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PubMed1988

DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community.

We developed a protocol which yields purified bacterial DNA from the soil bacterial community. The bacteria were first dispersed and separated from soil particles in the presence of polyvinylpolypyrrolidone, which removes humic acid contaminants by adsorption to this insoluble polymer. The soil bacteria were then collected by centrifugation and lysed by using a comprehensive protocol designed to maximize disruption of the various types of bacteria present. Total bacterial DNA was purified from the cell lysate and remaining soil contaminants by using equilibrium density gradients. The isolated DNA was essentially pure as determined by UV spectral analysis, was at least 48 kilobases long, and was not subject to degradation, which indicated that there was no contaminating nuclease activity. The isolated DNA was readily digested by exogenously added restriction endonucleases and successfully analyzed by slot blot and Southern blot hybridizations. Using single-stranded, P-labeled DNA probes, we could detect and quantitate the presence of a specific microbial population in the natural soil community on the basis of the presence of a DNA sequence unique to that organism. The sensitivity of our methodology was sufficient to detect Bradyrhizobium japonicum at densities as low as 4.3 x 10 cells per g (dry weight) of soil, which corresponds to about 0.2 pg of hybridizable DNA in a 1-mug DNA sample.

Journal Article↗
PubMed1982

Demonstration of previously undetected hepatitis B viral determinants in an Australian Aboriginal population by monoclonal anti-hbs antibody radioimmunoassays.

High-affinity IgM and IgG monoclonal antibodies (anti-HBs) against hepatitis B surface antigen (HBsAg) determinants were used to study a confined Australian Aboriginal population, 51% of which showed evidence of exposure to hepatitis B virus (HBV). A conventional radioimmunoassay which uses polyvalent anti-HBs antisera indicated that 4.4% of the subjects were positive for HBsAg; a monoclonal IgM anti-HBs radioimmunoassay detected all these HBsAg-positive samples and showed enhanced binding activity in a further 5.4% of subjects. Detailed analysis of this binding activity in serum by different IgG and IgM monoclonal anti-HBs antibodies demonstrated additional HBsAg-associated determinants as well as remarkable homogeneity of the determinants in this population. It was concluded that there are HBV or HBV-like agents in this community not previously detected by conventional assays.

Adult↗
PubMed2006

Impacts of 2,4-D application on soil microbial community structure and on populations associated with 2,4-D degradation.

The effect of 2,4-dichlorophenoxyacetic acid (2,4-D) application rate on microbial community structure and on the diversity of dominant 2,4-D degrading bacteria in an agricultural soil was examined using cultivation-independent molecular techniques coupled with traditional isolation and enumeration methods. Fingerprints of microbial communities established under increasing concentrations of 2,4-D (0-500 mg kg-1) in batch soil microcosms were obtained using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene segments. While a 2,4-D concentration of at least 100 mg kg-1 was required to obtain an apparent change in the community structure as visualized by DGGE, the greatest impact of 2,4-D concentration occurred in the 500 mg kg-1 treatment, resulting in significantly reduced diversity of the dominant populations and enrichment by Burkholderia-like populations. The greatest diversity of 2,4-D degrading isolates was cultivated from the 10 mg kg-1 treatment, indicating that under these conditions, cultivation was more sensitive than DGGE for detecting changes in community structure. Most of these isolates harbored homologs of Ralstonia eutrophus JMP134 and Burkholderia cepacia tfdA catabolic genes. Results from this study revealed that agriculturally relevant application rates of 2,4-D may provide a temporary selective advantage for organisms capable of utilizing 2,4-D as a carbon and energy source.

2,4-Dichlorophenoxyacetic Acid↗
PubMed1998

Human cystic echinococcosis in a Uruguayan community: a sonographic, serologic, and epidemiologic study.

