Inter-Simple Sequence Repeat (ISSR) Marker Analysis in Parkia timoriana (DC.) Merr. Populations from Northeast India

Genetic variation in three populations of Parkia timoriana (DC.) Merr. grown in the Manipur state of northeast India was analysed using inter-simple sequence repeat (ISSR) markers. A total of 30 individual trees representing three populations were sampled and studied using 22 University of British Columbia (UBC set no. 9) primers in the present study. Of the total 22 primers, 19 primers produced distinct, reproducible and well-resolved fragments. Overall, a total number of 111 fragments were generated by the 19 primers and of which, 51 were polymorphic (45.94 %). The average number of loci and polymorphic loci generated per primer were 5.84 and 2.68, respectively. The genetic variation generated by ISSR markers within the three populations studied ranges from 33.33 to 18.92 %. The overall genetic differentiation (Gst) among populations was estimated to be 0.29, and the number of gene flow (Nm) was estimated to be 1.23 per generation between populations. Of the total genetic variance, 70.04 % was attributed to within-population diversity while 4.72 % differences to the among-populations. The genetic similarity across the individuals belonging to the three populations was represented by the dendrogram showing the grouping of the individuals into three major groups which is also supported by the principle component analysis. The present finding asserts the effectiveness of ISSR procedure for assessing genetic variations of P. timoriana populations and provides valuable genetic information that can be utilized for breeding and conservation strategies.     

Towards the identification of plant and animal binders on Australian stone knives

There is limited information regarding the nature of plant and animal residues used as adhesives, fixatives and pigments found on Australian Aboriginal artefacts. This paper reports the use of FTIR in combination with the chemometric tools principal component analysis (PCA) and hierarchical clustering (HC) for the analysis and identification of Australian plant and animal fixatives on Australian stone artefacts. Ten different plant and animal residues were able to be discriminated from each other at a species level by combining FTIR spectroscopy with the chemometric data analysis methods, principal component analysis (PCA) and hierarchical clustering (HC). Application of this method to residues from three broken stone knives from the collections of the South Australian Museum indicated that two of the handles of knives were likely to have contained beeswax as the fixative whilst Spinifex resin was the probable binder on the third.     

SSR-Based DNA Fingerprinting and Diversity Assessment Among Indian Germplasm of <Emphasis Type="Italic">Euryale ferox</Emphasis>: an Aquatic Underutilized and Neglected Food Crop

Euryale ferox is native to Southeast Asia and China, and it is one of the important aquatic food crops propagated mostly in eastern part of India. The aim of the present study was to characterize and evaluate the genetic diversity of ex situ collections of E. ferox germplasm from different geographical states of India using microsatellite (simple sequence repeats (SSRs)) markers. Ten SSR markers were analyzed to assess DNA fingerprinting and genetic diversity of 16 cultivated germplasm of E. ferox. Total 37 polymorphic alleles were recorded with an average of 3.7 allele frequency per primer. The polymorphic information content value varied from 0.204 to 0.735 with mean of 0.448. A high range of heterozygosity (Ho 0.228; He 0.512) was detected in the present study. The neighbor-joining (N-J) tree and the principle coordinate analysis showed that the germplasm divided in to three main clusters. The results of the present investigation comply that SSR markers are effective for computing genetic assessment of genetic diversity and similarity with classifying cultivated varieties of E. ferox. Evaluation of genetic diversity among Indian E. ferox germplasm could provide useful information for genetic improvement.     

RAPD and ISSR Marker-Based Comparative Evaluation of Genetic Diversity Among Indian Germplasms of <Emphasis Type="Italic">Euryale ferox</Emphasis>: an Aquatic Food Plant

