Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny

The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.      

Adipose tissue R2* signal is increased in subjects with obesity: A preliminary MRI study

Objective : Circulating and adipose tissue markers of iron overload are increased in subjects with obesity. The aim is to study iron signals in adipose tissue. Methods: Adipose tissue R2* values and hepatic iron concentration (HIC) were evaluated using magnetic resonance imaging (MRI) in 23 middle‐aged subjects with obesity and 20 subjects without obesity. Results: Subcutaneous (SAT) and visceral adipose tissue (VAT) R2* were increased in subjects with obesity (P = 0.004 and P = 0.008) and correlated significantly and positively with HIC in all subjects. Strikingly, most of the associations of liver iron with metabolic parameters were replicated with SAT and VAT R2*. BMI, waist circumference, fat mass, HOMA value, and C‐reactive protein positively correlated with HIC and SAT and VAT R2*. BMI or percent fat mass (but not insulin resistance) contributed independently to 26.8‐34.8% of the variance in sex‐ and age‐adjusted SAT or VAT R2* (β > 0.40, P < 0.005). Within subjects with obesity, total cholesterol independently contributed to 14.8% of sex‐ and age‐adjusted VAT iron variance (β = 0.50, P = 0.025). Conclusions: Increased R2* in adipose tissue, which might indicate iron content, runs in parallel to liver iron stores of subjects with obesity. VAT iron seems also associated with serum cholesterol within subjects with obesity.     

盐生植物角果碱蓬种子二型性对环境的适应策略

角果碱蓬(Suaeda corniculata)是藜科一年生盐生植物, 在我国分布于北方盐碱滩涂和盐碱荒漠地区。角果碱蓬具有棕色和黑色两种异型体种子(简称棕色和黑色种子)。对采自内蒙古鄂托克前旗盐渍化生境的角果碱蓬二型种子的形态、休眠和萌发特性开展对比研究, 测定了二型种子休眠和萌发行为对温度、光照和盐分(NaCl)的响应, 以揭示盐生植物异型种子对温带盐漠生境的适应对策。结果表明: (1)二型性种子在大小、种皮特性和结实比例方面有显著差异。与黑色种子相比, 棕色种子个体较大, 种皮透水性强。黑色种子与棕色种子的结实比例约为5.6 : 1。(2)新成熟的棕色种子的萌发对各温度梯度和光照条件不敏感, 萌发率较高(84%-100%); 而新成熟的黑色种子萌发率较低(8%-78%), 萌发对光照敏感。(3)黑色种子具有浅度生理休眠, 种皮划破、赤霉素处理和低温层积均可有效地提高种子的萌发率。(4)二型种子萌发对土壤盐分的胁迫具有不同的响应。与黑色种子相比, 棕色种子对盐分胁迫不敏感, 在较高的盐分浓度下仍有较高的萌发率, 低温层积处理能够降低黑色种子对盐胁迫的敏感性, 有效地提高种子的初始萌发率、萌发恢复率和最终萌发率。角果碱蓬二型种子不同的形态、休眠和萌发特性, 提高了该物种在高度异质性生境中的适合度, 对种群成功地适应温带盐漠环境具有重要的意义。     

荷木树干CO_2释放通量与木质部液流和CO_2浓度的关系

采用红外气体分析仪,于2008年10月17-19日连续3个昼夜原位监测了荷木的树干CO_2释放通量、树干温度、木质部液流密度和CO_2浓度.结果表明:树干CO_2释放通量(EA)日变化呈S形曲线,不同径级间差异显著.EA与树干温度呈显著幂函数关系(0.24

Abstract：

By using a Li-820 infra-red CO_2 gas analyzer, an in situ measurement of Schima super-ba stem CO_2 efflux was conducted for three consecutive days from 17 to 19 October 2008. In the meantime, the stem temperature, xylem sap efflux density, and xylem CO_2 concentration were measured. The stem CO_2 efflux had a diurnal variation of "S" pattern, and differed significantly with stem diameter. There was a significant exponential relationship between stem CO_2 efflux and stem temperature (0. 24 < R~2 < 0. 78). The temperature coefficient (b) and regression coeffi-cient (R~2) were higher at nighttime than at daytime, and the Q_(10) value ranged from 2. 01 to 2. 79. The stem CO_2 efflux correlated significantly with the xylem CO_2 concentration, and the best regression curve was cubic (R~2= 0. 48). Excluding the effects of stem temperature, the stem CO_2 efflux showed a significant negative correlation with xylem sap flux density (r =-0.462). Therefore, only using simple temperature function to estimate stem CO_2 efflux would yield a significant error, and xylem sap flux should be taken into consideration in the stem CO_2 emux estimation.     