A prevalence and transmission study of human cystic echinococcosis (CE), due to infection with the dog tapeworm Echinococcus granulosus, was undertaken in the village of La Paloma in central Uruguay. The human population was registered and screened for CE by abdominal ultrasound scan as well as a number of serologic tests. Dogs were screened for E. granulosus infection by arecoline purgation as well as specific coproantigen testing. The total prevalence of human CE (new cases and those with a previous history) was 5.6% (64 of 1,149); 3.6% (40) of the cases were new ultrasound detected asymptomatic cases (mean age = 45 years). Age prevalence increased from 1.1% in the 4-6-year-old group to > 11% in the > 60-year-old group; the 20-29-year-old group had a significantly higher CE rate of 7.4%, compared with younger and older age groups, and there was no difference between sexes. A CE rate of 3.9% (20 of 514) was also recorded by ultrasound for new cases in the population residing outside the village. Most of the hydatid cysts were located in the liver presenting as either univesicular cysts or a solid mass, and of those 71% and 63%, respectively, with such cyst presentations were seropositive against E. granulosus cyst fluid antigens. Two of eight individuals who were filter paper blood spot seropositive, but ultrasound scan negative, were subsequently diagnosed respectively with pulmonary hydatidosis after radiography, and hepatic hydatidosis after computed tomography scan. Of 36 households with a CE patient, 32 were single cases while four households each harbored two CE cases. This did not represent a clustered distribution within families (23 of 117). Almost 20% of the dogs from La Paloma were found infected with E. granulosus after purge examination, with a mean worm number of 67 (range = 1-1,020). An additional eight dogs that were purge negative were Echinococcus coproantigen positive. The study showed that human CE is highly endemic in Uruguay, with one of the highest local prevalence rates in the world. Transmission appears to occur readily within well-developed towns, as well as on rural sheep ranches. Mass screening by ultrasound scanning with confirmatory serologic testing is an effective approach to case detection at the community level.

Adolescent↗
PubMed2001

Comparison of detection limits in environmental analysis--is it possible? An approach on quality assurance in the lower working range by verification.

Detection limit, reporting limit and limit of quantitation are analytical parameters which describe the power of analytical methods. These parameters are used for internal quality assurance and externally for competing, especially in the case of trace analysis in environmental compartments. The wide variety of possibilities for computing or obtaining these measures in literature and in legislative rules makes any comparison difficult. Additionally, a host of terms have been used within the analytical community to describe detection and quantitation capabilities. Without trying to create an order for the variety of terms, this paper is aimed at providing a practical proposal for answering the main questions for the analysts concerning quality measures above. These main questions and related parameters were explained and graphically demonstrated. Estimation and verification of these parameters are the two steps to get real measures. A rule for a practical verification is given in a table, where the analyst can read out what to measure, what to estimate and which criteria have to be fulfilled. In this manner verified parameters detection limit, reporting limit and limit of quantitation now are comparable and the analyst himself is responsible to the unambiguity and reliability of these measures.

Journal Article↗
PubMed2006

Phylogenetic dispersion of host use in a tropical insect herbivore community.

Theory has long predicted that insect community structure should be related to host plant phylogeny. We examined the distribution of insect herbivore associations with respect to host plant phylogeny for caterpillars (Lepidoptera), beetles (Coleoptera), and grasshoppers and relatives (orthopteroids) in a New Guinea rain forest. We collected herbivores from three lineages of closely related woody plants and from more distantly related plant lineages in the same locality to examine the phylogenetic scale at which host specificity can be detected in a community sample. By grafting molecular phylogenies inferred from three different genes into a supertree, we developed a phylogenetic hypothesis for the host community. Feeding experiments were performed on more than 100 000 live insects collected from the 62 host species. We examined patterns of host use with respect to the host plant phylogeny. As predicted, we found a negative relationship between faunal similarity, defined as the proportion of all herbivores feeding on two hosts that are shared between the hosts, and the phylogenetic distance between hosts based on DNA sequence divergence. Host phylogenetic distance explained a significant fraction of the variance (25%) in herbivore community similarity, in spite of the many ecological factors that probably influence feeding patterns. Herbivore community similarity among congeneric hosts was high (50% on average) compared to overlap among host families (20-30% on average). We confirmed this pattern using the nearest taxon index (NTI) and net relatedness index (NRI) to quantify the extent of phylogenetic clustering in particular herbivore associations and to test whether patterns are significantly different from chance expectations. We found that 40% of caterpillar species showed significant phylogenetic clustering with respect to host plant associations, somewhat more so than for beetles or orthopteroids. We interpret this as evidence that a substantial fraction of tropical forest insect herbivores are clade specialists.

