Genome analysis with gene expression microarrays

Advances in biochemistry, chemistry and engineering have enabled the development of a new gene expression assay. This ‘chip-based’ approach utilizes microscopic arrays of cDNAs printed on glass as high-density hybridization targets. Fluorescent probe mixtures derived from total cellular messenger RNA (mRNA) hybridize to cognate elements on the array, allowing accurate measurement of the expression of the corresponding genes. Array densities of >1,000 cDNAs per cm² enable quantitative expression monitoring of a large number of genes in a single hybridization. A two-color fluorescence detection scheme allows rapid and simultaneous differential expression analysis of independent biological samples. Mass-produced microarrays provide a new tool for genome expression analysis that may revolutionize genetic dissection, drug discovery and human disease diagnostics.     

Analysis of In Situ Distribution of Inorganic Elements in Plants by Micro-XRF

植物的无机元素分布特征对植物生理过程具有重要的指标作用, 可揭示营养物质分布、代谢途径及毒理耐受性等多种生命过程。用微区XRF技术测试样品中无机元素的分布, 具有原位无损、可进行较大面积样品连续成像分析以及前处理过程简单等诸多优势。将微区XRF技术应用于植物样品不同器官的无机元素分布检测, 旨在探讨该技术在植物样品测试中的仪器参数选择、样品前处理方法和数据后处理手段等对测试结果的影响。为得到可靠的实验结果, 对不同含水量的器官进行不同的前处理, 并比较不同驻留时间、测试腔体真空与否等仪器条件对测试结果的影响, 同时对数据处理方法进行探索, 包括对获得的数据进行图像叠加及对不同元素浓度比例进行半定量分析。研究结果表明, 微区XRF技术测试植物样品中无机元素分布具有一定的技术优势。     

微区XRF技术分析无机元素在植物中的原位分布

植物的无机元素分布特征对植物生理过程具有重要的指标作用, 可揭示营养物质分布、代谢途径及毒理耐受性等多种生命过程。用微区XRF技术测试样品中无机元素的分布, 具有原位无损、可进行较大面积样品连续成像分析以及前处理过程简单等诸多优势。将微区XRF技术应用于植物样品不同器官的无机元素分布检测, 旨在探讨该技术在植物样品测试中的仪器参数选择、样品前处理方法和数据后处理手段等对测试结果的影响。为得到可靠的实验结果, 对不同含水量的器官进行不同的前处理, 并比较不同驻留时间、测试腔体真空与否等仪器条件对测试结果的影响, 同时对数据处理方法进行探索, 包括对获得的数据进行图像叠加及对不同元素浓度比例进行半定量分析。研究结果表明, 微区XRF技术测试植物样品中无机元素分布具有一定的技术优势。     

Comparative analysis of borate fusion versus sodium carbonate extraction for quantification of silicon contents in plants

Journal of Plant Research - Studies of plant-silicon (Si) interaction benefit from safe, affordable and accurate methods to measure acid-insoluble silica (phytoliths) for a large number of plant...     

Flow infusion electrospray ionisation mass spectrometry for high throughput,non-targeted metabolite fingerprinting: a review

Producing a comprehensive overview of the chemical content of biologically-derived material is a major challenge. Apart from ensuring adequate metabolome coverage and issues of instrument dynamic range, mass resolution and sensitivity, there are major technical difficulties associated with data pre-processing and signal identification when attempting large scale, high-throughput experimentation. To address these factors direct infusion or flow infusion electrospray mass spectrometry has been finding utility as a high throughput metabolite fingerprinting tool. With little sample pre-treatment, no chromatography and instrument cycle times of less than 5 min it is feasible to analyse more than 1,000 samples per week. Data pre-processing is limited to aligning extracted mass spectra and mass-intensity matrices are generally ready in a working day for a month’s worth of data mining and hypothesis generation. ESI-MS fingerprinting has remained rather qualitative by nature and as such ion suppression does not generally compromise data information content as originally suggested when the methodology was first introduced. This review will describe how the quality of data has improved through use of nano-flow infusion and mass-windowing approaches, particularly when using high resolution instruments. The increasingly wider availability of robust high accurate mass instruments actually promotes ESI-MS from a merely fingerprinting tool to the ranks of metabolite profiling and combined with MS/MS capabilities of hybrid instruments improved structural information is available concurrently. We summarise current applications in a wide range of fields where ESI-MS fingerprinting has proved to be an excellent tool for “first pass” metabolome analysis of complex biological samples. The final part of the review describes a typical workflow with reference to recently published data to emphasise key aspects of overall experimental design.

