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Background: Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. The computational approach to SNP mining is becoming increasingly popular because of the continuously increasing number of sequences deposited in databases, which allows a more accurate identification of SNPs. Several software packages have been developed for SNP mining from databases. From these, QualitySNP is the only tool that combines SNP detection with the reconstruction of alleles, which results in a lower number of false positive SNPs and also works much faster than other programs. We have build a web-based SNP discovery and allele detection tool (HaploSNPer) based on QualitySNP. Results: HaploSNPer is a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species. It includes BLAST for finding homologous sequences in public EST databases, CAP3 or PHRAP for aligning them, and QualitySNP for discovering reliable allelic sequences and SNPs. All possible and reliable alleles are detected by a mathematical algorithm using potential SNP information. Reliable SNPs are then identified based on the reconstructed alleles and on sequence redundancy. Conclusion: Thorough testing of HaploSNPer (and the underlying QualitySNP algorithm) has shown that EST information alone is sufficient for the identification of alleles and that reliable SNPs can be found efficiently. Furthermore, HaploSNPer supplies a user friendly interface for visualization of SNP and alleles. HaploSNPer is available from http://www.bioinformatics.nl/tools/haplosnper/. [ABSTRACT FROM AUTHOR]

Background: Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs. Results: We have developed PolySSR, a new pipeline to identify polymorphic SSRs rather than just SSRs. Sequence information is obtained from public EST databases derived from heterozygous individuals and/or at least two different genotypes. The pipeline includes PCR-primer design for the putatively polymorphic SSR markers, taking into account Single Nucleotide Polymorphisms (SNPs) in the flanking regions, thereby improving the success rate of the potential markers. A large number of polymorphic SSRs were identified using publicly available EST sequences of potato, tomato, rice, Arabidopsis, Brassica and chicken. The SSRs obtained were divided into long and short based on the number of times the motif was repeated. Surprisingly, the frequency of polymorphic SSRs was much higher in the short SSRs. Conclusion: PolySSR is a very effective tool to identify polymorphic SSRs. Using PolySSR, several hundred putative markers were developed and stored in a searchable database. Validation experiments showed that almost all markers that were indicated as putatively polymorphic by polySSR were indeed polymorphic. This greatly improves the efficiency of marker development, especially in species where there are low levels of polymorphism, like tomato. When combined with the new sequencing technologies PolySSR will have a big impact on the development of polymorphic SSRs in any species. [ABSTRACT FROM AUTHOR]

With the aim of finding genes involved in the floral transition of woody species four MADS box genes containing cDNAs from apple (Malus domestica) have been isolated. Three genes were isolated from vegetative tissue of apple, but were homologues of known genes that specify floral organ identity. MdMADS13 is an AP3‐like B class MADS box gene, and was mainly expressed in petals and stamens as demonstrated by Northern blot analysis. MdMADS14 and –15 are AGAMOUS‐like genes. They differed slightly in expression patterns on Northern blots, with MdMADS15 mRNA levels equally high in stamens and carpels, but MdMADS14 preferably expressed in carpels. MdMADS14 is likely to be the apple orthologue of one of the Arabidopsis thaliana SHATTERPROOF genes, and MdMADS15 closely resembled the Arabidopsis AGAMOUS gene. It has been shown with RT‐PCR that the three floral apple MADS box genes are expressed in vegetative tissues of adult as well as juvenile trees, albeit at low levels. MdMADS12 is an AP1‐like gene that is expressed at similar levels in leaves, vegetative shoots, and floral tissues, and that may be involved in the transition from the juvenile to the adult stage. [ABSTRACT FROM PUBLISHER]

