Characteristic features of porcine endogenous retroviruses in Vietnamese native pigs

We aimed to clarify the genomic characteristics of porcine endogenous retroviruses (PERVs) in Vietnamese native pig (VnP) breeds. First, we investigated genetic polymorphisms in β‐ and γ‐like PERVs, and we then measured the copy numbers of infectious γ‐like PERVs (PERV‐A, B, and C). We purified genomic DNA from 15 VnP breeds from 12 regions all over the country and three Western pig breeds as controls, and investigated genetic polymorphisms in all known PERVs, including the beta (β)1–4 and gamma (γ)1–5 groups. PERVs of β1, β2, β3, and γ4 were highly polymorphic with VnP‐specific haplotypes. We did not identify genetic polymorphisms in β4, γ1, or γ2 PERVs. We then applied a real‐time polymerase chain reaction–based method to estimate copy numbers of the gag, pol, and env genes of γ1 PERVs (defined as A, B, and C). VnP breeds showed significantly lower copy number of the PERV genes compared with the Western pig breeds (on average, 16.2 and 35.7 copies, respectively, p < .05). Two VnP breeds showed significantly higher copy number compared with the other VnPs (p < .05). Our results elucidated that VnPs have specific haplotypes and a low copy number of PERV genes.     

中国畜禽品种资源网络数据库系统的构建

在规范化《中国畜禽品种志》和重新调查搜集到的大量畜禽种质资源信息后,利用TBF全文信息非结构数据库,构建了“中国畜禽品种资源网络数据库”,并通过Internet以http：／／www．cdad-is．org．cn／网址发布。在网站内系统提供了包括全文检索、组合检索、二次检索、字段检索和多库检索等功能,并指出了本网络数据库的今后发展目标是如何获取我国畜禽品种资源的动态信息,以及实现资源信息从内容管理到知识管理的逐步过渡。     

Practical implications of using non-relational databases to store large genomic data files and novel phenotypes

The objective of our study was to provide practical directions on the storage of genomic information and novel phenotypes (treated here as unstructured data) using a non-relational database. The MongoDB technology was assessed for this purpose, enabling frequent data transactions involving numerous individuals under genetic evaluation. Our study investigated different genomic (Illumina Final Report, PLINK, 0125, FASTQ, and VCF formats) and phenotypic (including media files) information, using both real and simulated datasets. Advantages of our centralized database concept include the sublinear running time for queries after increasing the number of samples/markers exponentially, in addition to the comprehensive management of distinct data formats while searching for specific genomic regions. A comparison of our non-relational and generic solution, with an existing relational approach (developed for tabular data types using 2 bits to store genotypes), showed reduced importing time to handle 50M SNPs (PLINK format) achieved by the relational schema. Our experimental results also reinforce that data conversion is a costly step required to manage genomic data into both relational and non-relational database systems, and therefore, must be carefully treated for large applications.     

东北虎（Panthera tigris altaica）个体识别技术研究进展

对东北虎种群的科学监测是采取有效保护、管理及恢复措施的基础,而准确的个体识别又是保证有效监测的前提。尤其是在中国,在野生东北虎种群数量很少,种群密度极低的情况下,能根据它留下的各种信息进行个体识别就显得尤为重要。目前,用于野生东北虎个体识别的技术主要有：足迹识别、DNA识别、条纹识别以及气味识别等。本文对这几种技术的特点、研究进展、应用注意事项等做了介绍,并且结合中国的实际情况,分析每种技术在中国的适用性,认为如果要建立中国的东北虎种群数量数据库,足迹识别和DNA识别比较适合在中国现有东北虎分布区推广使用。通过足迹识别,信息容易获取,也是最经济和比较成熟的方法;由于种群密度低,含DNA的遗传样本虽不能每次都采集到,但可以长期积累;现阶段条纹和气味识别只能起到辅助的作用。     

Associations between genetics, farm characteristics and clinical disease in field outbreaks of porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS) is a disease of domestic swine characterized by exceptionally high clinical variability. This study addresses the question of whether clinical variability in PRRS results from (a) genetic variation among viral isolates and/or (b) variation in management practices among farms on which isolates are found. Genetic data (open reading frame 5 gene sequences) and data on farm characteristics and associated clinical disease signs were collected for 62 PRRS virus (PRRSV) field isolates, representing 52 farms. Clinical disease signs were interrelated — confirming that a true reproductive syndrome exists (involving abortions, infertility in sows, deaths of sows and preweaning mortality).

