主成分分析在麦蚜发生量预报中的应用

介绍了主成分分析的计算方法。对利用主成分建立回归方程的一些问题进行了探讨。建立了山东菏泽地区麦蚜发生量预报模式,预报效果理想。     

Predation of bacteria by the protozoa Tetrahymena pyriformis in toluene-degrading cultures

The influence of the toluene concentration on predation of toluene-degrading bacteria by the protozoa Tetrahymena pyriformis was investigated in suspended batch cultures continuously aerated with toluene-contaminated air. At gas phase concentrations of 0.035 to 0.74 g m–3, toluene did not significantly affected protozoan activity and the final bacteria concentration was reduced by growing protozoa by 98 to 99.9% compared to protozoa-free controls. As the toluene concentration was increased to 1.16–1.33 g m–3, the reduction of the bacteria cell concentration was 80%. At 3.35 g toluene m–3, growth of T. pyriformis was completely inhibited. Overall, the results presented herein demonstrate that protozoa grazing on bacteria play a major role in controlling bacterial cell concentration, but that the toxicity of the treated pollutants to the protozoa is an important factor that needs to be taken into account in biological treatment processes.     

Accurate root length measurement by image analysis

Algorithms for estimating root length by image analysis should lead to results that have no systematic error (bias), be insensitive to preferential root orientation, valid across a wide range of sample sizes and adjust for overlap between roots in samples, to reduce the effort needed in spreading out root systems. We propose a new algorithm that forms a compromise between small bias and robustness (insensitivity to variation in sample size and preferential root orientation), and provide a simple way of dealing with root overlap. Image analysis was performed on a Macintosh computer using the public domain NIH Image program. The digital image of the root was processed to get the thinned image (skeleton). The numbers of orthogonally and diagonally connected pairs of pixels (N _o and N _d, respectively) in the skeleton were counted separately and used for length (L) calculation. A new length calculation equation was introduced so that the effect of orientation on length calculation was minimized; L=[N d ²+(N _d+N _o/2)²]^1/2+N _o/2. The maximum error due to orientation of a single line was evaluated for an ideal line, and the analysis revealed that the new equation was less affected by orientation than previous equations. Copper wire and rice (Oryza sativa L.) roots containing both primary and fine secondary root were measured manually and with image analysis. The two methods showed good agreement within 1.5%. The proposed image analysis method yielded length estimates with CV from 0.23 to 0.88%, which was lower than the CVs of the line-intersect method. Moreover, the lengths of overlapping samples were calculated correctly because the image analysis method distinguished an overlapping pixel from a thinned image, while the calculation with the line-intersect method showed underestimation because overlaps were not considered in that method. This revised version was published online in June 2006 with corrections to the Cover Date.     

Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods

Protozoa are common inhabitants of the rumen where they play roles in host nutrition and methanogenesis. Knowledge of how changes in the composition of protozoa communities affect these processes is limited in part due to a lack of efficient methods for protozoa community analysis. In this study, a terminal-restriction fragment length polymorphism (T-RFLP) assay targeting the 18S rRNA gene was developed for comparative analysis of rumen protozoa communities. Comparison of diversity and structure of protozoa communities from hay-fed versus silage/grain-fed cattle via T-RFLP analysis yielded similar overall results to microscopy analysis. According to both methods, Entodinium spp. were more abundant in the silage/grain-fed cattle and protozoa diversity (as calculated using the Shannon index) was higher for the hay-fed cattle due to greater species evenness. Type B protozoa were more prevalent in the hay-fed cattle, whereas Type A protozoa were more prevalent in the silage/grain-fed cattle. Analysis of similarity (ANOSIM) indicated that the protozoa communities from hay-fed and silage/grain-fed cattle were different, and multivariate analysis indicated that pen mates (i.e., cattle fed the same diet and housed together) tended to have similar protozoa communities types. In summary, we present a T-RFLP method for analyzing rumen protozoa communities which complements traditional microscopy approaches but has the advantage of being amenable to high-throughput.     