     

Flow infusion electrospray ionisation mass spectrometry for high throughput,non-targeted metabolite fingerprinting: a review

Producing a comprehensive overview of the chemical content of biologically-derived material is a major challenge. Apart from ensuring adequate metabolome coverage and issues of instrument dynamic range, mass resolution and sensitivity, there are major technical difficulties associated with data pre-processing and signal identification when attempting large scale, high-throughput experimentation. To address these factors direct infusion or flow infusion electrospray mass spectrometry has been finding utility as a high throughput metabolite fingerprinting tool. With little sample pre-treatment, no chromatography and instrument cycle times of less than 5 min it is feasible to analyse more than 1,000 samples per week. Data pre-processing is limited to aligning extracted mass spectra and mass-intensity matrices are generally ready in a working day for a month’s worth of data mining and hypothesis generation. ESI-MS fingerprinting has remained rather qualitative by nature and as such ion suppression does not generally compromise data information content as originally suggested when the methodology was first introduced. This review will describe how the quality of data has improved through use of nano-flow infusion and mass-windowing approaches, particularly when using high resolution instruments. The increasingly wider availability of robust high accurate mass instruments actually promotes ESI-MS from a merely fingerprinting tool to the ranks of metabolite profiling and combined with MS/MS capabilities of hybrid instruments improved structural information is available concurrently. We summarise current applications in a wide range of fields where ESI-MS fingerprinting has proved to be an excellent tool for “first pass” metabolome analysis of complex biological samples. The final part of the review describes a typical workflow with reference to recently published data to emphasise key aspects of overall experimental design.     

Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates

Several procedures were compared for reliable PCR detection of Ralstonia solanacearum in common substrates (plant, seed, water and soil). In order to prevent the inhibition of PCR by substances contained in crude extracts, numerous DNA extraction procedures as well as additives to buffers or PCR mixtures were checked. Our results showed that the efficiency of these methods or compounds depended greatly upon the nature of the sample. Consequently, preparation of samples prior to PCR depended upon sample origin. Simple methods such as a combined PVPP/BSA treatment or the association of filtration and centrifugation for detecting the bacterium in plant or water samples were very powerful. DNA capture also efficiently overcame PCR inhibition problems and ensured the detection of R. solanacearum in environmental samples. However, the commercial DNA extraction QIAamp kit appeared to be the most effective tool to guarantee the accurate PCR detection of the pathogen whatever the origin of the sample; this was particularly true for soil samples where the commonly used methods for the detection of R. solanacearum were inefficient. This study demonstrates that using an appropriate procedure, PCR is a useful and powerful tool for detecting low levels of R. solanacearum populations in their natural habitats.     

Quantitative beta-galactosidase assay suitable for high-throughput applications in the yeast two-hybrid system

Measurement of beta-galactosidase (beta-gal) activity is an important step in every yeast two-hybrid assay, yet many commonly used methods have distinct disadvantages, such as being only qualitative, time-consuming, and cumbersome when processing large numbers of samples. To overcome these drawbacks, we have implemented a novel technique, termed pellet X-gal assay, that allows simultaneous quantitative measurements from large numbers of samples with a minimum of hands-on time. The method was tested using five different, previously described protein-protein interactions and compared to two standard methods, the colony filter lift and the liquid ONPG assay. Our assay allows accurate quantitative measurements of protein-protein interactions and covers a greater dynamic range than the classic ONPG assay. The novel assay is robust and requires very little handling, making it suitable for applications in which several hundreds of individual protein interaction pairs need to be measured simultaneously.     

Charged-particle activation analysis of biological material

Charged-particle activation analysis offers a number of interesting possibilities for the determination of trace elements in biological material. It allows the determination of those elements that are difficult or impossible to determine by neutron activation, such as Li, B, Al, Si, V, Cr, Ni, Cd, Sn, Tl, and Pb. Up to now, protons have been successfully applied to samples of both vegetale and human origin. A number of difficulties have to be overcome, one of which is excessive heating of the samples owing to the limited range of the charged particles, thus giving rise to a high energy deposition in a small volume. Moreover, the sample composition has to be known to allow the calculation of the range of the particles. an interesting alternative has been proposed using an internal standard together with a standard additions procedure. Proton activation analysis was tested on a wide variety of reference materials, giving evidence that accurate results can be obtained for many trace elements, even when applying a purely instrumental method. Thus, the method can also be applied in the certification of reference materials, since nuclear methods are independent of chemical properties of the sample.     

