Practical implications of using non-relational databases to store large genomic data files and novel phenotypes

The objective of our study was to provide practical directions on the storage of genomic information and novel phenotypes (treated here as unstructured data) using a non-relational database. The MongoDB technology was assessed for this purpose, enabling frequent data transactions involving numerous individuals under genetic evaluation. Our study investigated different genomic (Illumina Final Report, PLINK, 0125, FASTQ, and VCF formats) and phenotypic (including media files) information, using both real and simulated datasets. Advantages of our centralized database concept include the sublinear running time for queries after increasing the number of samples/markers exponentially, in addition to the comprehensive management of distinct data formats while searching for specific genomic regions. A comparison of our non-relational and generic solution, with an existing relational approach (developed for tabular data types using 2 bits to store genotypes), showed reduced importing time to handle 50M SNPs (PLINK format) achieved by the relational schema. Our experimental results also reinforce that data conversion is a costly step required to manage genomic data into both relational and non-relational database systems, and therefore, must be carefully treated for large applications.     

Roraimine: a bisbenzylisoquinoline alkaloid from Cissampelos sympodialis roots

The roots of Cissampelos sympodialis yielded Roraimine (1), a novel bisbenzylisoquinoline alkaloid and liriodenine (2), a known oxoaporphine alkaloid.     

Inferred longevity of Amazonian rainforest trees based on a long-term demographic study

We used data from a long-term (14–18 years) demographic study to infer the maximum longevity for populations of 93 relatively abundant tree species in central Amazonia. We also assessed the influence of several life-history features (wood density, growth form, mortality rate, recruitment rate, stem diameter, growth increment, population density) on tree longevity. Data on 3159 individual trees were collected in 24 permanent, 1 ha plots in undisturbed forest arrayed across a large (ca. 1000 km²) study area. For each species, three estimates of longevity were generated (by dividing the stem diameter of the largest tree by the median, upper quartile, and upper decile of observed diameter-growth rates), and the mean of these three values was used as a longevity estimate. Longevity values ranged from 48 years in the pioneer Pourouma bicolor (Cecropiaceae) to 981 years for the canopy tree Pouteria manaosensis (Sapotaceae), with an overall mean of 336±196 years. These growth-based estimates of maximum tree age were concordant with those derived from analyses of mean mortality rates. Tree longevity was positively correlated with wood density, maximum stem diameter, and population density, and negatively correlated with annual mortality, recruitment, and growth rates. On average, pioneer species had much lower longevity than did non-pioneers, whereas among old-growth trees, emergent species had greater longevity than did canopy species. Our results are consistent with radiocarbon-based studies that suggest that Amazonian trees can occasionally exceed 1000 years of age.     

Arbuscular Mycorrhizal Fungi and Glomalin‐Related Soil Protein as Potential Indicators of Soil Quality in a Recuperation Gradient of the Atlantic Forest in Brazil

This study aimed at surveying arbuscular mycorrhizal fungi (AMF) species and glomalin‐related soil protein (GRSP) to understand their role as presumable biological indicators of soil quality in an undisturbed forest site (NT) and three sites with different management histories, soil textures, and different ages of recovery after reforestation for 20 (R20), 10 (R10) and 5 years (R05). Our objective was to determine how physical, chemical and microbiological soil attributes influence AMF species distribution, total‐GRSP (T‐GRSP) and easily extractable‐GRSP (EE‐GRSP). Glomus and Acaulospora were related to impacted sites, Gigaspora rosea to sites R10 and R20 that have different management histories and soil textures and Glomus geosporum to sites NT and R10, suggesting some influence of texture on its distribution. Scutellospora pellucida and other species were found only in one season. Correlations between EE‐GRSP and T‐GRSP on the one hand and total carbon and nitrogen, dehydrogenase and urease activity, microbial biomass carbon and microbial biomass nitrogen, on the other, reached values of 40–70% and were especially strong in summer. Soil bulk density had a negative and macroporosity a positive effect only on EE‐GRSP, suggesting the necessity to choose either EE‐GRSP or T‐GRSP as biological indicator depending on the soil characteristics and management. This study demonstrates the effect of recovery age, seasonality and other soil attributes on AMF and GRSP distribution and shows that these biological attributes may be used as indicators of soil quality in the Atlantic forest in Brazil. Copyright © 2013 John Wiley & Sons, Ltd.     