Cystatin-like cysteine proteinase inhibitors of parasitic protozoa

A new method has been developed for detecting cystatins and other cysteine proteinase inhibitors. The method, which involves protein separation by SDS-PAGE followed by a cysteine proteinase overlay step, is more sensitive than previously reported techniques: as little as 1 ng of recombinant human cystatin C can be detected and cysteine proteinase inhibitors could also be detected in complex protein mixtures such as bovine foetal serum. The method has been used to show, for the first time, cysteine proteinase inhibitors in lysates of a range of parasitic protozoa (Trypanosoma brucei, Leishmania mexicana mexicana, Toxoplasma gondii and Tritrichomonas foetus) and to confirm that one occurs in the free-living ciliate Tetrahymena pyriformis. Cystatin-like inhibitory activity was also demonstrated in boiled lysates of L. mexicana mexicana using conventional assays methods.     

A comparative study of ciliated protozoa communities in activated-sludge plants

Abstract: Ciliated protozoa present in ten activated sludge plants at Madrid (Spain) were identified. The abundance of key groups of ciliates was determined at each plant; attached ciliates made up the most abundant and representative group. Multivariate statistical analysis was employed to study relationships between ciliates and both the physico-chemical and operational parameters of the plants. Partial correlation analysis revealed: (1) The indicator value of attached ciliates in assessing management and performance of the activated sludge process, (2) the relationship of swimming ciliates with short-aged sludges and lower quality effluents and (3) the direct association between swimming-crawling ciliates and bad settlement conditions of the sludge. Factor analysis showed the associations of the most frequent species of ciliates with the operational parameters of the plants, suggesting the indicator value of some of the species: Vorticella striata was related with poor quality of effluent; Aspidisca cicada with stable plant conditions, and Litonotus lamella with a deficiently settling sludge.     

Multivariate analysis of the Vicia sativa L. aggregate

GIL, J. & CUBERO, J. I., 1993. Multivariate analysis of the Vicia sativa L. aggregate . The sativa group of species was studied by using multivariate analysis and karyological analysis. Thirty biometrical characters were studied by using 92 Vicia sativa L. accessions from a variety of geographical sources. The four main taxa analysed were: sativa, macrocarpa, cordata and angustifolia. Principal component analysis provided clear separation among sativa, cordata and angustifolia in terms of the first two components. Karyotype analysis confirmed the PCA results, and by combining both methods, misclassed specimens can be correctly determined. Cluster analyses using the characters which displayed the greatest loads over the first components were performed in order to identify the most valuable characters from the taxonomic point of view. These were flower length, calyx length, pod width, constriction of the pod between seeds, leaf length, leaflet width, seed length and seed width. Our results suggest an early separation of angustifolia from the ancestral stem. The taxon cordata may be useful in future plant breeding programmes not only for crossing with V. saliva to increase the leaflet size of this taxon, but also as a bridge species between sativa and angustifolia.     

Morphological characterization of yeast by image analysis

A semiautomatic image analysis method, with minimal operator intervention, has been developed to characterize the morphology of yeast cells under the assumption that they have an ellipsoidic shape. The cells are observed by optical microscopy and the surface and the minor and major half-axes of the projection of the ellipsoid on the image plane are determined. Using this method, yeast size distributions and population kinetics (single and budding cells, cell clusters) are determined during alcoholic fermentations. Combination of image analysis with a methylene blue viability test is examined but the staining procedure induces a change in the size of the cells. .     

Classification and measurement of fungal pellets by automated image analysis

An automated image analysis method for classifying and measuring pellets of filamentous fungi growing in submerged fermentations has been developed. The method discriminates between pelleted mycelial growth and loose aggregates of dispersed hyphae. Pellets are classified into smooth and hairy types. In both cases, the core of the pellet is identified and its shape and size characterized. For hairy pellets the annular region is also characterized. The method was tested on pellets of Aspergillus niger ATCC 11414 grown in a defined medium in shake flasks. This rapid method makes practical extensive studies on the morphology of pellets in submerged fermentations and the influence of fermentation conditions on that morphology.     