Lithologic controls on biogenic silica cycling in South African savanna ecosystems

The efficacy of higher plants at mining Si from primary and secondary minerals in terrestrial ecosystems is now recognized as an important weathering mechanism. Grassland ecosystems are a particularly large reservoir of biogenic silica and are thus likely to be a key regulator of Si mobilization. Herein, we examine the effects of parent material (basaltic and granitic rocks) on the range and variability of biogenic silica pools in grass-dominated ecosystems along two precipitation gradients of Kruger National Park, South Africa. Four soil pedons and adjacent dominant plant species were characterized for biogenic silica content. Our results indicate that although soils derived from basalt had less total Si and dissolved Si than soils derived from granite, a greater proportion of the total Si was made up of biogenically derived silica. In general, plants and soils overlying basaltic versus granitic parent material stored greater quantities of biogenic silica and had longer turnover times of the biogenic silica pool in soils. Additionally, the relative abundance of biogenic silica was greater at the drier sites along the precipitation gradient regardless of parent material. These results suggest that the biogeochemical cycling of Si is strongly influenced by parent material and the hydrologic controls parent material imparts on soils. While soils derived from both basalt and granite are strongly regulated by biologic uptake, the former is a “tighter” system with less loss of Si than the latter which, although more dependent on biogenic silica dissolution, has greater losses of total Si. Lithologic discontinuities span beyond grasslands and are predicted to also influence biogenic silica cycling in other ecosystems.     

A rapid, high resolution high performance liquid chromatography profiling procedure for plant and microbial aromatic secondary metabolites

High performance liquid chromatography protocols have been developed to allow the simultaneous analysis of a very wide range of soluble aromatic secondary metabolites in unfractionated biological extracts. The methods are simple, sensitive, and highly reproducible. They are applicable to a wide variety of natural product investigations in both plants and microorganisms. High resolution of metabolites is achieved in 25 minutes by chromatography on a reverse phase C18 column in a gradient of 0 to 55% acetonitrile in water at pH 3. For example, near-baseline resolution of over 20 phenylpropanoid metabolites and 18 naturally occurring metabolites of indole-3-acetic acid can be obtained. The methods can be applied directly to whole tissue extracts without prepurification or enrichment. Moreover, the simplicity and sensitivity of the protocols allow their application to a large number of very small tissue samples, such as those encountered in research on host-microbe interactions. Such profiles allow one to monitor simultaneously the various alternative metabolic fates of a complex array of molecules. Examination of the profiles over time thus provides one with a powerful tool to correlate many concurrent molecular events that may relate to a given biological phenomenon. The final protocol requires as little as 1 milligram of tissue, which is extracted directly in a microfuge tube in 80% ethanol. With a variable wavelength detector, as little as 100 femtomoles of a given metabolite can be analyzed. Examples of the application of the protocols to a number of plant and microbial secondary product investigations and to screening for flavonoid mutants of Arabidopsis thaliana (L.) Heynh. are given.     

A fast method for multi-metal determination in soil samples by high-resolution inductively-coupled plasma-mass spectrometry (HR–ICP–MS)

Abstract

Methods for multi-elemental quantitative analysis of soil samples by high-resolution inductively-coupled plasma-mass spectrometry (HR–ICP–MS) with preceding one-step wet digestion in a high-pressure microwave system have been developed. The application of aqua regia as a reagent for wet digestion using a high-pressure microwave digestion system, followed by determination using HR–ICP–MS, allows an accurate, simultaneous determination of a large number of heavy metals and metalloids that are considered as potentially hazardous for the environment and health. The values of the concentrations of the elements in the analysed certified reference material (CRM) that have been obtained in this study can be used as indicative values where this CRM is used as a control for the quality of the measurements.     

植物反转录转座子及其在功能基因组学中的应用

高等植物中的反转录转座子是构成植物基因组的重要成分之一.它分病毒家族和非病毒家族两类,病毒家族包括反转录病毒和类似于反转录病毒的非病毒转座子,病毒家族中的反转录转座子可再细分为Ty3-gypsy类和Ty1-copia类;非病毒家族可细分为LINE类和SINE类.正常情况下大部分反转录转座子不具有活性,某些生物或非生物因素胁迫可激活部分反转录转座子转座.反转录转座子自身编码反转录酶进行转录,以"拷贝-粘贴"的转座模式导致基因组扩增和进化.具有活性的反转录转座子通过插入产生新的突变,可作为一种基因标签技术,应用于功能基因组学研究,并成为研究植物基因功能和表达的重要技术平台.本文综述了近几年来在植物反转录转座子方面的研究进展,主要包括植物反转录转座子的结构、特征、活性及其对基因组的影响和它们在功能基因组学中的应用.     

