玉米耐旱自交系在干旱条件下的mRNA差异表达

用16%PEG-6000对玉米耐旱自交系“81565”进行模拟干旱处理,用DD-PCR技术研究干旱与正常浇水对照的mRNA差异表达,发现3个干旱条件下差异表达的特异片段MD1、MD2和MD3。MD1和MD2在干旱条件下减量表达,MD3为干旱诱导表达。序列分析和同源性比对表明,MD1与玉米叶绿体基因组中编码参与RNA转录本Ⅱ型内含子剪切的成熟酶的matK基因有93%的相似性,MD2与极端耐旱的Sporobolus stapfianus的丝氨酸/苏氨酸2C型蛋白磷酸酶基因PP2C的相似性达99%,MD3与属天冬氨酸特异性半胱氨酸蛋白酶类的水稻metacaspase基因有99%的相似性。根据各自序列相似同源基因的功能推测,MD1、MD2和MD3三个片段可能与“81565”的耐旱机制有关。     

番茄花药特异表达启动子LAT52的克隆与表达载体构建

采用半巢式PCR方法,从番茄基因组中扩增出了花药特异表达启动子LAT52。该序列与GenBank公布的同源序列相似度达98%,并鉴别到一个TAAAAAA简单重复序列。将LAT52启动子与GUS基因拼接,构建成了双元表达载体。     

植物GH3基因家族的生物信息学分析

植物生长素在植物的生长发育过程中至关重要,GH3基因家族是植物生长素早期应答的成员。本研究采用比较基因组学的方法,利用已经分离的拟南芥GH3(Gretchen Hagen3)蛋白为检索序列,在全基因组水平上搜索拟南芥、水稻、葡萄、白杨和苜蓿的GH3基因的同源序列。最终确定了59个GH3候选基因,其中拟南芥19个,水稻14个,葡萄9个,白杨14个,苜蓿3个。对同源序列作进一步的多序列联配、MEME、ESTs和系统发生表达分析,结果表明:GH3基因家族的基本特征在单双子叶植物分离之前就已经形成;GH3结构域在蛋白质间较保守,可以分为3个亚家族,其中个别蛋白发生了基序丢失;59个同源蛋白中的40个成员找到了ESTs的证据,且表达部位多样,不同成员之间的表达部位存在差异。该研究结果将为植物的GH3基因家族的研究提供参考。     

番茄Hsp70基因鉴定及系统发育关系分析

热激蛋白70(heat shock protein 70,Hsp70)是植物应对高温和其他胁迫环境时所产生的一类特定的应激蛋白。本文以番茄基因组数据为基础,利用生物信息学方法对Hsp70基因家族进行鉴定与分析。结果表明,番茄至少含有22个Hsp70基因成员,蛋白质序列长度为210-890个氨基酸之间,具有0~12个内含子;具有4对重复基因;滑动窗口分析结果表明,这些基因中的一些区段(或者位点)可能受到正选择的压力。此外,序列比对发现这些Hsp70基因家族成员具有多个保守基序;染色体定位发现他们不均匀分布在番茄的11条染色体上;系统发育关系揭示番茄和拟南芥Hsp70基因家族成员可以分为4组,每组成员数目是变异的,并且存在3对旁系同源基因和7对直系同源基因,表明Hsp70基因家族在番茄和拟南芥分化之前就已经存在。     

玉米HSP70基因家族的全基因组鉴定与分析

热激蛋白70(HSP70)是生物体应答各种胁迫反应产生的一类蛋白,广泛存在于生物体中,在几乎所有的活细胞中都起着重要的作用。为全面解析玉米基因组HSP70基因信息,利用从Pfam数据库中下载的隐马氏模型文件PF00012在Gramene数据库进行基因搜索,并利用多种生物软件或在线工具对所鉴定的基因进行生物信息学分析。结果表明,试验共鉴定得到35个玉米HSP70基因,分别命名为Zm HSP70-1~Zm HSP70-35。这些基因不均衡地分布在玉米的10条染色体上,其中5号染色体上分布最多(6个),9号染色体上分布最少(1个)。进化树分析显示35个基因聚为6组,且同组基因具有相似的基因结构,其基序数量、类型和顺序也是相似的。物种间进化树分析不同物种的86个基因,存在8对直系同源基因和17对旁系同源基因,直系同源基因中7对存在于玉米和水稻之间,仅1对存在于水稻和拟南芥之间,说明起源于共同祖先基因的直系同源基因对虽在单/双子叶植物差异分离前就存在,但玉米与水稻间的进化关系要比与拟南芥间更为亲近。表达谱分析表明,大多数Zm HSP70基因属组成型表达,但表达模式和表达量不同。本研究结果为进一步研究玉米HSP70家族基因的功能奠定了理论基础。     

