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PubMed2005

A soil-based microbial biofilm exposed to 2,4-D: bacterial community development and establishment of conjugative plasmid pJP4.

A soil suspension was used as a source to initiate the development of microbial communities in flow cells irrigated with 2,4-dichlorophenoxyacetic acid (2,4-D) (25 microg ml(-1)). Culturable bacterial members of the community were identified by 16S rRNA gene sequencing and found to be members of the genera Pseudomonas, Burkholderia, Collimonas and Rhodococcus. A 2,4-D degrading donor strain, Pseudomonas putida SM1443 (pJP4::gfp), was inoculated into flow cell chambers containing 2-day old biofilm communities. Transfer of pJP4::gfp from the donor to the bacterial community was detectable as GFP fluorescing cells and images were captured using confocal scanning laser microscopy (GFP fluorescence was repressed in the donor due to the presence of a chromosomally located lacI(q) repressor gene). Approximately 5-10 transconjugant microcolonies, 20-40 microm in diameter, could be seen to develop in each chamber. A 2,4-D degrading transconjugant strain was isolated from the flow cell system belonging to the genus Burkholderia.

2,4-Dichlorophenoxyacetic Acid↗
PubMed2000

Measuring soil microbial community diversity using polar lipid fatty acid and denaturing gradient gel electrophoresis data.

The possibility of calculating useful microbial community diversity indices from environmental polar lipid fatty acid and 16S rDNA PCR-DGGE data was investigated. First, the behavior of the species richness, Shannon's, and Simpson's diversity indices were determined on polar lipid fatty acid profiles of 115 pure cultures, communities constructed from those profiles with different numbers of species, and constructed communities with different distributions of species. Differences in the species richness of these artificial communities was detected by all three diversity indices, but they were insensitive to the evenness of the distribution of species. Second, data from a field experiment with substrate addition to soil was used to compare the methods developed for lipid- and DNA-based diversity indices. Very good agreement was found between indices calculated from environmental polar lipid fatty acid profiles and denaturing gradient gel electrophoresis profiles from matched samples (Pearson's correlation coefficient r=0.95-0.96). A method for data pre-treatment for diversity calculations is described.

Bacteria↗
PubMed2004

Bacterial populations associated with the oxidation and reduction of arsenic in an unsaturated soil.

Microbial populations responsible for the oxidation and reduction of As were examined in unsaturated (aerobic) soil columns treated with 75 microM arsenite [As(III)] or 250 microM arsenate [As(V)]. Arsenite [As(III)] was rapidly oxidized to As(V) via microbial activity, whereas no apparent reduction of As(V) was observed in the column experiments. Eight aerobic heterotrophic bacteria with varying As redox phenotypes were isolated from the same columns. Three isolates, identified as Agrobacterium tumefaciens-, Pseudomonas fluorescens-, and Variovorax paradoxus-like organisms (based on 16S sequence), were As(III) oxidizers, and all were detected in community DNA fingerprints generated by PCR coupled with denaturing gradient gel electrophoresis. The five other isolates were identified (16S gene sequence) as A. tumefaciens, Flavobacterium sp., Microbacterium sp., and two Arthrobacter sp. -like organisms and were shown to rapidly reduce As(V) under aerobic conditions. Although the two A. tumefaciens-like isolates exhibited opposite As redox activity,their 16S rDNA sequences (approximately 1400 bp) were 100% identical, and both were shown to contain putative arsC genes. Our results support the hypothesis that bacteria capable of either oxidizing As(III) or reducing As(V) coexist and are ubiquitous in soil environments, suggesting that the relative abundance and metabolic activity of specific microbial populations plays an important role in the speciation of inorganic As in soil pore waters.

Agrobacterium tumefaciens↗
PubMed2002

Field and pulping performances of transgenic trees with altered lignification.

