Principal Component 1 Research Articles

Gene expression profiling in rat liver treated with compounds inducing elevation of bilirubin

We have constructed a large-scale transcriptome database of rat liver treated with various drugs. In an effort to identify a biomarker for the diagnosis of elevated total bilirubin (TBIL) and direct bilirubin (DBIL), we extracted 59 probe sets of rat hepatic genes from the data for seven typical drugs, gemfibrozil, phalloidin, colchicine, bendazac, rifampicin, cyclosporine A, and chlorpromazine, which induced this phenotype from 3 to 28 days of repeated administration in the present study. Principal component analysis (PCA) using these probes clearly separated dose- and time-dependent clusters in the treated groups from their controls. Eighteen more drugs in the database, reported to elevate TBIL and DBIL, were estimated by PCA using these probe sets. Of these, 12 drugs, that is methapyrilene, thioacetamide, ticlopidine, ethinyl estradiol, alpha-naphthylisothiocyanate, indomethacin, methyltestosterone, penicillamine, allyl alcohol, aspirin, iproniazid, and isoniazid were also separated from the control clusters, as were the seven typical drugs causing elevation of TBIL and DBIL. The principal component 1 (PC1) value showed high correlation with TBIL and DBIL. In the cases of colchicine, bendazac, chlorpromazine, gemfibrozil, and phalloidin, the possible elevation of TBIL and DBIL could be predicted by expression of these genes 24 h after single administration. We conclude that these identified 59 probe sets could be useful to diagnose the cause of elevation of TBIL and DBIL, and that toxicogenomics would be a promising approach for prediction of this type of toxicity.

Assessing management impacts on soil organic matter quality in subtropical Australian forests using physical and chemical fractionation as well as 13C NMR spectroscopy

Successful soil organic matter (SOM) quality assessment is needed to improve our ability to manage forest soils sustainably. Our objective was to use a multivariate data set to determine whether the land use conversion from native forest (NF) to hoop pine plantation and the following rotation and site preparation practices had altered SOM quality at three adjacent sites of NF, first (1R) and second rotation (2R, including tree planting row (2R–T) and windrow of harvest residues (2R–W)) of hoop pine plantations in southeast Queensland, Australia. Cross-polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS 13C NMR) spectroscopy and sequential hot water and acid hydrolysis were conducted on SOM fractions separated by wet-sieving and density fractionation procedures to characterize SOM quantitative and qualitative relevant parameters, including carbon (C) functional groups, C and nitrogen (N) contents, C/N ratios, and C and N recalcitrant indices. Analysis of variance (ANOVA) and principal component analysis (PCA) of these multivariate parameters together indicated a complicated interaction between physical protection and biochemical recalcitrance, making the land use and management induced changes of SOM quality more complex. Knowledge of PCA based on the refined set of 41 SOM quantitative and qualitative parameters identified that principal component 1 (PC1), which explained 55.7% of the total variance, was most responsible for the management induced changes in soil processes. This was reflected by the dynamics of SOM regarding the aspects of total stock, soil basal and substrate induced respirations, gross and net N mineralization and nitrification, and microbial biomass, microbial diversity of C utilization patterns. Further, the macroaggregates ( F 250–2000 μm) and the C/N ratio of acid extracts of SOM physical fractions, which represented the most informative and unique variables loading on PC1, might be the most promising physical and chemical measures for SOM quality assessment of land use and management impacts in subtropical Australian forests.

Description of Chemical Changes Implied During Bread Dough Mixing by FT‐ATR Mid‐Infrared Spectroscopy