萝卜胞质雄性不育正常花蕾与败育花蕾DD-PCR及EST序列分析

提取了萝卜雄性不育系BT-18败育花蕾和正常花蕾的DNA,并且采用DD-PCR技术研究了败育花蕾与正常花蕾的mRNA差异表达。败育花蕾DNA表现有规则的Ladder,而正常花蕾只有单一DNA条带,该结果为萝卜败蕾发生了细胞程序化死亡提供了生化证据;DD-PCR得到107个差异表达片段,其中败育花蕾差异表达片段94个,正常花蕾差异表达片段13个。BLAST结果显示,与功能蛋白同源的差异序列50%以上来源于叶绿体,推测萝卜败蕾与叶绿体有很大关系;叶绿体Mat K在不同的引物组合扩增中出现3次,序列分析后发现长度为282bp和283bp的为同一片段,长度为396bp的片段与长度为282bp和283bp的片段无同源性,可能为编码Mat K的不同亚基。Mat K参与叶绿体中RNA转录本Ⅱ型内含子剪切,通过对内含子剪接的影响来调节基因的表达,推测Mat K等叶绿体基因上调表达使其蛋白质的合成发生变化,导致萝卜叶绿体代谢紊乱,最终导致败蕾;而甲基转移酶可能通过DNA甲基化调控萝卜发育,使其发育异常表现花蕾败育。对BLASTx比对分值小于80及无同源性的片段进行BLASTn分析,根据比对结果推测:细胞程序化死亡可能是萝卜败蕾、植物衰老和植物受逆境胁迫时普遍发生的一种生理生化现象。     

诸葛菜OvCYP86MF基因的克隆及其特性分析

为进一步阐明细胞色素P450基因CYP86MF在诸葛菜发育中的分子机理,本文根据已知同源基因保守序列设计特异引物,利用RT-PCR和RACE技术从诸葛菜中获得一个细胞色素P450基因(OvCYP86MF)全长cDNA序列,该序列全长为1876bp,含有1605bp的完整开放阅读框,可编码534个氨基酸,分子量和等电点分别为61.4kDa和6.90,具有细胞色素P450蛋白的典型特征,即保守结构域FNAGPRLCIG;原核表达显示该基因的融合蛋白在体外可以诱导表达;DANSTAR和Clustal W软件分析表明该基因的全长cDNA序列及其编码氨基酸序列与十字花科物种拟南芥相似性很高,达到80%以上,亲缘关系最近;与CYP86C亚家族成员在氨基酸水平上的相似性均高于50%,因此推断该基因属于CYP86C这个亚家族。Northern杂交分析表明该基因在花蕾中特异表达。     

绿色杜氏藻DvGGPS生物信息学及转录差异研究

香叶酰香叶酰焦磷酸合成酶(GGPS)能够催化焦磷酸异戊烯酯(IPP)与二甲基丙烯焦磷酸(DMAPP)反应形成二萜化合物通用前体香叶酰基香叶酰焦磷酸(GGPP)。为深入了解GGPS蛋白在类胡萝卜素合成途径中的作用,通过Illumina Hi Seq TM 2000高通量测序获得Dv GGPS基因c DNA全长序列,对GGPS基因序列进行生物信息学分析,并研究花生四烯酸(AA)、乙酰水杨酸(ASA)和硫酸铈铵(ACS)对Dv GGPS基因转录水平的影响及绿色杜氏藻类胡萝卜素含量变化。生物信息学分析结果表明,Dv GGPS基因c DNA全长2 229 bp,含1 041 bp开放阅读框,编码346个氨基酸。GGPS蛋白质序列理论等电点(p I)为5.82,相对分子质量为37.66 k Da,该蛋白为疏水性蛋白,无信号肽和跨膜区域。二级结构预测显示该蛋白分子中α-螺旋结构最多,占57.23%。同源比对结果表明,绿色杜氏藻GGPS蛋白与雨生红球藻亲缘关系最近。qRT-PCR结果表明,62.5 mg·L~(-1)AA、50 mg·L~(-1)ASA和0.8 mg·L~(-1)ACS处理的Dv GGPS基因转录水平达到最高,此时类胡萝卜素含量也均有提高,说明绿色杜氏藻类胡萝卜素的生物学合成可能是通过诱导Dv GGPS基因表达实现的,Dv GGPS基因在类胡萝卜素生物合成中起关键作用。Dv GGPS基因的克隆及表达调控研究为今后探明类胡萝卜素积累的分子机理提供了重要参考,也为进一步通过代谢工程手段提高绿色杜氏藻类胡萝卜素含量奠定了理论基础。     

