Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.     

Evaluation of Mercury Contamination in Fungi Boletus Species from Latosols,Lateritic Red Earths,and Red and Yellow Earths in the Circum-Pacific Mercuriferous Belt of Southwestern China

For the first time, highly elevated levels of mercury (Hg) have been documented for several species of the edible Fungi genus Boletus growing in latosols, lateritic red earths, and red and yellow earths from the Yunnan province of China. Analysis of Hg concentrations in the genus suggests that geogenic Hg is the dominant source of Hg in the fungi, whereas anthropogenic sources accumulate largely in the organic layer of the forest soil horizon. Among the 21 species studied from 32 locations across Yunnan and 2 places in Sichuan Province, the Hg was found at elevated level in all samples from Yunnan but not in the samples from Sichuan, which is located outside the mercuriferous belt. Particularly abundant in Hg were the caps of fruiting bodies of Boletus aereus (up to 13 mg kg^-1 dry matter), Boletus bicolor (up to 5.5 mg kg^-1 dry matter), Boletus edulis (up to 22 mg kg^-1 dry matter), Boletus luridus (up to 11 mg kg^-1 dry matter), Boletus magnificus (up to 13 mg kg^-1 dry matter), Boletus obscureumbrinus (up to 9.4 mg kg^-1 dry matter), Boletus purpureus (up to 16 mg kg^-1 dry matter), Boletus sinicus (up to 6.8 mg kg^-1 dry matter), Boletus speciosus (up to 4.9mg kg^-1 dry matter), Boletus tomentipes (up to 13 mg kg^-1 dry matter), and Boletus umbriniporus (up to 4.9 mg kg^-1 dry matter). Soil samples of the 0–10 cm topsoil layer from the widely distributed locations had mercury levels ranging between 0.034 to 3.4 mg kg^-1 dry matter. In Yunnan, both the soil parent rock and fruiting bodies of Boletus spp. were enriched in Hg, whereas the same species from Sichuan, located outside the mercuriferous belt, had low Hg concentrations, suggesting that the Hg in the Yunnan samples is mainly from geogenic sources rather than anthropogenic sources. However, the contribution of anthropogenically-derived Hg sequestered within soils of Yunnan has not been quantified, so more future research is required. Our results suggest that high rates of consumption of Boletus spp. from Yunnan can deliver relatively high doses of Hg to consumers, but that rates can differ widely because of large variability in mercury concentrations between species and locations.     

Variations in Temperature Sensitivity (Q10) of CH4 Emission from a Subtropical Estuarine Marsh in Southeast China

Understanding the functional relationship between greenhouse gas fluxes and environmental variables is crucial for predicting the impacts of wetlands on future climate change in response to various perturbations. We examined the relationships between methane (CH₄) emission and temperature in two marsh stands dominated by the Phragmites australis and Cyperus malaccensis, respectively, in a subtropical estuarine wetland in southeast China based on three years of measurement data (2007–2009). We found that the Q₁₀ coefficient of CH₄ emission to soil temperature (Q_s10) from the two marsh stands varied slightly over the three years (P > 0.05), with a mean value of 3.38 ± 0.46 and 3.89 ± 0.41 for the P. australis and C. malaccensis stands, respectively. On the other hand, the three-year mean Q_a10 values (Q₁₀ coefficients of CH₄ emission to air temperature) were 3.39 ± 0.59 and 4.68 ± 1.10 for the P. australis and C. malaccensis stands, respectively, with a significantly higher Q_a10 value for the C. malaccensis stand in 2008 (P < 0.05). The seasonal variations of Q₁₀ (Q_s10 and Q_a10) differed among years, with generally higher values in the cold months than those in the warm months in 2007 and 2009. We found that the Q_s10 values of both stands were negatively correlated with soil conductivity, but did not obtain any conclusive results about the difference in Q₁₀ of CH₄ emission between the two tidal stages (before flooding and after ebbing). There were no significant differences in both Q_s10 and Q_a10 values of CH₄ emission between the P. australis stand and the C. malaccensis stands (P > 0.05). Our results show that the Q₁₀ values of CH₄ emission in this estuarine marsh are highly variable across space and time. Given that the overall CH₄ flux is governed by a suite of environmental factors, the Q₁₀ values derived from field measurements should only be considered as a semi-empirical parameter for simulating CH₄ emissions.     

