UV spectral fingerprinting and analysis of variance-principal component analysis: a useful tool for characterizing sources of variance in plant materials

UV spectral fingerprints, in combination with analysis of variance-principal components analysis (ANOVA-PCA), can differentiate between cultivars and growing conditions (or treatments) and can be used to identify sources of variance. Broccoli samples, composed of two cultivars, were grown under seven different conditions or treatments (four levels of Se-enriched irrigation waters, organic farming, and conventional farming with 100 and 80% irrigation based on crop evaporation and transpiration rate). Freeze-dried powdered samples were extracted with methanol-water (60:40, v/v) and analyzed with no prior separation. Spectral fingerprints were acquired for the UV region (220-380 nm) using a 50-fold dilution of the extract. ANOVA-PCA was used to construct subset matrices that permitted easy verification of the hypothesis that cultivar and treatment contributed to a difference in the chemical expression of the broccoli. The sums of the squares of the same matrices were used to show that cultivar, treatment, and analytical repeatability contributed 30.5, 68.3, and 1.2% of the variance, respectively.     

Constructing DNA fingerprinting of Hemarthria cultivars using EST-SSR and SCoT markers

DNA fingerprinting of known cultivars may provide much-needed data to assist with the identification of such cultivars. From 86 pairs of expressed sequence tag SSRs (EST-SSR) and 45 start-codon targeted polymorphism (SCoT) primers, eight pairs of EST-SSR primers and seven SCoT primers were chosen to construct the DNA fingerprinting of six Hemarthria cultivars in this study. Using genomic DNA from six cultivars, a total of eight pairs of EST-SSR primers were able to amplify 193 bands, producing an average of 24.1 bands per primer pair. The percentage of polymorphic bands (PPB) was 83.4 %, and the polymorphism information content (PIC) ranged from 0.480 to 0.695, with an average of 0.602. A total of seven SCoT primers amplified 105 bands with an average of 15 bands per sample. The PPB was 84.8 %, and the PIC ranged from 0.471 to 0.758, with an average of 0.612. The unweighted pair-group method with arithmetic mean dendrogram from EST-SSR and SCoT markers grouped the six Hemarthria cultivars into two major groups of the same. These clusters are in accordance with their known species and origin. Our results indicate a rich genetic diversity in these six Hemarthria cultivars. The six cultivars we assayed could be easily identified using these eight pairs of EST-SSR and seven pairs of SCoT primers.     

甜菜品种（系）的ISSR标记数字指纹图谱构建及聚类分析

摘要：本文针对来源于荷兰的4个引进甜菜品种和国内的6个甜菜品系（其中2个为一年生野生甜菜）进行了ISSR指纹图谱构建和聚类分析研究。筛选出稳定性高且多态性好的6个引物用于试验。利用筛选的6条引物ISSR-PCR 共扩增出51个条带, 其中多态性条带百分率为86.3%. 利用该6条引物ISSR-PCR建立的指纹图谱能将试验中的全部甜菜品种都鉴定区分开。只利用2条引物L1和UBC846 扩增的8个多态性条带构建了10个甜菜品种（系）的数字指纹识别码,该数字指纹图谱能完全区分10个甜菜品种（系）,结果显示ISSR 指纹图谱能非常有效的鉴定不同的甜菜品种。利用生物软件NTSYS-pc针对10个试验甜菜品种（系）的ISSR 扩增条带进行遗传相似性聚类分析,结果显示10个甜菜品种（系）的相似系数为0.43与0.83之间,平均为0.62。利用非加权组平均法（UPGMA）进行聚类分析,结果显示10个甜菜品种（系）聚类为2个组和3个亚组。UPGMA 聚类分析能清楚的显示10个甜菜群体间的遗传关系并且聚类结果与10个甜菜群体的特性一致, 说明ISSR标记能用于甜菜不同群体间遗传距离的评估。     

