乐陵金丝小枣区生态环境地质特征

乐陵金丝小枣区生态环境地质研究表明,层状沉积的河流相及其变异体,心、底土层层位为壤质、粘壤质的土体构型,以不稳定原生矿物为主的土壤,中性或微碱性的重碳酸盐型地球化学环境,钾素丰富、理化性状良好的潮土、褐土化潮土、盐化潮土为该枣区生态环境地质特征的重要标志．对枣生长发育适宜区进行了划分．     

桂西北白云岩坡地典型土体构型石灰土水文特征

综合运用传统水文学、氢氧稳定同位素和原位模拟降雨等方法,研究了桂西北白云岩坡地典型土体构型石灰土微区(2 m×1.2 m)土壤水文功能.白云岩峰丛坡地沿坡向下表现出通体砂、上壤下砂、通体壤、上黏下砂4种典型石灰土土链格局,所有构型土体微区地表稳定入渗速率高达41～48 mm·h^-1,地表径流少,且表现为蓄满产流,壤中流和深层渗漏是重要水文过程;壤中流依据土壤发生层层次分为A、C层壤中流,对于A层壤中流,通体砂、上黏下砂以及上壤下砂构型土体微区以基质流为主,通体壤构型土体表现为优先流;对于C层壤中流,所有构型土体微区均表现为优先流特征.白云岩坡地土壤连续分布,虽土层浅薄但仍表现出沿坡向下的土链格局,不同土体构型土壤水文性质的差异主要体现在地表以下各界面产流过程,研究证实该区土壤水文功能的研究应具备三维立体视角,发展更加侧重地下水文过程观测和研究的新方法,才能全面揭示喀斯特坡地近地表水文过程.     

基于GIS的农田土壤肥力评价及其与土体构型的关系

以河南省延津县中低产田为例,选取土壤有机质、全氮、全磷、全钾、速效氮、速效磷、速效钾、pH和阳离子交换量（CEC）等指标作为评价因子,利用ArcGIS 9.2软件和模糊数学方法对土壤肥力进行了综合评价,根据评价结果,分析不同土体构型土壤肥力状况差异.结果表明：该区土壤呈偏碱性状态,全氮、全磷、速效氮、CEC、有机质、速效钾含量偏低,速效磷、全钾含量中等,土壤肥力综合指数为0.14～0.63,整体水平偏低.除速效磷和全钾外,其他土壤肥力指标在不同土体构型间均表现出显著差异,土壤肥力与土体构型关系密切,上壤下粘型土壤的肥力等级相对较高,上壤下砂型次之,通体砂型最低.根据各指标在剖面上的分布状况判断,该区土体结构不良,保水保肥能力差,可针对此特征进行土壤改良.     

海南岛东寨港几种红树植物种间生态位研究

采用3种常见的生态位宽度和生态位重叠计测公式,以外来种无瓣海桑扩散区的秋茄+桐花树群落演替系列作为资源轴,定量计测了几种红树植物的生态位宽度和重叠值.结果表明,各树种生态位宽度值排序为桐花树(3.8357)＞秋茄(3.3421)＞木榄(3.3180)＞白骨壤(3.0975)＞无瓣海桑(2.9137)＞海桑(2.5724)＞角果木(1.8523)＞红海榄(1.6897)＞海莲(1.0000),很好地表征了其生态适应性和分布幅度.各树种重叠值中,以秋茄、桐花树、木榄、白骨壤之间的生态位重叠较大,表明其间存在较强的资源利用性竞争.无瓣海桑生态位宽度处于中等程度,与中低潮滩红树植物海桑、桐花树、秋茄和白骨壤的重叠值相对较高,与红海榄、木榄有中度重叠,与角果木有少量重叠,与海莲完全没有重叠.     

大亚湾红树林研究Ⅱ,澳头港部分红树植物的生态生理

对大亚湾澳头港的３种红树植物的光合速率、呼吸速率和蒸腾速率进行测定,结果表明：桐花树、白骨壤和木榄的光合速率日进程呈双峰曲线,日平均光合速率的大小为桐花树＞木榄＞白骨壤,而日均呼吸速率的大小为桐花树＞白骨壤＞木榄,呼吸速率的变化幅度小于光合速率,提示白骨壤的生产力最低,可能与其所处的生境含盐量更高有关。蒸腾速率日进程呈单峰曲线,且泌盐植物桐花树和白骨壤的日均值很接近,都高于拒盐种木榄,表明蒸腾速率与它们的泌盐或拒盐生理特性密切相关。总体上,这些红树植物具有较高的光合速率、较低的呼吸速率和蒸腾速率,有利于生长在盐渍淹水的特殊海滩环境。     