菊分支NCED酶分子特征及进化分析

为探究9-顺式-环氧类胡萝卜素双加氧酶(NCED)基因家族进化特性,本文利用生物信息学方法,对菊分支类群已完成测序的植物(包括番茄、马铃薯、烟草、甜菜、猴面花)基于全基因组进行NCED基因家族鉴定,并对其蛋白序列特征,保守基序,次级结构以及系统发育关系进行分析。结果表明,NCED酶是由小基因家族编码的酶,其成员为2~4个。蛋白质氨基酸大小在505~652aa之间,分子质量为56.23~71.42 k Da,除Sl NCED6外,其余各蛋白的等电点均表现为酸性,保守基序分析发现各成员均包含10个保守基序,其长度在29~50之间。此外,NCEDs蛋白结构分析显示,一级结构氨基酸序列N端保守性较低,而次级结构均表现为高度保守。系统发育关系发现,来自番茄的Sl NCED5、Sl NCED6与来自马铃薯的St NCED5、St NCED6分别为直系同源蛋白,这与生物学上的亲缘关系一致。     

镜鲤体重的QTL定位

本研究利用217个微卫星标记和336个SNPs标记对德国镜鲤F2代68个个体基因组DNA进行基因型检测。其中507个标记共组成62个连锁群,覆盖基因组总长度为2805．85cM,标记问平均距离为6-31cM;利用软件MapQTL4．0采用区间作图法对体重性状进行QTL定位分析。研究结果共检测到14个与体重性状有关的QTLs,分布于9个连锁群。其中BIV-5-J有最大的LOD值,为4．46;BIV—I-1的LOD值最小,为2．25。单个QTL平均解释表型变异介于14．10％～45．50％之间,其中贡献率大于20％的主效QTLs有9个。通过BLASTX与斑马鱼蛋白质序列数据库进行序列比对,找到了与斑马鱼酰基辅酶A脱氢酶蛋白、胰淀粉酶仅2蛋白、Apoebprotein和甘油醛-3-磷酸脱氢酶蛋白同源的分子标记。本研究结果对分子标记辅助育种具有重要应用价值。     

Trace metals in precipitation in Sweden

Trace metals (Cd, Cu, Fe, Mn, Pb, and Zn) concentrations in atmospheric precipitation have been routinely monitored in Sweden since the autumn of 1983. Concentrations are highest in southern Sweden and decrease northward. It is postulated that the long range transport of anthropogenic pollutants from the rest of Europe is the major source of Cd, Pb, and Zn in precipitation. Evidence for this hypothesis is that enrichment factors indicate anthropogenic origin, and Swedish atmospheric emissions of Zn and Cd are 2 to 3 times smaller than deposition fluxes. Also, Cd, Pb, and Zn concentrations are correlated in both space and time and are also well correlated with exSO₄ ⁺, a substance known to be of anthropogenic origin transported long distances.     

Patterns in trace elements in lichens

Water, Air, & Soil Pollution - Epiphytic lichens were sampled in a Dutch national monitoring survey, which was carried out twice within 5 yr. The samples were analyzed by neutron activation...     