基于主成分分析的高丛蓝莓品种果实品质综合评价

比较分析不同品种蓝莓果实品质特性,确定代表性品质指标,建立蓝莓品质综合评价体系,为蓝莓品质合理评价和优良蓝莓品种筛选提供理论参考。以26个高丛蓝莓品种果实为材料,测定其11项品质指标（单果质量、果实横径、果实纵径、果形指数、果实硬度、可溶性固形物质量分数 可溶性糖质量分数、可滴定酸质量分数、糖酸比、维生素C质量分数、花色苷质量分数）,并采用主成分分析方法进行果实品质综合评价。结果表明：26个蓝莓品种的11项果实品质性状中糖酸比、可滴定酸质量分数、单果质量和花色苷质量分数的变异系数较大,其变异系数分别为33.67%、32.25%、30.84%和28.48%。通过主成分分析确定单果质量、果形指数、可溶性糖质量分数、可滴定酸质量分数、花色苷质量分数和果实硬度可作为评价蓝莓果实品质的代表性指标;建立综合品质评价模型,并依据各品种的综合品质得分进行优良度排序,得分排名前10位的蓝莓品种依次为'大果蓝金'莱格西'公爵'日出'维口'蓝片'早蓝'蓝丰'爱国者'红利',研究结果为大连地区蓝莓品种合理开发和应用提供了依据。     

樱桃品种果实品质因子主成分分析及模糊综合评价

研究不同品种甜樱桃果实品质指标差异,确定代表性品质指标,从而筛选出品质优良的甜樱桃品种。以24种甜樱桃果实为材料,测定其11项品质指标(单果质量、硬度、可食率、出汁率、p H值、总糖含量、还原糖含量、可滴定酸含量、糖酸比、维生素C含量、花色苷含量),并运用主成分分析、模糊评判法进行综合评价。结果表明:不同甜樱桃品种各项指标存在差异,其中单果质量与维生素C之间,可食率与出汁率、可滴定酸之间,花色苷与p H值、可滴定酸之间,总糖、还原糖、糖酸比与p H值之间均呈及极显著正相关。因子分析提取了甜味、口感、抗氧化、可食、质量5项主因子,累计方差贡献率为82.948%,包含了大部分指标信息,因此筛选总糖、出汁率、维生素C、可食率、单果质量作为评价甜樱桃的关键指标;利用PAST软件绘制各品种在5个主因子的分布状况,并对品种因子综合得分进行排序,得分排名前10的樱桃品种依次为"Red"(0.70)、"早露"(0.63)、"红蜜"(0.60)、"彩玉"(0.47)、"秦樱一号"(0.44)、"S2S1"(0.38)、"早大果实生"(0.35)、"13-33"(0.28)、"明珠"(0.13)、"秦林"(0.07);对11个分析指标进行模糊综合评判,综合品质表现排名前10的品种分别为"Red"(0.642)、"红蜜"(0.566)、"早露"(0.545)、"明珠"(0.524)、"彩玉"(0.521)、"秦樱一号"(0.512)、"秦林"(0.501)、"美早"(0.491)、"S2S1"(0.482)、"早大果实生"(0.470),以上结果一致表明"Red"、"早露"、"红蜜"、"彩玉"、"秦樱一号"、"S2S1"、"早大果实生"、"明珠"、"秦林"等9种樱桃综合品质较其他15种樱桃更优,其中"Red"樱桃品质最优,可作为樱桃资源开发利用、育种及品质改良的原材料。因子分析与综合评价结果基本一致,该试验初步确定排名前9位的樱桃优良品种,为樱桃品种选育和加工利用提供理论依据。     

Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting

Genetic diversity is an area of concern for sustaining crop yield. Information on genetic relatedness/diversity among Gossypium arboreum L. cultivars/genotypes is scanty. We have used random amplified polymorphic DNA (RAPD) analysis to assess the genetic divergence/relationship among 30 genotypes/cultivars of G. arboreum. Of 45 primers surveyed, 63% were polymorphic. Out of the total number of loci amplified, 36% were polymorphic. The calculated genetic similarity between the cultivars/genotypes was in the range of 47.05–98.73%. Two genotypes, HK-244 and Entry-17, were the most distantly related. The average genetic relatedness among all the genotypes was 80.46%. However, most of the cultivated varieties showed a close genetic relationship, indicating a narrow genetic base in comparison to the non-cultivated germplasm. The calculated coefficients were used to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA) algorithm, which grouped the genotypes/cultivars into two major and three smaller clusters. The study is the first comprehensive analysis of the genetic diversity of G. arboreum germplasm and identifies cultivars that will be useful in extending the genetic diversity of cultivated varieties and future genome mapping projects.     

Analysis of water quality data using spectral analysis

Considerable effort has been expended by many State, Federal and private agencies in collecting data by installing automatic water quality monitoring stations on many streams and estuaries. This work discusses techniques for analyzing the data and presents some results based on the analysis of monitoring stations along the Ohio, Detroit, Missouri, and Coosa Rivers. Autocorrelation, spectral estimates, cross correlation, amplitude of transfer function and coherence square have been evaluated to correlate a water quality variable measured at different positions or different variables measured at the same location. Results from the different rivers have been compared and some conclusions have been drawn.     

