Development of Use Cases, Part I

For determining requirements and constructs appropriate for a Web query language, or in fact any language, use cases are of essence. The W3C has published two sets of use cases for XML and RDF query languages. In this article, solutions for these use cases are presented using Xcerpt. a novel Web and Semantic Web query language that combines access to standard Web data such as XML documents with access to Semantic Web metadata such as RDF resource descriptions with reasoning abilities and rules familiar from logicprogramming. To the best knowledge of the authors, this is the first in depth study of how to solve use cases for accessing XML and RDF in a single language: Integrated access to data and metadata has been recognized by industry and academia as one of the key challenges in data processing for the next decade. This article is a contribution towards addressing this challenge by demonstrating along practical and recognized use cases the usefulness of reasoning abilities, rules, and semistructured query languages for accessing both data (XML) and metadata (RDF)

Analyse der Chromosomenverteilung in menschlichen Fibroblasten mittels 3D-Vielfarben Fluoreszenz in situ Hybridisierung

In human diploid fibroblasts (HDFs) the cell nucleus is oval in shape, quite large in xy-diameter (10-20µm), but flat in z-direction (5µm). In these nuclei chromosome territories typically lie side by side or slightly above each other. The question whether these arrangements are ordered or variable has yielded conflicting answers. We hybridised an improved 7-fluorochrome MFISH probe set on 3D-preserved cell nuclei, fixed with buffered 4% paraformaldehyde. A LEICA wide field microscope with an 8-filter-wheel and an automated z-step motor was used for imaging of the 7 fluorochromes plus DAPI. Multicolor images from nuclei were taken as serial sections in z-direction. After deconvolution, a specifically developed Program goldFISH Saracoglu K. et al. 2001 was used to classify the images according to the labelling scheme. The classification algorithm corresponds to the procedure previously used for metaphase spreads, now adopted to 3-D studies of chromosome territory arrangements in the cell nucleus. The analysis of 30 G0-fibroblast nuclei and 30 prometaphase rosettes revealed a pronounced variability of chromosome territory neighbourhoods, as described by Allison D. C. et al. 1999, but in contrast to Nagele R. et al. 1995. However we noted a distinct radial order: small chromosomes were located close to the centre while large chromosomes were positioned towards the nuclear rim. This non-random radial positioning could also be observed in prometaphase rosettesDie Erforschung von Chromosomenpositionen im menschlichen Zellkern führte zu kontroversen Ergebnissen: In Lymphozyten konnte eine radiale Chromosomenposition entdeckt werden, die von der Gendichte der Chromosomen abhing (Boyle A. L. et al. 1990; Cremer M. et al. 2001). Genreiche Chromosomen lagen zentraler im Zellkern als genarme. In Fibroblasten wurde zwar ebenfalls eine radiale Verteilung gefunden, jedoch korreliert diese besser mit der genomischen Größe der Chromosomen. Hier lagen kleinere Chromosomen zentraler als größere (Sun et al. 2000). Darüberhinaus finden einige Publikationen eine starr gegenüberliegende und fixierte nachbarschaftliche Anordnung (Nagele et al. 1995), andere hingegen eine zufällige Nachbarschaft (Allison und Nestor 1999). Weitfeldmikroskoptechnik, Dekonvolution und Klassifikation: Ein Großteil der Arbeit betraf die Etablierung und das Testen eines 3D-Mikroskopie- und Dekonvolutions-System für M-FISH Präparate. Ein Leica Weitfeld-Epifluoreszenzmikroskop wurde mit einem Filterrad für acht Bandpassfilter und einem z-Schrittmotor für den Mikroskoptisch ausgestattet. Die Software zu Steuerung wurde in Zusammenarbeit mit Leica Microsystems angepasst. Nach Aufnahme der Bildstapel wurden sie der Dekonvolution unterzogen, um sie auf die Qualität konfokaler Bilder anzuheben. Für die Dekonvolution war es nötig die richtigen Programme und Parameter herauszufinden. ReFISH-Präparate konnten mit einem konfokalen Mikroskop aufgenommen werden, jedoch war es nötig das Präparat nach der ersten Hybridisierung erneut zu waschen und zu denaturieren, um den zweiten, komplementären Sondensatz zu hybridisieren. Die zwei nacheinander aufgenommenen Bildstapel mussten mit einem Alignmentprogramm aneinander angeglichen werden. Schließlich wurde es durch die Erweiterung des Karyotypisierungsprogramms auf 3 Dimensionen möglich, Chromosomenterritorien im Zellkern automatisch zu bestimmen. Das Programm klassifiziert die Regionen anhand des Markierungsschemas und weist jedem erkannten Chromosomenterritorium eine Klassifikationsfarbe zu. Die Schwerpunkte der Chromosomenterritorien wurden in eine Ausgabetabelle geschrieben. Die daraus berechneten Abstände und Winkel liessen eine Aussage bezüglich der Chromosomentopologie zu. Chromosomenpositionen in Fibroblasten: In allen Experimenten an G0-Fibroblasten und Prometaphaserosetten wur-de in den Kernen eine größenabhängige, radiale Verteilung der Chromoso-menterritorien gefunden, wobei kleinere Chromosomen allgemein zentraler lagen als größere. Eine starre Ordnung, wie sie in Nagele et al. (1995) pro-pagiert wurde, konnte nicht nachvollzogen werden. Vielmehr stellte sich heraus, dass die nachbarschaftliche Anordnung der Chromosomen im Zell-kern weitgehend zufällig is