中国华北地区近40年物候春季变化

根据华北地区7个观测站物候资料,分析了华北地区1963-1996年及北京1963-2005年物候春季的变化特征及其与气温的关系。结果表明:华北地区的物候春季有明显提早来临的趋势,而造成这一变化的主要因素是本地区近40 a来冬春季气温的明显上升。其中1963-1996年间华北地区1-3月及4月的平均气温分别上升了2.3℃与1.7℃,物候春季起止日期分别提前了9d和4d,因而使得春季长度也延长了5d;北京1963-2003年间1-3月及4月的平均气温分别上升了3.5℃与2.6℃,物候春季的起止日期分别提前了11d和10d,但春季长度没有明显变化。     

Sediment denitrification in waterways in a rice-paddy-dominated watershed in eastern China

Purpose

Rice-paddy-dominated watersheds in eastern China are intensively cultivated, and lands with two crops receive as much as 550–600 kg?ha^–1?year^–1 of nitrogen (N), mainly through the addition of N-based fertilizers. However, stream N concentrations have been found to be relatively low. Waterways in the watersheds are assumed to be effective “sinks” for N, minimizing its downstream movement. We directly measured net sediment denitrification rates in three types of waterways (ponds, streams/rivers, and a reservoir) and determined the key factors that control net sediment denitrification. Such information is essential for evaluating the impact of the agricultural N cycle on the quality of surface water.

Materials and methods

The pond–stream–reservoir continuum was sampled every 2 months at nine sites in an agricultural watershed between November 2010 and December 2011. Net sediment N₂ fluxes/net sediment denitrification rates were determined by membrane inlet mass spectrometry and the N₂/Ar technique. A suite of parameters known to influence denitrification were also measured.

Results and discussion

Net denitrification rates ranged between 28.2?±?18.2 and 674.3?±?314.5 μmol N₂–N?m^–2?h^–1 for the streams, 23.7?±?23.9 and 121.2?±?38.7 μmol N₂–N?m^–2?h^–1 for the ponds, and 41.8?±?17.7 and 239.3?±?49.8 μmol N₂–N?m^–2?h^–1 for the reservoir. The mean net denitrification rate of the stream sites (173.2?±?248.4 μmol N₂–N?m^–2?h^–1) was significantly higher (p?<?0.001) than that of the pond sites (48.3?±?44.5 μmol N₂–N?m^–2?h^–1), and the three types of waterways all had significantly higher (p?<?0.01) mean net denitrification rates in summer than in other seasons. Linear regression and linear mixed effect model analysis showed that nitrate (NO₃ ^?–N) concentration in surface water was the primary controlling factor for net sediment denitrification, followed by water temperature. Using monitoring data on NO₃ ^?–N concentrations and temperature of the surface water of waterways and an established linear mixed effect model, total N removed through net sediment denitrification in the pond–stream–reservoir continuum was estimated at 46.8?±?24.0 t?year^–1 from July 2007 to June 2009, which was comparable with earlier estimates based on the mass balance method (34.3?±?12.7 t?year^–1), and accounted for 83.4 % of the total aquatic N. However, the total aquatic N was only 4.4 % of the total N input to the watershed, and thus most of the surplus N in the watershed was likely to be either denitrified or stored in soil.

Conclusions

High doses of N in a rice-paddy-dominated watershed did not lead to high stream N concentrations due to limited input of N into waterways and the high efficiency of waterways in removing N through denitrification.     

天津半干旱地区不同种植年限菜田土壤微生物变化特征的研究

对天津周边半干旱地区不同种植年限的菜田土壤微生物状况调查研究表明 ,该地区土壤微生物以细菌为主 ,夏季微生物总量大大高于冬季 ;随着种菜年限的增加 ,耕层和亚耕层微生物总量都有增加趋势 ,其中细菌和放线菌增加明显 ,真菌有下降趋势 ;真菌类群分析表明 ,少数纤维素分解菌 ,如青霉 (Penicillium)、木霉 (Trichoderma)等为优势菌 ,而糖和木质素分解菌仅占少数。用尖孢镰刀霉 (Fusariumuoxysporum)、大肠杆菌 (Escherichia coli)接种不同种菜年限土壤 ,检测土壤拮抗菌状况发现 ,拮抗菌仅在种植年限长的老菜田的放线菌中发现。表明北方半干旱地区菜田土壤细菌为优势菌 ,主要存在于土壤微孔隙中 ;而适于生活在土壤疏松大孔隙中的真菌数量极少。应注意土壤结构的改良 ,为丰富土壤微生物提供良好的生态环境     