Animals↗
PubMed2004

Spatial patterns and relations with site factors in a campos grassland under grazing.

Spatial distribution patterns and their relations with environmental factors at different scales were identified in ca. 100-ha grassland under cattle and sheep grazing, in Eldorado do Sul, RS, Brazil (30 degrees 05'S, 51 degrees 40'W). The field survey used 138 0.5 x 0.5 m quadrats located systematically on transects along relief gradients. The quadrats were arranged in groups of 3 contiguous quadrats, which were pooled for the analysis, thus forming 46 quadrats 1.5 x 0.5 m, in this way defining two observation scales. Vegetation description involved recording the presence and the visual estimation of cover-abundance of species in each quadrat. A total of 148 species belonging to 30 families was detected. The environmental conditions at each site were described by 30 variables related to soil chemical and physical properties, slope, exposure and relief position. Data analysis used cluster analysis, evaluation of group partition sharpness, ordination, significance of ordination axes, evaluation of environmental congruence and randomization testing. The results of the analysis with 46 quadrats supported those found with 138 quadrats. The vegetation patterns in the study area are associated to relief position and other related factors such as soil moisture. Two clearly defined grassland community types were detected, one occurring on the slopes and another on the wet lowlands.

Animals↗
PubMed1989

[Prevalence of handicapped individuals in a rural community].

A specially designed questionnaire was used to detect handicapped individuals in a rural community. The type and magnitude of incapacity was evaluated by a physician. Overall prevalence was 4.2% with a peak incidence in the 45 to 64 year age group (111.1 per 1000). Leading causes of incapacity were bone and muscle disorders and nervous or sensory problems. Chronic back pain was the leading individual problem. 66.7% of handicapped individuals require assistance for their everyday life activities and 47.2% are unable to engage in any productive job.

Adolescent↗
PubMed2002

Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters.

Microbial diversity in four wells along a groundwater flowpath in a coal-tar-waste-contaminated aquifer was examined using RFLP analysis of both 16S rDNA and naphthalene dioxygenase (NDO) genes. Amplified ribosomal DNA restriction analysis (ARDRA) relied upon eubacteria-specific primers to generate four clone libraries. From each library, 100 clones were randomly picked for analysis. Sixty percent of 400 clones contained unique ARDRA patterns. Diversity indices calculated for each community were high (Shannon-Weaver, H = 3.53 to 3.69). Clones representing ARDRA patterns found in the highest abundance were sequenced (31 total). Sequences related to aerobic bacteria (e.g., Nitrospira, Methylomonas, and Gallionella) predominated among those retrieved from the uncontaminated area of the site, whereas sequences related to facultatively aerobic and anaerobic bacteria (e.g. Azoarcus, Syntrophus, and Desulfotomaculum) predominated among those retrieved from contaminated areas of the site. Using NDO-specific primers and low-stringency PCR conditions, variability in RFLP patterns was only detected in community-derived DNA (3 of 4 wells) and not in 5 newly isolated naphthalene-degrading pure cultures. The ARDRA patterns of the pure culture isolates were not found in the clone libraries. Polymorphisms in community 16S rDNA and NDO genes found in well-water microorganisms reflected distinctive geochemical conditions across the site. Sequences related to sulfate-reducing bacteria were found in groundwater that contained sulfide, while sequences related to Gallionella, Syntrophus, and nitrate-reducing aromatic hydrocarbon-degrading bacteria were found in groundwater that contained ferrous iron, methane, and naphthalene, respectively.

Bacteria, Aerobic↗
PubMed2006

Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities.