Identificação e gestão da dor em bovinos leiteiros

Existem poucos métodos objetivos para identificar os diferentes tipos de dor em animais de produção o que torna mais difícil a gestão desta. No entanto, há uma preocupação crescente por parte dos consumidores que está a levar os produtores e os médicos veterinários a considerarem cada vez mais a questão da gestão da dor. No caso dos animais de produção, a identificação da dor é difícil, daí a importância de uma abordagem multiparamétrica. Esta revisão bibliográfica pretende discutir as diferentes manifestações e fenómenos dolorosos em bovinos leiteiros, bem como as moléculas existentes e disponíveis para aliviar os efeitos da dor nas capacidades de produção dos animais.There are few objective methods to identify the different types of pain in farm animals, which makes pain management more difficult. However, there is an increasing consumer concern that is causing farmers and veterinarians to look more closely at the issue of pain management. In the case of farm animals, pain identification is difficult, hence the importance of a multiparametric approach is needed. This review attempts to discuss the different manifestations of pain in dairy cattle, as well as the molecules that available to alleviate them and the effects of pain on the production capabilities of animals

Towards many colors in FISH on 3D-preserved interphase nuclei

The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process. We discuss (1) M-FISH (combinatorial labeling + deconvolution + widefield microscopy); (2) multicolor labeling + SIM (structured illumination microscopy); (3) the standard approach to multicolor FISH + CLSM (confocal laser scanning microscopy; one fluorochrome - one color channel); (4) combinatorial labeling + CLSM; (5) non-combinatorial labeling + CLSM + linear unmixing. Two related issues, deconvolution of images acquired with CLSM and correction of data for chromatic Z-shift, are also discussed. All methods are illustrated with practical examples. Finally, several rules of thumb helping to choose an optimal labeling + microscopy combination for the planned experiment are suggested. Copyright (c) 2006 S. Karger AG, Basel

Development of Use Cases, Part I

For determining requirements and constructs appropriate for a Web query language, or in fact any language, use cases are of essence. The W3C has published two sets of use cases for XML and RDF query languages. In this article, solutions for these use cases are presented using Xcerpt. a novel Web and Semantic Web query language that combines access to standard Web data such as XML documents with access to Semantic Web metadata such as RDF resource descriptions with reasoning abilities and rules familiar from logicprogramming. To the best knowledge of the authors, this is the first in depth study of how to solve use cases for accessing XML and RDF in a single language: Integrated access to data and metadata has been recognized by industry and academia as one of the key challenges in data processing for the next decade. This article is a contribution towards addressing this challenge by demonstrating along practical and recognized use cases the usefulness of reasoning abilities, rules, and semistructured query languages for accessing both data (XML) and metadata (RDF)

Development, validation, and application of a fast, simple, and robust SPE-based LC-MS/MS method for quantification of angiotensin I-converting enzyme inhibiting tripeptides Val-Pro-Pro, Ile-Pro-Pro, and Leu-Pro-Pro in yoghurt and other fermented dairy products