ABSTRACTThe aim of the present study was to investigate the ability of mid‐infrared (MIR) spectroscopy to identify physicochemical changes in the French bread dough mixing process. An ATR FT‐MIR spectrometer at 4000–800 cm–1 was used. The MIR spectra collections recorded during mixing were analyzed after standard normal variate using principal component analysis (PCA) and after second‐derivative treatment. The results were interpreted in terms of chemical changes involved in dough development and more particularly in terms of secondary structural protein changes (amide III). The loading spectrum associated with principal component 1 (PC1) allows three MIR wave number regions of variations (3500–3000, 1700–1200, and 1200–800 cm–1) to be identified. The loading spectrum associated with PC1 describes an increase in the relative protein band intensities and a decrease in relative water and starch band intensities. The variation during bread dough mixing time of the different amide III bands identified after the second‐derivative show that α‐helical, β‐turn, and β‐sheet structures increase while random coil structure decreases, suggesting that the gluten structure is becoming a more ordered structure. The MIR mixing time identified as being the maximum scores value on the PC1 scores plots was associated with the time at which the dough apparent torque begin to collapse, suggesting that the MIR spectroscopy could monitor bread dough development.

Mathematical modeling and systems biology approach to study biomaterial composition‐mediated inflammatory signals in endothelial cells

Understanding of intracellular signaling in response to biomaterials is crucial for rational design of bioactive materials that elicit desired cellular behavior. To understand correlation of signaling to recruitment of inflammation by endothelial cells, human umbilical vein endothelial cells (HUVECs) were cultured on substrates prepared by adsorbing nine different extracellular matrix components to tissue culture plates in addition to a non‐adsorbed plate. Activation of kinases (ERK1/2, JNK‐1, Akt and IKK) was quantified by high‐throughput kinase assays for HUVECs exposed to these surfaces for various times. Principal component analysis (PCA), a well‐known matrix analysis technique, indicates that principal component 1 (PC1), captured the most information, is positively correlated to JNK activity, gelatin, polystyrene and negatively to chondroitin sulfate. PC2 correlated positively to ERK1/2 activity, vitronectin and negatively to Akt activity, chondroitin sulfate and heparin sulfate. PC3 correlated mostly with IKK activity, and PC3 is high for matrigel and laminin but low for vitronectin and heparan sulfate. Correlating these observations with ICAM‐1/E‐selectin expression and leukocyte adhesion will provide further insight into biomaterial composition‐mediated inflammatory signals in endothelial cells.Source of research support: K22 DE014846 (NIDCR), R21 EB004386 (NIBIB)

Time-of-Flight Secondary Ion Mass Spectrometry of a Range of Coal Samples: A Chemometrics (PCA, Cluster, and PLS) Analysis

This paper documents time-of-flight secondary ion mass spectrometry (ToF−SIMS) analyses of 34 different coal samples. In many cases, the inorganic Na+, Al+, Si+, and K+ ions dominate the spectra, eclipsing the organic peaks. A scores plot of principal component 1 (PC1) versus principal component 2 (PC2) in a principal components analysis (PCA) effectively separates the coal spectra into a triangular pattern, where the different vertices of this pattern come from (i) spectra that have a strong inorganic signature that is dominated by Na+, (ii) spectra that have a strong inorganic signature that is dominated by Al+, Si+, and K+, and (iii) spectra that have a strong organic signature. Loadings plots of PC1 and PC2 confirm these observations. The spectra with the more prominent inorganic signatures come from samples with higher ash contents. Cluster analysis with the K-means algorithm was also applied to the data. The progressive clustering revealed in the dendrogram correlates extremely well with the cluster...

Simultaneous determination of iridoids, phenolic acids, flavonoids, and saponins in Flos Lonicerae and Flos Lonicerae Japonicae by HPLC‐DAD‐ELSD coupled with principal component analysis

A method, HPLC coupled with diode-array and evaporative light scattering detectors (HPLC-DAD-ELSD), was newly developed to evaluate the quality of Flos Lonicerae (FL) and Flos Lonicerae Japonicae (FLJ), through a simultaneous determination of multiple types of bioactive components. By employing DAD, the detection wavelengths were set at 240 nm for the determination of iridoids, 330 nm for phenolic acids, and 360 nm for flavonoids, respectively. While ELSD, connected in series after DAD, was applied to the determination of saponins. This assay was fully validated with respect to precision, repeatability, and accuracy. Moreover, principal component analysis (PCA) was used for the similarity evaluation of different samples, and it was proven straightforward and reliable to differentiate FL and FLJ samples from different origins. For PCA, two principal components have been extracted. Principal component 1 (PC1) influences the separation between different sample sets, capturing 54.598% variance, while principal component 2 (PC2) affects differentiation within sample sets, capturing 12.579% variance. In conclusion, simultaneous quantification of bioactive components by HPLC-DAD-ELSD coupled with PCA would be a well-acceptable strategy to differentiate the sources and to comprehensively control the quality of the medicinal plants FL and FLJ.

