Use of base excision sequence scanning for detection of genetic variations in St. Louis encephalitis virus isolates.
(17/6654)
Twenty-two isolates of St. Louis encephalitis (SLE) virus of various geographical origins (Brazil, Argentina, Panama, Texas, Missouri, Maryland, California, and Florida) were examined for genetic variation by the base excision sequence scanning (BESS T-scan) method. A fragment was amplified in the envelope gene with the forward primer labeled in the PCR. The BESS T-scan method determined different clusters according to the profiles generated for the isolates and successfully grouped the isolates according to their geographical origins. Two major clusters, the North American cluster (cluster A) and the South and Central American cluster (cluster B), were defined. Two subgroups, the Texas-California subgroup (subgroup A1) and the Missouri-Maryland-Florida subgroup (subgroup A2), were distinguished within group A. Similarly, group B strains were subclustered to a South American subgroup (subgroup B1) and a Central American subgroup (subgroup B2). These results were consistent with those obtained by DNA sequencing analysis. The ability of the BESS T-scan method to discriminate between strains that present with high degrees of nucleotide sequence similarity indicated that this method provides reliable results and multiple applications for other virus families. The method has proven to be suitable for phylogenetic comparison and molecular epidemiology studies and may be an alternative to DNA sequencing. (+info)
World food trends and prospects to 2025.
(18/6654)
This paper reviews food (especially cereal) production trends and prospects for the world and its main regions. Despite fears to the contrary, in recent years we have seen continued progress toward better methods of feeding humanity. Sub-Saharan Africa is the sole major exception. Looking to the future, this paper argues that the continuation of recent cereal yield trends should be sufficient to cope with most of the demographically driven expansion of cereal demand that will occur until the year 2025. However, because of an increasing degree of mismatch between the expansion of regional demand and the potential for supply, there will be a major expansion of world cereal (and noncereal food) trade. Other consequences for global agriculture arising from demographic growth include the need to use water much more efficiently and an even greater dependence on nitrogen fertilizers (e.g., South Asia). Farming everywhere will depend more on information-intensive agricultural management procedures. Moreover, despite continued general progress, there still will be a significant number of undernourished people in 2025. Signs of heightened harvest variability, especially in North America, are of serious concern. Thus, although future general food trends are likely to be positive, in some respects we also could be entering a more volatile world. (+info)
Ecological and geographic characteristics predict nutritional status of communities: rapid assessment for poor villages.
(19/6654)
The quality of poverty alleviation programmes relies heavily on appropriate targeting and priority setting. Major problems in assessing poverty include identification of the indicators of poverty and the methods used for its assessment. Nutritional status, expressed by anthropometric indices, has been proposed as a poverty indicator because of its validity, objectivity, reliability and feasibility. This study was conducted to explore the application of remote sensing to poverty mapping based on nutritional status at the community level. Relationships between the nutritional status within a community and the ecological characteristics of the community were investigated. Multiple linear regression tests were executed, and the resultant equations were tested for their validity in predicting communities with poor nutritional status. Among geographical and ecological indicators used, distance to the nearest market, main soil type, rice field area, and perennial cultivation area were found to be most useful predictors for the ranking of the communities by nutritional status. Among non-ecological determinants, food consumption, health service status and living conditions were also found as predictors. The highest correlation was found if total population was also taken into account in the regression model (R2 = 0.69; p < 0.0001). In the assessment of the sensitivity and specificity of the eight models studied, 'undernutrition' was defined as a condition where a community belongs in the first quartile for nutritional status (highest prevalence of undernutrition), and the baseline nutritional survey was considered as a standard method for final diagnosis. Most models which included only ecological factors in the equations had lower sensitivity and specificity than models which included all determinant factors in the equations. All models which took into account the total population had higher sensitivity and specificity than those that did not take total population into account. The best model of those that took into account only the geographical and ecological characteristics of the community's living environment had similar sensitivity and specificity (80% and 94.1%, respectively) as the models that considered non-geographical and non-ecological variables in addition to geographical and ecological variables. In the case of West Sumatra, only four ecological and geographic characteristics were sufficient to predict poverty in village. Since these characteristics could be surveyed by remote sensing, it may well be possible to use remote sensing for a rapid method for poverty mapping. (+info)
Geographic information systems and the environmental risk of schistosomiasis in Bahia, Brazil.
