Genome assembly and annotation of Arabidopsis halleri,a model for heavy metal hyperaccumulation and evolutionary ecology

The self‐incompatible species Arabidopsis halleri is a close relative of the self‐compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability make A. halleri a useful model for ecological genomics studies. We used long‐insert mate‐pair libraries to improve the genome assembly of the A. halleri ssp. gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high‐quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold. The assembly will enhance the genomewide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri.     

Metal concentrations and mycorrhizal status of plants colonizing copper mine tailings: potential for revegetation

A field survey of metal concentrations and mycorrhizal status of plants growing on copper mine tailings was conducted in Anhui Province, China. Available phosphorus and organic matter in the tailings were very low. High concentrations of Pb, Zn, As and Cd as well as Cu were observed on some sites. The dominant plants growing on mine tailings belonged to the families Gramineae and Compositae, and the most widely distributed plant species were Imperata cylin-drica, Cynodon dactylon and Paspalum distichum. Coreopsis drummondii also grew well on the arid sites but not on wet sites. Very low or zero arbuscular mycorrhizal (AM) fungal colonization was observed in most of the plants, but extensive mycorrhizal colonization was recorded in the roots of C. drummondii and C. dactylon. Metal concentrations in plant tissues indicated that /. cylindrica and P. distichum utilized avoidance mechanisms to survive at high metal concentrations. The investigation suggests that remediation and revegetation of heavy metal con     

Effect of Extracellular Factors on Growth and Dimorphism of Rhizopus oryzae with Multiple Enzyme Synthesizing Ability

Rhizopus oryzae PR7 MTCC 9642 was a dimorphic fungus that showed a regular 90 days cycle of filament (mycelium) to pellet (yeast) transformation through a distinct bottom dwelling intermediate state and the pellets never revert back to filamentous form. Apart from the normal cycle, high temperature (37°C and above) and extreme pH also induced the yeast formation. Among the ions tested, calcium and chloride ions were found to restore the filamentous morphology, even in extreme pH and temperature. Cysteine HCl also played noteworthy role in maintaining mycelial growth even at adverse condition. Immobilized spores showed the appearance of intermediate form instead of typical yeast form even at high temperature. The strain could produce a number of extracellular hydrolytic enzymes like cellulolytic, xylanolytic, pectinolytic and amylolytic enzymes. The pellet and mycelial forms were found to be a better producer of cellulase–lignocellulase enzymes and amylolytic enzymes respectively, which might be correlated with their infectivity. Increase in inoculum size, agitation during cultivation, change in carbon and nitrogen source failed to induce mycelial growth in extreme conditions, which might be explained as irreversible change of configuration of protein responsible for mycelial development.     

Characterization of the Catalytic and Nucleotide Binding Properties of the α-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A

The α-kinases are a widely expressed family of serine/threonine protein kinases that exhibit no sequence identity with conventional eukaryotic protein kinases. In this report, we provide new information on the catalytic properties of the α-kinase domain of Dictyostelium myosin-II heavy chain kinase-A (termed A-CAT). Crystallization of A-CAT in the presence of MgATP yielded structures with AMP or adenosine in the catalytic cleft together with a phosphorylated Asp-766 residue. The results show that the β- and α-phosphoryl groups are transferred either directly or indirectly to the catalytically essential Asp-766. Biochemical assays confirmed that A-CAT hydrolyzed ATP, ADP, and AMP with k_cat values of 1.9, 0.6, and 0.32 min⁻¹, respectively, and showed that A-CAT can use ADP to phosphorylate peptides and proteins. Binding assays using fluorescent 2′/3′-O-(N-methylanthraniloyl) analogs of ATP and ADP yielded K_d values for ATP, ADP, AMP, and adenosine of 20 ± 3, 60 ± 20, 160 ± 60, and 45 ± 15 μm, respectively. Site-directed mutagenesis showed that Glu-713, Leu-716, and Lys-645, all of which interact with the adenine base, were critical for nucleotide binding. Mutation of the highly conserved Gln-758, which chelates a nucleotide-associated Mg²⁺ ion, eliminated catalytic activity, whereas loss of the highly conserved Lys-722 and Arg-592 decreased k_cat values for kinase and ATPase activities by 3–6-fold. Mutation of Asp-663 impaired kinase activity to a much greater extent than ATPase, indicating a specific role in peptide substrate binding, whereas mutation of Gln-768 doubled ATPase activity, suggesting that it may act to exclude water from the active site.     