Discriminating between village and commercial hunting of apes

Hunting is the major driver of large mammal decline in Central African forests. In slowly reproducing species even low hunting pressure leaves spatial gradients with wildlife density increasing with distance from transport routes and human settlements. Park management can use this pattern formation to identify sources of threats, but also to discriminate between different threat scenarios, such as the impact of subsistence vs. commercial hunting. We conducted an ape survey in the mountainous Moukalaba Doudou National Park, Gabon, to evaluate whether potential population gradients would emanate from the three human population centers in the region or the villages surrounding the park. Using generalized linear modeling we found hill slope as a good predictor of ape nest occurrence probability and the distance to human population centers a better predictor of ape nest density and ape nest group size than distance to villages. In fact ape nest density was three times lower at the park borders close to the human population centers than in the park’s interior. The results indicate that Moukalaba’s ape population is more impacted by commercial than subsistence hunting and suggest that park management should focus conservation efforts on the human population centers. We conclude that in particular for slowly reproducing species geographic information on wildlife population gradients are of additional value for guiding protected area management. The hunting impact on those species might be easily underestimated, if derived only from market surveys or transport route controls, where they are only rarely found.     

Kinetics of the stability of broccoli (Brassica oleracea Cv. Italica) myrosinase and isothiocyanates in broccoli juice during pressure/temperature treatments

The Brassicaceae plant family contains high concentrations of glucosinolates, which can be hydrolyzed by myrosinase yielding products having an anticarcinogenic activity. The pressure and temperature stabilities of endogenous broccoli myrosinase, as well as of the synthetic isothiocyanates sulforaphane and phenylethyl isothiocyanate, were studied in broccoli juice on a kinetic basis. At atmospheric pressure, kinetics of thermal (45-60 degrees C) myrosinase inactivation could be described by a consecutive step model. In contrast, only one phase of myrosinase inactivation was observed at elevated pressure (100-600 MPa) combined with temperatures from 10 up to 60 degrees C, indicating inactivation according to first-order kinetics. An antagonistic effect of pressure (up to 200 MPa) on thermal inactivation (50 degrees C and above) of myrosinase was observed indicating that pressure retarded the thermal inactivation. The kinetic parameters of myrosinase inactivation were described as inactivation rate constants (k values), activation energy (Ea values), and activation volume (Va values). On the basis of the kinetic data, a mathematical model describing the pressure and temperature dependence of myrosinase inactivation rate constants was constructed. The stability of isothiocyanates was studied at atmospheric pressure in the temperature range from 60 to 90 degrees C and at elevated pressures in the combined pressure-temperature range from 600 to 800 MPa and from 30 to 60 degrees C. It was found that isothiocyanates were relatively thermolabile and pressure stable. The kinetics of HP/T isothiocyanate degradation could be adequately described by a first-order kinetic model. The obtained kinetic information can be used for process evaluation and optimization to increase the health effect of Brassicaceae.     

玉米果穗图像单一特征的品种鉴别力评价

寻找新的果穗性状并评价它们单独鉴别品种的能力,是玉米新品种特异性、一致性和稳定性（DUS）测试研究的重要内容。采集了4个品种各50个果穗的RGB图像,用图像处理法提取了4大类形态特征共计145个性状,逐一性状对品种进行判别分析,以性状的品种识别率表示性状鉴别品种的能力大小。单一性状的品种识别率变化在0.244～0.634之间,在前17个高鉴别力性状中,果穗长宽比等具有与指南性状同等的甚至更高的品种区分能力。单一性状的广义遗传力一般都小于0.66,且与鉴别力高度一致（y = 0.29 + 0.44x, r=0.897, P<0.01）。总体上,四大属性的鉴别力从大到小依次为形状类>纹理类>颜色类>大小类。从受试的145个特征中筛选出许多具有较高品种鉴别能力的性状,可望应用于玉米新品种DUS测试工作。     

Forest soil acidification assessment using principal component analysis and geostatistics