Post-weaning body morphology to sexual maturity and carcass characteristics of rabbits in the humid rainforest zone of Nigeria

Data on some linear measurements of rabbits at weaning and post weaning ages to sexual maturity were recorded on weekly interval to quantify rabbit conformation and determine their interrelationships and how well they can predict body weight of rabbits. The rabbits were of mixed breeds raised at the University of Benin Farm Project between May and November 2003. Data obtained were on body weight (BWT), shoulder-to-tail-drop (STD), heart girth (HGT), hind limb length (HLL), thigh girth (TGT) and half hind limb length (HHL). Analyses of different carcass cuts (hind limb, fore limb, waist region, back bone area, skin offal and viscera organs) were also done. Body measurements increased in mean value from 396.43g, 23.57cm, 20.93cm, 18.29cm and 10.00cm to 1621.43g, 31.11cm, 27.39cm, 23.67cm, 12.75cm and 13.79cm for BWT, STD, HGT, HLL, TGT and HHL at weaning to 15 weeks post weaning ages respectively. High and positive relationship exited among linear measurements and body weight with values ranging from –0.49 to 0.89. Results of principal component indicated that body size was influenced most by the TGT at Principal component 1 (PC1) but at Principal component 2 (PC2) HLL had the highest weight (eigenvector) thus suggesting that in rabbits hind limb measurement seems to better predict body weight by accounting for more than 98% of the total variation in body weight. Rabbit had a dressing percentage of 50.67 with the hind limbs accounting for over 42% of the carcass weight. International Journal of Agriculture and Rural Development Vol. 7(2) 2006: 40-47

Analysis of Environmental Variation in a Great Plains Reservoir Using Principal Components Analysis and Geographic Information Systems

We present a method for spatial interpretation of environmental variation in a reservoir that integrates principal components analysis (PCA) of environmental data with geographic information systems (GIS). To illustrate our method, we used data from a Great Plains reservoir (Skiatook Lake, Oklahoma) with longitudinal variation in physicochemical conditions. We measured 18 physicochemical features, mapped them using GIS, and then calculated and interpreted four principal components. Principal component 1 (PC1) was readily interpreted as longitudinal variation in water chemistry, but the other principal components (PC2-4) were difficult to interpret. Site scores for PC1-4 were calculated in GIS by summing weighted overlays of the 18 measured environmental variables, with the factor loadings from the PCA as the weights. PC1-4 were then ordered into a landscape hierarchy, an emergent property of this technique, which enabled their interpretation. PC1 was interpreted as a reservoir scale change in water chemistry, PC2 was a microhabitat variable of rip-rap substrate, PC3 identified coves/embayments and PC4 consisted of shoreline microhabitats related to slope. The use of GIS improved our ability to interpret the more obscure principal components (PC2-4), which made the spatial variability of the reservoir environment more apparent. This method is applicable to a variety of aquatic systems, can be accomplished using commercially available software programs, and allows for improved interpretation of the geographic environmental variability of a system compared to using typical PCA plots.