Pairs of farms experiencing deaths in their sow populations also tended to share viral isolates which were more similar to one another than expected by chance alone. This implies that sow death (one of the more-severe manifestations of PRRS) is under genetic influence. Large herd size was a significant risk factor for the death of sows and for respiratory disease in nursery pigs. All-in–all-out management practices in the nursery were protective against reproductive signs in the sow herd. All-in–all-out management practices in the finishing stages of production were protective against respiratory disease in nursery pigs — but were paradoxically associated with an increased risk of infertility in sows. These results suggest that farm-management practices can also influence which PRRS clinical signs are manifested during an outbreak. In general, signs associated with PRRS appear to result from a combination of genetic factors and herd-management characteristics. The relative contributions of these two influences differ depending on the specific clinical sign in question.     

Database system for herd health management of dairy herds especially for udder health

Integrated herd health management is an effective method to improve animal health as mastitis and fertility disorders in dairy herds. For optimizing the costs and work load for the herd health management, it is necessary to have a data tool that enables a quick and comfortable data handling and provides practicable handouts for extension. The Research Institute of Organic Agriculture in Switzerland (FiBL) has developed such a database-system for the animal health management project "pro-Q". Objective of this database is to combine external available and on-farm collected data and to provide routine tools on herd and cow level (incl. udder quarter level) for farmers, veterinarians and advisers. These tools should give a comprehensive overview over the animal health situation of the herd and the single animal level. Furthermore, the database presented in this article, meets the requirements of a multi-user system with remote-access which enables different instances to gain the requested information.     

Progress in Identifying High Nature Value Montados: Impacts of Grazing on Hardwood Rangeland Biodiversity

Due to their complex structure and traditional low-intensity management, Portuguese oak woodland rangelands known as montados are often considered high nature value (HNV) farming systems, and as such, they may be deemed eligible for subsidies and incentives by governmental and nongovernmental agencies. Too little is known about how the HNV concept might be applied to conserve complex silvopastoral systems. These systems, due to their structural and functional complexity at multiple scales, tend to support high levels of biodiversity. Montados are in sharp decline as a result of the rapid specialization of land management that, through simplification, undermines multifunctionality. Understanding how changes in management influence these systems and their biodiversity is needed for prioritizing conservation efforts and for ensuring they remain HNV systems. On the basis of a field survey in 58 plots distributed among 29 paddocks on 17 farms, we conducted an integrated analysis of the relationship between grazing intensity and biodiversity in montados of similar biophysical and structural characteristics. Data on management were obtained through interviews, and biodiversity data (vegetation, macrofungi, birds, herpetofauna) were obtained through specific field protocols. Additional spatial data, such as soil characteristics, slope, land cover, and linear landscape elements, were also analyzed. The results show no overall biodiversity variation as a result of different management practices. However, different groups of species react differently to specific management practices, and within a pasture, grazing impacts are heterogenous. In low grazing intensity plots, macrofungi species richness was found to be higher, while bird species richness was lower. Using tree regeneration as proxy for montado sustainability, results show less tree regeneration in areas with higher forage quality and more intense grazing. Pathways for future progress are proposed, including creating areas within a paddock that attract grazing away from where regeneration is desired.     

A small animal clinical and epidemiological relational database

A mainframe relational database management system (RDBMS), ORACLE, has been applied to small animal clinical records to facilitate storage and querying of case data for clinical and epidemiological use. Coded records are entered into the computer via a “user-friendly” interface which validates the input. Clinicians' queries similarly utilise an interface that generates query commands from four simple queries. Epidemiologists' queries, in contrast, require considerable flexibility and so use the main RDBMS language, SQL*Plus. A data administrator manages the security and integrity of the RDBMS.     