Dairy products are an important part of a nutritionally balanced diet as their constituents can affect the human state of health. By inhibiting the angiotensin I-converting enzyme, the tripeptides Val-Pro-Pro, Ile-Pro-Pro, and Leu-Pro-Pro can lower blood pressure. As these peptides are produced during fermentation, they are found in various dairy products like cheese, yoghurt, etc., but except for cheese only little is known about their content. To investigate how other dairy products contribute to a supply of these antihypertensive peptides, we developed and validated a fast and sensitive assay for quantification of the three tripeptides with LC-MS/MS combined with a simple protocol for extraction and SPE-purification from yoghurt, curd, or other products. Finally, the entire method was successfully applied to survey peptide concentrations in samples from local dairies and thus expands our awareness on the content of antihypertensive peptides in our food. (C) 2019 Elsevier Ltd. All rights reserved.Peer reviewe

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

A growing body of experimental evidence supports the hypothesis that the 3D structure of chromatin in the nucleus is closely linked to important functional processes, including DNA replication and gene regulation. In support of this hypothesis, several research groups have examined sets of functionally associated genomic loci, with the aim of determining whether those loci are statistically significantly colocalized. This work presents a critical assessment of two previously reported analyses, both of which used genome-wide DNA–DNA interaction data from the yeast Saccharomyces cerevisiae, and both of which rely upon a simple notion of the statistical significance of colocalization. We show that these previous analyses rely upon a faulty assumption, and we propose a correct non-parametric resampling approach to the same problem. Applying this approach to the same data set does not support the hypothesis that transcriptionally coregulated genes tend to colocalize, but strongly supports the colocalization of centromeres, and provides some evidence of colocalization of origins of early DNA replication, chromosomal breakpoints and transfer RNAs

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag 2008.In the nuclei of human lymphocytes, chromosome territories are distributed according to the average gene density of each chromosome. However, chromosomes are very heterogeneous in size and base composition, and can contain both very gene-dense and very gene-poor regions. Thus, a precise analysis of chromosome organisation in the nuclei should consider also the distribution of DNA belonging to the chromosomal bands in each chromosome. To improve our understanding of the chromatin organisation, we localised chromosome 7 DNA regions, endowed with different gene densities, in the nuclei of human lymphocytes. Our results showed that this chromosome in cell nuclei is arranged radially with the gene-dense/GC-richest regions exposed towards the nuclear interior and the gene-poorest/GC-poorest ones located at the nuclear periphery. Moreover, we found that chromatin fibres from the 7p22.3 and the 7q22.1 bands are not confined to the territory of the bulk of this chromosome, protruding towards the inner part of the nucleus. Overall, our work demonstrates the radial arrangement of the territory of chromosome 7 in the lymphocyte nucleus and confirms that human genes occupy specific radial positions, presumably to enhance intra- and inter-chromosomal interaction among loci displaying a similar expression pattern, and/or similar replication timing

Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues

Copyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and 85 reproduction in any medium, provided the original author and source are credited. The article was made available through the Brunel University Open Access Publishing Fund.BACKGROUND: In interphase nuclei of a wide range of species chromosomes are organised into their own specific locations termed territories. These chromosome territories are non-randomly positioned in nuclei which is believed to be related to a spatial aspect of regulatory control over gene expression. In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome re-positioning during differentiation. The pig is an important model organism both economically and as a closely related species to study human disease models. This is why great efforts have been made to accomplish the full genome sequence in the last decade. RESULTS: This study has positioned most of the porcine chromosomes in in vitro cultured adult and embryonic fibroblasts, early passage stromal derived mesenchymal stem cells and lymphocytes. The study is further expanded to position four chromosomes in ex vivo tissue derived from pig kidney, lung and brain. CONCLUSIONS: It was concluded that porcine chromosomes are also non-randomly positioned within interphase nuclei with few major differences in chromosome position in interphase nuclei between different cell and tissue types. There were also no differences between preferred nuclear location of chromosomes in in vitro cultured cells as compared to cells in tissue sections. Using a number of analyses to ascertain by what criteria porcine chromosomes were positioned in interphase nuclei; we found a correlation with DNA content.This study is partly supported by Sygen International PLC