Multivariate statistical methods for evaluating biodegradation of mineral oil

Two methods were developed for evaluating natural attenuation and bioremediation of mineral oil after environmental spills and during in vitro experiments. Gas chromatography–mass spectrometry (GC–MS) in selected ion monitoring (SIM) mode was used to obtain compound-specific data. The chromatographic data were then preprocessed either by calculating the first derivative, retention time alignment and normalization or by peak identification, quantification and calculation of diagnostic ratios within homologue series of polycyclic aromatic compounds (PACs). Finally, principal component analysis (PCA) was applied to the preprocessed chromatograms or diagnostic ratios to study the fate of the oil. The methods were applied to data from an in vitro biodegradation experiment with a North Sea crude oil exposed to three mixtures of bacterial strains: R (alkane degraders and surfactant producers), U (PAC degraders) and M (mixture of R- and U-strains) over a 1-year-period with five sampling times. Assessment of variation in degradability within isomer groups of methylfluorenes ( m/ z 180), methylphenanthrenes ( m/ z 192) and methyldibenzothiophenes ( m/ z 198) was used to evaluate the effects of microbial degradation on the composition of the oil. The two evaluation methods gave comparable results. In the objective pattern matching approach, principal component 1 (PC1) described the general changes in the isomer abundances, whereas M samples were separated from U and R samples along PC2. Furthermore, in the diagnostic ratio approach, a third component (PC3) could be extracted; although minor, it separated R samples from U and M samples. These results demonstrated that the two methods were able to differentiate between the effects due to the different bacterial activities, and that bacterial strain mixtures affected the PAC isomer patterns in different ways in accordance with their different metabolic capabilities.

Hydroclimatic variability of the upper Nazas basin: Water management implications for the irrigated area of the Comarca Lagunera, Mexico

Earlywood ring-width chronologies derived primarily from Douglas-fir trees were used to reconstruct winter–spring (November–May) precipitation and fall–spring (September–June) streamflow volumes for the period 1765–1993 in the forested upper Nazas watershed in Durango, Mexico. The tree-ring data were obtained from mixed conifer stands within or adjacent to the upper Nazas watershed. Precipitation data were derived from one of the longest regional records. The streamflow data were obtained from a guage located in the upper Nazas watershed. The Principal Component 1 (PC1) of nine residual earlywood chronologies accounted for 73% of the variance in November–May precipitation 1967–1993, and 64% for the total period with available data 1941–1993. The mean of three residual earlywood chronologies from Douglas-fir explained 51% of the normalized streamflow at Sardinas from 1971–1992. The 20th century was characterized by severe droughts, especially between 1950 and 1963 that also affected other regions of Mexico and the southwestern United States. Additional droughts of similar or greater magnitude occurred in the 1790s, 1810s, 1860–1870s and 1890–1910s. Similar periods of low flow occur in the September–June streamflow reconstruction between 1765 and 1993. These results indicate that tree-ring chronologies from this region document a high percentage of the precipitation and streamflow variance. Spectral analysis detected significant high periodicities in both records at peaks of 4 and 7 years that could be related to the ENSO frequency bands (approximately 4.0 and 6.25 years). Analysis of the reconstructed records show strong influence of ENSO on precipitation and streamflow amounts on an interannual basis. These results can provide significant inputs to decisions regarding management of water resources that are used to irrigate land in the Comarca Lagunera: specifically they indicate that water budgeting should be managed over longer time periods to account for this ENSO-related variability rather than on the year-to-year basis that is presently used.

MICRO-ARCHITECTURAL ALTERATIONS IN ENDOSCOPICALLY-NORMAL MUCOSA PROVIDES ACCURATE RISK STRATIFICATION FOR COLORECTAL NEOPLASIA

Purpose: The “field effect” is frequently exploited for colorectal cancer (CRC) screening; however, the most common markers (i.e. the distal adenoma) lacks both sensitivity and positive predictive value. Micro-alterations in the colonocytes (i.e. the “field”) may reflect the earliest events in colon carcinogenesis although, to date, practical detection of these subtle changes have not been possible. We have pioneered optics for the detection of dysplasia in general (Nature 2000) and in the colon (Nature Med 2001). We have recently developed 4D-ELF, a new generation of light-scattering technology, that allows heretofore unattainable insights into the nano-scale cellular architecture (IEEE 2003). In experimental models, 4D-ELF analysis of uninvolved mucosa had unprecedented sensitivity for CRC risk (Gastroenterology 2004). The aim of this study was to evaluate the ability of 4D-ELF to predict neoplasia in humans. Methods: Forty-five patients undergoing colonoscopy had two mid-transverse colon biopsies from endoscopically normal mucosa. 4D-ELF analysis was performed on fresh tissue using our advanced light-scattering apparatus. Parameters that were evaluated included principal component 1 (PC1) and spectral slope. Patients were divided into high and low risk based on current and past colonoscopy findings (presence of adenoma or carcinoma). Results: PC1 and spectral slope were dramatically and highly statistically significantly altered in colonic neoplasia patients (high risk) when compared to those with normal colonoscopies (low risk) (see figure).Figure 1Conclusions: We demonstrate, for the first time, that micro-architectural changes in the endoscopically normal mucosa could predict the risk of colonic neoplasia. These parameters were markedly superior to any previously described biomarkers. This suggests that that 4D-ELF analysis may have potential applicability in CRC risk-stratification. [figure 1]