Comparison of SR-excited X-ray fluorescence analysis with neutron activation analysis for hair and fiber

Human scalp hair and some kinds of vegetable and animal fibers were analyzed by means of the SR excited X-ray fluorescence method (SRXFA) and the neutron activation method (NAA). Human hair samples collected from five males and five females were washed by the IAEA method prior to analysis. In the SRXFA analysis, samples were excited by monochromated X-rays. Fluorescence X-rays were measured by an Si(Li) detector. The elements detected in all hair samples were S, Ca, Cu, Fe, Zn, Br, and Sr. The elements K, Ti, Cr, Mn, Ni, Se, Hg, and Pb were also detected in several samples. After SRXFA analysis these same samples were analyzed by the NAA method. Elements such as Cu, Zn, and Br were detected by both methods, and their relative concentrations show a good agreement of variation between individuals. However, Pb was only detected by SRXFA, and Na, Au, and Sb were only detected by NAA. Therefore, these two methods are complementary to each other for trace element analysis.     

Whole plant cell wall characterization using solution-state 2D NMR

Recent advances in nuclear magnetic resonance (NMR) technology have made it possible to rapidly screen plant material and discern whole cell wall information without the need to deconstruct and fractionate the plant cell wall. This approach can be used to improve our understanding of the biology of cell wall structure and biosynthesis, and as a tool to select plant material for the most appropriate industrial applications. This is particularly true in an era when renewable materials are vital to the emerging bio-based economies. This protocol describes procedures for (i) the preparation and extraction of a biological plant tissue, (ii) solubilization strategies for plant material of varying composition and (iii) 2D NMR acquisition (for typically 15 min-5 h) and integration methods used to elucidate lignin subunit composition and lignin interunit linkage distribution, as well as cell wall polysaccharide profiling. Furthermore, we present data that demonstrate the utility of this new NMR whole cell wall characterization procedure with a variety of degradative methods traditionally used for cell wall compositional analysis.     

空间分辨代谢组学进展和挑战

空间分辨代谢组学即整合质谱成像和代谢组学技术,对动/植物组织和细胞中内/外源性代谢物的种类、含量和差异性空间分布进行精准测定。质谱成像技术因其具有无标记、非特异、高灵敏度、高化学覆盖、元素/分子同时检测等优势,被广泛应用于动/植物组织中各类代谢物、多肽和蛋白的时空分布研究。首先介绍了代谢组学和质谱成像技术的研究现状,然后重点综述了空间分辨代谢组学在动物组织、植物组织和单细胞水平上的前沿应用。最后展望了空间分辨代谢组学技术的现有瓶颈和未来发展方向。空间分辨代谢组学是继代谢组学之后又一门新兴的分子成像组学技术,能够无标记、可视化检测动物组织中外源性药物的吸收、分布、代谢和排泄,以及植物组织中多种代谢产物的生物合成、转运途径和积累规律。该技术将推动靶向药物发现、病理机制解析和动植物生长发育密切关联的空间代谢网络调控等前沿应用研究。     

Spatial Variability of Soil Properties in a Floodplain Forest in Northwest Spain

Floodplain forests are generally areas of high plant diversity compared with upland forests. Higher environmental heterogeneity, especially variation in belowground properties may help explain this high diversity. However, there is little information available on the spatial scale and pattern of belowground resources in floodplain forests. Geostatistics and coefficient of variation (CV) were used to describe the spatial variability of 20 soil properties ranging from essential plant nutrients, such as NH₄ or PO₄, to nonessential elements like Ti or V. The spatial variation of Si-to-(Al + Fe) ratio, an index of soil development, was also analyzed. Semivariograms and maps of selected properties were used to discriminate between the effect of flooding (and other mechanisms that may contribute to large scale trends in data) and local heterogeneity. The hypothesis that elements mainly cycled through biological processes (such as N) show different spatial properties than elements cycled through both biological and geological processes (such as P) or elements under strict geological control (such as Ti or V) is also presented. Redox potential was the most variable property (CV = 1.35) followed by mineral N, phosphate, organic matter, and carbon. Nonessential elements for organisms such as Si, Al, Ti, Rh, or V were less variable, supporting the hypothesis that biological control on soil properties leads to higher spatial variability. The range (the average distance within which the samples correlate spatially) varied between 3.89 m for water content to 18.5 m for the Si-to-(Al + Fe) ratio. The proportion of the total variance that can be modeled as spatial dependence (structural variance) was very variable, ranging between 0.34 for Fe and 0.96 for K. The addition of the large trend had a strong influence on the CV of most soil variables and created a gradient in C accumulation and the mineral weathering rate. The results suggest that flooding and other processes that are responsible for large spatial trends in the floodplain forest differentially affect biologically and geologically controlled variables with different turnover rates, thus providing a heterogeneous edaphic environment.     