XQuery Injection Attack and Countermeasures

As a database that allows data to be stored in XML format, XML database suffers from some similar attacks as traditional relational database does. These attacks include injection attack by XQuey function in application software. These include BaseX, eXist and MarkLogic. In order to defeat these attacks, countermeasures are proposed.     

辽宁省草原资源管理系统的设计与应用

为提高辽宁省草原资源管理水平, 实现草原数字化与信息化管理, 以辽宁省1∶1 000 000、1∶250 000和1∶50 000比例尺的电子地图为基础本底数据, 结合实地调查的草原GPS数据和草原属性数据建立了辽宁省草原地理信息数据库。通过综合运用地理信息、数据库和网络信息技术, 采用B/S辅以C/S架构, 构建了包含辽宁省草原资源、属性、工程、灾害、监测、知识、文献和报表等信息的辽宁省草原资源管理系统, 为辽宁省草原管理提供了系统、高效、便捷和直观的网络信息交互平台。     

Monitoring tigers with confidence

With only 5% of the world's wild tigers (Panthera tigris Linnaeus, 1758) remaining since the last century, conservationists urgently need to know whether or not the management strategies currently being employed are effectively protecting these tigers. This knowledge is contingent on the ability to reliably monitor tiger populations, or subsets, over space and time. In the this paper, we focus on the 2 seminal methodologies (camera trap and occupancy surveys) that have enabled the monitoring of tiger populations with greater confidence. Specifically, we: (i) describe their statistical theory and application in the field; (ii) discuss issues associated with their survey designs and state variable modeling; and, (iii) discuss their future directions. These methods have had an unprecedented influence on increasing statistical rigor within tiger surveys and, also, surveys of other carnivore species. Nevertheless, only 2 published camera trap studies have gone beyond single baseline assessments and actually monitored population trends. For low density tiger populations (e.g. <1 adult tiger/100 km²) obtaining sufficient precision for state variable estimates from camera trapping remains a challenge because of insufficient detection probabilities and/or sample sizes. Occupancy surveys have overcome this problem by redefining the sampling unit (e.g. grid cells and not individual tigers). Current research is focusing on developing spatially explicit capture-mark-recapture models and estimating abundance indices from landscape-scale occupancy surveys, as well as the use of genetic information for identifying and monitoring tigers. The widespread application of these monitoring methods in the field now enables complementary studies on the impact of the different threats to tiger populations and their response to varying management intervention.     

Genetic origin and dispersal of the invasive soybean aphid inferred from population genetic analysis and approximate Bayesian computation

Biological invasion is considered among the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines, is among the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using 8 microsatellite loci and the mitochondrial cytochrome c oxidase subunit I gene. We were able to identify a significant isolation by distance pattern and 3 genetic lineages in the microsatellite data but not in the mtDNA dataset. The genetic structure showed that the USA population had the closest relationship with those from Korea and Japan, indicating that the 2 latter populations might be the sources of the invasion to the USA. Both population genetic analyses and approximate Bayesian computation showed that the northeastern populations in China were the possible sources of the further spread of A. glycines to Indonesia. The dispersal history of this aphid can provide useful information for pest management strategies and can further help predict areas at risk of invasion.     

畜禽遗传资源的地理信息系统

畜禽品种资源信息由于具有明显的分散地域特征,因而宜用地理信息系统对其各种数据进行综合与分析。基于这样的考虑,我们进行了畜禽品种资源信息系统的前期研究,结合信息系统、数据库系统和数量遗传学的理论,开发了该系统的部分软件,主要的研究工作包括：１．图形、图像数据库的建立,录入了部分家畜家禽的图像资料和有关的特性特征的数字和文字资料,建立了全国及分省区的地图库。可以方便地按品种名称和地图两种途径进行检索。２．可视化操作环境的制作。本系统采用了多窗口切换、图形菜单及事件管理等手段,使系统具有良好的人机交互界面,适于具有不同计算机应用水平的人员使用。３．品种资源状态预警系统的前期研究。可根据群体数量对品种资源状态做简单预警。     