Proteomic analysis of agar gel-entrapped Pseudomonas aeruginosa.

We have compared the protein maps of agar-entrapped Pseudomonas aeruginosa cells to those of free counterparts grown in the presence or absence of the immobilized-cell gel support. Principal component analyses (PCAs) were used to interpret spot quantity variations observed on electropherograms obtained by two-dimensional gel electrophoresis. PCA of the data matrix (923 rows x 6 columns) in which spot density values were standardized horizontally extracted three principal components (PCs) with eigenvalues higher than 1, accounting together for 71.6% of the variability in the data. Principal component 1 (PC1) opposed free (F) and agar-entrapped (AE) cultures, with a low contribution of agar-released, free (ARF) cultures to PC1. Inversely, the contribution of ARF cultures to PC2 was high, opposing those of AE and F cultures. Component 3 was related to the duration of incubation. Only 10% of total proteins were upregulated in AE cells during the first 18 h of incubation, the number of underexpressed peptides balancing that of overexpressed ones. Downregulation clearly became the dominant tendency when the incubation time was extended to 48 h. These results demonstrate that AE and ARF bacteria are physiologically different from F organisms.

Metabolomic Differentiation of Cannabis sativa Cultivars Using 1H NMR Spectroscopy and Principal Component Analysis

The metabolomic analysis of 12 Cannabis sativa cultivars was carried out by 1H NMR spectroscopy and multivariate analysis techniques. Principal component analysis (PCA) of the 1H NMR spectra showed a clear discrimination between those samples by principal component 1 (PC1) and principal component 3 (PC3) in cannabinoid fraction. The loading plot of PC value obtained from all 1)H NMR signals shows that Delta9-tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA) are important metabolites to differentiate the cultivars from each other. The discrimination of the cultivars could also be obtained from a water extract containing carbohydrates and amino acids. The level of sucrose, glucose, asparagine, and glutamic acid are found to be major discriminating metabolites of these cultivars. This method allows an efficient differentiation between cannabis cultivars without any prepurification steps.

ToF-SIMS characterization of hybridization onto self-assembled single-stranded DNA monolayers

DNA hybridization onto solid surfaces forms the basis for applications of DNA microarrays. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is an excellent tool for chemical characterization of surfaces because of its molecular specificity, surface sensitivity and excellent mass resolution. Previous studies have indicated the possibility to follow hybridization based on the phosphate signal from the backbone. We have employed DNA molecules which have a C6 thiol linker at its 3′ end and self-assemble onto gold surfaces. The positive spectrum has peaks from the sugar backbone as well as peaks from the individual bases [base+H] +. The negative spectrum has intense peaks from the phosphate backbone as well as peaks from the bases [base−H] −. Our hypothesis that hybridization onto these single-stranded DNA (ss DNA) should change the fragmentation pattern of these molecules in ToF-SIMS is confirmed by principal component analysis (PCA) of these ToF-SIMS spectra. Briefly, principal component 1 (PC1) of the positive ToF-SIMS spectra separates the hybridized DNA from the ss DNA. Similar results were observed for the negative spectra. These results were supported by surface plasmon resonance experiments (SPR), which indicate that hybridization does occur and is believed to be reason for the change in the fragmentation pattern of the ToF-SIMS spectra.