Euryale ferox Salisbury is an important aquatic food plant cultivated largely in eastern India. E. ferox is a monotypic genus, and breeding programmes have mostly relied on the variability present in the primary gene pool. Knowledge of the genetic structure of the population is limited, and there are very few reports available on the genetic diversity of E. ferox. In this study, comprehensive research on the genetic diversity of 16 germplasms of E. ferox was carried out using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 320 RAPD and 95 ISSR primers screened initially, 61 primers (40 RAPD and 21 ISSR) gave reproducible bands and were selected for further work. Amplification of the 40 RAPD primers gave 533 polymorphic bands with an average of 13.32 polymorphic bands per primer. The percentage of polymorphism ranged from 37.5 to 100, with an average of 88.3 %. The 21 ISSR primers produced 259 bands, of which 214 were polymorphic, with an average of 10.19 polymorphic bands per primer. The percentage of polymorphism using ISSR primers ranged from 50 to 100, with a mean of 82.6 %. Jaccard’s coefficient ranged from 0.45 to 0.69 (RAPD), 0.50 to 0.77 (ISSR) and 0.48 to 0.71 (RAPD and ISSR). Molecular characterization of different germplasms of E. ferox not only is essential for its conservation but also can be used in further breeding programmes.     

Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species

Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in Sesamum (Sesamum indicum L.). More than 200 SSR motifs were detected (SSR motifs ??2 repeat units or 6?bp); 80?% of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10?bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60 Sesamum germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.     

Correlation between the genetic diversity and variation of total phenolic acids contents in Fructus Xanthii from different populations in China

Fructus Xanthii (Cang-Er-Zi) is a traditional Chinese medicine that is used in curing nasal diseases and headache according to the Chinese Pharmacopoeia. For the effective quality control of its medicinal values, reflected by chemical variation patterns, in addition to the relationship with genetic diversity, analyses based on UV spectrophotometry, HPLC fingerprinting and inter-simple sequence repeat (ISSR) molecular markers were carried out, involving 16 Xanthium populations from different locations in China. The HPLC data showed considerable variation of chemical constituents among the 16 Xanthium populations, and they were classified to three chemotypes by hierarchical clustering analysis. Abundant genetic diversity was detected among the Xanthium populations, which were also clustered into three groups based on their ISSR data and varied according to different species. Combining the genetic divergence and chemical differences showed an important result that, in the two chemotypes, the higher contents of total phenolic acids (TPA) in Fructus Xanthii showed greater genetic diversity (I). We suggest that genetic diversity affects the contents of TPA. Since variable phenolic acid contents may affect therapeutic efficacy, it is important to point out that combining the use of genetic base with chemotype will help control the favourable chemotypes and breed new cultivars with more desirable chemical constituents.     

Isotopic Indications of Late Pleistocene and Holocene Paleoenvironmental Changes at Boodie Cave Archaeological Site,Barrow Island,Western Australia

This paper presents the first application of mammal tooth enamel carbonate stable isotope analysis for the purpose of investigating late Pleistocene–early Holocene environmental change in an Australian archaeological context. Stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotope ratios were analyzed from archaeological and modern spectacled hare wallaby (Lagorchestes conspicillatus) and hill kangaroo (Osphranter robustus) tooth enamel carbonates from Boodie Cave on Barrow Island in Western Australia. δ¹⁸O results track the dynamic paleoecological history at Boodie Cave including a clear shift towards increasing aridity preceding the onset of the Last Glacial Maximum and a period of increased humidity in the early to mid-Holocene. Enamel δ¹³C reflects divergent species feeding ecology and may imply a long-term shift toward increasing diversity in vegetation structure. This study contributes new data to the carbonate-isotope record for Australian fauna and demonstrates the significant potential of stable isotope based ecological investigations for tracking paleoenvironment change to inter-strata resolution.     

Fatty Acid Distribution in the Lipoid Extracts of Various Algae

The fatty acid composition of the lipoid extracts of four marine alga species, Halopteris scoparia (L.) Sauvagau, Scinaia furcellata L., Sargassum natans (L.) J. Meyer, Padina vickersiae Hoyt, and the sea grass Posidonia oceanica L. as well as six freshwater alga species, namely Cladophora fracta (Dilw.) Kutz, C. glomerata (Dilw.) Kutz, Zygnema pectinatum (Vauch.) C. A. Agardh, Maugeotia sp. (C. A. Agardh), Vaucheria sessilis (Vauch.) De Candolle, and Spyrogyra gratiana Link. together with the aquatic plant Potomogeton perfoliatus L., collected from Turkish waters, was characterized by capillary GC-MS. Only the saturated fatty acids were found in the species investigated.     