连续免耕对不同质地稻田土壤理化性质的影响

以我国南方地区典型的单季水稻生产大田为研究对象,按土壤质地分为壤质和粘质两个系列,探讨不同质地稻田土壤理化性质变化对连续免耕的响应规律。结果表明,在无秸秆覆盖条件下,随着免耕年限的增加,壤质和粘质稻田土壤的耕层均有紧实度提高的趋势,特别是粘质土壤,导致耕层变浅。与常年翻耕土壤相比,免耕6a后壤质水稻土0—20 cm土层的紧实度值平均增加了32%,而粘质的平均增加了90%。在相同免耕年限条件下粘质稻田土壤容重的增加也比壤质土壤的明显。壤质土壤0—10 cm土层有机质和碱解氮含量随免耕年限延长而提高,而在粘质土壤则显著降低。无论是壤质还是粘质土壤,连续免耕多年后土壤速效磷均在耕层(0—20 cm)富集,而速效钾则相反。总体而言,壤质水稻土对免耕的适宜性要优于粘质土壤;应根据土壤质地的不同选择性地实施免耕技术,并结合秸秆覆盖,以实现免耕稻田土壤的可持续利用。     

北京市平原区土壤有机碳垂直分布特征

研究土壤有机碳垂直分布特征规律对精确测算土壤有机碳储量具有重要意义。通过野外调查实地挖取北京市平原区40个典型土壤剖面共169个样品数据,研究土壤有机碳垂直分布特征。结果表明:1)北京市平原区0—150 cm土壤平均有机碳含量为(5.98±2.62) g/kg,垂直分布上,随剖面深度增加土壤有机碳含量逐渐降低,且在浅层(≤60 cm)下降速度显著快于深层(60 cm); 2)各发生层次不同土壤质地的有机碳含量差异整体上均表现为粉粒及黏粒含量比例越高,即质地越黏重,土壤有机碳含量越高; 3)不同土体构型的平均土壤有机碳含量大小关系为通体砂通体壤上壤下黏夹黏,通体砂型土壤有机碳含量垂直变化相对平缓,上壤下黏型土壤有机碳含量在垂直方向呈"降-升-降"趋势,通体壤及夹黏型则均呈先快速下降后缓慢下降趋势; 4)耕地和园地土壤平均有机碳含量高于荒草地,耕地在整个剖面中土壤有机碳含量均居于三种土地利用类型之首,耕地和园地的土壤有机碳含量在0—20 cm和40—60 cm之间下降速度高达40.10%和55.92%,剖面深度超过60 cm后下降速度显著放缓,受人类活动直接影响相对较少的荒草地在垂直方向上变化相对平缓。     

北京市平原区土壤有机碳垂直分布特征

研究土壤有机碳垂直分布特征规律对精确测算土壤有机碳储量具有重要意义。本文通过野外调查实地挖取北京市平原区40个典型土壤剖面共169个样品数据,研究土壤有机碳垂直分布特征。结果表明:1)北京市平原区0—150 cm土壤平均有机碳含量为(5.98±2.62)g/kg,垂直分布上,随剖面深度增加土壤有机碳含量逐渐降低,且在浅层(≤60 cm)下降速度显著快于深层(60 cm);2)各发生层次不同土壤质地的有机碳含量差异整体上均表现为粉粒及黏粒含量比例越高,即质地越黏重,土壤有机碳含量越高;3)不同土体构型的平均土壤有机碳含量大小关系为通体砂通体壤上壤下黏夹黏,通体砂型土壤有机碳含量垂直变化相对平缓,上壤下黏型土壤有机碳含量在垂直方向呈“降—升—降”趋势,通体壤及夹黏型则均呈先快速下降后缓慢下降趋势;4)耕地和园地土壤平均有机碳含量高于荒草地,耕地在整个剖面中土壤有机碳含量均居于三种土地利用类型之首,耕地和园地的土壤有机碳含量在0—20 cm和40—60 cm之间下降速度高达40.10%和55.92%,剖面深度超过60 cm后下降速度显著放缓,受人类活动直接影响相对较少的荒草地在垂直方向上变化相对平缓。     

稻茬麦根系构型的定向分型分析

为探索稻茬麦根构型的方向性,使用田间数字化仪实现稻茬麦根系的数值化,将根系数据导入Pro-E重构出根系的空间状态图,然后将根构型每隔10°进行各向投影,计算根系构型在18个维度的分形维数与分形丰度.结果表明:小麦苗期根构型在各维度的分形特征具有较强的规律性,表明根系在土体中的分布具有明显的方向性.在苗期到返青期,根构型在18个维度的分形指标波动性大,表明这一时期内根系生长处于持续的动态变化过程.在拔节期,根构型在各维度的分形再次呈现出一定的规律性,表明根系在土体中的分布重新表现出明显的方向性.该研究方法可以精准描述和分析植物根系在田间环境中的分布状况.     