A comparative study of methods for diagnosis of obesity in an urban mixed-race population in Minas Gerais, Brazil

BACKGROUND: Obesity is defined as an excess of total body fat and may be assessed by different methods. The objective of the present study was to establish the discriminatory power of anthropometric data in determining obesity. METHODS: The subjects comprised 685 individuals, aged 20-79 years, sampled from a population-based survey. The following indicators were used: body mass index (BMI), waist circumference (WC) and total body fat percentage estimated with both Siri's equation (%BF Siri) and foot-to-foot bioelectrical impedance analysis (%BF BIA). Sensitivity and specificity of different cut-off points for each method were determined using %BF BIA as reference. RESULTS: Of 685 participants, 57.6% were aged >/= 40 years, 69.9% were women and 72.6% self-referred themselves as non-white. To classify obesity based on sex and age among women aged 0.05). Classifying according to skin colour did not change cut-off points in any indicator. CONCLUSION: BMI and WC better discriminate obesity among women and men aged >/= 40 years from a mixed-race population.     

Effect of the citrus flavanone naringenin on oxidative stress in rats

Flavonoids are non-nutrient plant phenolic compounds proposed to provide health benefits in humans. The antioxidant and prooxidant effects of the citrus flavanone naringenin have been tested only in vitro. The dose-response effect of naringenin consumption was tested in weanling rats (n=6-8/group) with a 2x4 factorial design using high or low oxidative stress (Hox or Lox, respectively) diets, created by adequate or deficient amounts of vitamin E and selenium, with three increasing naringenin concentrations (30, 60, or 120 mg/kg of diet). Hox compared to Lox rats exhibited reduced growth and liver hypertrophy, which was not prevented by naringenin consumption. Also, Hox rats exhibited severalfold higher liver NAD(P)H:quinone oxidoreductase-1 activity, which was further elevated in proportion to naringenin intake, but this was not sufficient to protect against oxidative stress indicated by higher liver total aldehydes. In addition, dietary naringenin did not affect antioxidant nutrient status or physiological markers of growth under Lox conditions. Thus, dietary naringenin did not exhibit antioxidant or prooxidant effects in vivo in this rat model.     

Two Resistance Modes to Clover yellow vein virus in Pea Characterized by a Green Fluorescent Protein-Tagged Virus

ABSTRACT This study characterized resistance in pea lines PI 347295 and PI 378159 to Clover yellow vein virus (ClYVV). Genetic cross experiments showed that a single recessive gene controls resistance in both lines. Conventional mechanical inoculation did not result in infection; however, particle bombardment with infectious plasmid or mechanical inoculation with concentrated viral inocula did cause infection. When ClYVV No. 30 isolate was tagged with a green fluorescent protein (GFP) and used to monitor infection, viral cell-to-cell movement differed in the two pea lines. In PI 347595, ClYVV replicated at a single-cell level, but did not move to neighboring cells, indicating that resistance operated at a cell-to-cell step. In PI 378159, the virus moved to cells around the infection site and reached the leaf veins, but viral movement was slower than that in the susceptible line. The viruses observed around the infection sites and in the veins were then recovered and inoculated again by a conventional mechanical inoculation method onto PI 378159 demonstrating that ClYVV probably had mutated and newly emerged mutant viruses can move to neighboring cells and systemically infect the plants. Tagging the virus with GFP was an efficient tool for characterizing resistance modes. Implications of the two resistance modes are discussed.     

Effects of region, soil, land use, and terrain type on fuelwood properties of five tree/shrub species in the Sahelian and Sudanian ecozones of Mali

? Context

There is little information about inter- and intra-specific variation in fuelwood properties of trees/shrubs in West Africa.

? Aims

We studied variation in fuelwood properties of Balanites aegyptiaca, Combretum glutinosum, Guiera senegalensis, Piliostigma reticulatum, and Zizyphus mauritiana in the Sahelian and Sudanian ecozones of Mali.

? Methods

Trees were sampled on different soil (sandy, sandy/loam, or rocky), land use (parkland agroforest or woodland), and terrain (flat, temporarily flooded, or hill slope) types in five regions extending from the drier eastern to the more humid western parts of Mali. Basic density, volatile matter, fixed carbon, ash content, moisture content, gross calorific value, and fuel value index were measured for each tree and adjusted for tree age.

? Results

All fuelwood properties differed significantly among species, but there were significant species by region interactions. Most fuelwood properties of four species differed significantly among regions. Soil and/or land use type had significant effects on a few fuelwood properties of four species.

? Conclusion

In general, fuelwood production is recommended in all regions for G. senegalensis, in drier regions for B. aegyptiaca and C. glutinosum, in more humid regions for Z. mauritiana, and on rocky soils for all species. Fuelwood production of P. reticulatum is not recommended.