The agronomic and pulping performance of transgenic trees with altered lignin has been evaluated in duplicated, long-term field trials. Poplars expressing cinnamyl alcohol dehydrogenase (CAD) or caffeate/5-hydroxy-ferulate O-methyltransferase (COMT) antisense transgenes were grown for four years at two sites, in France and England. The trees remained healthy throughout the trial. Growth indicators and interactions with insects were normal. No changes in soil microbial communities were detected beneath the transgenic trees. The expected modifications to lignin were maintained in the transgenics over four years, at both sites. Kraft pulping of tree trunks showed that the reduced-CAD lines had improved characteristics, allowing easier delignification, using smaller amounts of chemicals, while yielding more high-quality pulp. This work highlights the potential of engineering wood quality for more environmentally benign papermaking without interfering with tree growth or fitness.

Alcohol Oxidoreductases↗
PubMed2001

Support for teenage mothers: a qualitative study into the views of women about the support they received as teenage mothers.

AIM OF THE STUDY: To gain insight into the support teenage mothers received during pregnancy, birth and their child's pre-school years and young women's perceptions of the usefulness of a support group for teenage mothers. BACKGROUND: Most qualitative studies have focused on teenage mothers around the time of the birth of their first child. For this study, women were recruited several years after the birth (median 8.5 years), so that they would have had time to reflect on the support they had received. DESIGN: The qualitative method of semi-structured interviews was chosen to obtain in-depth information and to allow teenage mothers' own views to be heard. Ten individual interviews and one paired interview were undertaken. FINDINGS: Recruitment was difficult because taking part in research was not a priority for many of the women. The study confirmed the strong link between deprivation and teenage pregnancy found in other studies, and suggested that mental health problems in teenage mothers may be more difficult to detect. Teenage women need more information on mental health and on services available to them. The fear, expressed by some of the women in this study, of becoming different from other women in their social network should be considered by health workers when establishing intervention programmes. CONCLUSIONS: Professional bodies of health workers should lobby government to provide a minimum standard of living and sufficient child-care to combat deprivation. Former teenage mothers should be involved in the recruitment, planning and implementation stages of research and interventions. Health professionals should be aware that mental health problems in teenage mothers may be particularly difficult to detect. Key community health workers or a support group may provide information on services, mental health and education facilities available that would benefit teenage mothers. A support group may also give emotional support.

Adolescent↗
PubMed2003

A Canadian programme for early intervention in non-affective psychotic disorders.

OBJECTIVES: To provide a brief overview of the development of clinical services and research for early intervention in psychotic disorders in Canada; to describe components of a comprehensive clinical/research programme for nonaffective psychotic disorders; and to present a summary of results of clinical and social outcomes achieved. METHOD: This is a descriptive paper providing some details of how clinical services are being developed in Canada and concentrating on one particular early intervention programme, Prevention and Early intervention Programme for Psychoses (PEPP) London, Ontario, which is using a historical control design to evaluate the impact of an assertive approach to community case detection. Components of a phase-specific treatment programme and early case detection are described followed by results based on clinical and psychosocial data collected according to a defined protocol. RESULTS: One year outcome for patients treated in PEPP shows use of low dose, pre-dominantly novel antipsychotics and high (81.5%) retention and remission (75%) rates. Highly significant improvements were also reported for self-rated quality of life and cognition. Duration of untreated psychosis (DUP) and premorbid adjustment were associated with improvement in positive and negative symptoms, respectively. Systemic changes to improve access to the service resulted in substantial increases in number of cases treated and a> 50% decline in DUP. CONCLUSIONS: Phase-specific treatment approach and case identification strategies to reduce delay in treatment are likely to substantially improve outcome in nonaffective psychotic disorders compared with what has been reported with traditional approaches.

Canada↗
PubMed1990

Detection of malaria endemicity in community villages in North Sumatra, Indonesia by enzyme linked immunosorbent assay.