BACKGROUND: The beta-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable. RESULTS: We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. This has been shown by analysis of samples from an enrichment of activated sludge on testosterone resulting in an increase in abundance and finally isolation of C. testosteroni. Additionally, we have successfully used quantitative PCR to follow the C. testosteroni abundance during a laboratory scale wastewater bioaugmentation experiment. CONCLUSION: The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities.

Colony Count, Microbial↗
PubMed1986

Onchocerciasis in Sudan: the Southern Darfur focus.

The prevalence, intensity and clinical manifestations of onchocerciasis were investigated in three village communities along the Bahr El Arab and its tributaries in Southern Darfur, Western Sudan. Onchocerca volvulus has not been reported from this region before. Over 300 people were examined and the selection of patients was aimed at obtaining a cross-sectional view of the disease at all ages and in both sexes. Prevalence rates were high (67.5%, 28.6% and 32% in Titribi, Radom and Kafia Kingi, respectively). The intensity of infection in young adults was generally about 30 mf/mg, but ranged up to 100 mf/mg. Infections were detected in subjects as young as two years old; about one quarter of those sampled in Titribi had nodules, mostly in the pelvic region. Clinical signs of acute and chronic dermal changes were especially marked in Titribi. This village was located closest to the breeding sites, which appear in the rainy season only. More than a third of those samples had severe pruritus and showed many self-inflicted excoriations. Both anterior and posterior eye segment changes were detected in each community, and cases of onchocercal blindness were attributed to sclerosing keratitis and to optic and chorioretinal atrophy. One case typical of intensely localized disease was seen, where the affliction was unilateral and severe with oedema and pigment changes, but very few microfilariae present. Onchocerciasis appears to be well established in this region and has apparently caused abandonment of some settlements in recent years.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed2002

Effect of an industrial discharge on water quality and periphyton structure in a pampeam stream.

Seasonal sampling was carried out at four sites on a pampean stream that receives industrial effluent from two textile factories. To evaluate water quality, several physical and chemical parameters were examined and the periphyton growing on cattail (Typha latifolia L.) were analyzed. Water quality and periphyton structure differed significantly between sites upstream and downstream of the discharge. Differences in temperature and also in concentrations of phosphate, dissolved oxygen, and phaeopigment were detected. At the same time, changes in the dominant algae groups were observed. Downstream of the industrial discharge, the number of Bacillariophyta decreased, while species of Cianophyta and Euglenophyta were more abundant. This abundance correlated with increased phosphate and organic matter content and decreased oxygen concentration. Although this study did not detect a reduction in the number of species, similarity between stands decreased downstream of the industrial discharge. Changes in community structure were readily detected in this situation because the communities of the polluted and unpolluted zones were qualitatively different. Periphyton growing naturally on Typha latifolia is a useful indicator of the impact of waste waters on the biota and can also be used to evaluate water body recovery.

Environmental Monitoring↗
PubMed2003

Plasmid introduction in metal-stressed, subsurface-derived microcosms: plasmid fate and community response.

The nonconjugal IncQ plasmids pMOL187 and pMOL222, which contain the metal resistance-encoding genes czc and ncc, were introduced by using Escherichia coli as a transitory delivery strain into microcosms containing subsurface-derived parent materials. The microcosms were semicontinuously dosed with an artificial groundwater to set a low-carbon flux and a target metal stress (0, 10, 100, and 1,000 micro M CdCl(2)), permitting long-term community monitoring. The broad-host-range IncPalpha plasmid RP4 was also transitorily introduced into a subset of microcosms. No novel community phenotype was detected after plasmid delivery, due to the high background resistances to Cd and Ni. At fixed Cd doses, however, small but consistent increases in Cd(r) or Ni(r) density were measured due to the introduction of a single pMOL plasmid, and this effect was enhanced by the joint introduction of RP4; the effects were most significant at the highest Cd doses. The pMOL plasmids introduced could, however, be monitored via czc- and ncc-targeted infinite-dilution PCR (ID-PCR) methods, because these genes were absent from the indigenous community: long-term presence of czc (after 14 or 27 weeks) was contingent on the joint introduction of RP4, although RP4 cointroduction was not yet required to ensure retention of ncc after 8 weeks. Plasmids isolated from Ni(r) transconjugants further confirmed the presence and retention of a pMOL222-sized plasmid. ID-PCR targeting the RP4-specific trafA gene revealed retention of RP4 for at least 8 weeks. Our findings confirm plasmid transfer and long-term retention in low-carbon-flux, metal-stressed subsurface communities but indicate that the subsurface community examined has limited mobilization potential for the IncQ plasmids employed.

