R统计软件在地理信息上的应用

R软件是一种开源软件,提供了丰富的算法,是一种非常适合林业工作者应用的软件.它为林木育种的基因序列分析、野生动物保护的环境分析、环境保护的污染分析、地理学的分析等都可以提供有力的支持.在R中有许多可用的扩展包,其中RArcinfo、Maptools、spdev等为进行空间分析提供了很大的便利.一旦地理数据读入R软件,就可以使用其丰富的软件包进行空间分析,且R可以通过数据库读入数据,将这些数据进行统一分析,R为使用者提供了数据挖掘的有力手段.     

新疆引进扁桃品种与当地品种间种质资源的RAPD分析

利用7个多态性稳定的引物,对18个扁桃品种进行遗传多样性和亲缘关系RAPD分析.共扩增出54条DNA片段,其中多态性DNA带30条,占总扩增片段的55.6;.根据RAPD扩增结果,应用DPS(V3.01)软件进行Jaccard相似系数和遗传距离计算,并利用UPGMA法构建聚类树状图,结果表明,供试的18个扁桃品种可分为2个大类,聚类结果与种质分布结果基本一致.     

Adoption of new technologies by smallholder farmers: the contributions of extension,research institutes,cooperatives, and access to cash for improving tef production in Ethiopia

Agricultural intensification and extensification are standard responses to ecological and economic vulnerability among smallholder communities. Climate change has exacerbated this vulnerability and thrown the complexity of and critical need for managing a healthy natural resource base while increasing on-farm productivity into sharp light. Sustainable intensification is one of many mechanisms for accomplishing this balancing act. This study examines the adoption of sustainable intensification practices, namely input packages focused on tef row planting—designed to boost yield and promote more efficient use of inputs. This study utilized a mix methods approach to survey 115 smallholder farmers in the South Wollo zone of the Amhara region in Ethiopia. This study found that cash and capital, more so than contact with the AIS, influenced farmers’ decisions to adopt row planting input packages. Khat production was an important source of cash for inputs and was more likely to be available to farmers with irrigation schemes. Long-term, farmers who cultivate khat may not successfully engage in SI, as khat replaces traditional food crop production in the region. Yet, for farmers who do not grow khat, long-term investment in SI practices is unlikely unless access to affordable credit options is improved.     

Sequence analysis on microcomputers

Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further complicated their documentation by mixing instructions for the version based on floppy disk operation with that for the hard disk version.(ABSTRACT TRUNCATED AT 400 WORDS)     

基因组转座子鉴别与注释方法研究进展

转座子是一类可以在基因组不同位置间移动的、重复的序列,广泛存在于真核和原核生物基因组中,并对基因组的结构、功能和进化有着重要影响。转座子鉴别与注释是基因组注释工作的重要一步,相关软件可分为3类:从头算法、基于同源性的算法和联合算法,不同的软件实现方法和功能各不相同,并各有优缺点。文中对此进行了综述,并提出在今后的开发中将会出现更多结合多种算法的综合流程程序包,它们整合多种方法的优点,针对性强,可根据不同的需求来解决实际问题。     

利用ArcGIS建立县级永久基本农田数据库——以甘肃省古浪县为例

以古浪县为例,根据当地基本农田现状,运用Arc GIS10.2软件的数据处理功能,利用年度遥感监测影像数据进行有效核查比对。通过建设基本农田数据库,确定了保护目标,落实了空间位置,实现动态管理,为切实保护基本农田提供参考依据。     

New ways to study developmental genes in spore-forming bacteria

The regulated activation of numerous sets of genes in multiple chromosomal locations is a hallmark of cellular differentiation in both eukaryotes and prokaryotes. Certain species of bacteria that experience complex developmental cycles are especially attractive as systems in which to study the mechanisms of this kind of gene regulation because they are highly amenable to both biochemical and genetic approaches. Bacillus subtilis, which undergoes extensive cellular differentiation when it sporulates, is one such system. Many new methods are now available in this Gram-positive species for identifying, manipulating, and studying the regulation of genes involved in spore formation, including the use of transposable genetic elements that create gene fusions in vivo as an automatic consequence of insertions into genes.     

陕西石门电站微机测控系统抗干扰措施

结合石门电站微机测控工程实践论述了硬件及软件抗干扰措施。     

浙江近海三疣梭子蟹4个群体的控制区序列分析

以浙江近海三疣梭子蟹大螯肌肉的线粒体DNA作为模板,对4群体共67个个体的控制区（D-loop）序列进行了PCR扩增。通过对PCR产物进行双向测序,最终得到了控制区3’端的rRNA部分序列（64 bp）、D-loop全序列（1179 bp）及控制区5’端tRNA-Ile部分序列（73 bp）。经DNASP软件分析得知,67个D-loop序列定义了65个单倍型,在65个单倍型中,除去插入/缺失位点,所有单倍型共检测到344个多态位点,主要发生在D-loop序列的中间区域;D-loop序列检测到26个插入或缺失位点,碱基插入主要发生在中央后端区域,以13 bp重复片断插入的形式进行。每个个体含有0～3个连续重复片断。通过对三疣梭子蟹的遗传多样性分析发现,D-loop序列的单倍型多样性为0.982～1.000,核苷酸多样性指数为0.02770～0.03633,平均核苷酸差异数为31.790～43.304。综合分析,三个成蟹群体的遗传多样性相近,都低于仔蟹的遗传多样性,说明经过遗传育种,可以提高三疣梭子蟹的种质情况,真正实现对三疣梭子蟹的科学利用。     

