly grouped according to whether they colonize the gastric or enterohepatic niche. GastricHelicobacter species are widely distributed in mammalian hosts and are often nearly universally prevalent. In many cases they cause an inflammatory response resembling that seen with H. pylori in humans. Although usually not pathogenic in their natural host, these organisms serve as models of human disease. Enterohepatic Helicobacter species are an equally diverse group of organisms that have been identified in the intestinal tract and the liver of humans, other mammals, and birds. In many cases they have been linked with inflammation or malignant transformation in immunocompetent hosts and with more severe clinical disease in immunocompromised humans and animals. The purpose of this review is to describe these other Helicobacter species, characterize their role in the pathogenesis of gastrointestinal and enterohepatic disease, and discuss their implications for our understanding of H. pylori infection in humans.
Global Impact of Human Immunodeficiency Virus and AIDS
Authors: Gayle Helene D. , Hill Gena L. 
Published: July 2002

SUMMARYThis review provides information on the epidemiology, economic impact, and intervention strategies for the human immunodeficiency virus (HIV)/AIDS pandemic in developing countries. According to the World Health Organization and the Joint United Nations Programme on HIV/AIDS (UNAIDS) at the end of 1999, an estimated 34.3 million people were living with HIV/AIDS. Most of the people living with HIV, 95% of the global total, live in developing countries. Examples of the impact of HIV/AIDS in Africa, Asia, Latin America, the Caribbean, and the Newly Independent States provide insight into the demographics, modes of exposure, treatment and prevention options, and the economic effect of the epidemic on the global community. The epidemic in each region of the world is influenced by the specific risk factors that are associated with the spread of HIV/AIDS and the responses that have evolved to address it. These influences are important in developing HIV/AIDS policies and programs to effectively address the global pandemic.
Lack of Association between Maternal Antibody and Protection of African Infants from Malaria Infection
Authors: Riley E. M. , Wagner G. E. , Ofori M. F. , Wheeler J. G. , Akanmori B. D. , Tetteh K. , McGuinness D. , Bennett S. , Nkrumah F. K. , Anders R. F. , Koram K. A. 
Published: July 2002

ABSTRACT

Maternally derived antibodies are believed to protect infants against infection, but there is little direct evidence for a protective role of passively acquired antibodies against malaria. A longitudinal study of malaria infection in 143 infants was conducted in a region of southern Ghana where
Plasmodium falciparum
is endemic. Infants born in the high-transmission season were less likely to become infected in the first 20 weeks of life than children born in the low-transmission season. Plasma, obtained at birth, was tested for immunoglobulin G (IgG) and IgG subclasses to
P. falciparum
schizonts and recombinant circumsporozoite antigen, MSP-1
19
, MSP-2, AMA-1, and Pf155 (also called ring-infected erytrocyte surface antigen). Antibody levels at birth were not associated with resistance to malaria infection. On the contrary, antibodies at birth were positively associated with infection, indicating that high levels of maternally derived antibodies represent a marker for intensity of exposure to malaria infection in infants. However, all five children who experienced high-density infections (>100 parasites/μl of blood) were seronegative for MSP-1
19
at the time of infection.
pMGA Phenotypic Variation in
Mycoplasma gallisepticum
Occurs In Vivo and Is Mediated by Trinucleotide Repeat Length Variation
Authors: Glew M. D. , Browning Glenn F. , Markham Philip F. , Walker Ian D. 
Published: July 2002

ABSTRACT

Chickens were infected with a pathogenic strain of
Mycoplasma gallisepticum
, and the expression of pMGA, the major surface protein, was inferred by examination of colonies from ex vivo cells. Within 2 days postinfection, 40% of cells had ceased the expression of the original pMGA surface protein (pMGA1.1), and by day 6, the majority of recovered cells were in this category. The switch in pMGA phenotype which had occurred in vivo was reversible, since most colonies produced from ex vivo progenitors exhibited frequent pMGA1.1
+
sectors. After prolonged in vivo habitation, increasing proportions of recovered cells gave rise to variant pMGA colonies which had switched from the expression of pMGA1.1 to another gene, pMGA1.2, concomitant with the acquisition of a (GAA)
12
motif 5′ to its promoter. Collectively, the results suggest that changes in
M. gallisepticum
pMGA gene expression in vivo are normal, common, and possibly obligate events for successful colonization of the host. Surprisingly, the initial cessation of pMGA1.1 expression occurred in the absence of detectable pMGA antibodies and seemed to precede the adaptive immune response.
Strain Diversity in Major Surface Protein 2 Expression during Tick Transmission ofAnaplasma marginale
Authors: Rurangirwa Fred R. , Stiller David , Palmer Guy H. 
Published: July 2002

ABSTRACTSpecific major surface protein 2 (MSP2) variants are expressed byAnaplasma marginalewithin the tick salivary gland and, following transmission, are expressed during acute rickettsemia. In previous work, we have shown that a restricted pattern of MSP2 variants is expressed in the salivary glands ofDermacentor andersoniticks infected with the South Idaho strain ofA. marginale. Now we demonstrate that the identical restriction does not apply to two other strains ofA. marginale, and that different variants are also expressed when the same strain is transmitted by differentDermacentorspp. This indicates that antigenic diversity among strains is maintained in tick transmission and may be a significant constraint to MSP2 vaccine development.