Bacteria↗
PubMed1989

Biotransformation and detoxification of T-2 toxin by soil and freshwater bacteria.

Bacterial communities isolated from 17 of 20 samples of soils and waters with widely diverse geographical origins utilized T-2 toxin as a sole source of carbon and energy for growth. These isolates readily detoxified T-2 toxin as assessed by a Rhodotorula rubra bioassay. The major degradation pathway of T-2 toxin in the majority of isolates involved side chain cleavage of acetyl moieties to produce HT-2 toxin and T-2 triol. A minor degradation pathway of T-2 toxin that involved conversion to neosolaniol and thence to 4-deacetyl neosolaniol was also detected. Some bacterial communities had the capacity to further degrade the T-2 triol or 4-deacetyl neosolaniol to T-2 tetraol. Two communities, TS4 and KS10, degraded the trichothecene nucleus within 24 to 48 h. These bacterial communities comprised 9 distinct species each. Community KS10 contained 3 primary transformers which were able to cleave acetate from T-2 toxin but which could not assimilate the side chain products, whereas community TS4 contained 3 primary transformers which were able to grow on the cleavage products, acetate and isovalerate. A third community, AS1, was much simpler in structure and contained only two bacterial species, one of which transformed T-2 toxin to T-2 triol in monoculture. In all cases, the complete communities were more active against T-2 toxin in terms of rates of degradation than any single bacterial component. Cometabolic interactions between species is suggested as a significant factor in T-2 toxin degradation.

Bacteria↗
PubMed2006

Community influenza activity and risk of acute influenza-like illness episodes among healthy unvaccinated pregnant and postpartum women.

This study investigated the relation between weekly levels of influenza activity and the risk of acute influenza-like illness episodes among 8,323 healthy pregnant and postpartum women enrolled in a Puget Sound region, Washington, health maintenance organization, Group Health Cooperative, between June 1991 and December 1997. The authors classified weeks between October and May for isolate activity level based on surveillance data for influenza, respiratory syncytial virus, parainfluenza, and adenovirus infection. Influenza-like illness episodes were identified from medical encounters assigned a diagnostic code consistent with a symptomatic influenza infection. The authors compared the occurrence of influenza-like illness episodes within each pregnancy stage for periods with varying levels of influenza isolate detection in the community. Repeated-measures logistic regression methods accounted for time-dependent factors. The adjusted strength of association between influenza exposure and influenza-like illness episodes increased as the pregnancy stage progressed (first trimester odds ratio = 1.12, 95% confidence interval: 0.79, 1.59; second trimester odds ratio = 1.30, 95% confidence interval: 0.97, 1.73; third trimester odds ratio = 1.84, 95% confidence interval: 1.31, 2.59; postpartum period odds ratio = 2.28, 95% confidence interval: 1.42, 3.68). Pregnancy stage modified the association between influenza activity and influenza-like illness episodes. Findings estimate that 20-43 pregnant/postpartum women would need to be vaccinated with an 80% effective vaccine to prevent one influenza-like illness episode.

Acute Disease↗
PubMedDate not supplied

[Biogeochemical processes in the algal-bacterial mats of the Urinskii alkaline hot spring].