小麦生长模拟过程可视化软件的研究

本文介绍了小麦生长模拟过程可视化软件的设计思想和实现的关键技术，该软件具有通用性和独立于模型的特点，并通过器官库的支持来实现小麦的造型部分。最后讨论了实现的关键技术，包括器官库的构建技术、三维图形的绘制技术、用户交互技术。     

Construction of a general human chromosome jumping library, with application to cystic fibrosis

In many genetic disorders, the responsible gene and its protein product are unknown. The technique known as "reverse genetics," in which chromosomal map positions and genetically linked DNA markers are used to identify and clone such genes, is complicated by the fact that the molecular distances from the closest DNA markers to the gene itself are often too large to traverse by standard cloning techniques. To address this situation, a general human chromosome jumping library was constructed that allows the cloning of DNA sequences approximately 100 kilobases away from any starting point in genomic DNA. As an illustration of its usefulness, this library was searched for a jumping clone, starting at the met oncogene, which is a marker tightly linked to the cystic fibrosis gene that is located on human chromosome 7. Mapping of the new genomic fragment by pulsed field gel electrophoresis confirmed that it resides on chromosome 7 within 240 kilobases downstream of the met gene. The use of chromosome jumping should now be applicable to any genetic locus for which a closely linked DNA marker is available.     

西藏高校“3S”技术课程教学现状与对策

西藏民族学生在语言文化、学习特点、思维方式等诸多方面与内地高校学生有相当大的差异,加之目前西藏高校＂3S＂技术课程的开设、师资力量、软硬件设施、管理程序等方面都存在不足,因而在学习内容复杂多样、实践性强等特点的＂3S＂技术课程方面存在着许多困难。提高学生思想认识,配置足够的教学设备和软件,为学生创造实践机会,简化管理程序,改革教学手段,一定程度上可以为西藏社会经济建设培养更多的既有专业知识又具备现代农林业信息技术理论和实践能力的高素质复合型人才。     

Molecular genetics: applications to the clinical neurosciences

Application of molecular biology, by means of linkage analysis and DNA probes that demonstrate restriction fragment length polymorphisms (RFLPs), has resulted in the chromosomal localization of the genes responsible for a number of neurological disorders. Characterization of the structure and function of individual genes for these diseases is in an early stage, but information available indicates that the molecular mechanisms underlying phenotypic expression of neurological diseases encompass a wide range of genetic errors ranging from the most minor (a single-base pair mutation) to large chromosomal deletions. Linkage analysis can now be used for genetic counseling in several of these disorders.     

玉米耐低磷研究现状及磷高效育种策略的探讨

土壤缺磷是影响作物产量提高和资源持续性发展利用的世界性问题．解决这一问题的根本途径是筛选土壤磷利用效率高的作物品种,玉米是中国主要的粮食作物,但在中国以西南、华南为代表的一部分地区,由于土壤有效磷含量偏低,严重制约玉米产量的提高,而在其他玉米产区由于磷肥的高度滥用,导致土壤结构发生改变,有效磷积累并不能满足玉米等作物的可持续性吸收利用。因此选择和培育玉米磷高效品种是提高土壤磷素利用效率．解决中国部分土壤有效磷缺乏对玉米产量影响的一条有效途径。综述了目前国内外在玉米耐低磷种质资源的筛选、遗传研究及相关性状QTL定位的研究进展,并在此基础上对玉米磷高效育种策略作了初步的探讨。     

On-farm computing software in the United Kingdom — a brief review

Since 1980 there has been huge growth in the commercial use of computers in relation to daily farming activities in the U.K. Three main types of application are involved, Bureau services, stand-alone computers on the farm, and on-line services such as Prestel Farmlink through the farmer's television set.Over 120 companies offer computer services to farmers, and 88 were surveyed for this study. Between them they offered 253 different packages of which the most common are for dairy and pig herd management, financial management, arable crops management and other livestock applications.There are no hard data on the number of farmers who use computers, but the proportion is greater than in most other countries. At present at least a third of the companies in the sector have formed joint ventures to market existing packages or develop new applications, and the recent rapid pace of change in the sector is expected to continue.     