The presence of serum anti-Ascaris lumbricoides IgE antibodies and of Trichuris trichiura infection are risk factors for wheezing and/or atopy in preschool-aged Brazilian children

Background

The elucidation of factors that trigger the development of transient wheezing in early childhood may be an important step toward understanding the pathogenesis of asthma and other allergic diseases later in life. Transient wheezing has been mainly attributed to viral infections, although sensitisation to aeroallergens and food allergens may occur at an early age. In developing countries, intestinal helminthic infections have also been associated with allergy or atopy-related disorders.

Objective

The aim of this study was to explore the association of Trichuris trichiura and Ascaris lumbricoides infections with wheezing and atopy in early childhood.

Study design

A cross-sectional study using a Portuguese-language ISAAC phase I questionnaire, adapted for preschool-aged children, nested in a cohort study of childhood diarrhoea, was conducted on 682 children. Two faecal samples per child were examined for the presence of intestinal helminthic infection. IgE antibodies against three allergenic preparations (Dermatophagoides pteronyssinus, Blomia tropicalis and common child food), as well as against A. lumbricoides antigens, were measured in a sub-sample of these children, whose parents allowed the procedure. Atopy was defined by the presence of levels of serum IgE antibodies ≥0.35 kU/L against at least one of the three tested allergenic preparations.

Results

Active T. trichiura infection but not A. lumbricoides infection was positively associated with wheezing in the total studied children population [adjusted OR = 2.60; CI = 1.54;4.38] and in the atopic children sub-population [adjusted OR = 3.07; CI = 1.00;9.43]. The association with atopy was also positive and statistically significant only in the brute analysis [OR = 2.13; CI = 1.03;4.40]. Anti-A. lumbricoides IgE antibodies, but not current A. lumbricoides infection, were positively associated with wheezing in atopic children [adjusted OR = 2.01; CI = 1.00;4.50] and in non-atopic children [adjusted OR = 3.07; CI = 1.13;8.35] and it was also associated with atopy [adjusted OR = 7.29; CI = 3.90; 13.4]. On the other hands, reports of wheezing were not significantly associated with atopy.

Conclusions

These data corroborate previous studies showing that wheezing is predominantly associated with infection in early childhood and shows that anti-A. lumbricoides IgE antibodies, but not active Ascaris infections, are associated with wheezing and atopy. Additionally, the data demonstrate that T. trichiura infection may play a role in the pathogenesis of atopic wheezing in early childhood.     

Spatial prediction of malaria prevalence in an endemic area of Bangladesh

Background

Malaria is a major public health burden in Southeastern Bangladesh, particularly in the Chittagong Hill Tracts region. Malaria is endemic in 13 districts of Bangladesh and the highest prevalence occurs in Khagrachari (15.47%).

Methods

A risk map was developed and geographic risk factors identified using a Bayesian approach. The Bayesian geostatistical model was developed from previously identified individual and environmental covariates (p < 0.2; age, different forest types, elevation and economic status) for malaria prevalence using WinBUGS 1.4. Spatial correlation was estimated within a Bayesian framework based on a geostatistical model. The infection status (positives and negatives) was modeled using a Bernoulli distribution. Maps of the posterior distributions of predicted prevalence were developed in geographic information system (GIS).

Results

Predicted high prevalence areas were located along the north-eastern areas, and central part of the study area. Low to moderate prevalence areas were predicted in the southwestern, southeastern and central regions. Individual age and nearness to fragmented forest were associated with malaria prevalence after adjusting the spatial auto-correlation.

Conclusion

A Bayesian analytical approach using multiple enabling technologies (geographic information systems, global positioning systems, and remote sensing) provide a strategy to characterize spatial heterogeneity in malaria risk at a fine scale. Even in the most hyper endemic region of Bangladesh there is substantial spatial heterogeneity in risk. Areas that are predicted to be at high risk, based on the environment but that have not been reached by surveys are identified.

     

Ontogenetic variations in the venom proteome of the Amazonian snake Bothrops atrox

Background  

Bothrops atrox is responsible for the majority of snakebite accidents in the Brazilian Amazon region. Previous studies have demonstrated that the biological and pharmacological activities of B. atrox venom alter with the age of the animal. Here, we present a comparative proteome analysis of B. atrox venom collected from specimens of three different stages of maturation: juveniles, sub-adults and adults.