The structure and production characteristics of microbial communities from the Urinskii alkaline hot spring (Buryat Republic, Russia) have been investigated. A distinctive characteristic of this hot spring is the lack of sulfide in the issuing water. The water temperature near the spring vents ranged from 69 to 38.5 degrees C and pH values ranged from 8.8 to 9.2. The total mineralization of water was less than 0.1 g/liter. Temperature has a profound effect on the species composition and biogeochemical processes occurring in the algal-bacterial mats of the Urinskii hot spring. The maximum diversity of the phototrophic community was observed at the temperatures 40 and 46 degrees C. A total of 12 species of cyanobacteria, 4 species of diatoms, and one species of thermophilic anoxygenic phototrophic bacteria, Chloroflexus aurantiacus, have been isolated from mat samples. At temperatures above 40 degrees C, the filamentous cyanobacterium Phormidium laminosum was predominant; its cell number and biomass concentration were 95.1 and 63.9%, respectively. At lower temperatures, the biomass concentrations of the cyanobacterium Oscillatoria limosa and diatoms increased (50.2 and 36.4%, respectively). The cyanobacterium Mastigocladus laminosus, which is normally found in neutral or slightly acidic hydrothermal systems, was detected in microbial communities. As the diatom concentration increases, so does the dry matter concentration in mats, while the content of organic matter decreases. The concentrations of proteins and carbohydrates reached their maximum levels at 45-50 degrees C. The maximum average rate of oxygenic photosynthesis (2.1 g C/m2 day), chlorophyll a content (343.4 mg/m2), and cell number of phototrophic microorganisms were observed at temperatures from 45 to 50 degrees C. The peak mass of bacterial mats (56.75 g/m2) occurred at a temperature of 65-60 degrees C. The maximum biomass concentration of phototrophs (414.63 x 10(-6) g/ml) and the peak rate of anoxygenic photosynthesis [0.42 g C/(m2 day)] were observed at a temperature of 35-40 degrees C.

Algal Proteins↗
PubMedDate not supplied

[Q-fever in the Zadar region].

The occurrence of Q fever in a population of Zadar region (2787 km2) which has five microregions (Zadar, Benkovac, Biograd, Obrovac and Pag microregion) is presented. In 1986, nine cases of Q fever were reported. Five patients were detected in Zadar community, one in Pag microregion and 3 in Biograd community and microregion, respectively. In 1989, two cases in Zadar and, in 1988 and 1991, one case in each year from the territory of Zadar were found. A total of 13 cases of Q fever were treated and reported. The personnel of the Zadar Veterinary Stations were not able to provide information since blood samples from the suspected animals were not taken. The agent was therefore not isolated. It is known that there were more serologically proven cases of Q fever, but they were not registered by the Epidemiologic Service of the Zadar Department for Health Protection. Clinical manifestation in a form of pulmonary affection is a very significant data in this zoonosis and it is therefore most commonly detected at the hospital departments for lung diseases, what was one of the reasons for undertaking this study.

Adult↗
PubMed1999

Detection and control of high blood pressure in the community : Do we need a wake-up call?

At the community level, the effect of national programs in increasing hypertension awareness, prevention, treatment, and control is unclear. This study evaluated the degree of detection and control of high blood pressure in a random population-based sample of Olmsted County, Minnesota, residents >/=45 years old, of whom 636 subjects among 1245 eligible residents agreed to participate. Home interview and home and office measurements of blood pressure were used to estimate awareness, treatment, and control rates for hypertension in the community. Mean blood pressures (+/-SD) were 138/80+/-20/12 mm Hg for men and 137/76+/-23/11 mm Hg for women. The overall prevalence of hypertension was 53%. The percentage of subjects with treated and controlled hypertension was 16.6%. Thirty-nine percent of subjects were unaware of their hypertension. Despite clinical trial evidence of reduced morbidity and mortality with antihypertensive therapy, recently reported national data suggest a leveling-off trend for treatment and control of hypertension. This population-based study supports these observations and suggests that at a community level, hypertension awareness and blood pressure control rates are suboptimal, presumably because of decreased attention to the detection and control of hypertension.

Aged↗