Methods for integration site distribution analyses in animal cell genomes.

The question of where retroviral DNA becomes integrated in chromosomes is important for understanding (i) the mechanisms of viral growth, (ii) devising new anti-retroviral therapy, (iii) understanding how genomes evolve, and (iv) developing safer methods for gene therapy. With the completion of genome sequences for many organisms, it has become possible to study integration targeting by cloning and sequencing large numbers of host-virus DNA junctions, then mapping the host DNA segments back onto the genomic sequence. This allows statistical analysis of the distribution of integration sites relative to the myriad types of genomic features that are also being mapped onto the sequence scaffold. Here we present methods for recovering and analyzing integration site sequences.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach.

AbstractText BACKGROUND: Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim's epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim's DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim's fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim's fraction, and then digest the residual victim's DNA with a nuclease. METHODS: The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. RESULTS: For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. CONCLUSIONS: In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.

Dynamic graphics of parametrically linked multivariate methods used in compositional data analysis

Many multivariate methods that are apparently distinct can be linked by introducing oneor more parameters in their definition. Methods that can be linked in this way arecorrespondence analysis, unweighted or weighted logratio analysis (the latter alsoknown as "spectral mapping"), nonsymmetric correspondence analysis, principalcomponent analysis (with and without logarithmic transformation of the data) andmultidimensional scaling. In this presentation I will show how several of thesemethods, which are frequently used in compositional data analysis, may be linkedthrough parametrizations such as power transformations, linear transformations andconvex linear combinations. Since the methods of interest here all lead to visual mapsof data, a "movie" can be made where where the linking parameter is allowed to vary insmall steps: the results are recalculated "frame by frame" and one can see the smoothchange from one method to another. Several of these "movies" will be shown, giving adeeper insight into the similarities and differences between these methods.

Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine.

Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.

The application of NMR and MS methods for detection of adulteration of wine, fruit juices, and olive oil. A review

This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration.

Variance reduction methods for simulation of densities on Wiener space

We develop a general error analysis framework for the Monte Carlo simulationof densities for functionals in Wiener space. We also study variancereduction methods with the help of Malliavin derivatives. For this, wegive some general heuristic principles which are applied to diffusionprocesses. A comparison with kernel density estimates is made.

When rare is just a matter of sampling: unexpected dominance of clubtail dragonflies (Odonata, Gomphidae) through different collecting methods at Parque Nacional da Serra do Cipó, Minas Gerais State, Brazil

When rare is just a matter of sampling: Unexpected dominance of clubtail dragonflies (Odonata, Gomphidae) through different collecting methods at Parque Nacional da Serra do Cipó, Minas Gerais State, Brazil. Capture of dragonfly adults during two short expeditions to Parque Nacional da Serra do Cipó, Minas Gerais State, using three distinct collecting methodsaerial nets, Malaise and light sheet trapsis reported. The results are outstanding due the high number of species of Gomphidae (7 out of 26 Odonata species), including a new species of Cyanogomphus Selys, 1873, obtained by two non-traditional collecting methods. Because active collecting with aerial nets is the standard approach for dragonfly inventories, we discuss some aspects of the use of traps, comparing our results with those in the literature, suggesting they should be used as complementary methods in faunistic studies. Furthermore, Zonophora campanulata annulata Belle, 1983 is recorded for the first time from Minas Gerais State and taxonomic notes about Phyllogomphoides regularis (Selys, 1873) and Progomphus complicatus Selys, 1854 are also given.

