An optimized method for the generation of AFLP markers in a stingless bee (Melipona quadrifasciata) reveals a high degree of intracolonial genetic polymorphism

This study describes an optimized protocol for the generation of Amplified Fragment Length Polymorphism (AFLP) markers in a stingless bee. Essential modifications to standard protocols are a restriction enzyme digestion (EcoRI and Tru1I) in a two-step procedure, combined with a touchdown program in the selective PCR amplification step and product labelling by incorporation of alpha[P-33]dATP. In an analysis of 75 workers collected from three colonies of Melipona quadrifasciata we obtained 719 markers. Analysis of genetic variability revealed that on average 32% of the markers were polymorphic within a colony. Compared to the overall percentage of polymorphism (44% of the markers detected in our bee samples), the observed rates of within-colony polymorphism are remarkably high, considering that the workers of each colony were all of spring of a singly mated queen.

Studying genetic relationships among coconut varieties/populations using microsatellite markers

The extent of genetic diversity and the genetic relationships among 94 coconut varieties/populations (51 Talls and 43 Dwarfs) representing the entire geographic range of cultivation/distribution of the coconut was assessed using 12 pairs of coconut microsatellite primers. A high level of genetic diversity was observed in the collection with the mean gene diversity of 0.647+/-0.139, with that of the mean gene diversity of Talls 0.703+/-0.125 and 0.374+/-0.204 of Dwarfs. A phenetic tree based on DAD genetic distances clustered all the 94 varieties/ populations into two main groups, with one group composed of all the Talls from southeast Asia, the Pacific, west coast of Panama, and all Dwarfs and the other of all Talls from south Asia, Africa, and the Indian Ocean coast of Thailand. The allele distribution of Dwarfs highlighted a unique position of Dwarf palms from the Philippines exhibiting as much variation as that in the Tall group. The grouping of all Dwarfs representing the entire geographic distribution of the crop with Talls from southeast Asia and the Pacific and the allele distribution between the Tall and Dwarf suggest that the Dwarfs originated from the Tall forms and that too from the Talls of southeast Asia and the Pacific. Talls from Pacific Islands recorded the highest level of genetic diversity (0.6+/-0.26) with the highest number of alleles (51) among all the regions.

Levels and distribution of genetic diversity of coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka assessed by microsatellite markers

The coconut variety Typica, form typica, commonly known as Sri Lanka tall coconuts is the most widely exploited and grown variety in Sri Lanka. Under the coconut bio-diversity conservation programme, several Typica populations have been collected by island-wide surveys and planted ex situ. Thirty-three coconut populations were subjected to microsatellite assay with eight coconut-specific microsatellite primer pairs in order to study the levels and distribution of genetic variation of the collected materials for formulating future collection strategies and selecting parents for the breeding programme. A total of 56 alleles were detected ranging from 3 to 10 alleles per primer pair with an average of 7 alleles per locus. Overall a very high level of genetic diversity was detected (0.999) for all the populations studied ranging from 0.526 for population Debarayaya to 0.683 for population Dickwella. Only four introduced coconut populations, i.e. Clovis, Margeret, Dickwella, Mirishena and an embryo-cultured population were clearly separated from the resulting dendrogram. A very high level of within population variation (99%) accounted for native populations suggests a common history and a restricted genetic base for native Sri Lankan tall coconuts. Categorization of alleles into different classes according to their frequency and distribution confirmed the results of the dedrogram and concluded the adequacy of single large collection from the entire target area to represent the total genetic diversity in Sri Lanka. This study discusses useful information regarding conservation and breeding of coconut in Sri Lanka.

Genetic variation of the razor clam Ensis siliqua (Jeffreys, 1875) along the European coast based on random amplified polymorphic DNA markers

Ensis siliqua is regarded as an increasingly valuable fishery resource with potential for commercial aquaculture in many European countries. The genetic variation of this razor clam was analysed by randomly amplified polymorphic DNA (RAPD) in six populations from Spain, Portugal and Ireland. Out of the 40 primers tested, five were chosen to assess genetic variation. A total of 61 RAPD loci were developed ranging in size from 400 to 2000 bp. The percentages of polymorphic loci, the allele effective number and the genetic diversity were comparable among populations, and demonstrated a high level of genetic variability. The values of Nei's genetic distance were small among the Spanish and Portuguese populations (0.051-0.065), and high between these and the Irish populations. Cluster and principal coordinate analyses supported these findings. A mantel test performed between geographic and genetic distance matrices showed a significant correlation (r=0.84, P

Raman spectroscopy of advanced glycation end products (AGEs), possible markers for progressive retinal dysfunction

Raman microscopy is used to investigate the spectral features of selected compounds known to be involved in the development of the eye disease age-related macular degeneration (AMD). Diagnostic features were identified in synthetic samples of these compounds and in a biological matrix. The study demonstrates the potential of Raman microscopy for the development of diagnostic markers of the onset of AMD. Copyright (C) 2008 John Wiley & Sons, Ltd.

Probabilistic classification of acute myocardial infarction from multiple cardiac markers

Logistic regression and Gaussian mixture model (GMM) classifiers have been trained to estimate the probability of acute myocardial infarction (AMI) in patients based upon the concentrations of a panel of cardiac markers. The panel consists of two new markers, fatty acid binding protein (FABP) and glycogen phosphorylase BB (GPBB), in addition to the traditional cardiac troponin I (cTnI), creatine kinase MB (CKMB) and myoglobin. The effect of using principal component analysis (PCA) and Fisher discriminant analysis (FDA) to preprocess the marker concentrations was also investigated. The need for classifiers to give an accurate estimate of the probability of AMI is argued and three categories of performance measure are described, namely discriminatory ability, sharpness, and reliability. Numerical performance measures for each category are given and applied. The optimum classifier, based solely upon the samples take on admission, was the logistic regression classifier using FDA preprocessing. This gave an accuracy of 0.85 (95% confidence interval: 0.78-0.91) and a normalised Brier score of 0.89. When samples at both admission and a further time, 1-6 h later, were included, the performance increased significantly, showing that logistic regression classifiers can indeed use the information from the five cardiac markers to accurately and reliably estimate the probability AMI. © Springer-Verlag London Limited 2008.