Soil acidification and consequent Al release is a problem particularly under forests in mountainous areas of the Czech Republic. It is controlled by a number of factors, like acid deposition, forest type, parent rock, altitude, etc. The Jizera Mountains region presents an area heavily influenced by acidification and forest decline. This paper focused on the effect of stand factors on spatial distribution of soil characteristics of the surface organic (O) and sub-surface (B) horizons from 98 sites using a combination of principal component analysis (PCA) and geostatistics. In the PCA, five principal components (PC) describing more than 70% of total variation were selected. The properties of the O and B horizons (pH, C, N, and S content, potentially dangerous Al forms) were in most cases separated, suggesting different processes and effects in each horizon. Spatial variation of PC scores was analysed using variograms, maps of their distribution were created using kriging. Spatial correlation with stand factors (altitude, slope aspect, forest type and age, soil unit, liming, and grass cover) was analysed using cross-variograms. The surface horizons are more sensitive to external influence (acid deposition, liming, grass expansion) and their spatial variation is stronger. The B horizons are more influenced by forest type (beech vs. spruce) and age, and by soil units (cambic vs. spodic horizons). The effect of stand factors is complex and often indirect. Nevertheless, used combination of pedometrical methods provided concise information about spatial variation and relationships between soil characteristics and the effect of stand factors.     

Spatial and temporal analysis of mass movement using dendrochronology

Tree growth and inclination on sloping land is affected by mass movement. Suitable analysis of tree growth and tree form can therefore provide considerable information on mass movement activity.This paper reports a new, automated method for studying the temporal and spatial aspects of mass movement activity. Ringwidth data from only a few cores per tree are required. The method uses filtering techniques and statistical time series analysis.Preliminary results for two landslides in the Barcelonnette area of the French Alps show a relative stability of movement activity over the last hundred years (no trend) and short periodicity (six to seven year periods) of mass movement activity.The advantages of the method (over other, mostly visual, methods) are its clearness, flexibility, repeatability and rapidity. However, further testing is needed to examine its reliability.     

Assessment of cocoa input needs using soil types and soil spectral analysis

In this study, diffuse reflectance spectroscopy (DRS) approach was examined for making input recommendations in the smallholder cocoa farms of Papua New Guinea (PNG). Soil samples were collected from four provinces of PNG. Soil samples from four different depths (0–10, 10–30, 30–60 and 60–90 cm) of 32 profiles in each of these site were used to create a database of soil chemical and physical properties. Spectral reflectance values at 1 nm interval covering visible to shortwave‐infrared (350–2,500 nm) were collected for each of these soil samples to develop partial least squares regression models. Soil textural fractions, soil organic carbon contents and available N were well predicted by the DRS approach with R² values larger than 0.75. Moderate to poor estimation efficiencies were observed for remaining parameters. Nevertheless, the estimated soil attributes and their corresponding measured soil parameters were used as inputs to an input recommendation model of soil diagnosis to create input recommendation for a targeted cocoa yield of 1,000 kg dry cocoa beans ha^‐1 Resulting input recommendations were similar for both of these input sources (measured and DRS‐estimated) suggesting that the DRS approach may provide an easy way to create input recommendations.     

Screening and mass spectral confirmation of beta-lactam antibiotic residues in milk using LC-MS/MS.

Milk is typically screened for beta-lactam antibiotics by nonspecific methods. Although these methods are rapid and sensitive, they are not quantitative and can yield false positive findings. A sensitive and specific method for the quantitation and mass spectral confirmation of five beta-lactam and two cephalosporin antibiotics commonly or potentially used in the dairy industry is described using high-performance liquid chromatography with tandem mass spectrometry. The antibiotics studied were ampicillin, amoxicillin, penicillin G, penicillin V, cloxacillin, cephapirin, and ceftiofur. The antibiotics were extracted from milk with acetonitrile, followed by reversed-phase column cleanup. The extract was analyzed by liquid chromatography coupled with a mass spectrometer, using a water/methanol gradient containing 1% acetic acid on a C-18 reversed-phase column. Determination was by positive ion electrospray ionization and ion trap tandem mass spectrometry. Quantitation was based on the most abundant product ions from fragmentation of the protonated ion for amoxicillin, cephapirin, ampicillin, and ceftiofur and on the fragmentation of the sodium adduct for penicillin G, penicillin V, and cloxacillin. The method was validated at the U.S. FDA tolerance or safe level and at 5 or 2.5 ng/mL for these compounds in bovine milk. Theoretical method detection limits in milk based on a 10:1 signal to noise ratio were 0.2 ng/mL (ampicillin), 0.4 ng/mL (ceftiofur), 0.8 ng/mL (cephapirin), 1 ng/mL (amoxicillin and penicillin G), and 2 ng/mL (cloxacillin and penicillin V) using a nominal sample size of 5 mL.     