Comparative abundance and diversity of Dryininae (Hymenoptera, Dryinidae) in three savannah phytophysiognomies in southeastern Brazil, under three sampling methods

Comparative abundance and diversity of Dryininae (Hymenoptera, Dryinidae) in three savannah phytophysiognomies in southeastern Brazil, under three sampling methods. This study aimed to assess the abundance and diversity of Dryininae in riparian vegetation, Brazilian savannah, and savannah woodland vegetation at the Estação Ecológica de Jataí, in Luiz Antônio, State of São Paulo, Brazil, by using Moericke, Malaise, and light traps. The sampling was carried out from December 2006 to November 2009, and 371 specimens of Dryininae were caught, with the highest frequencies in spring and summer. Fourteen species of Dryinus Latreille, 1804 and one of Thaumatodryinus Perkins, 1905 were identified. The highest frequencies of Dryinus in the riparian vegetation differed significantly from those obtained in the Brazilian savannah and savannah woodland vegetation. In the riparian vegetation, the highest number of Dryinus was collected using light traps and the interactions between abundance and the collection method used were significant. The number of specimens of Dryinus collected in the Brazilian savannah and savannah woodland vegetation using Malaise traps did not differ significantly from those obtained using Moericke traps. Males significantly outnumbered females in the sex ratio of Dryinus. The species diversity of Dryinus based on females collected using Malaise traps was high in the Brazilian savannah. Furthermore, high species richness of female Dryinus was observed in riparian vegetation (six species) and Brazilian savannah (five). The light trap was the most successful method for sampling diversity of Dryininae.

Conceptos generales y métodos de estudio en farmacogenética [General concepts and study methods in pharmacogenetics.]

Pharmacogenetics, the study of how individual genetic profiles influence the response to drugs, is an important topic. Results from pharmacogenetics studies in various clinical settings may lead to personalized medicine. Herein, we present the most important concepts of this discipline, as well as currently-used study methods.

Minimum requirements for application of ink dating methods based on solvent analysis in casework

Several ink dating methods based on solvents analysis using gas chromatography/mass spectrometry (GC/MS) were proposed in the last decades. These methods follow the drying of solvents from ballpoint pen inks on paper and seem very promising. However, several questions arose over the last few years among questioned documents examiners regarding the transparency and reproducibility of the proposed techniques. These questions should be carefully studied for accurate and ethical application of this methodology in casework. Inspired by a real investigation involving ink dating, the present paper discusses this particular issue throughout four main topics: aging processes, dating methods, validation procedures and data interpretation. This work presents a wide picture of the ink dating field, warns about potential shortcomings and also proposes some solutions to avoid reporting errors in court.

Simple and fast methods based on solid-phase extraction coupled to liquid chromatography with UV detection for the monitoring of caffeine in natural and waste waters as marker of anthropogenic impact

Two concentration methods for fast and routine determination of caffeine (using HPLC-UV detection) in surface, and wastewater are evaluated. Both methods are based on solid-phase extraction (SPE) concentration with octadecyl silica sorbents. A common “offline” SPE procedure shows that quantitative recovery of caffeine is obtained with 2 mL of an elution mixture solvent methanol-water containing at least 60% methanol. The method detection limit is 0.1 μg L−1 when percolating 1 L samples through the cartridge. The development of an “online” SPE method based on a mini-SPE column, containing 100 mg of the same sorbent, directly connected to the HPLC system allows the method detection limit to be decreased to 10 ng L−1 with a sample volume of 100 mL. The “offline” SPE method is applied to the analysis of caffeine in wastewater samples, whereas the “on-line” method is used for analysis in natural waters from streams receiving significant water intakes from local wastewater treatment plants

Active learning methods for remote sensing image classification

In this paper, we propose two active learning algorithms for semiautomatic definition of training samples in remote sensing image classification. Based on predefined heuristics, the classifier ranks the unlabeled pixels and automatically chooses those that are considered the most valuable for its improvement. Once the pixels have been selected, the analyst labels them manually and the process is iterated. Starting with a small and nonoptimal training set, the model itself builds the optimal set of samples which minimizes the classification error. We have applied the proposed algorithms to a variety of remote sensing data, including very high resolution and hyperspectral images, using support vector machines. Experimental results confirm the consistency of the methods. The required number of training samples can be reduced to 10% using the methods proposed, reaching the same level of accuracy as larger data sets. A comparison with a state-of-the-art active learning method, margin sampling, is provided, highlighting advantages of the methods proposed. The effect of spatial resolution and separability of the classes on the quality of the selection of pixels is also discussed.