植物氮素吸收利用相关NPF基因家族研究进展

氮(N)是植物生长发育需要量最大的矿质营养元素,也是作物产量的限制因子。硝态氮(NO₃^--N)是植物吸收利用氮素的主要形态之一。目前,植物中已报道4个基因家族(NPF、NRT2、CLC和SLAC1/SLAH)参与硝态氮的吸收和利用,其中NPF基因家族成员数量众多且功能多样化,近年来获得较多关注和深入研究。模式植物拟南芥和主要粮食作物水稻、玉米和小麦中,分别含有53、93、79和331个NPF基因。拟南芥NPF家族中已有超过一半成员(31/53)的生物学功能被解析,粮食作物水稻中NPF基因功能亦有较多报道。研究表明,NPF基因广泛参与了植物对氮素的吸收及其调控、转运、分配/再分配等过程,一些成员对于改良和提高作物氮素利用率(nitrogen use efficiency, NUE)具有重要作用。因此,从氮素进入植物体及其在植物体内流动的层面出发,发掘具有重要功能的候选NPF基因,对于解析植物利用氮素的分子机制及其遗传改良具有重要意义。本文综述了模式植物拟南芥以及粮食作物中已报道的NPF基因在氮素吸收和利用中的生物学功能。目前粮食作物玉米中仅有4...     

Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms

This review mainly discusses three related topics: the application of ecological theories to soil, the measurement of microbial diversity by molecular techniques and the impact of transgenic plants and microorganisms on genetic diversity of soil. These topics were debated at the Meeting on Soil Emergency held in Erice (Trapani, Italy) in 2001 for the celebration of the 50th anniversary of the Italian Society of Soil Science. Ecological theories have been developed by studying aboveground ecosystems but have neglected the belowground systems, despite the importance of the latter to the global nutrient cycling and to the presence of life on the Earth. Microbial diversity within the soil is crucial to many functions but it has been difficult in the past to determine the major components. Traditional methods of analysis are useful but with the use of molecular methods it is now possible to detect both culturable and unculturable microbial species. Despite these advances, the link between microbial diversity and soil functions is still a major challenge. Generally studies on genetically modified bacteria have not addressed directly the issue of microbial diversity, being mainly focused on their persistence in the environment, colonization ability in the rhizosphere, and survival. Concerns have been raised that transgenic plants might affect microbial communities in addition to environmental factors related to agricultural practice, season, field site and year. Transgenic plant DNA originating from senescent or degraded plant material or pollen has been shown to persist in soil. Horizontal transfer of transgenic plant DNA to bacteria has been shown by the restoration of deleted antibiotic resistance genes under laboratory in filter transformations, in sterile soil or in planta. However, the transformation frequencies under field conditions are supposed to be very low. It is important to underline that the public debate about antibiotic resistant genes in transgenic plants should not divert the attention from the real causes of bacterial resistance to antibiotics, such as the continued abuse and overuse of antibiotics prescribed by physicians and in animal husbandry.     

Semiparametric Kernel-Based Regression for Evaluating Interaction Between Pathway Effect and Covariate

Pathway-based analysis has the ability to detect subtle changes in response variables that could be missed when using gene-based analysis. Since genes interact with other covariates such as environmental or clinical variables, so do pathways, which are sets of genes that serve particular cellular or physiological functions. However, since pathways are sets of genes and since environmental or clinical variables do not have parametric relationships with response variables, it is difficult to model unknown interaction terms between high-dimensional variables and low-dimensional variables as environmental or clinical variables. In this paper, we propose a semiparametric interaction model for two unknown functions to evaluate the interaction between a pathway and environmental or clinical variable: for the pathway, we use an unknown high-dimensional function, and for environmental or clinical variable, we use an unknown low-dimensional function. We model the environmental or clinical variable nonparametrically via a natural cubic spline. We model both the pathway effect and the interaction between the pathway and environmental or clinical effect nonparametrically via a kernel machine. Since both interactions among genes within the same pathway and the interaction between the pathway and the environmental or clinical variables are complex, we allow for the possibility that a pathway is interacting with environmental or clinical variables and the genes within the same pathway are interacting with each other. We illustrate our approach using simulated data and genetic pathway data for type II diabetes. Supplementary materials accompanying this paper appear online.     

