Detecting the Guttman effect with the help of ordinal correspondence analysis in synchrotron X-ray diffraction data analysis.

We propose a method for detecting a Guttman effect in a complete disjunctive table U with Q questions. Since such an investigation is a nonsense when the Q variables are independent, we reuse a previous unpublished work about the chi-squared independence test for Burt's tables. Then, we introduce a two-steps method consisting in plugging the first singular vector from a preliminary Correspondence Analysis (CA) of U as a score x into a subsequent singly-ordered Ordinal Correspondence Analysis (OCA) of U . OCA mainly consists in completing x by a sequence of orthogonal polynomials superseding the classical factors of CA. As a consequence, in presence of a pure Guttman effect, we should in principle have that the second singular vector coincide with the polynomial of degree 2, etc. The hybrid decomposition of the Pearson chi-squared statistics (resulting from OCA) used in association with permutation tests makes possible to reveal such relationships, i.e. the presence of a Guttman effect in the structure of U , and to determine its degree - with an accuracy depending on the signal to noise ratio. The proposed method is successively tested on artificial data (more or less noisy), a well-known benchmark, and synchrotron X-ray diffraction data of soil samples.

Diversity of microbial community structure and their association with phthalic acid esters and physicochemical parameters in informal landfills.

Informal landfill is a common waste treatment method employed in rural areas of China, and phthalic acid esters (PAEs) are one of the typical pollutants in landfill leachate. However, there is no corresponding theoretical basis for whether microbial treatment technology can be used to reduce environmental risk of PAEs in informal landfills. Thus, a typical informal landfill site in northern China was selected and approximately 1,133,023 effective sequences were obtained from 21 samples collected from three layers (different deposit depths) of the landfill. This research explored the correlation between PAEs and the composition and distribution of microbial community in specific environments of informal landfill sites. Here we found that dis(2-ethylhexyl) phthalate (DEHP), di-n-octyl phthalate (DOP), and diethyl phthalate (DEP) were positively and significantly correlated with Bhargavaea, Planococcus, Virgibacillus, and Oceanobacillus, respectively. The redundancy analysis demonstrated that moisture content, pH, NO2--N, and SUVA254 among the seven physicochemical factors (pH, TN, NO3--N,NO2--N,NH4+-N, SUVA254, and moisture content) significantly affected bacterial communities. The research conclusion can provide theoretical basis for the degradation technology of PAEs by microorganism and research basis for the treatment of informal landfill sites.

Influences of environmental parameters and phytoplankton productivity on benthic invertebrates in a tropical oligotrophic lake, northern Malaysia.

Studies that associate environmental parameters with aquatic organisms in man-made lakes remain limited by accessibility and interest particularly in many Asian countries. With missed opportunities to monitor environmental transitions at Lake Kenyir, our knowledge of lake transition is restricted to the non-mixing shallow waters only. Triplicate monthly benthic invertebrate samples were collected concurrently with various environmental parameters at three locations (zones A-C) of Kenyir Lake, Malaysia. Our results affirmed that the northeast part of Lake Kenyir is oligotrophic. Abundance of phytoplankton, total suspended solids, phosphate, nitrite and nitrate drive the abundance of various groups of benthic invertebrates. All of these extrinsic variables (except phosphate) negatively influenced the density of Trichoptera and positively influenced (P<0.05) the densities of Polychaeta, Oligochaeta, Bivalvia, Gastropod, Isopoda and Copepod in all zones. Phosphate negatively influenced the density of Trichoptera and positively influenced (P<0.05) the densities of Oligochaeta, Bivalvia and Copepod. Its influences on the Polychaeta, Gastropod and Isopoda densities were zone-specific. Overall, seasons equally influenced the relationships between extrinsic and response variables in all zones. The results of this study are useful to evaluate the lake's environmental quality, in conservation and in similar projects involving environmental handling, monitoring and recovery.

Topography and soil content contribute to plant community composition and structure in subtropical evergreen-deciduous broadleaved mixed forests.

Topography and soil factors are known to play crucial roles in the species composition of plant communities in subtropical evergreen-deciduous broadleaved mixed forests. In this study, we used a systematic quantitative approach to classify plant community types in the subtropical forests of Hubei Province (central China), and then quantified the relative contribution of drivers responsible for variation in species composition and diversity. We classified the subtropical forests in the study area into 12 community types. Of these, species diversity indices of three communities were significantly higher than those of others. In each community type, species richness, abundance, basal area and importance values of evergreen and deciduous species were different. In most community types, deciduous species richness was higher than that of evergreen species. Linear regression analysis showed that the dominant factors that affect species composition in each community type are elevation, slope, aspect, soil nitrogen content, and soil phosphorus content. Furthermore, structural equation modeling analysis showed that the majority of variance in species composition of plant communities can be explained by elevation, aspect, soil water content, litterfall, total nitrogen, and total phosphorus. Thus, the major factors that affect evergreen and deciduous species distribution across the 12 community types in subtropical evergreen-deciduous broadleaved mixed forests include elevation, slope and aspect, soil total nitrogen content, soil total phosphorus content, soil available nitrogen content and soil available phosphorus content.