Analytical pyrolysis-based study on intra-skeletal organic matrices from Mediterranean corals

Off-line analytical pyrolysis combined with gas chromatography–mass spectroscopy (GC–MS), directly or after trimethylsilylation, along with infrared spectroscopy and amino acid analysis was applied for the first time to the characterization of the intra-skeletal organic matrix (OM) extracted from four Mediterranean hard corals. They were diverse in growth form and trophic strategy namely Balanophyllia europaea and Leptopsammia pruvoti—solitary corals, only the first having zooxanthelle—and Cladocora caespitosa and Astroides calycularis—colonial corals, only the first with zooxanthelle. Pyrolysis products evolved from OM could be assigned to lipid (e.g. fatty acids, fatty alcohols, monoacylglicerols), protein (e.g. 2,5-diketopiperazines, DKPs) and polysaccharide (e.g. anhydrosugars) precursors. Their quantitative distribution showed for all the species a low protein content with respect to lipids and polysaccharides. A chemometric approach using principal component analysis (PCA) and clustering analysis was applied on OM mean amino acidic compositions. The small compositional diversity across coral species was tentatively related with coral growth form. The presence of N-acetyl glucosamine markers suggested a functional link with other calcified tissues containing chitin. The protein fraction was further investigated using novel DKP markers tentatively identified from analytical pyrolysis of model polar linear dipeptides. Again, no correlation was observed in relation to coral ecology. These analytical results revealed that the bulk structure and composition of OMs among studied corals are similar, as it is the textural organization of the skeleton mineralized units. Therefore, they suggest that coral’s biomineralization is governed by similar macromolecules, and probably mechanisms, independently from their ecology.     

Does the Phytochemical Diversity of Wild Plants Like the Erythrophleum genus Correlate with Geographical Origin?

Secondary metabolites are essential for plant survival and reproduction. Wild undomesticated and tropical plants are expected to harbor highly diverse metabolomes. We investigated the metabolomic diversity of two morphologically similar trees of tropical Africa, Erythrophleum suaveolens and E. ivorense, known for particular secondary metabolites named the cassaine-type diterpenoids. To assess how the metabolome varies between and within species, we sampled leaves from individuals of different geographic origins but grown from seeds in a common garden in Cameroon. Metabolites were analyzed using reversed phase LC-HRMS(/MS). Data were interpreted by untargeted metabolomics and molecular networks based on MS/MS data. Multivariate analyses enabled us to cluster samples based on species but also on geographic origins. We identified the structures of 28 cassaine-type diterpenoids among which 19 were new, 10 were largely specific to E. ivorense and five to E. suaveolens. Our results showed that the metabolome allows an unequivocal distinction of morphologically-close species, suggesting the potential of metabolite fingerprinting for these species. Plant geographic origin had a significant influence on relative concentrations of metabolites with variations up to eight (suaveolens) and 30 times (ivorense) between origins of the same species. This shows that the metabolome is strongly influenced by the geographical origin of plants (i.e., genetic factors).     

Association between chemical and genetic variation of Vitex rotundifolia populations from different locations in China: its implication for quality control of medicinal plants

Vitex rotundifolia is a widely distributed plant species that has been extensively used in traditional Chinese medicine. Its fruits, Fructus Viticis, are recorded as Manjingzi in the Pharmacopoeia of the People's Republic of China. For the effective quality control of its medicinal values reflected by chemical variation patterns, in addition to the relationship with genetic diversity, analyses based on high-performance liquid chromatographic (HPLC) fingerprinting and inter simple sequence repeat (ISSR) molecular markers were carried out, involving 14 V. rotundifolia populations from different locations in China. The HPLC data showed considerable variation of chemical constituents among the V. rotundifolia populations. The hierarchical clustering analysis further revealed four major groups based on their chemotype variation. Abundant genetic diversity was detected among the V. rotundifolia populations that also were clustered into four groups based on their ISSR data. It is important to point out that the genetic variation pattern revealed by molecular markers was closely associated with that indicated by chemical constitutes in the fruits of V. rotundifolia. This finding provides a solid basis for the combined use of chemical and genetic fingerprints in efficiently evaluating qualities and choosing favourable chemotypes with appropriate pharmacological properties of V. rotundifolia, in addition to establishing good agricultural practices for medicinal plants.     