Brassicaceae,a Plant Family Well Suited for Modern Biotechnology

Abstract

A survey of recent progress in various biotechnological areas, on various Brassica crops, is presented. Wide hybridization and subsequent culture of embryos, ovaries and ovules can facilitate sexual gene transfer between species. The protoplast fusion technique extends the possibilities of transferring genes between species, even from different genera and tribes, it being independent of sexual incompatibility barriers. Furthermore, somatic hybridization provides novel possibilities for modifying the organelle composition of plants. Genetic engineering for crop improvements and fundamental studies in plant biology involve isolation of genes, studies of gene expression and gene regulation. In order to change or improve agronomically desirable traits, or to investigate further specific gene functions, methods for transfer of cloned genes into plants have developed. Furthermore, cryopreservation would enable conservation of genetic material, including genetically modified plants deriving from various biotechnological manipulations.     

土壤宏基因组学研究方法与进展

土壤微生物驱动着土壤中的物质循环和养分转化。在土壤学的研究中,长期将土壤作为一个黑箱系统来对待,对其中的生物组成及其参与的生化过程知之甚少。土壤中绝大部分微生物目前尚难以分离培养,因此基于传统的培养方法对于认识土壤微生物群落组成和功能有其局限性。宏基因组学直接从环境样品中提取全部微生物的DNA,或通过测序探究环境中微生物的群落结构和功能(序列驱动),或构建宏基因组文库,筛选新的基因或生物活性物质(功能驱动),克服了传统培养方法的缺陷,极大地丰富了对土壤微生物多样性及其功能的认知。本文在综述土壤宏基因组学研究基本流程的基础上,重点介绍了日益重要的第二代测序平台在土壤宏基因组学研究中的应用及其产生的海量数据的分析处理方法,并简要探讨了宏基因组学在土壤微生物生态学中的应用。最后,作者建议在国家层面上展开相关土壤宏基因组学研究,调查微生物群落及其变化,为生物资源开发、农业生产和环境保护作出应有的贡献。     

Intragenic crop improvement: combining the benefits of traditional breeding and genetic engineering

New crop varieties are developed by applying traditional breeding methods that rely on random genome modifications. These varieties combine multiple traits that support farm efficiency and acceptable yields but also contain genes associated with the production of toxins, allergens, and/or antinutritional compounds that were not considered during the selection process. Furthermore, existing cultivars frequently lack the functional genes required for specific sensory traits and the formation of health-promoting antioxidants. One new method efficiently addresses some of these issues by either silencing undesirable genes or enhancing the expression of genes that are linked to dormant beneficial traits. Rather than incorporating foreign DNA into the plant's genome, these methods transform crops with plant-derived transfer (P-) DNAs that consist of only native genetic elements. The genetic modification can be characterized molecularly so that any inadvertent transfer of undesirable DNA, as may be the case with traditional methods, is excluded. A recently developed intragenic potato plant is silenced for the polyphenol oxidase, dikinase R1, and phosphorylase-L genes in a tuber-specific manner. French fries derived from these tubers lack discolorations, display an enhanced potato flavor, and produce greatly reduced amounts of the suspected carcinogen acrylamide. It is argued that intragenic modification is unlikely to trigger phenotypic, biochemical, or physiological variation that is new to the species. Similarly, the targeted traits are similar to those that breeders select for and often have a history of domestication and reduced fitness. For these reasons, an updated regulatory system is proposed whereby intragenic crops are considered as low risk and should be cleared for commercial release in a timely and cost-effective manner. By using modern techniques to modify the same genetic material that is used by breeders, intragenic approaches may be perceived as an acceptable extension of traditional methods in crop improvement.     