An enzyme linked immunosorbent assay for malaria was used in North Sumatra, Indonesia as an epidemiological survey tool. The seroepidemiological investigation was concentrated on junior high schools. Serum samples obtained were classified according to the villages of origin of the students. The mean of ELISA values of each village group was compared with the parasite rate in primary schools in their native villages. A good correlation was observed between them (r = 0.96). The present results indicate that a survey of malaria in junior high schools by ELISA could give useful information on malaria prevalence in several peripheral villages. Province-wide information on malaria prevalence could easily be obtained by malaria-ELISA in junior high schools in tropical rural area.

Animals↗
PubMed2003

Prevalence of and risk factors for colonization with methicillin-resistant Staphylococcus aureus in an outpatient clinic population.

OBJECTIVES: To determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization in an outpatient population and to identify risk factors for MRSA colonization. DESIGN: Surveillance cultures were performed during outpatient visits to identify S. aureus colonization. A case-control study was performed to identify risk factors for MRSA colonization. SETTING: Primary care internal medicine clinic. PATIENTS: Adults presenting for non-acute primary care (N = 494). RESULTS: S. aureus was isolated from 122 (24.7%) of the patients for whom cultures were performed. Methicillin-susceptible S. aureus was isolated from 107 (21.7%) of the patients, whereas MRSA was isolated from 15 (3.0%) of the patients. All MRSA isolates were resistant to multiple non-beta-lactam antimicrobial agents. In multivariate analyses, MRSA colonization was independently associated with admission to a nursing home (adjusted odds ratio [OR], 103; 95% confidence interval [CI95], 7 to 999) or hospital in the previous year, although the association with hospital admission was observed only among those without chronic illness (adjusted OR, 7.1; CI95, 1.3 to 38.1). In addition, MRSA colonization was associated with the presence of at least one underlying chronic illness, although this association was observed only among those who had not been hospitalized in the previous year (adjusted OR, 5.1; CI95, 1.2 to 21.9). CONCLUSIONS: We found a low prevalence of MRSA colonization in an adult outpatient population. MRSA carriers most likely acquired the organism through contact with healthcare facilities rather than in the community. These data show that care must be taken when attributing MRSA colonization to the community if detected in outpatients or during the first 24 to 48 hours of hospitalization.

Ambulatory Care Facilities↗
PubMed1986

A comprehensive investigation of immunity to poliomyelitis in a developing country.

A comprehensive nationwide surveillance program of serologic immunity of two-year-old black children, combined with evaluation of vaccine quality and distribution, was carried out in South Africa during 1983-1984. Sera were randomly collected from urban and rural groups and cluster samples collected from the semi-urban group. The sample represented 0.23% of the total target population. Satisfactory levels of immunity were found in the urban (80%) and semi-urban (71%) groups but a disquietingly low level was found for the rural group (59%). Individual districts in the rural group could be singled out for directed cluster sampling at a later stage. History and documentation of immunization corresponded well to serologic findings and revealed also a fairly substantial level of natural immunization among individuals who, on history, had received no vaccine. Some 95% of random samples of vaccine recalled from the field showed satisfactory levels of potency. An immunity surveillance program such as this is ideally suited and highly cost-effective for developing countries with incomplete immunization to prevent large-scale buildup of immunity deficit. The technique, however, is too insensitive to detect localized community immunity defects.

Antibodies, Viral↗
PubMed1992

Screening for cystic fibrosis.

Neonatal screening for cystic fibrosis (CF) reduces short-term morbidity but its long term effects remain to be demonstrated. The best available method is the assay of immunoreactive trypsin in dried blood spots, and specificity can be improved by adding direct or indirect genetic analysis. Pregnancies known to be at risk of CF can also be screened by molecular methods, and affected pregnancies terminated. The application of genetic testing to whole communities, to detect unknown heterozygotes, raises many questions which require consideration by society and the health professions. The development of effective treatment of the basic abnormality of cell function in CF would enhance the need for neonatal screening, and possibly reduce the requirement for abortion.

Cystic Fibrosis↗
PubMed2006

Prevalence of methicillin-sensitive and methicillin-resistant Staphylococcus aureus in pregnant women.