天津半干旱地区不同种植年限菜田土壤微生物变化特征的研究

对天津周边半干旱地区不同种植年限的菜田土壤微生物状况调查研究表明 ,该地区土壤微生物以细菌为主 ,夏季微生物总量大大高于冬季 ;随着种菜年限的增加 ,耕层和亚耕层微生物总量都有增加趋势 ,其中细菌和放线菌增加明显 ,真菌有下降趋势 ;真菌类群分析表明 ,少数纤维素分解菌 ,如青霉 (Penicillium)、木霉 (Trichoderma)等为优势菌 ,而糖和木质素分解菌仅占少数。用尖孢镰刀霉 (Fusariumuoxysporum)、大肠杆菌 (Escherichia coli)接种不同种菜年限土壤 ,检测土壤拮抗菌状况发现 ,拮抗菌仅在种植年限长的老菜田的放线菌中发现。表明北方半干旱地区菜田土壤细菌为优势菌 ,主要存在于土壤微孔隙中 ;而适于生活在土壤疏松大孔隙中的真菌数量极少。应注意土壤结构的改良 ,为丰富土壤微生物提供良好的生态环境     

Trends in soil science in Switzerland

Phytoremediation is an emerging technology based on the use of green plants to remove, contain, inactivate or destroy harmful environmental pollutants. Recent developments in Europe and the USA show that the approach is somewhat different on both sides of the Atlantic. In Europe, phytoremediation has more basically been research driven and, based on the outcomes, applications have been envisaged. By contrast, the approach in the USA is more application and experience driven. In spite of a growing track record of commercial success, more demonstration projects are needed to prove that phytoremediation is effective in order to rigorously measure its underlying economics, and to expand its applications. More fundamental research is also required to better understand the complex interactions between pollutants, soil, plant roots and micro-organisms at the rhizosphere level, to increase the bioavailability of pollutants, to fully exploit the metabolic diversity of plants and, thus, to successfully implement this new green technology.     

沈阳市城市表土中微生物区系变化的初步研究

在沈阳市远郊-近郊-市区等不同城市化水平区内选取林地、草地和路边土几种不同利用方式下的表层土壤,对土壤中的微生物状况进行了初步分析。结果表明,随着城市化水平的提高,土壤中微生物的数量表现为明显的减少趋势。其中变化较大的是细菌,而真菌和放线菌的变化不明显。     

Changes in proteolytic bacteria in paddy soils in response to organic management

Proteolytic bacterial communities, which mineralize organic nitrogen, play a key role in agricultural systems. In this study, alkaline metalloprotease (apr) gene fragments from proteolytic bacteria were investigated in bulk and rhizosphere paddy soil from four fields under organic management (for 2, 3, 5, and 9 years), and from one field under conventional management (for 2 years). We analyzed the abundance and structure of the proteolytic bacterial communities using real-time quantitative PCR and denaturing gradient gel electrophoresis. Our results showed that the abundance of proteolytic bacteria ranged from 1.57?×?10⁸ to 8.02?×?10⁸?copies/g of soil. In addition, the abundance of the proteolytic bacteria in the paddy soils under organic management was significantly higher than those in the paddy soil under conventional management. Moreover, the gene copy numbers in the rhizosphere soils were significantly higher than those in the bulk soils. The abundance of proteolytic bacteria tended to increase with the duration of organic management, with the highest abundance being found in the soil that had been under organic management for 5 years. However, the proteolytic bacteria communities in the paddy soils were not significantly affected by management practices. Phylogeny analysis showed that all gel bands obtained represented genes from Pseudomonas. Additionally, correlation analysis and canonical correspondence analysis showed that C/N, C, and N were important factors that influenced the abundance and community structure of the proteolytic bacteria. These results suggest that proteolytic bacteria are indicators in organic management systems, depolymerize organic N and hence maintain soil sustainability.

Abbreviations: CM: conventional management; OM: organic management; DGGE: denaturing gradient gel electrophoresis; qPCR: real-time quantitative PCR detecting system; COFCC: China organic food certification center; CCA: canonical correspondence analysis