基于高光谱成像和主成分分析的水稻茎叶分割

在单株水稻表型测量研究中,为了实现绿叶面积和茎叶相关表型参数的准确计算提供技术保障,茎叶的分割是非常重要的一步。传统的人工测量方法费时费力,且主观性较强,而基于普通相机拍摄的彩色图像进行分割效果很差。本研究介绍了一种使用可见光-近红外高光谱成像系统自动区分单株盆栽水稻茎叶的方法。首先将各波长下的图像从原始二进制数据中提取出来,接着使用主成分分析所有波长下的图像,并提取出主要的主成分图像,再基于数字图像处理技术将茎叶区分开。实验结果表明,本系统以及文中所用方法对分蘖盛期的水稻茎叶有很好的分割效果,这为后续水稻茎叶表型性状高通量、数字化、无损准确提取提供了重要的技术保障,并进一步促进植物表型组学的发展。     

Diversity of Antarctic terrestrial protozoa

Heterotrophic protozoa have a global distribution in terrestrial habitats. The functional groups significantly represented are zooflagellates, cillates, gymnamoebae and testate amoebae. Their range extends into the Antarctic zone, but the species richness of the communities is rarely of the same order of magnitude as those in temperate latitudes. Species diversity is usually very low owing to dominance of the communities by single, or a few, species which are best adapted to the Antarctic terrestrial environment. This is characterized by seasonal, diurnal or unpredictable fluctuations in moisture, temperature and bacterial food supply of high amplitude. The fauna shows pauperization with latitude and climatic severity. Nearly all records of species distribution are consistent with the model that community composition is determined by local conditions. An important exception is the distribution of the testate amoeba genus Nebela whose species distribution is influenced by biogeographical factors. Successional changes in community composition in fellfield habitats are characterized by the sequence: pioneer microflagellate colonizers, larger flagellates and small ciliates, and finally testate amoebae. The succession is most closely correlated with the accumulation of organic matter. A model of the strategies of dominant microflagellate species can be constructed by ordinating them on a two-dimensional habitat template of A-r-K selection continuum. The globally ubiquitous microflagellate Heteromita globosa emerges as the most strongly A-selected and K-selected. The occurrence of terrestrial protozoa near their latitudinal limits of distribution can serve as sensitive indicators of the biological effects of climatic change. Having short generation times and effective means of cyst dispersal, changes in the gross distribution can provide rapid warning of critical changes in thermal regimes.     

Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences

AIMS: To examine the diversity of protozoa in the rumen contents of cow. METHODS AND RESULTS: Protozoa that inhabit the rumen were detected by PCR using protozoan-specific primers. Libraries of protozoan rDNA sequences were constructed from rumen fluid, solid tissues and epithelium. Twenty-three clones isolated from rumen fluid fell into two genera identified as Entodinium (69.6% of clones) and Epidinium (31.4% of clones). Of the clones isolated from rumen fluid, a moderate number were unidentifiable (30.4%). CONCLUSIONS: The predominant protozoan genus identified in the whole rumen belonged to the Entodinium group (81.1%). Protozoa were not detected in the rumen epithelium. SIGNIFICANCE AND IMPACT OF THE STUDY: These findings suggest that rumen fluid and solid tissues contain different protozoan populations that may play specific roles in rumen function. Quantitative PCR techniques and a more specific set of phylogenetic probes that distinguish between protozoan species are needed to determine the significance of newly identified groups and to determine the distribution of identified protozoan clusters in rumen microbial communities.     

Survival of protozoa in cooling tower biocides

Protozoa from cooling towers may serve as hosts for legionellae, but such protozoa have not been examined with respect to effects of cooling tower biocides. In this study, two ciliate species,Tetrahymena sp andColpoda sp, and two amoebae species,Vannella miroides andAcanthamoeba hatchetti, were isolated from a cooling tower and tested for survival in the presence of four cooling tower biocides. The protozoa were exposed for 24 h to a thiocarbamate compound, an isothiazolone compound, quaternary ammonium compounds (QAC), and tributyltin neodecanoate with quarternary ammonium compounds (TBT/QAC). After exposure, cells were examined for viability. The highest concentration of each biocide in which cells could survive was compared to the manufacturers' recommended maintenance dosage (MRMD) of the biocides.Tetrahymena andColpoda survived concentrations within the range of the MRMD of thiocarbamate and QAC.Vannella andAcanthamoeba survived concentrations within the MRMD of thiocarbamate, isothiazolone, and QAC.Colpoda cysts andAcanthamoebae cysts remained viable after exposure to concentrations much greater than the MRMD of thiocarbamate, isothiazolone, and QAC. None of the protozoa in any stage could survive the MRMD of TBT/QAC. These results show that protozoa indigenous to cooling towers may survive the recommended concentration of certain biocides, and this information may be important in devising procedures for eradicating hosts for legionellae.     