OBJECTIVE: To estimate the extent of Staphylococcus aureus vaginal-rectal colonization among pregnant women as severe S aureus infections have emerged in pregnant and postpartum women and infants. METHODS: We conducted a prospective surveillance study for methicillin-sensitive S aureus and methicillin-resistant S aureus on all routine de-identified vaginal-rectal prenatal group B streptococcus (GBS) screening cultures submitted to the microbiology laboratory of a tertiary-care facility from January to July 2005. Standard microbiologic techniques and molecular analyses were used to detect community-associated methicillin-resistant S aureus strains. As opposed to health care-associated methicillin-resistant S aureus isolates, community-associated methicillin-resistant S aureus isolates were defined as those possessing the type IV or type V staphylococcal chromosomal cassette mec element and usually lacking a multidrug-resistant phenotype. RESULTS: A total of 2,963 GBS screening cultures were analyzed, from which 743 (25.1%, 95% confidence interval [CI] 23.5-26.7%) GBS isolates and 507 (17.1%, 95% CI 15.7-18.5%) S aureus isolates were identified. Group B streptococcus colonization was significantly associated with S aureus colonization (prevalence odds ratio 2.1, 95% CI 1.7-2.5, P < .001). Of the S aureus isolates, 14 (2.8%, 95% CI 1.4-4.2%) were methicillin-resistant, and 13 of these were determined to be community-associated methicillin-resistant S aureus. CONCLUSION: The prevalence of S aureus colonization identified in GBS screening cultures from pregnant women was substantial and associated with GBS co-colonization. Although we do not advocate routine screening of pregnant women for methicillin-sensitive S aureus and methicillin-resistant S aureus colonization, we recommend continued monitoring of both methicillin-sensitive S aureus and methicillin-resistant S aureus infections in this population and their infants.

Anti-Bacterial Agents↗
PubMed2005

Methanogen communities and Bacteria along an ecohydrological gradient in a northern raised bog complex.

Mires forming an ecohydrological gradient from nutrient-rich, groundwater-fed mesotrophic and oligotrophic fens to a nutrient-poor ombrotrophic bog were studied by comparing potential methane (CH(4)) production and methanogenic microbial communities. Methane production was measured from different depths of anoxic peat and methanogen communities were detected by detailed restriction fragment length polymorphism (RFLP) analysis of clone libraries, sequencing and phylogenetic analysis. Potential CH(4) production changed along the ecohydrological gradient with the fens displaying much higher production than the ombrotrophic bog. Methanogen diversity also decreased along the gradient. The two fens had very similar diversity of methanogenic methyl-coenzyme M reductase gene (mcrA), but in the upper layer of the bog the methanogen diversity was strikingly lower, and only one type of mcrA sequence was retrieved. It was related to the Fen cluster, a group of novel methanogenic sequences found earlier in Finnish mires. Bacterial 16S rDNA sequences from the fens fell into at least nine phyla, but only four phyla were retrieved from the bog. The most common bacterial groups were Deltaproteobacteria, Verrucomicrobia and Acidobacteria.

Bacteria↗
PubMed2006

Characterization and quantification of ammonia-oxidizing bacteria in eutrophic coastal marine sediments using polyphasic molecular approaches and immunofluorescence staining.

Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia-oxidizing bacteria were most numerous at B30, where the ammonium concentration in the porewater was markedly lower and the nitrite concentration was slightly higher than nearby sites. These results reveal spatial distribution and shifts in the population structure of AOB corresponding to nutrients and organic inputs from the river run-off and phytoplankton bloom.

Ammonia↗
PubMed1999

Characterization of mercury resistance mechanisms in marine sediment microbial communities.