农杆菌介导的玉米遗传转化研究进展

农杆菌介导的转基因法是目前玉米遗传转化的主流方法之一。目前,模式玉米种质幼胚的转化体系已程式化,且开发了新筛选基因和获得不含筛选基因转基因玉米的方法,但是大多数育种骨干自交系转化频率低和转化受体基本上是幼胚。从农杆菌、受体及培养条件多方面各种因素对问题进行分析,多数研究认为针对特定基因型和受体材料建立好的受体再生系统,结合高效率农杆菌转化体系,获得多目的基因聚合（无其它外源片段）的转基因玉米将是农杆菌介导玉米转化体系研究的最终目标。本文主要从农杆菌介导（转基因）法应用于玉米遗传转化的历史、现状、问题等方面进行综述,为同领域的研究者提供一定的参考。     

Quantitative approach to classification of gray forest soils in the Volga-Kama forest-steppe region

On the basis of factual data obtained by the Soil Science Department of the Privolzhskii Federal University and available from literary, virtual reference “images” of gray forest soils as distinguished in classification systems of 1977 and 2004 have been obtained with the use of the methods of multivariate statistics for the Volga-Kama forest-steppe region. Discriminant functions and have been obtained, and classification functions have been developed with the help of numerical methods to diagnose new representatives of gray forest soils. The virtual “images” of the soils can be used for the improvement of soil systematization and for solving various applied problems of land use.     

Call for Papers--Bt Research （ISSN 1925-1939）

Bt Research （ISSN 1925-1939） is a new launched, open access and peer-reviewed journal that disseminates significant creative reviews and opinions or innovative research work in the area of Bacillus thuringiensis, including the isolation and identification of novel Bt strains, identification of novel Bt toxic genes and their functions, the insecticidal mechanism Bt toxics, Bt genetic engineering, transgenic Bt plants, the resistance mechanism of target-insect to Bt toxins, and the development of novel experimental methods and techniques for Bt Research.     

点突变的酶学检测技术

研究点突变有助于深入认识高等生物的遗传特性、解释个体的表型差异、揭示基因和蛋白质的正常功能、变异的成因以及不同个体对环境变化的响应机制,对功能基因组学研究和建立分子标记都具有重要意义。本文在概述点突变常用的非酶学检测技术基础上,重点介绍了不同酶学检测系统的原理和方法,并对影响点突变酶学检测效果的因素进行了讨论。     

禾本科植物富甲硫氨酸蛋白基因的克隆及其进化分析

甲硫氨酸(Met)是豆科植物的第一限制性氨基酸。为了获取富Met贮藏蛋白基因,通过比对禾本科富Met贮藏蛋白基因序列来设计引物,以千金子、芦苇、稗、光头稗、东乡野生稻、茶陵野生稻和湖南野生稻等几种常见禾本科植物种子RNA为模板,经RT-PCR扩增获得c DNA片段,并进行序列比对、Motif预测和进化分析。测序结果显示,禾本科植物富Met贮藏蛋白基因序列存在保守程度不同的区域,在同一个属内的植物间,富Met贮藏蛋白基因的序列高度保守。Motif预测显示,富Met贮藏蛋白可能与植物抗病性等功能有关。进化分析表明,不同科的植物种子富Met贮藏蛋白基因存在较大差异,禾本科植物则较为保守,尤其是稻属中富Met贮藏蛋白基因高度保守,玉米中则存在不同类型的富Met贮藏蛋白。本研究丰富了富Met贮藏蛋白基因库,为豆科植物富Met基因工程提供了更多选择,为进一步理解富Met贮藏蛋白在植物发育代谢中的作用机理提供了参考。     