Extraction Optimization,Characterization and Bioactivities of a Major Polysaccharide from Sargassum thunbergii

Sargassum thunbergii is a kind of natural edible algae. STP (S. thunbergii polysaccharides) was considered as the main bioactive compounds in S. thunbergii. To obtain the optimal processing conditions for maximum total sugar yield, single factor investigation and response surface methodology (RSM) were employed. The optimal processing conditions were as follows: liquid to solid ratio 120 mL/g, extraction time 210 min, extraction temperature 97°C. The experimental yield 7.53% under optimized conditions was closely agreed with the predicted yield 7.85% of the model. The major polysaccharide fraction from S. thunbergii (named STP-II) was purified by DEAE-Sepharose CL-6B column chromatography. High-performance size-exclusion chromatography (HPSEC), gas chromatography (GC) and high-performance liquid chromatography (HPLC) were used to identify its characterizations, and in vitro antioxidant assays and cytotoxicity assays were used to research its bioactivities. The purified fraction STP-II (63.75%) was a single peak in HPSEC with Sugar KS-804 column, had a molecular weight of 550KD, and comprised mainly of fucose, xylose, galactose, glucose and glucuronic acid. STP-II had higher scavenging activities on hydroxyl radical (76.72% at 0.7 mg/mL) and superoxide radical (95.17% at 2 mg/mL) than Vitamin C (Vc). STP-II also exhibited the capability of anti-proliferation in Caco-2 cells. STP-II possessed good antioxidant and inhibitory activity against human colon cancer Caco-2 cells in vitro and could be explored as novel natural functional food.     

Cross-Sectional Associations between Body Size,Circulating Sex-Steroid Hormones and IGF Components among Healthy Chinese Women

The incidence of breast cancer has increased in Asian countries and rates of hormone receptor (HR) negative breast cancer exceed those of Western countries. Epidemiologic data suggest that the association between body size and BC risk may vary by HR status, and could differ geographically. While body size may influence BC risk by moderating the synthesis and metabolism of circulating sex-steroid hormones, insulin-like growth factor (IGF)-1 and related binding proteins, there is a dearth of literature among Asian women. We aimed to examine these specific associations in a sample of Chinese women. In Sichuan Province 143 women aged ≥40 years were recruited through outpatient services (2011–2012). Questionnaires, anthropometric measurements, and blood samples were utilized for data collection and linear regression was applied in data analyses. Among women <50 years we observed a non-monotonic positive association between body mass index (BMI) and 17β-estradiol, and a reversed J-shaped association between BMI and IGF-1 (p ≤0.05). We observed similar associations between waist-to-hip ratio and these markers. Our finding of augmented IGF-1 among women with low body mass may have implications for understanding breast tumor heterogeneity in diverse populations and should be evaluated in larger prospective studies with cancer outcomes.     

Association between COMT SNP variation and timidity in Golden and Labrador Retrievers

Timidity in dogs is a trait with high heritability. However, the relevant genetic factors and markers associated with this condition are largely unknown. The function of the catechol‐O‐methyl transferase (COMT) gene has been found to be associated with human fearful or anxious emotions, and the COMT:p.Val158Met polymorphism locus is significantly related to anxious behavior. In the present study, the correlation between timidity and four single nucleotide polymorphism (SNP) variations (C.‐1666C>G c.39A>G, c.216G>A, c.482G>A) of the COMT gene was investigated in dogs. The evaluation was based on the dog courage assessment assay and a genotype and haplotype analysis in Labrador Retrievers (LR) and Golden Retrievers (GR). The principal components analysis factor structure of the courage phenotype was invariant between LR and GR. Sex, breed and age had no statistically significant effect on the timidity of the dogs. All SNP loci detected were in Hardy–Weinberg equilibrium. The c.39A>G locus was removed in the subsequent association analysis due to the significant difference between LR and GR in genotype distributions. Intriguingly, the genotypes and haplotypes of the COMT gene were significantly and highly correlated with the timidity of LR and GR. The A alleles of the COMT:c.216G>A and c.482G>A loci appeared to play a dominant role in the timid behavior of the dogs. This result supports and broadens the warrior/worrier hypothesis and will have important implications for the understanding of the evolution of temperament in dogs. Additionally, the results provide predictive genetic markers for temperament in dogs.     

厚壳贻贝whirlin类贝壳基质蛋白的重组表达与功能分析

贝壳历来是生物工程和材料学研究的重要对象。贝壳中的贝壳基质蛋白质在贝壳的形成与发育过程中具有重要的调控作用。Whirlin类蛋白质(Whirlin-like protein,WLP)是一种从厚壳贻贝(Mytilus coruscus)中鉴定的新型贝壳基质蛋白质。序列分析结果显示,该蛋白质含有PDZ(postsynaptic density/Discs large/Zonula occludens)结构域,而该结构域对贝壳生物矿化的影响目前尚无报道。为深入了解WLP在贝壳形成中对碳酸钙晶体的影响,在序列分析基础上,采用密码子优化结合原核重组表达,获得其重组表达产物后,开展了重组WLP对碳酸钙晶体形貌及晶型的影响研究,结晶速度抑制以及碳酸钙晶体结合分析。分析结果表明,重组WLP能诱导文石型碳酸钙晶体的形貌和方解石型碳酸钙晶体的晶型发生改变;同时重组WLP对碳酸钙晶体具有结合作用,且能抑制碳酸钙晶体的结晶速度。上述结果表明,WLP对贝壳的形成及发育具有重要影响,并可能在贝壳肌棱柱层的形成中发挥了重要作用。