While estuarine sediments are often severely polluted with mercury, few studies have focused on the mechanisms of adaptation to mercury contamination in marine sediment microbial communities. In this study, we report a high frequency of Gram-negative bacterial isolates that are resistant to the heavy metal mercury obtained from the aerobic culturable marine microbial community. We detected a low frequency of genes homologous to mer(Tn21) in isolates from three out of four different estuarine environments. Other mercury resistant culturable bacterial isolates lacking homology to the known mer genes were able to reduce Hg(II) to its volatile Hg(0) form, indicating the presence of divergent mer genes. In addition, a number of mercury resistant isolates, obtained from three of the four marine sites investigated, exhibited decreased resistance to mercury in the presence of the protonophore carbonyl cyanide m-chlorophenylhydrazone. Representative mercury resistant bacterial isolates were identified by phylogenetic analysis as belonging to the alpha and gamma subclasses of the class Proteobacteria.

Journal Article↗
PubMed2001

Microcosm-based analyses of Scots pine seedling growth, ectomycorrhizal fungal community structure and bacterial carbon utilization profiles in boreal forest humus and underlying illuvial mineral horizons.

We report on the identity of indigenous mycorrhiza forming fungi and rhizosphere/mycorrhizosphere bacterial community carbon source utilization profiles of Scots pine (Pinus sylvestris L.) seedlings grown in boreal forest humus (O) or illuvial (B) mineral horizon containing microcosm growth systems. Based on rDNA (ITS)-RFLP analyses, a total of 10 fungal RFLP taxa were identified from pre-morphotyped mycorrhizas on 7-month-old seedling roots. Hierarchical cluster analysis, including corresponding RFLPs of known fungal species, confirmed root colonization by eight mycorrhizal species. In the O horizon, roots were colonized by e.g. Suillus bovinus, Suillus variegatus, Cenococcum geophilum, Piloderma croceum, Thelephora terrestris and Russula vinicolor. Mycobiont diversity in the mineral B horizon was lower but included Piceirhiza bicolorata and both Suillus species which produced extensive extramatrical mycelium. In comparison to non-colonized soils, rhizosphere and mycorrhizosphere compartments supported significantly higher numbers of bacteria (mean range 10(8)-10(11) cells g(-1) fresh weight (fw)). Specific rhizosphere/mycorrhizosphere 'niche'-linked bacterial communities were detected following multivariate analyses (PCA and CA) of bacterial carbon utilization profiles (Biolog(R) GN microplate). Distinct preferences for amino and carboxylic acids were identified in mineral B horizon rhizospheres whereas a wider range of carbon sources were utilized in the fungal-dominated mycorrhizospheres irrespective of soil types.

Journal Article↗
PubMed2000

Rampant early childhood dental decay: an example from Italy.

OBJECTIVES: This study sought to estimate the prevalence and related prediction factors for dental caries in 3- to 5-year-old children in Rome, Italy. METHODS: From a sample of 2,025 children, 1,494 (73.8%) were included in the analysis. Children with at least two primary maxillary incisors showing evidence of caries experience were considered affected by rampant early childhood dental decay (RECDD). Behavioral and socioeconomic variables, mutans streptococci counts, diet, and nutritional status were investigated for their association with RECDD using regression analysis. RESULTS: The prevalence of any caries was 27.3 percent, and was 7.6 percent for RECDD. Among all children, mean dft and dt scores per person were 1.1 (SD = 2.4) and 0.9 (SD = 2.3), respectively; among those classified as having RECDD, scores were 6.9 (SD = 4.2) and 6.7 (SD = 4.3), respectively. Children with RECDD had 56 percent of all the decayed teeth in the sample. Low and medium social classes, use of a baby bottle filled with sweetened beverages, high salivary mutans streptococcal levels, and malnutrition were directly associated with RECDD; milk and yogurt consumption and low Plaque Index scores were inversely associated with the condition. CONCLUSIONS: The high prevalence of RECDD suggests that the implementation of preventive programs should be a priority for dental public health. Because of its high prevalence among children as young as 3 years of age, preventive measures targeted toward pregnant women and toddlers should be developed and tested, while kindergarten students could be used for monitoring RECDD prevalence and for detection of communities at risk.

Animals↗
PubMed2005

Community proteomics of a natural microbial biofilm.

Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

Amino Acids↗