利用病毒诱导的基因沉默(VIGS)技术快速鉴定两个马铃薯晚疫病抗性相关EST片段EL732276和EL732318的功能

马铃薯晚疫病是由致病疫霉[Phytophthora infestans(Mont.)deBary]引起的第一大作物病害,目前已严重限制了全球马铃薯的生产和发展。马铃薯晚疫病抗性分子机理的研究一直是抗病育种中的热点问题。本研究利用病毒诱导的基因沉默(virus-induced gene silencing,VIGS)技术,在本氏烟草(Nicotina benthamiana)中沉默两个马铃薯晚疫病水平抗性相关的基因片段EL732276和EL732318。目的基因沉默后的烟草接种晚疫病菌P.infestans,根据病斑生长速率LGR(length grow rate)来了解这两个基因是否参与烟草对晚疫病的抗性反应。结果表明,目的基因片段EL732276和EL732318被成功地插入烟草脆裂病毒(Tobacco rattle virus,TRV)载体中。利用携带八氢番茄红素脱氢酶基因(phytoene desaturae,PDS)的TRV重组载体病毒接种烟草,感染病毒的烟草植株表现光漂白现象,说明VIGS体系有效。用携带目的片段的重组载体病毒TRV:EL732276和TRV:EL732318感染烟草植株,一个月后,烟草叶片接种晚疫病菌P.infestans,从接种P.infestans的烟草叶片上可以看出,感染TRV空载体的对照烟草叶片上病斑扩展速率非常缓慢,而目的片段EL732276和EL732318沉默后的烟草叶片可见明显的水浸状病斑和少量白色的晚疫病菌菌丝。进一步的分析表明TRV:EL732276重组载体病毒侵染的烟草接种P.infestans后LGR值极显著上升,TRV:EL732318病毒侵染的烟草接种P.infestans后LGR值显著上升,表明EL732276和EL732318同源基因在烟草中沉默后,烟草对P.infestans的抗性显著降低。研究结果认为,病毒诱导的基因沉默技术可在本氏烟草中初步快速鉴定马铃薯抗病相关基因的功能。     

Heavy metals potentially drive co-selection of antibiotic resistance genes by shifting soil bacterial communities in paddy soils along the middle and lower Yangtze River

Heavy metals (HMs) and antibiotic resistance have become serious environmental problems affecting soil and human health. Soil microorganisms play key roles in pollutant degradation and biogeochemical cycling processes; however, the interactions among HMs, soil microbial communities, and antibiotic resistance genes (ARGs) in agricultural soils remain unclear. Using quantitative real-time polymerase chain reaction and NovaSeq sequencing, we evaluated heavy metal contents, abundances of ARGs, soil bacterial community structure and functions, and their correlations in paddy soils at 43 sampling sites along the middle and lower reaches of the Yangtze River, central and eastern China. Our results showed the co-occurrence of HMs, ARGs, and HM resistance genes across all paddy soils. Additionally, significant positive associations were detected between HMs and resistance genes. Cadmium, czcA, and int1 were positively correlated with bacterial community diversity. The Mantel test showed that bacterial community composition and functions were significantly associated with HMs and resistance genes, such as Cd, Cr, Zn, copA, czcA, int1, and sul1. Moreover, HMs and ARGs were the major factors shaping soil bacterial communities; thus, HMs triggered proliferation of HM and antibiotic resistances by influencing the mobile genetic element (int1) and soil microbial communities. Our study revealed that HMs potentially drive the co-selection of ARGs by shifting soil bacterial community structure and functions, thereby increasing the potential risks to human health as well as ecological environment in the paddy soils along the middle and lower reaches of the Yangtze River.     

6天龄与10天龄大鼠的睾丸组织的基因差异表达

通过基因芯片技术,利用Roche-NimbleGen公司制作的大鼠12×135K全基因组表达谱芯片,对日龄为6d和10d的大鼠睾丸组织进行全基因组表达差异分析。结果显示：具有2倍以上的差异表达基因有4298个,其中表达上调的基因共1878个,表达下调的基因共2420个。这些差异表达的基因中有3154个基因具有基因本体注释,参与了154个生物学通路。进一步分析表明具有8倍以上差异表达的基因有13个,这些基因参与了生物学过程、细胞组分和分子功能等基因本体分类,进一步选择3个差异表达的基因,LOC686076、Cxcl6和Trib3,做了实时定量RT-PCR检测。其结果趋势与芯片数据一致。因此,我们初步认为精原干细胞的发生与增殖在大鼠早期的发育过程中已经有大量的基因参与,是一个多基因协调表达的过程。     

A new perspective on functional redundancy and phylogenetic niche conservatism in soil microbial communities