Multivariate analysis of apple cultivar susceptibility to Venturia inaequalis under greenhouse conditions

Apple scab, caused by Venturia inaequalis, is a disease of great importance in apple production regions in eastern North America. However, little is known regarding the relative susceptibility of North American cultivars to this disease since the majority of previous researches on apple scab were conducted on a highly susceptible cultivar, 'McIntosh'. We evaluated 21 cultivars commonly grown in eastern and central Canada for their responses to V. inaequalis by measuring the following components of partial resistance: the number of lesions per leaf, the number of lesions per square centimetre of leaf, the lesion surface area per leaf, the proportion of leaf area diseased, the number of conidia per lesion, the number of conidia per square centimetre of lesion, the incubation period, and the latent period. All of the components examined were effective in assessing relative cultivar susceptibility, but those related to disease severity, latent period, and conidia production were the most important and accounted for 86% of the variation among cultivars. Numbers of lesions per leaf and per square centimetre of leaf were highly positively correlated with principal component 1 (PC1). Incubation and latent periods were highly negatively correlated with PC1. 'McIntosh' and 'Vista Bella' were found to be highly susceptible whereas 'Golden Russet', 'Idared', 'Paulared', 'Red Delicious', and 'Sunrise' were the least susceptible.

Influence of water pressure on the final quality of arabica espresso coffee. Application of multivariate analysis.

Water pressure is one of the most important factors which influence the final quality of espresso coffee (EC). However, few studies dealing with this issue have been found. The aim of this work was to study the effect of water pressure on the final quality of Arabica ECs as well as to classify ECs prepared at different pressures (7, 9, and 11 atm) according to their physicochemical and sensory characteristics, key odorants, by means of multivariate analysis. Statistically, principal component 1 (PC1) separated ECs prepared at 7 and 9 atm from ECs prepared at 11 atm and included the main foam and taste characteristics as well as some key odorants and flavor compounds. ECs prepared at 7 and 9 atm were separated by principal component 2 (PC2). Coffees prepared at 9 atm showed consistency of foam and a high percentage of key odorants related to freshness and fruity, malty, and buttery flavors. A simple discriminate function was obtained by discriminate analysis, allowing the classification of ECs prepared at three pressures into their respective groups with a success rate of 100%.

Facial growth: separating shape from size

Optical surface scanning technologies produce dense three-dimensional (3D) data sets, which allow detailed analysis of surface morphology. This paper describes a method of analysing change in facial shape independently of change in size. The 3D data from three male subjects from the age of 6-21 years were recorded using an optical surface scanner. A series of 22 conventional landmarks were located with the aid of horizontal and vertical profiles across the face, and were analysed using geometric morphometrics. The 3D landmark co-ordinates were scaled and aligned using Generalized Procrustes Analysis (GPA) and analysed by Principal Component Analysis (PCA) to determine the shape change over the growth period for each individual. The results show that the centroid size reaches a steady value at different times for each of the subjects. When analysing shape versus age, highly significant correlations were found with principal component 1 (PC-1), but not with other principal components. PC-1 encompassed 40 per cent of the total variance for each subject. The movement of facial landmarks with time that is represented by PC-1 in each of the individuals is described. The use of these techniques has enabled the individual characteristics of facial growth to be identified and also has revealed the subtle changes in shape that continue after change in size has ceased.

Paleoceanographic implications of a 90,000 year long diatom record in piston core KH94-3, LM-8 off NE Japan