A polarographic method for the simultaneous determination of total glucosinolates and free glucose of cruciferous material

A rapid method for the simultaneous analysis of total free glucose and total glucosinolates in aqueous extracts of cruciferous material is described. The technique, which appears suitable for plant-breeding programs as it allows the processing of more than 100 samples per day, involves the polarographic determination of O2 uptake of free glucose by a system of double-coupled enzymes, such as myrosinase-glucose oxidase. The method has advantages over current methods, because it is very rapid (4 min per analysis), allows two determinations for each analysis, and appears to be very reproducible, accurate, and sensitive.     

Consumptive and nonconsumptive effect ratios depend on interaction between plant quality and hunting behavior of omnivorous predators

Predators not only consume prey but exert nonconsumptive effects in form of scaring, consequently disturbing feeding or reproduction. However, how alternative food sources and hunting mode interactively affect consumptive and nonconsumptive effects with implications for prey fitness have not been addressed, impending functional understanding of such tritrophic interactions. With a herbivorous beetle, two omnivorous predatory bugs (plant sap as alternative food, contrasting hunting modes), and four willow genotypes (contrasting suitability for beetle/omnivore), we investigated direct and indirect effects of plant quality on the beetles key reproductive traits (oviposition rate, clutch size). Using combinations of either or both omnivores on different plant genotypes, we calculated the contribution of c onsumptive (eggs predated) and n onc onsumptive (fewer eggs laid) effect on beetle fitness, including a prey density‐independent measure (c:nc ratio). We found that larger clutches increase egg survival in presence of the omnivore not immediately consuming all eggs. However, rather than lowering mean, the beetles generally responded with a frequency shift toward smaller clutches. However, female beetles decreased mean and changed clutch size frequency with decreasing plant quality, therefore reducing intraspecific exploitative competition among larvae. More importantly, variation in host plant quality (to omnivore) led to nonconsumptive effects between one‐third and twice as strong as the consumptive effects. Increased egg consumption on plants less suitable to the omnivore may therefore be accompanied by less searching and disturbing the beetle, representing a “cost” to the indirect plant defense in the form of a lower nonconsumptive effect. Many predators are omnivores and altering c:nc ratios (with egg retention as the most direct link to prey fitness) via plant quality and hunting behavior should be fundamental to advance ecological theory and applications. Furthermore, exploring modulation of fitness traits by bottom‐up and top‐down effects will help to explain how and why species aggregate.     

不同竹龄雷竹中硅及其他营养元素吸收和积累特征

在浙江省临安市的雷竹主产区,分别采集不同竹龄(1～4 a)和不同器官(叶、枝、秆)的雷竹样品,分析了Si和其他营养元素含量、吸收和积累特征,以及Si和其他营养元素之间的相互关系.结果表明： 雷竹各器官中C含量的大小顺序为竹秆>竹枝>竹叶,Si、N、P、K、Ca、Mg、Al、Fe和Mn含量的大小顺序为竹叶>竹枝>竹秆.除Mn主要积累在竹叶中外,其他9种营养元素主要积累在1年生雷竹的秆中.3～4年生雷竹竹叶的Si平均含量为13.66 g · kg^-1. 雷竹属于Si积累植物.随竹龄的增加,雷竹叶中的N、P、K和Mg含量减少,C、Al和Mn含量增加.雷竹对Si的吸收主要集中在第2年(57.1%),对N和K的吸收主要集中在前两年(67.7%～93.7%),此后N和K从植株体内流出,其流失量分别占总积累量的19.1%～39.1%.雷竹中Si与Ca、Al、Mn呈显著正相关,与N、P、K、Mg呈显著负相关.