Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes

Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on over 10,000 genes, including approximately 1,500 previously associated with lifespan, and additional approximately 9,000 for which an association with longevity has never been suggested. We analyzed dN/dS rates, positive selection, gene expression (RNA-seq), and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan, and body mass, we identified 276 genes whose rate of evolution positively correlates with maximum lifespan in primates. Further, we identified five genes, important for tumor suppression, adaptive immunity, metastasis, and inflammation, under positive selection exclusively in the great ape lineage. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that 8% of approximately 1,500 genes previously associated with longevity are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel “ape-specific” enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE–Vntr–Alus. In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.     

Horizontal transmission versus vertical inheritance of P elements in Drosophila and Scaptomyza: has the M-type subfamily spread from East Asia?

Polymerase chain reaction (PCR) screening for P elements was carried out in 77 species with a primer set highly specific for the M-type subfamily. In the course of this search M-type elements were detected in 29 species: In the melanogaster (subgroups montium and rhopaloa ) and obscura species groups of Drosophila (25 out of 71 species examined), and in the genus Scaptomyza (four out of six species). M-type elements are present in all species of the montium subgroup investigated so far (21), but occur only sporadically in other groups. Within the montium subgroup 20 species possess only incomplete copies, only one species ( D. lacteicornis ) harbours apparently full-sized elements. In contrast, outside the montium subgroup almost all species with M-type elements carry full-sized copies suggesting transpositional activity, at least in the recent past. The interior section of the full-sized M-type element of D. lacteicornis was partially sequenced (936 bp). In addition, the complete sequences of four internally deleted M-type elements of D. lacteicornis, D. rufa, D. quadraria , and D. triauraria were determined. Sequence comparisons (including sequence data from previous investigations) revealed striking discrepancies between P element phylogeny and the cladogenesis of their host species. Among several possible pathways for interspecific transfers of M-type elements, we favour the hypothesis assuming the invasion of Scaptomyza as well as the obscura group species of Drosophila via independent transmission routes originating from Asian species of the montium subgroup of Drosophila . The logical geographic scenario for these events would be East-Asia.     

微波消解-FAAS法分析并比较旱芹(Apium graveolens L.)不同部位八种金属元素的含量

采用微波消解法处理旱芹根、茎、叶,并用火焰原子吸收法测定其中的Na、K、Ca、Mg、Fe、Mn、Zn、Cu 8种金属元素的含量。结果表明:旱芹中富含人体必需的Na、K、Mg、Fe、Ca等元素,各元素在不同部位含量有一定差异。Fe元素在旱芹根中含量为883.57μg.g-1,明显高于茎和叶;Ca、Zn和Mn元素在旱芹叶中的含量分别为11 103.74,214.04,88.07μg.g-1,明显高于茎和根;K、Na和Mg元素在旱芹茎中的含量高于根和叶中,Cu元素含量在各部位差异不大。方法的加标回收率为96.8%～105.8%,相对标准偏差(RSD)≤3.36%。     

南极地区苔藓地衣植物的地球化学元素营养富集特征

研究南极苔藓地衣中地球化学元素的营养富集特征,发现K,Ca为苔藓地衣中最活跃元素,主要以主动吸收的方式累积于苔藓地衣植物中,P极易富集在地衣的藻层,参与藻类的有机合成过程,苔藓容易富集环境中的S,Al,Si以被动吸收的方式累积于地衣中,同时Fe,Mg以被动吸收的方式累积于苔藓体内,根据元素的含量和营养作用,研究认为K,Ca苔地衣的大量无机营养元素,S,P为苔藓地衣的中等营养元素,Al,Si为苔藓地衣的环境累积元素。     

Multianalysis of trace elements in mosses with inductively coupled plasma-mass spectrometry

As a part of an air-pollution biomonitoring survey, a procedure using inductively coupled plasma-mass spectrometry (ICP-MS) and microwave digestion was developed to achieve a high sample throughput and guarantee the accuracy of the results. This article presents an analytical method to measure 22 trace elements. As, Ba, Cd, Ce, Co, Cr, Cs, Cu, Fe, Hg, La, Mo, Ni, Pb, Rb, Sb, Sr, Th, Tl, U, V, W were analyzed in 563 mosses collected in France. The digestion was performed in polytetrafluoroethylene (PTFE) vessel using the mixture HNO₃-H₂O₂-HF. The data were reprocessed taking into account the drift curve calculated for each element. The detection limits (DL) calculation was based on the standard deviations of the reagent blanks concentrations. The DL varied from one batch to another, because of the heterogeneity of the mosses’ elemental contents. The DL ranged between 0.001 μg/g (Cs, Tl) and 70 μg/g (Fe) and were mainly around 0.01 μg/g (As, Cd, Ce, Co, Hg, La, Mo, Sb, Sr, U, V, W). The detection limits obtained were in agreement with the concentrations observed in the samples, except for Hg and Ni. The reproducibility between duplicates and the analytical precision were near 10%. The procedure was tested with the mosses’ reference materials.     