Classification of Ilex species based on metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis

The metabolomic analysis of 11 Ilex species, I. argentina, I. brasiliensis, I. brevicuspis, I. dumosavar. dumosa, I. dumosa var. guaranina, I. integerrima, I. microdonta, I. paraguariensis var. paraguariensis, I. pseudobuxus, I. taubertiana, and I. theezans, was carried out by NMR spectroscopy and multivariate data analysis. The analysis using principal component analysis and classification of the (1)H NMR spectra showed a clear discrimination of those samples based on the metabolites present in the organic and aqueous fractions. The major metabolites that contribute to the discrimination are arbutin, caffeine, phenylpropanoids, and theobromine. Among those metabolites, arbutin, which has not been reported yet as a constituent of Ilex species, was found to be a biomarker for I. argentina,I. brasiliensis, I. brevicuspis, I. integerrima, I. microdonta, I. pseudobuxus, I. taubertiana, and I. theezans. This reliable method based on the determination of a large number of metabolites makes the chemotaxonomical analysis of Ilex species possible.     

水稻谷粒与脱粒元件碰撞过程的接触力学分析

针对中国水稻在机械化收获过程中稻谷损伤严重,脱粒装置的设计仍以经验为主等现状,从碰撞的角度,建立了谷粒与脱粒元件接触过程的位移量和最大压力分布方程,并以钉齿脱粒滚筒为例,求得了稻谷产生应力裂纹或破碎时稻谷与脱粒元件碰撞的临界相对速度,室内台架试验验证了理论分析的正确性,为深入研究水稻谷粒与脱粒元件的相互作用、稻谷的脱粒损伤机理以及脱粒装置的设计提供了理论依据。     

Rapid differentiation of three Chamaecyparis species (Cupressaceae) grown in Taiwan using solid-phase microextraction-gas chromatography/mass spectrometry, cluster analysis, and principal component analysis

Three Chamaecyparis species (C. formosensis, C. obtusa, and C. obtusa var. formosana) are difficult to distinguish by the naked eye. Therefore, from the chemotaxonomic point of view, it would be valuable to find a simple and rapid method to differentiate these three Chamaecyparis species. In this study, the chemical compositions of biogenic volatile organic compounds (BVOCs) from mature leaves were analyzed using solid-phase microextraction-gas chromatography/mass spectrometry (SPME-GC/MS). Then cluster analysis (CA) and principal component analysis (PCA) were conducted for the BVOC constituents to reveal the differences among these three species. Results from SPME-GC/MS showed that the compositions of BVOCs from the three species were distinctly different. Moreover, these species were clearly differentiated according to the results of CA and PCA. In conclusion, the findings of this study suggest that SPME-GC/MS coupled with CA and PCA is a feasible and rapid technique to differentiate Chamaecyparis species with similar morphological characteristics.     

The effect of post-harvest and packaging treatments on glucoraphanin concentration in broccoli (Brassica oleracea var. italica)

The effects of post-harvest and packaging treatments on glucoraphanin (4-methylsulfinylbutyl glucosinolate), the glucosinolate precursor of anticancer isothiocyanate sulforaphane [4-methylsulfinylbutyl isothiocyanate], were examined in broccoli (Brassica oleracea var. italica) during storage times. The results showed that at 20 degrees C, 55% loss of glucoraphanin concentration occurred in broccoli stored in open boxes during the first 3 days of the treatment and 56% loss was found in broccoli stored in plastic bags by day 7. Under both air and controlled atmosphere (CA) storage, glucoraphanin concentration appeared to fluctuate slightly during 25 days of storage and the concentrations under CA was significantly higher than those stored under air treatment. In modified atmosphere packaging (MAP) treatments, glucoraphanin concentration in air control packaging decreased significantly whereas there were no significant changes in glucoraphanin concentration in MAP with no holes at 4 degrees C and two microholes at 20 degrees C for up to 10 days. Decreases in glucoraphanin concentration occurred when the broccoli heads deteriorated. In the present study, the best method for preserving glucoraphanin concentration in broccoli heads after harvest was storage of broccoli in MAP and refrigeration at 4 degrees C. This condition maintained the glucoraphanin concentration for at least 10 days and also maintained the visual quality of the broccoli heads.