A Comparison of Rosetta Stones in Adapter Protein Families.

The inventory of proteins used in different kingdoms appears surprisingly similar in all sequenced eukaryotic genome. Protein domains represent the basic evolutionary units that form proteins. Domain duplication and shuffling by recombination are probably the most important forces driving protein evolution and hence the complexity of the proteome. While the duplication of whole genes as well as domain encoding exons increases the abundance of domains in the proteome, domain shuffling increases versatility, i.e. the number of distinct contexts in which a domain can occur. In this study we considered five important adapter domain families namely WD40, KELCH, Ankyrin, PDZ and Pleckstrin Homology (PH domain) family for the comparison of Domain versatility, Abundance and domain sharing between them. We used ecological statistics methods such as Jaccard's Similarity Index (JSI), Detrended Correspondence Analysis, k-Means clustering for the domain distribution data. We found high propensity of domain sharing between PH and PDZ. We found higher abundance of only few selected domains in PH, PDZ, ANK and KELCH families. We also found WD40 family with high versatility and less redundant domain occurrence, with less domain sharing. Hence, the assignments of functions to more orphan WD40 proteins that will help in the identification of suitable drug targets.

Eutrophication strengthens the response of zooplankton to temperature changes in a high-altitude lake.

To assess whether and how zooplankton communities respond to variations in temperature and how these assemblages change with eutrophication, we performed a large-scale, monthly survey from August 2011 to July 2012 to determine the seasonal and spatial variations in these communities in a high-altitude lake. A detrended correspondence analysis and a path analysis demonstrated that temperature and chlorophyll a were important factors influencing zooplankton. The path diagram showed that Daphnia was negatively affected directly by chlorophyll a and indirectly by temperature, whereas Bosmina was directly and positively affected by temperature. Daphnia spp. decreased in both absolute and relative biomass during warm seasons, whereas Bosmina spp. showed the opposite trend. Moreover, the lowest Daphnia spp. biomass was observed in the southern region, which was the most eutrophic. Our results indicate that increasing temperatures will continue to shift the dominant genus from Daphnia to Bosmina, and this change will be exacerbated by eutrophication. In addition, the zooplankton of Lake Erhai have shifted to smaller species over time as temperature and eutrophication have increased, which implies that zooplankton succession to small cladocerans may be markedly accelerated under further climate change and the increased eutrophication that has been observed in recent decades.

Examining relationship between environmental gradients and Lesser Himalyan forest vegetation of Nikyal valley, Azad Jammu and Kashmir using ordination analysis.

OBJECTIVE: To report the relationship of vegetation structure and environmental gradient and physiochemical properties of soil at Nikyal valley, Azad Jammu and Kashmir . METHODS: A survey of natural vegetation and soil of Nikyal valley was undertaken. Phytosociological survey was conducted by using Braun-Blanquet's approach. The study also investigated the vegetation structure and its relationship with altitude and edaphic factors. The floristic data was analyzed by cluster anlaysis, detrended correspondence analysis and canonical correspondence analysis using CANACOO 5.0. RESULTS: A total of 110 plant species and 13 stands were merged into five major associations as dema rcated by cluster analysis and detrended correspondence analysis. The associations were Olea-Pinus-Themeda association, Myrsine-Rhus-Quercus association, Quercus-Rubus-Pinus association and Quercus association. Soil organic matter, saturation, pH and altitude play the major role in distribution of species. CONCLUSIONS: The variation in vegetation structure is controlled by the altitudinal gradient and physiochemical properties of soil. These results indicate a deteriorated forest structure and reduced regeneration pattern, demanding immediate attention of forest management authorities.

Primary succession in Mount Pinatubo: Habitat availability and ordination analysis.

Vegetation structure on the east flank of Mount Pinatubo was investigated to determine the inventory of species at 15 y post-eruption, then to ascertain environmental variables that have influenced the early patterns of primary succession. Unconstrained and constrained ordination methods were used to determine the influence of spatial, elevation, and substrate patterns on vegetation. Vegetation was assigned to one of 3 habitat types. Scours were eroded flat surfaces, terraces were perched flat surfaces, and talus piles were created along the canyon edges as mass waste events. The influence of habitat type on vegetation was multifaceted because they represent different conditions and different histories. The talus piles have preferential access to colonists from the vegetation on the canyon walls above and a more benign microclimate than the exposed terrace and scour sites. Scoured sites on the valley floor exhibited the least vegetation cover, as these substrates had the least mature surfaces and the most restricted capacity for root exploration. Perched terraces exhibited greater plant dominance than did the other habitats in the early stages of succession because of the ubiquitous appearance of Parasponia rugosa as initial colonists on these relatively flat surfaces. Polynomial canonical correspondence analysis was more closely aligned with the pattern of vegetation than linear canonical correspondence analysis, and therefore more closely approximated accurate descriptions of correlations among site ordination positions and measured variables. These results confirm that a variety of statistical approaches can clarify applications for restoration ecology following landslide and volcanic disturbances or agriculture and forestry anthropogenic disturbances in the lowland tropics.