原生动物在活性污泥中的作用

处理污水有三个重要作用 ,保护环境 ,维护生态系统的健康 ;除去污水中的病菌 ,维护人类健康 ;通过中水的回用 ,提高水资源的利用率。 1913年英国的Ａｒｄｅｒｎ和Ｌｏｃｋｅｔｔ在曼彻斯特建立了世界上第一座活性污泥试验工厂 ,现在活性污泥法已经成为世界各国广泛采用的污水处理方法。在我国城市污水处理厂中 ,采用活性污泥法的占 85 %以上 ,该法的中心环节是曝气形成活性污泥 ,通过生物消耗分解污染物 ,随后活性污泥在沉淀池中沉淀分离 ,从而净化污水。该过程的主要目的是通过微生物的吸收和降解 ,尽量减少污泥的生成量。原生动物是活性污…     

Characterization of the Mucor circinelloides life cycle by on-line image analysis

AIMS: The life cycle of the dimorphic fungus Mucor circinelloides was studied in a temperature-controlled flow-through cell, which constitutes an ideal tool when following the development of individual cells, with a view to understanding the growth and differentiation processes occurring in and between the different morphological forms of the organism. METHODS AND RESULTS: Mycelial growth and the transformation of hyphae into chains of arthrospores were characterized by image analysis techniques and described quantitatively. The influence of the nature (glucose and xylose) and concentration of the carbon source on specific growth rate and hyphal growth unit length were studied. The organism branched more profusely on xylose than on glucose while the specific growth rates determined were rather similar. Methods were developed to study the yeast-like growth phase of M. circinelloides in the flow-through cell, and combined with fluorescent microscopy which allowed new insights to bud formation. Additionally, numbers and distribution of nuclei in arthrospores, hyphae and yeasts were studied. CONCLUSIONS: The results give essential information on the morphological development of the organism. SIGNIFICANCE AND IMPACT OF STUDY: Development of any industrial process utilizing this organism will be dependent on the information obtained here for effective process optimization.     

Semi-automated relative quantification of cell culture contamination with mycoplasma by Photoshop-based image analysis on immunofluorescence preparations

Mycoplasma contamination in cell culture is a serious setback for the cell-culturist. The experiments undertaken using contaminated cell cultures are known to yield unreliable or false results due to various morphological, biochemical and genetic effects. Earlier surveys revealed incidences of mycoplasma contamination in cell cultures to range from 15 to 80%. Out of a vast array of methods for detecting mycoplasma in cell culture, the cytological methods directly demonstrate the contaminating organism present in association with the cultured cells. In this investigation, we report the adoption of a cytological immunofluorescence assay (IFA), in an attempt to obtain a semi-automated relative quantification of contamination by employing the user-friendly Photoshop-based image analysis. The study performed on 77 cell cultures randomly collected from various laboratories revealed mycoplasma contamination in 18 cell cultures simultaneously by IFA and Hoechst DNA fluorochrome staining methods. It was observed that the Photoshop-based image analysis on IFA stained slides was very valuable as a sensitive tool in providing quantitative assessment on the extent of contamination both per se and in comparison to cellularity of cell cultures. The technique could be useful in estimating the efficacy of anti-mycoplasma agents during decontaminating measures.     

An approach to incorporate linkage disequilibrium structure into genomic association analysis

In this study, we propose to use the principal component analysis (PCA) and regression model to incorporate linkage disequilibrium (LD) in genomic association data analysis. To accommodate LD in genomic data and reduce multiple testing, we suggest performing PCA and extracting the PCA score to capture the variation of genomic data, after which regression analysis is used to assess the association of the disease with the principal component score. An empirical analysis result shows that both genotype-basod correlation matrix and haplotype-based LD matrix can produce similar results for PCA. Principal component score seems to be more powerful in detecting genetic association because the principal component score is quantitatively measured and may be able to capture the effect of multiple loci.