Q-mode principal component analysis (PCA) of a fossil diatom assemblage reveals the late Quaternary paleoceanography of the NW Pacific margin, based on submarine core KH94-3, LM-8 recovered off the Sanriku coast of NE Japan (38°53.46′N, 143°22.19′E). Overall, diatoms were abundant during interglacials, but low in abundance and poor in preservation during the last glacial, with each oxygen isotope stage having its own characteristic assemblage. The results of PCA are: principal component 1 (PC1) is composed mainly of Thalassionema nitzschioides, which predominated during the coldest oxygen isotopic Stages 4 (75–58 ka) and 2 (25–11 ka), and by allochthonous taxa. The diatom tests are poorly preserved and the diatom mass accumulation rate (DMAR) is the lowest in these stages. PC2 is characterized by ice-related diatoms that predominate in Stage 3 (the interstadial), whereas PC3, which is characterized by Neodenticula seminae and Odontella aurita, shows high values in Stage 1. Diatom assemblages exhibit drastic changes between oxygen isotopic Stages 3 and 1 (11–0 ka). Distinct increases of DMAR occurred during both periods. We infer an intensified advection of sea ice from the Sea of Okhotsk toward the area off Sanriku during Stage 3. This interpretation explains the high DMAR in Stage 3, owing to high productivity at the sea ice edge. Our study can contribute to marine environmental reconstruction since the last glaciation because fewer micropaleontological data exist in the NW Pacific margin for these time intervals, compared with other oceans.

The use of phospholipid fatty acids (PL-FA) in the determination of rhizosphere specific microbial communities (RSMC) of two wheat cultivars

To determine differences in microbial community structure, phospholipid fatty acids (PL-FA) from rhizosphere bacteria of two different wheat cultivars Triticum aestivum L. (cv. Bohouth-6 and cv. Salamouni) were extracted and analyzed by gas chromatography. This approach was used to overcome the methodological underestimation of microbial densities obtained with isolation, culture techniques and microscopic observations. Our objective was to verify differences in PL-FA profiles from two wheat cultivars grown under controlled environmental conditions. Principal component analysis (PCA) and cluster analysis were used to detect dissimilarities between rhizosphere microbial communities of the two wheat cultivars and signature fatty acids (FA) were used to determine specific differences in the community structures. PCA of the two cultivars explained 79.18% of the variance on principal component 1 (PC1), which accounted for Bohouth-6 rhizosphere soil. The rhizosphere soil of Salamouni accounted for 11.66% of the variance on principal component 2 (PC2). The results demonstrated repeatedly the clustering of the samples into two distinct groups; each group belonging specifically to one of the two wheat cultivars. Profiles of Bohouth-6 showed higher amounts of cyclopropane acid 19:0cy and Sif 7 (Sum in feature 7) than Salamouni. Those FA are known as signature molecules for Gram-negative bacteria. This was also reflected by the higher bacterial counts (cfu g−1 fresh root weight) of Gram-negative bacteria from the rhizosphere of the former than the latter. The results indicated that under controlled environmental conditions, wheat cultivars of different genotypes exhibit distinct microbial colonization in their rhizosphere.

Soil Quality Assessment of Tillage Impacts in Illinois

Successful soil quality assessment strategies are needed to improve our ability to manage soils sustainably. Our objective was to use a multivariate data set to determine whether recent adoption of no‐tillage (NT) practices had altered soil quality in Illinois. In 1995 and 1996, we sampled thirty‐six farm fields under conventional tillage (CT) or NT practices and relatively nondisturbed (ND) areas. Soils were Mollisols or Alfisols. Tillage or region affected 20 of the 23 parameters characterized. Soil chemical parameters were less variable than biological or physical measures. Principal component analysis (PCA) was used to assess soil quality overall. Principal component 1 (PC1) scores, which explained 39% of the total variance of the overall data set, were affected by tillage (ND > NT > CT) and increased with particulate and organic C and total N, biological activity, mineralizable N, and wet aggregate stability, and decreased with bulk density and dry aggregate mean weight diameter. The only significant factor contributing to PC2 was penetration resistance; PC2 explained 13% of the variance and decreased as follows: NT ≥ ND > CT. Multivariate assessment of soil quality indicated use of NT practices improved the biological and physical condition of the soil (0–15 cm) despite increased consolidation. It also showed that those biological and physical aspects of soils influenced by organic matter were the properties most altered by agronomic practices. Particulate organic matter (POM) was identified as a promising soil quality measure. A next step is to determine the biological and environmental relevance of a refined set of soil quality measures in conjunction with soil processes of regional concern.