Functional redundancy in soil microbial communities seems to contradict the notion that individual species have distinct metabolic niches in multi-species communities.All soil microbiota have the metabolic capacity for"basic"functions(e.g.,respiration and nitrogen and phosphorus cycling),but only a few soil microbiota participate in"rare"functions(e.g.,methanogenesis and mineralization of recalcitrant organic pollutants).The objective of this perspective paper is to use the phylogenetic niche conservatism theory as an explanation for the functional redundancy of soil microbiota.Phylogenetic niche conservatism is defined as the tendency for lineages to retain ancestral functional characteristics through evolutionary time-scales.The present-day soil microbiota is the result of a community assembly process that started when prokaryotes first appeared on Earth.For billions of years,microbiota have retained a highly conserved set of core genes that control the essential redox and biogeochemical reactions for life on Earth.These genes are passed from microbe to microbe,which contributes to functional redundancy in soil microbiota at the planetary scale.The assembly of microbial communities during soil formation is consistent with phylogenetic niche conservatism.Within a specific soil,the heterogeneous matrix provides an infinite number of sets of diverse environmental conditions,i.e.,niches that lead to the divergence of microbial species.The phylogenetic niche conservatism theory predicts that two or more microbial species diverging from the same clade will have an overlap in their niches,implying that they are functionally redundant in some of their metabolic processes.The endogenous genetic factors that constrain the adaptation of individuals and,thus,populations to changing environmental conditions constitute the core process of phylogenetic niche conservatism.Furthermore,the degree of functional redundancy in a particular soil is proportional to the complexity of the considered function.We conclude with a conceptual model that identifies six patterns of functional redundancy in soil microbial communities,consistent with the phylogenetic niche conservatism theory.     

镉胁迫下的实验室放线菌种群结构变化的DGGE分析

The actinomycete populations and functions in cadmium (Cd) contaminated soil were investigated by the cultivationindependent molecular methods. The genomic DNA was extracted and purified from soil adulterated with various concentrations of Cd in the laboratory. The partial 16S rDNA genes were amplified by polymerase chain reaction (PCR) using specific primers bound to evolutionarily conserved regions within these actinomycete genes. The diversity in PCRamplified products, as measured by denaturing gradient gel electrophoresis (EGGE), was used as a genetic fingerprint of the population. Principle component analysis and Shannon-Weaver diversity index (H) analyses were used to analyze the DGGE results. Results showed that the two principal components accounted for only a low level of the total variance. The value H in contaminated soil was lower than that in the control at later stages of cultivation, whereas at earlier stages it was higher. Among the six sampling time points, the first, fifth and sixth weeks had the highest values of H. Significantly negative correlations between bioavailable Cd concentration and H values existed in the samples from weeks 2 (R = 0.929, P < 0.05) and 4 (R =0.909, P < 0.05). These results may shed light on the effect of Cd on the soil environment and the chemical behavior and toxicity of Cd to actinomycetes.     

生物多样性对生态系统功能及其稳定性的影响

生物多样性导致生态系统功能优化学说、组分有机体功能特点决定生态系统功能观点及一些中间观点的提出使生态学界对生物多样性与生态系统功能之间关系的研究结果各异,但关键种的丧失会严重损害生态系统功能是肯定的。对结构多样性的生态系统来说,关键种能稳定生态系统功能,并在一定程度上缓冲波动带来的压力。生物多样性与生态系统稳定性间关系的研究亦未形成共识,一般看法是生物多样性降低会导致生态系统稳定性下降。但也有与之不同的看法,认为多样性与稳定性间无任何关系。对局部多样性、区域多样性及全球范围内生物多样性改变及其相应保护措施的研究比较后认为,应为不同物种提供适合其繁殖条件的局部试验地块,用个体小的物种来控制区域生物多样性及通过各种自然试验方法增加不同范围内的生物多样性。     

大中型拖拉机残值模型的研究

折旧是农业生产中的一项重要成本,而科学的折旧要以正确估计农业机器的残值为基础,ASABE的残值函数对估计农业机器残值提供了通用的方法,但这些模型是根据美国的实际情况模拟,并不能适合中国的实际情况.该文以上海农场近15年出售的116台拖拉机历史数据为观察样本,以机龄和年平均工作小时数为自变量,对6种不同的备选残值模型进行了回归分析和比较,在此基础上优选了双平方根模型为最佳残值模型,并用实际观察数据进行了验证.结果表明,用ASABE的模型来预测中国大中型拖拉机残值偏差很大,而本模型的预测精度是满意的,可用来预测中国大中型拖拉机残值;在残值模型变量中,机龄为决定残值的主要因素.