不同质地土壤的水热状况及其对冬小麦产量形成的影响

对豫东平原３种质地土壤的水热状况和冬小麦籽粒生长特征进行了研究．结果表明,冬小麦籽粒生长阶段,粘壤土５ｃｍ处的日平均温度最低,为１８．３℃,砂壤土最高,为１９．５℃,中壤居中,为１９．１℃．３种土壤的含水量大小顺序为粘壤＞中壤＞砂壤,粘壤土上小麦籽粒灌浆时间最长,千粒重最高,分别为３８ｄ和４５．５ｇ,砂壤土小麦籽粒灌浆时间最短,千粒重最低,分别为３３ｄ和４２．４ｇ,中壤土小麦２项指标居中,分别为３６ｄ和４３．１ｇ．高产栽培条件下,粘壤土冬小麦产量最高,为８２５３ｋｇ·ｈｍ－２,中壤次之,为７９８０ｋｇ·ｈｍ－２,砂壤最低,为７６１７ｋｇ·ｈｍ－２     

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs

MOTIVATION: The best quality multiple sequence alignments are generally considered to derive from structural superposition. However, no previous work has studied the relative performance of profile hidden Markov models (HMMs) derived from such alignments. Therefore several alignment methods have been used to generate multiple sequence alignments from 348 structurally aligned families in the HOMSTRAD database. The performance of profile HMMs derived from the structural and sequence-based alignments has been assessed for homologue detection. RESULTS: The best alignment methods studied here correctly align nearly 80% of residues with respect to structure alignments. Alignment quality and model sensitivity are found to be dependent on average number, length, and identity of sequences in the alignment. The striking conclusion is that, although structural data may improve the quality of multiple sequence alignments, this does not add to the ability of the derived profile HMMs to find sequence homologues. SUPPLEMENTARY INFORMATION: A list of HOMSTRAD families used in this study and the corresponding Pfam families is available at http://www.sanger.ac.uk/Users/sgj/alignments/map.html Contact: sgj@sanger.ac.uk     

Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome

MOTIVATION: Insertion mutagenesis, using transgenes or endogenous transposons, is a popular method for generating null mutations (knockouts) in model organisms. Insertions are mapped to specific genes by amplifying (via TAIL-PCR) and sequencing genomic regions flanking the inserted DNA. The presence of multiple TAIL-PCR templates in one sequencing reaction results in chimeric sequence of intermittently low quality. Standard processing of this sequence by applying Phred quality requirements results in loss of informative sequence, whereas not trimming low-quality sequence causes inclusion of low-complexity homopolymers from the ends of sequence runs. Accurate mapping of the flanking sequences is complicated by the presence of gene families. RESULTS: Methods for extracting informative regions from sequence traces obtained by sequencing multiple TAIL-PCR fragments in a single reaction are described. The completely sequenced Arabidopsis genome was used to identify informative TAIL-PCR sequence regions. Methods were devised to define and select high quality matches and precisely map each insert to the correct genome location. These methods were used to analyze sequence of TAIL-PCR-amplified flanking regions of the inserts from individual plants in a T-DNA-mutagenized population of Arabidopsis thaliana, and are applicable to similar situations where a reference genome can be used to extract information from poor-quality sequence.     