川西北高原鼠荒地危害程度分级及适应性管理对策

高原鼠兔和高原鼢鼠是青藏高原特有的食草型小动物,其啃食、掘洞、刈割、贮草行为对高寒草甸生态系统既具有破坏损伤系统的负面效应,也有利于维持和稳定系统的正面效应,这种益害转化完全取决于不同时间和空间尺度上的害鼠种群及其数量。通过对川西北的阿坝州、甘孜州和青海省果洛州的42个高寒草地样地的鼠类种群密度调查和已有文献的采集分析,明确了草原害鼠在高寒草地生态系统中的角色和作用,定义了鼠荒地的概念,对鼠荒地危害程度划分为轻度、中度、重度和极度4个等级;依据指标因子重要性排序,分级指标包含害鼠种群、植物群落和土壤养分3个主因子群;总洞穴数量、有效洞口数等11个单项因子;并对不同危害程度的鼠荒地提出了封育自然修复、人为干预修复、半人工草地改建和人工草地重建4种草原鼠害适应性管理策略,对于高寒草地生态系统草原害鼠适应性管理和害鼠灭除后二次发生防控具有指导意义。     

甘肃亚高山云杉人工林下植物种群生态位特征

根据野外110个样方的调查数据,应用Levins、Shannon-Wiener生态位宽度指数和Levins生态位重叠指数对甘肃亚高山云杉(Picea asperata)人工林下30个种(包括15种灌木和15种草本植物)的生态位特征进行定量分析。结果表明,灌木针刺悬钩子(Rubus pungens)、箭竹(Sinarundinaria nitida)、秀丽莓(Rubus amabilis)、草本东方草莓(Fragaria orientalis)、鸭茅(Dactylis glomerata)和紫花碎米荠(Cardamine tangutorum)的生态位宽度较大,表明这些物种适应能力强,分布范围广,倾向于泛化种。生态位宽的种群可能产生较小的生态位重叠,生态位较窄的种群间也会产生较大的生态位重叠,生态位宽度与生态位重叠程度无相关性。总体上看,亚高山云杉人工林下物种间生态位重叠程度均较小,种间竞争并不激烈。从生态响应来看,灌木层的红桦(Betula albo-sinensis)幼苗和草本层的老鹳草(Geranium wilfordii)发展性最强,今后可能会发展为云杉人工林下的优势种群。     

基于GIS牧草种植管理专家系统的分析与设计

介绍了牧草种植管理专家系统 (Expert System, ES)的结构体系与设计思路.系统基于地理信息系统 (GIS)、数据库管理系统(SQL server),建立以遥感图像数据、土壤养分数据、专题地图矢量数据、自然地理条件因子等为主体的数据库;由专业经验及领域知识建立了决策库;由相关模型建立模型库,将这4个库通过程序代码有机的整合在一起,形成4库一体化专家系统结构.实现了在牧草种植地区草种信息咨询服务,牧草种植优化配置分析,适宜性评价及预测预报,退耕还草的空间分布及其面积的估测等功能.     

Joint use of Disparate Data for the Surveillance of Zoonoses: A Feasibility Study for a One Health Approach in Germany

Zoonotic diseases concern human and animal populations and are transmitted between both humans and animals. Nevertheless, surveillance data on zoonoses are collected separately for the most part in different databases for either humans or animals. Bearing in mind the concept of One Health, it is assumed that a global view of these data might help to prevent and control zoonotic diseases. In following this approach, we wanted to determine which zoonotic data are routinely collected in Germany and whether these data could be integrated in a useful way to improve surveillance. Therefore, we conducted an inventory of the existing data collections and gathered information on possible One Health surveillance areas in Germany by approaching experts through a scoping survey, personal interviews and during a workshop. In matching the information between the status quo for existing data collections and the possible use cases for One Health surveillance, this study revealed that data integration is currently hindered by missing data, missing pathogen information or a lack of timeliness, depending on the surveillance purpose. Therefore, integrating the existing data would require substantial efforts and changes to adapt the collection procedures for routine databases. Nevertheless, during this study, we observed a need for different stakeholders from the human and animal health sectors to share information to improve the surveillance of zoonoses. Therefore, our findings suggest that before the data sets from different databases are integrated for joint analyses, the surveillance could be improved by the sharing of information and knowledge through a collaboration of stakeholders from different sectors and institutions.