Geographical origin of Sauvignon Blanc wines predicted by mass spectrometry and metal oxide based electronic nose

Analysis of 34 Sauvignon Blanc wine samples from three different countries and six regions was performed by gas chromatography-mass spectrometry (GC-MS). Linear discriminant analysis (LDA) showed that there were three distinct clusters or classes of wines with different aroma profiles. Wines from the Loire region in France and Australian wines from Tasmania and Western Australia were found to have similar aroma patterns. New Zealand wines from the Marlborough region as well as the Australian ones from Victoria were grouped together based on the volatile composition. Wines from South Australia region formed one discrete class. Seven analytes, most of them esters, were found to be the relevant chemical compounds that characterized the classes. The grouping information obtained by GC-MS, was used to train metal oxide based electronic (MOS-Enose) and mass spectrometry based electronic (MS-Enose) noses. The combined use of solid phase microextraction (SPME) and ethanol removal prior to MOS-Enose analysis, allowed an average error of prediction of the regional origins of Sauvignon Blanc wines of 6.5% compared to 24% when static headspace (SHS) was employed. For MS-Enose, the misclassification rate was higher probably due to the requirement to delimit the m/z range considered.     

Exposure Media and Nanoparticle Size Influence on the Fate,Bioaccumulation, and Toxicity of Silver Nanoparticles to Higher Plant Salvinia minima

Silver nanoparticles (AgNPs) are favoured antibacterial agents in nano-enabled products and can be released into water resources where they potentially elicit adverse effects. Herein, interactions of 10 and 40 nm AgNPs (10-AgNPs and 40-AgNPs) with aquatic higher plant Salvinia minima at 600 µg/L in moderately hard water (MHW), MHW of raised calcium (Ca²⁺), and MHW containing natural organic matter (NOM) were examined. The exposure media variants altered the AgNPs’ surface properties, causing size-dependent agglomeration. The bio-accessibility in the ascending order was: NOM < MHW < Ca²⁺, was higher in plants exposed to 10-AgNPs, and across all exposures, accumulation was higher in roots compared to fronds. The AgNPs reduced plant growth and the production of chlorophyll pigments a and b; the toxic effects were influenced by exposure media chemistry, and the smaller 10-AgNPs were commonly the most toxic relative to 40-AgNPs. The toxicity pattern was linked to the averagely higher dissolution of 10-AgNPs compared to the larger counterparts. The scanning electron microscopy and X-ray fluorescence analytical techniques were found limited in examining the interaction of the plants with AgNPs at the low exposure concentration used in this study, thus challenging their applicability considering the even lower predicted environmental concentrations AgNPs.     

Access to Phylogeny from Voltammetric Fingerprints of Seeds: the Asparagus Case

A methodology for characterizing vegetal taxonomic groups from the voltammetric fingerprints of polyphenolic components of seeds is described. It is based on recording the voltammetric response of microparticulate films deposited on glassy carbon electrodes from seed extracts using different organic solvents. The obtained responses in contact with aqueous electrolytes provided characteristic voltammetric profiles at the level of genera/subgenera and/or families using bivariant and multivariant chemometric methods. The voltammograms of 14 species from 5 different families provided family‐characteristic patterns. Analysis of voltammetric responses for a set of 20 species of the Asparagus genus from four continents permits to discriminate the genetic lines represented by the Asparagus , Protasparagus and Myrsiphyllum subgenera.     

Voltammetric identification of motor oils using an “electronic tongue”

The possibility of the voltammetric identification of motor oils using a chemometric method of the principal component analysis and voltammograms of metal ions and organic markers (Cu(II), Pb(II), o- and p-aromatic nitro compounds) on carbon paste electrodes containing analytes as binders.     