Hardware and software efficacy in assessment of fine root diameter distributions

Fine roots constitute the majority of root system surface area and thus most of the nutrient and water absorption surface. Fine roots are, however, the least understood of all plant roots. A sensitivity analysis of several software programs capable of providing root diameter distribution analyses was undertaken to determine if this software was capable of discriminating 10% changes in diameters of roots in the 0.05–0.2 mm diameter range. Digital images produced by drawing discrete lines, by scanning wires of various diameters, and by scanning roots from several legume species were analyzed and compared. None of the three packages were able to adequately analyze these images. Each introduced artifacts into the data that were severe enough to confound interpretation of the resulting diameter class length histograms at resolutions from 24 to 400 pixels (px) mm⁻¹, and root diameters from 0.06 to 0.5 mm or larger. One package was, however, clearly superior to the other two for routine digital analysis. All three packages require additional development before they are suitable for routine analysis of fine roots. Due to the 252 px mm⁻¹ resolution ceiling with currently available scanners, the smallest roots for which this level of discrimination is possible is 0.12 mm diameter. For many agricultural and forest species, up to 95% of their total root length is less than 0.1 mm in diameter. It is concluded that both hardware and software constraints currently inhibit the sensitivity of investigations into fine root diameter shifts in response to environmental conditions.     

Gene transfer in crop improvement

Transfer of genes between plant species has played an important role in crop improvement for many decades. Useful traits such as resistance to disease, insects, and stress have been transferred to crop varieties from noncultivated plants. Recombinant DNA methods greatly extend (even outside the plant kingdom) the sources from which genetic information can be obtained for crop improvement. Gene transfer systems based on recombinant DNA are available for several crop species and are under development for others. The concerted use of traditional and more recent methods for plant genetic manipulation will contribute to crop improvement.     

A simple way to visualize detailed phylogenetic tree of huge genome-wide SNP data constructed by SNPhylo

Phylogenetic trees based on genome-wide single nucleotide polymorphisms (SNPs) among diverse inbreds could provide valuable and intuitive information for breeding and germplasm management in crops. As a result of sequencing technology developments, a huge amount of whole genome SNP data have become available and affordable for breeders. However, it is a challenge to perform quick and reliable plotting based on the huge amount of SNP data. To meet this goal, a visualization pipeline was developed and demonstrated based on publicly available SNP data from the current important maize inbred lines, including temperate, tropical, sweetcorn, and popcorn. The detailed phylogenetic tree plotted by our pipeline revealed the authentic genetic diversity of these inbreds, which was consistent with several previous reports and indicated that this straightforward pipeline is reliable and could potentially speed up advances in crop breeding.     

植物育种模拟的原理和应用

传统植物育种很大程度上依赖于表型选择和育种家的经验，分子生物学积累的大量遗传数据使得在基因水平上进行目标性状的选择成为可能，但是由于缺乏必要的工具，大量的遗传信息尚未在育种中得以有效利用。模拟方法可以利用各类遗传信息，在育种家进行田间试验之前，对杂交组合的表现、后代选择效果以及整个育种过程进行模拟，提出最佳的亲本选配、杂交和后代选择策略，从而提高常规育种的预见性和效率。本文介绍育种模拟的一些基本原理，包括遗传模型的构建、杂交类型和选择方法的定义等，概述育种模拟工具QuLine的基本功能及其在育种方法的比较、利用已知基因信息的亲本选配和设计育种等方面的应用。模拟方法通过定义复杂的遗传模型和育种方法实现对育种过程的模拟，在更真实的情形下比较不同育种方法的优劣、预测不同亲本杂交后代的表现，从而为育种家有效利用大量的分子信息和遗传数据提供了手段。     

Simulation Modeling in Plant Breeding： Principles and Applications

Conventional plant breeding largely depends on phenotypic selection and breeder＇s experience, therefore the breeding efficiency is low and the predictions are inaccurate. Along with the fast development in molecular biology and biotechnology, a large amount of biological data is available for genetic studies of important breeding traits in plants, which in turn allows the conduction of genotypic selection in the breeding process. However, gene information has not been effectively used in crop improvement because of the lack of appropriate tools. The simulation approach can utilize the vast and diverse genetic information, predict the cross performance, and compare different selection methods. Thus, the best performing crosses and effective breeding strategies can be identified. QuLine is a computer tool capable of defining a range, from simple to complex genetic models, and simulating breeding processes for developing final advanced lines. On the basis of the results from simulation experiments, breeders can optimize their breeding methodology and greatly improve the breeding efficiency. In this article, the underlying principles of simulation modeling in crop enhancement is initially introduced, following which several applications of QuLine are summarized, by comparing the different selection strategies, the precision parental selection, using known gene information, and the design approach in breeding. Breeding simulation allows the definition of complicated genetic models consisting of multiple alleles, pleiotropy, epistasis, and genes, by environment interaction, and provides a useful tool for breeders, to efficiently use the wide spectrum of genetic data and information available.