Trypanosoma evansi is alike to Trypanosoma brucei brucei in the subcellular localisation of glycolytic enzymes

Trypanosoma evansi, which causes surra, is descended from Trypanosoma brucei brucei, which causes nagana. Although both parasites are presumed to be metabolically similar, insufficient knowledge of T. evansi precludes a full comparison. Herein, we provide the first report on the subcellular localisation of the glycolytic enzymes in T. evansi, which is a alike to that of the bloodstream form (BSF) of T. b. brucei: (i) fructose-bisphosphate aldolase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hexokinase, phosphofructokinase, glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase (glycolytic enzymes) and glycerol-3-phosphate dehydrogenase (a glycolysis-auxiliary enzyme) in glycosomes, (ii) enolase, phosphoglycerate mutase, pyruvate kinase (glycolytic enzymes) and a GAPDH isoenzyme in the cytosol, (iii) malate dehydrogenase in cytosol and (iv) glucose-6-phosphate dehydrogenase in both glycosomes and the cytosol. Specific enzymatic activities also suggest that T. evansi is alike to the BSF of T. b. brucei in glycolytic flux, which is much faster than the pentose phosphate pathway flux, and in the involvement of cytosolic GAPDH in the NAD+/NADH balance. These similarities were expected based on the close phylogenetic relationship of both parasites.

Examining relationship between environmental gradients and Lesser Himalyan forest vegetation of Nikyal valley, Azad Jammu and Kashmir using ordination analysis

Objective: To report the relationship of vegetation structure and environmental gradient and physiochemical properties of soil at Nikyal valley, Azad Jammu and Kashmir Methods: A survey of natural vegetation and soil of Nikyal valley was undertaken. Phytosociological survey was conducted by using Braun-Blanquet's approach. The study also investigated the vegetation structure and its relationship with altitude and edaphic factors. The floristic data was analyzed by cluster anlaysis, detrended correspondence analysis and canonical correspondence analysis using CANACOO 5.0. Results: A total of 110 plant species and 13 stands were merged into five major associations as dema rcated by cluster analysis and detrended correspondence analysis. The associations were Olea- Pinus- Themeda association, Myrsine- Rhus- Quercus association, Quercus- Rubus- Pinus association and Quercus association. Soil organic matter, saturation, pH and altitude play the major role in distribution of species. Conclusions: The variation in vegetation structure is controlled by the altitudinal gradient and physiochemical properties of soil. These results indicate a deteriorated forest structure and reduced regeneration pattern, demanding immediate attention of forest management authorities.

Examining relationship between environmental gradients and Lesser Himalyan forest vegetation of Nikyal valley, Azad Jammu and Kashmir using ordination analysis

OBJECTIVE@#To report the relationship of vegetation structure and environmental gradient and physiochemical properties of soil at Nikyal valley, Azad Jammu and Kashmir .@*METHODS@#A survey of natural vegetation and soil of Nikyal valley was undertaken. Phytosociological survey was conducted by using Braun-Blanquet's approach. The study also investigated the vegetation structure and its relationship with altitude and edaphic factors. The floristic data was analyzed by cluster anlaysis, detrended correspondence analysis and canonical correspondence analysis using CANACOO 5.0.@*RESULTS@#A total of 110 plant species and 13 stands were merged into five major associations as dema rcated by cluster analysis and detrended correspondence analysis. The associations were Olea-Pinus-Themeda association, Myrsine-Rhus-Quercus association, Quercus-Rubus-Pinus association and Quercus association. Soil organic matter, saturation, pH and altitude play the major role in distribution of species.@*CONCLUSIONS@#The variation in vegetation structure is controlled by the altitudinal gradient and physiochemical properties of soil. These results indicate a deteriorated forest structure and reduced regeneration pattern, demanding immediate attention of forest management authorities.

DCA on medicinal materials of three species of Isodon Kudo based on their UV spectra / 中草药

Object To observe the differences of Isodon amethystoides (Benth.) C. Y. Wu et Hsuan, I. nervosa (Hemsl) Kudo and I. macrocalyx (Dunn) Kudo from different regions in their UV spectra, to make the applicability of the method of Detrended Correspondence Analysis (DCA) clear in the comparison of Chinese medicinal materials based on the UV spectra. Methods The UV spectra of the 15 samples of I. amethystoides, I. nervosa and I. macrocalyx from different regions and organs were obtained, based on the indices of wavenumber absorbance, the differences of 15 UV spectra were compared by DCA. Results(1) the UV spectra of I. amthystoides from different regions were very different; (2) the samples of I. macrocalyx (or I. nervosa) from the same region were rather similar in their UV spectra; (3) there were resemblances among I. nervosa, I. macrocalyx and I. amethystoides in their UV spectra.; (4) the difference of UV spectra between the stems and leaves were obvious. Conclusion The above results indicate: (1) the medicinal effects of I. amethystoides from different regions may be very different; (2) the stems and leaves of I. amethystoides are of different medical effects; (3) I. macrocalyx and I. nervosa could be considered as the substitutes of I. amethystoides. It is practical to apply DCA on the basis of UV spectra to compare the chemical differences of plant samples.