Concentrations and flux of rare earth elements in a semifield plot as influenced by their agricultural application

The concentrations of rare earth elements (REs) in atmospheric particles, soil, soil water, surface runoff, and different parts of corn in an experimental plot in the suburb of Beijing, China were measured and the flux of REs was estimated. The concentration of REs in air particles with diameter less than 10 μm is 36 ng/m³ and, by ratio analysis, the origin of REs in the atmosphere was likely local soil. The concentration of soluble REs is 0.69 μg/L in rainwater, 5–7 μg/L in surface runoff, as well as 1–4 μg/L in soil water and the application of RE mixture has no observed influences on their concentrations. The concentration of soluble REs in surface runoff and soil water was dominated by aqueous-solid-phase partitioning. By estimation of the flux, most of the REs applied will remain in the soil phase and continued application of REs will cause an accumulation of REs in agricultural soil.     

Effects of Zn2+ and Cu2+ on growth,lignin degradation and ligninolytic enzymes in Phanerochaete chrysosporium

The influence of Zn²⁺ (6.0 × 10^–3 –18.0 × 10^–3 M) and Cu²⁺ (4 × 10^–4 –1.2 × 10^–4 M) in the basal medium on mycelial growth (dry weight), activities of lignin peroxidase (Lip), manganese peroxidase (Mnp), solubilization, and mineralization (¹⁴CO₂ evolution) of lignin during a period of 3 weeks was studied in Phanerochaete chrysosporium strain MTCC-787. Highest mycelial growth was obtained at 0.6 M Zn²⁺ and 0.4 M Cu²⁺ levels. Enzyme activities were found to increase up to the highest levels of both the trace elements. However, Zn²⁺ had a relatively more stimulatory effect on Lip production and the reverse was true in case of Cu²⁺. [¹⁴C]Lignin solubilization was also promoted by higher levels of both trace elements. Mineralization of [¹⁴C]lignin was optimal at 6.0 M Zn²⁺ and 1.2 M Cu²⁺. The stimulatory effect of Zn²⁺ on Lip production was correlated with higher rates of [¹⁴C]lignin mineralization.     

浙江镜湖湿地3种菌根植物根部真菌群落多样性及对金属元素富集能力的研究

城市湿地（urban wetland）植物多样性水平高,并具有积极的净化和美化环境的作用。本研究以浙江绍兴镜湖城市湿地公园为研究样地,通过ICP-AES检测了人工园区和次生林土壤中几种金属元素（Al、Cr、Cu、K和Zn）的含量,比较不同类型的菌根植物——黑麦草（Lolium perenne L.）（AM）、六月霜（Monochasma sauatieri Franch）（AM）和乌饭树（Vaccinium bracteatum Thunb）（ERM）对金属元素的富集作用。通过高通量测序分析各宿主植物根部真菌群落的组成和结构,比较其对宿主植物金属富集能力的影响。结果表明：（1）人工园区土壤中5种金属元素的含量均显著高于次生林下的土壤;（2）乌饭树对Al的富集能力较强,黑麦草和六月霜富集Cr能力都较强;（3）3种植物根部真菌主要来自Ascomycota,而乌饭树根部Basidiomycota也是优势真菌,AM真菌在黑麦草和六月霜根部真菌群落结构中较少,而公认的ERM真菌Helotiales和Sebacinales在乌饭树根部真菌群落中的比例较高,且与所测金属元素无显著相关性。绍兴镜湖城市湿地公园次生林土壤环境保持良好。     

Nucleotide sequence of the transposable element IS15

We have determined the complete nucleotide sequence of the right (R) copy of the insertion sequence IS15 which flanks, in direct orientation, the composite transposon Tn1525. IS15-R, which is capable of independent transposition, is 1648 bp long and has short (14 bp) perfect inverted repeats at its termini. Analysis of the nucleotide sequence indicates that IS15-R results from the transposition, in direct orientation, of a smaller (820 bp long) IS, designated IS15-Δ, into itself. This integration event is accompanied by the duplication of 8 bp in the target DNA. IS15-Δ possesses two large overlapping open reading frames (ORF) located on opposite strands. Because of this particular structure, IS15 possesses four large ORFs which, due to the integration event, exhibit some differences with those of the parental 1S15-Δ.