Genotypic Diversity of Mosquitocidal Bacteria (Bacillus sphaericus, B. thuringiensis, and B. cereus) Newly Isolated from Natural Sources

In the present study, to comprehend the genetic diversity of mosquitocidal bacteria, the genotypic analysis of 30 strains of Bacillus species isolated newly from diverse environmental sources has been conducted. Randomly amplified polymorphic DNA polymerase chain reaction was conducted to characterize the genotype diversity between the bacterial strains. The matrix of scores from each bacterial DNA was analyzed, and the correlation between the co-efficients and the similarity matrix data was computed. Clusters from dendrogram showing diversity among isolates could be distinguished genetically based on their origin of isolates. The first major cluster consists of 43 strains grouped under various subclusters (91.489 %). A second cluster contains only four strains (8.511 %). An average similarity value of 0.36 revealed the dendrogram split into 28 distinct “groups” or “clusters,” allowing almost a complete separation of strains within the Bacillus group isolated from various sources and thus facilitating assessment of genetic diversity of species and subspecies level. The conclusion from the result was that there was broad diversity among the mosquitocidal strains, and cluster analysis revealed the associations among the isolates based on their origin. A high level of polymorphism with distinct genetic lineages consequent to the source of origin of bacterial strains is the significant impact of this study.     

Application of a genomic model for high‐dimensional chemometric analysis

The rapid development of new technologies for large‐scale analysis of genetic variation in the genomes of individuals and populations has presented statistical geneticists with a grand challenge to develop efficient methods for identifying the small proportion of all identified genetic polymorphisms that have effects on traits of interest. To address such a “large p small n” problem, we have developed a heteroscedastic effects model (HEM) that has been shown to be powerful in high‐throughput genetic analyses. Here, we describe how this whole‐genome model can also be utilized in chemometric analysis. As a proof of concept, we use HEM to predict analyte concentrations in silage using Fourier transform infrared spectroscopy signals. The results show that HEM often outperforms the classic methods and in addition to this presents a substantial computational advantage in the analyses of such high‐dimensional data. The results thus show the value of taking an interdisciplinary approach to chemometric analysis and indicate that large‐scale genomic models can be a promising new approach for chemometric analysis that deserve to be evaluated more by experts in the field. The software used for our analyses is freely available as an R package at http://cran.r‐project.org/web/packages/bigRR/ . Copyright © 2014 John Wiley & Sons, Ltd.     

GC–MS combined with chemometric techniques for the quality control and original discrimination of Curcumae longae rhizome: Analysis of essential oils

Curcumae longae rhizome is a widely used traditional herb in many countries. Various geographical origins of this herb might lead to diversity or instability of the herbal quality. The objective of this work was to establish the chemical fingerprints for quality control and find the chemical markers for discriminating these herbs from different origins. First, chemical fingerprints of essential oil of 24 C. longae rhizome from four different geographical origins in China were determined by GC–MS. Then, pattern recognition techniques were introduced to analyze these abundant chemical data in depth; hierarchical cluster analysis was used to sort samples into groups by measuring their similarities, and principal component analysis and partial least‐squares discriminate analysis were applied to find the main chemical markers for discriminating these samples. Curcumae longae rhizome from Guangxi province had the highest essential oil yield (4.32 ± 1.45%). A total of 46 volatile compounds were identified in total. Consistent results were obtained to show that C. longae rhizome samples could be successfully grouped according to their origins, and turmerone, ar‐turmerone, and zingiberene were the characteristic components for discriminating these samples of various geographical origins and for quality control. This finding revealed that fingerprinting analysis based on GC–MS coupled with chemometric techniques could provide a reliable platform to discriminate herbs from different origins, which is a benefit for quality control.     

Study on Gas Chromatographic Fingerprint of Essential Oil from Stellera chamaejasme Flowers and Its Repellent Activities against Three Stored Product Insects

The objective of this study was to establish the chromatographic fingerprints of the essential oil (EO) from Stellera chamaejasme flowers collected from various natural sites by gas chromatography (GC) combined with chemometric methods. The EO was obtained by hydrodistillation, and its chemical composition was analyzed by gas chromatography−mass spectrometry (GC−MS). Most components were identified as ketones and the relatively high-content components were fitone (38.973%), n-hentriacontane (5.807%), myristic acid (4.944%) and phytol (3.988%). In addition, the repellent activities of the EO from S. chamaejasme flowers and its four main chemical compounds were evaluated against three stored product pests (Tribolium castaneum, Lasioderma serricorne, Liposcelis bostrychophila) for the first time. In this work, the EO and the four chemical compounds showed a repellent effect against three storage pests after 2 and 4 h exposure. The experimental method and repellent activity of S. chamaejasme flower EO could provide a basis for the development of botanical pesticide and the utilization of the rich plant resources of S. chamaejasme in the future.