新乡市水源地土壤重金属含量特征及其对地下水的影响

对新乡市自来水水源地土壤和地下水重金属含量特征进行分析,结果表明:土壤中Pb含量达标,Zn、Cr、Ni和Cu含量超标,其平均含量分别为1213.80、115.22、189.56和60.39mg.kg-1;用化学连续浸提法对超标元素化学形态分布进行研究表明,Zn、Cr、Ni和Cu残渣态含量最高,所占比例分别为87.81%、78.38%、84.26%和59.33%,可交换态含量最低,所占比例分别为0.21%、2.56%、1.00%和3.51%,由于Zn、Cr、Ni、Cu主要以迁移性最弱的残渣态为主,未发现地下水中重金属含量超标。     

芒属植物重金属耐性及其在矿山废弃地植被恢复中的应用潜力

芒属植物重金属耐性强,并且是重要的能源植物,其在矿山废弃地植被恢复中的应用备受关注.芒属植物对多种重金属耐性强,但不属于重金属超累积植物.目前的研究认为,根系代谢能力强、根际存在多种共生微生物及抗氧化和光合作用能力强是芒属植物重金属耐性强的重要原因,但更为全面的耐性机理需要深入研究.芒属植物在矿山废弃地植被恢复的应用潜力大,可以清除土壤重金属、改善土壤性质和促进生物多样性发展.本文总结分析了芒属植物生物学特性、重金属耐性特点、机理及其在矿山废弃地植被恢复中的应用潜力,提出了应用芒属植物进行矿山废弃地植被恢复的基本思路,并对芒属植物的重金属耐性机理及应用的未来研究方向进行展望,以期为利用芒属植物开展矿山废弃地植被恢复提供借鉴.     

汕头湾表层沉积物重金属污染与潜在生态风险评价

汕头湾作为华南地区重要的出海门户,汕头市主要的旅游区和水产养殖基地,其环境污染问题已成为制约当地经济发展的重要因素,为此2002年在此开展了重大科技术兴海项目,以海洋沉积物质量标准、单因子污染指数和潜在生态风险评价体系对汕头湾表层沉积物重金属污染现状和潜在生态风险进行了评价。结果表明:汕头湾表层沉积物中Cd,Cu,Pb,Zn的平均含量超过海沉积物质量标准(Ⅰ类);以单因子污染指数评价,Cd达到很强污染等级,Zn为强污染,Cu,Ni,Pb为中等污染;以单元素生态系数(E_rⁱ)评价,只有Cd的潜在生态风险达到很强等级,其它元素则只属于轻微潜在风险范畴;以多元素潜在生态风险指数(RI)评价,汕头湾的潜在生态风险水平处于中等强度;重金属含量分布特征与重金属污染及潜在生态风险的空间差异性一致,表现为由上游至下游呈波状递减趋势,其中以牛田洋和汕头港上游最为严重;这一污染特征主要是由集水区域内的产业结构特点、河流入海口及排污口的分布以及汕头湾的地理和水文特性所决定的。     

Articulated Knowledges: Environmental Forms after Universality's Demise

Critiques of universalism require rethinking when confronted with environmental political arenas, in which the very concepts of "universality" and "particularity" are in a constant process of self-conscious deployment. In this article, I attend to the analytic and political implications of such deployments in a recent incinerator controversy in Hong Kong. I suggest that an aesthetic of local appropriateness and its formal requirement of simultaneous universal and particular truth value normalize the politics of environmental expertise such that the only legible form for counterknowledge is one of articulated knowledges. To understand how the knowledges emergent in an NGO–village collaboration were scaled, linked, and mobilized, I analyze a translation of expert knowledge and the event's metapragmatic effects. A subsequent account of unarticulated knowledges emphasizes the political-economic conditions that limit whose knowledges can count as particular in articulations of counterexpertise.     

岷江上游祁连山圆柏群落结构研究

应用样方调查方法,对祁连山圆柏群落外貌和结构进行研究.结果表明,该群落生活型谱中以地面芽植物为主,但一年生植物也占有较大比率,具有一些温带植物群落特征.该群落垂直结构简单,只有乔、灌、草3层,无层间植物及地被层.乔木层只有祁连山圆柏1种;灌木层以高山绣线菊的重要值最大,为153.3;草本层以丛生苔草重要值最大,达到36.8.在不同坡度样地中,大坡度样地上具有相对较多的幼苗和幼树,而低坡度样地有刺灌木和适口性差的草本较多,这主要是由于坡度不同导致样地上放牧强度不同造成的.由年龄结构和高度结构的分析可以看出,祁连山圆柏种群总体上为衰退种群,如果任由放牧等干扰继续下去,群落将向灌丛草甸方向演替.群落上层盖度对下层盖度影响较大,且各层盖度大小与其多样性之间没有必然联系.     

Vanadium as a tracer of oil pollution in the sediments of Kuwait

Vanadium is important as an indicator of oil pollution since oil is one of the main contributors of vanadium to the environment and because most crude oils contain relatively high concentrations of vanadium (30.6 ± 14.3 mg kg^–1 were measured in nine different Kuwait crudes). If oil has settled to the bottom and biodegradation has taken place, it is obvious that enrichment of vanadium in the sediment may be observed.More than 200 sampling sites were selected in the coastal zone of Kuwait and sediment samples were analyzed for grain size distribution, CaC0₃ content, heavy metals and TOC. The analytical results were normalized by taking into account the natural background levels of vanadium in different sediment fractions.After evaluation of the results, vanadium enrichments of as much as 10 to 77 mg kg^–1 were found at 15 sampling locations and of 1 to 10 mg kg^–1 at many others. The areas of vanadium enrichment in the sediments were located 3–5 km from the shoreline in the areas of wastewater discharges, near oil loading piers and in the shipping channels. There was no correlation between vanadium and TOC indicating that biodegradation of oils had taken place. However, high TOC values in the sediments were determined in the near shore sediments around the outlets.