Benchmarking template selection and model quality assessment for high-resolution comparative modeling

Comparative modeling is presently the most accurate method of protein structure prediction. Previous experiments have shown the selection of the correct template to be of paramount importance to the quality of the final model. We have derived a set of 732 targets for which a choice of ten or more templates exist with 30-80% sequence identity and used this set to compare a number of possible methods for template selection: BLAST, PSI-BLAST, profile-profile alignment, HHpred HMM-HMM comparison, global sequence alignment, and the use of a model quality assessment program (MQAP). In addition, we have investigated the question of whether any structurally defined subset of the sequence could be used to predict template quality better than overall sequence similarity. We find that template selection by BLAST is sufficient in 75% of cases but that there are examples in which improvement (global RMSD 0.5 A or more) could be made. No significant improvement is found for any of the more sophisticated sequence-based methods of template selection at high sequence identities. A subset of 118 targets extending to the lowest levels of sequence similarity was examined and the HHpred and MQAP methods were found to improve ranking when available templates had 35-40% maximum sequence identity. Structurally defined subsets in general are found to be less discriminative than overall sequence similarity, with the coil residue subset performing equivalently to sequence similarity. Finally, we demonstrate that if models are built and model quality is assessed in combination with the sequence-template sequence similarity that a extra 7% of "best" models can be found.     

Evaluating and improving cDNA sequence quality with cQC

SUMMARY: Errors are prevalent in cDNA sequences but the extent to which sequence collections differ in frequencies and types of errors has not been investigated systematically. cDNA quality control, or cQC, was developed to evaluate the quality of cDNA sequence collections and to revise those sequences that differ from a higher quality genomic sequence. After removing rRNA, vector, bacterial insertion sequence and chimeric cDNA contaminants, small-scale nucleotide discrepancies were found in 51% of cDNA sequences from one Arabidopsis cDNA collection, 89% from a second Arabidopsis collection and 75% from a rice collection. These errors created premature termination codons in 4 and 42% of cDNA sequences in the respective Arabidopsis collections and in 7% of the rice cDNA sequences.     

小麦HMW-GS 12基因克隆及植物表达载体构建

目的:为了利用基因遗传转化改良小麦品质,采用聚合酶链式反应(PCR)技术。方法:从小麦品种东农7742基因组DNA中扩增并克隆了小麦高分子量谷蛋白12亚基基因(HMW-GS 12)。结果:序列分析结果表明,该基因全长1 980bp,其核苷酸顺序和推导的氨基酸顺序与已发表的序列相比,同源性分别为99.5%和99.7%。经过基因拼接,分别构建了胚乳特异性表达和组成型表达的高分子量谷蛋白12亚基基因的两个植物表达载体pDNPPBIHG和pUbPBIHG。     

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

MOTIVATION: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods. RESULTS: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.     

INTERALIGN: interactive alignment editor for distantly related protein sequences

SUMMARY: Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon alpha traces of corresponding protein structures. Profile alignment, using CLUSTALW, is implemented to improve the alignment of a sequence of unknown structure with the visually optimized structural alignment as compared with a standard multiple sequence alignment. Tree-based ordering further helps in identifying the structure closest to a given sequence.     

Optimization of primer-specific filter metrics for the assessment of mitochondrial DNA sequence data

Filter metrics are used as a quick assessment of sequence trace files in order to sort data into different categories (i.e. high quality, review, and low quality) without human intervention. The filter metrics consist of two numerical parameters for sequence quality assessment: trace score (TS) and contiguous read length (CRL). Primer-specific settings for the TS and CRL were established using a calibration dataset of 2817 traces and validated using a concordance dataset of 5617 traces. Prior to optimization, 57% of the traces required manual review before import into a sequence analysis program, whereas after optimization only 28% of the traces required manual review. After optimization of primer-specific filter metrics for mitochondrial DNA sequence data, an overall reduction of review of trace files translates into increased throughput of data analysis and decreased time required for manual review.     

PRIMO: A Primer Design Program That Applies Base Quality Statistics for Automated Large-Scale DNA Sequencing

PRIMO is a computer program that designs walking primers for large-scale DNA sequencing projects. Oligonucleotide primers are predicted automatically, using quality information associated with each base call, eliminating the need for manually viewing the sequence traces or inspecting contig assemblies to determine appropriate locations for primer design. This allows PRIMO to run in batch mode on an arbitrarily large number of templates. For shotgun sequencing, PRIMO reads assembled sequence contigs with corresponding base quality statistics and automatically designs walking primers as needed to extend and join contigs, or improve their overall quality. In the opposite extreme of single-pass or completely directed sequencing, PRIMO reads the unassembled sequence for each template and designs walking primers for extending each read. If the base-calling software does not provide base quality statistics, PRIMO assigns its own measure of base quality determined by the shapes of individual peaks in the trace data for each template. In this way, PRIMO can be used in the finishing stages of a shotgun sequencing project, in sequencing by directed primer walking, or in some intermediate strategy. The code is written in ANSI C and maintained in two versions: one for the Macintosh and the other for UNIX.