(20/6654)
A geographic information system was constructed using maps of regional environmental features, Schistosoma mansoni prevalence in 30 representative municipalities, and snail distribution in Bahia, Brazil to study the spatial and temporal dynamics of infection and to identify environmental factors that influence the distribution of schistosomiasis. Results indicate that population density and the duration of annual dry period are the most important determinants of prevalence of schistosomiasis in the areas selected for study. Maximum rainfall, total precipitation during three consecutive months, annual maximum or minimum temperatures, and diurnal temperature difference were not shown to be significant factors influencing S. mansoni prevalence in local populations or distribution of snail hosts. Prevalence of the disease was highest in the coastal areas of the state. Higher prevalence tended to occur in areas with latossolo soil type and transitional vegetation. (+info)
Gene genealogies in geographically structured populations.
(21/6654)
Population genetics theory has dealt only with the spatial or geographic pattern of degrees of relatedness or genetic similarity separately for each point in time. However, a frequent goal of experimental studies is to infer migration patterns that occurred in the past or over extended periods of time. To fully understand how a present geographic pattern of genetic variation reflects one in the past, it is necessary to build genealogy models that directly relate the two. For the first time, space-time probabilities of identity by descent and coalescence probabilities are formulated and characterized in this article. Formulations for general migration processes are developed and applied to specific types of systems. The results can be used to determine the level of certainty that genes found in present populations are descended from ancient genes in the same population or nearby populations vs. geographically distant populations. Some parameter combinations result in past populations that are quite distant geographically being essentially as likely to contain ancestors of genes at a given population as the past population located at the same place. This has implications for the geographic point of origin of ancestral, "Eve," genes. The results also form the first model for emerging "space-time" molecular genetic data. (+info)
Temporal and geographical distributions of reported cases of Escherichia coli O157:H7 infection in Ontario.
(22/6654)
The distribution of 3001 cases of verocytotoxigenic Escherichia coli (VTEC) reported in the Province of Ontario, Canada, were examined to describe the magnitude of this condition geographically and to evaluate the spatial relationship between livestock density and human VTEC incidence using a Geographical Information System. Incidence of VTEC cases had a marked seasonal pattern with peaks in July. Areas with a relatively high incidence of VTEC cases were situated predominantly in areas of mixed agriculture. Spatial models indicated that cattle density had a positive and significant association with VTEC incidence of reported cases (P = 0.000). An elevated risk of VTEC infection in a rural population could be associated with living in areas with high cattle density. Results of this study suggested that the importance of contact with cattle and the consumption of contaminated well water or locally produced food products may have been previously underestimated as risk factors for this condition. (+info)
Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods.
(23/6654)
Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended. (+info)
Salmonella enteritidis phage types 1 and 4: pheno- and genotypic epidemiology of recent outbreaks in Finland.
(24/6654)
In the 1990s, Salmonella enterica subsp. enterica serovar Enteritidis has caused 15 outbreaks in Finland; 12 of them were caused by phage type 1 (PT1) and PT4. Thus far, there has been no clear evidence as to the source of these Salmonella Enteritidis PT1 and PT4 strains, so it was necessary to try to characterize them further. Salmonella Enteritidis PT1 (n = 57) and PT4 (n = 43) isolates from different sources were analyzed by genomic pulsed-field gel electrophoresis (PFGE), plasmid profiling, and antimicrobial resistance testing to investigate the distribution of their subtypes in Finland. It was also hoped that this investigation would help in identifying the sources of the infections, especially the sources of the outbreaks caused by PT1 and PT4 in the 1990s. The results showed that both PFGE and plasmid profiling, but not antimicrobial susceptibility testing, were capable of differentiating isolates of Salmonella Enteritidis PT1 and PT4. By genotypic methods, it was possible to divide both PT1 and PT4 isolates into 12 subtypes. It could also be shown that all PT1 outbreak isolates were identical and, at least with this collection of isolates, that the outbreaks did not originate from the Baltic countries or from Russia, where this phage type predominates. It was also established that the outbreaks caused by PT4 all had different origins. Valuable information for future investigations was gained on the distribution of molecular subtypes of strains that originated from the tourist resorts that are popular among Finns and of strains that were isolated from livestock. (+info)