We investigated the ability of TNF-α to mediate damage of endothelial cells in the presence of Neutrophils, by measuring detachment of cultured human umbilical vein endothelial cells (HUVEC), Endothelial cell detachment was increased from 5% to about 75% by the presence of 1-10 ng/ml TNF-α during incubation with neutrophils, whereas negligible endothelial cell lysis was observed as measured by 51Cr release, TNF-α was compared with the cytokines IL-lα and IFN-γ and with PMA and LPS, Both TNF-α and PMA appeared to be strong triggers for neutrophil-induced endothelial cell detachment, whilst reduced injury was seen after addition of IL-α and LPS, IFN-γ did not induce endothelial cell detachment, but potentiated the effect of both TNF-α and IL-α, TNF-α-induced endothelial cell detachment was neutrophil dependent, since pre-incubation of neutrophils, but not pre-incubation of endothelial cells with TNF-α, caused endothelial cell detachment. Thus, TNF-α-induced increase in neutrophil-adhesiveness of HUVEC was found not to be essential for endothelial damage, Pre-incubation of neutrophils in suspension with TNF-α induced rapid activation, followed by nearly complete deactivation of neutrophils, as measured by their capacity to induce detachment of endothelial cells after removal of TNF-α. These results indicate that local presence of TNF-a might be critical in tissue or organ damage during early, neutrophil-mediated inflammatory processes, independent of enhanced adhesiveness of endothelium for neutrophils. [ABSTRACT FROM AUTHOR]

TNF plays a central role in septic shock induced by endotoxin or Gram-negative bacteria. Zymosan can elicit a septic shock-like syndrome in rodents in the absence of endoloxin. TNF and IL-6 release in mice treated with zymosan was investigated. One hour after intraperitoneal zymosan injection, maximal TNF levels were measured in serum, followed by lL-6peak levels 1 h later. Treatment with a monoclonal anlibody againsl TNF lowered zymosan-induced mortality from 63 to 1 !.6".., while maximal lL-6 levels were lowered by about 40"!.. Mechanisms triggering zymosan-induced cytokine release in murine macrophages were analysed in vitro. Cytokine release was only slightly triggered by uncoated zymosan particles. Thirty-nine per cent of TNF release by macrophages appeared to be triggered by zymosan-bound activated complement. Maximal TNF release also required the presence oT natural antibodies against zymosan and zymosan-activated serum. In contrast, maximal IL-6 release was reached upon stimulation with zymosan-activated serum only, while the presence of zymosan particles lowered this response. We conclude that TNF Is a crucial mediator in zymosan-induced shock. TNF release can be induced by different immunological pathways, without the need for the direct presence of endotoxins. Although IL-6 release during septic shock is partly dependent on TNF, in vitro trigger mechanisms for IL-6 and TNF differ remarkably. [ABSTRACT FROM AUTHOR]

The aim of this study was to examine the tumour necrosis factor (TNF)-a production by peripheral blood mononuclear cells activated by mitogens. Considerable amounts of TNF-α, ranging from 1.0 to 5.0 ng/ml, were present in the supernatants of cultures of human peripheral blood mononuclear cells (PBMC), stimulated with either the anti-CD3 monoclonal antibody OKT3 or the lectin phytohaemagglutinin (PMA) The amount of TNF-α secreted in the supernatant was closely correlated to the degree of T cell proliferation in such cultures, as measured by [3H]TdR incorporation. In the absence of proliferating T cells the mitogens did not induce secretion of TNF-α by monocytes. Supernatants of proliferating T cells were shown to induce TNF-α production by monocytes. The macrophage-activating factor gamma interferon (IFN-γ) was also shown to induce, in the absence of endoloxin. TNF-α secretion by monocytes in a dose-dependent manner. The induction of TNF-α production by supernatants of proliferating T cells could largely be abrogated by passaging the supernatants on an anti- IFN-γ column before adding them to the monocytes. It is therefore concluded from this study that the production of TNF-α by monocytes can be induced by proliferating T cells and that this induction can largely be attributed to the T cell lymphokine IFN-γ. [ABSTRACT FROM AUTHOR]

The cytokine tumour necrosis factor (TNF) is believed to be involved in the pathophysiology of several human disease states, both septic and non-septic. Different pathways of inductior are involved in the generation of TNF in these disease states. We therefore used four different stimulatory agents, lipopolysaccharide, phorbol myristate acetate, silica quartz, and anti-human IgG antibody to study the influence of the corticosteroids prednisolone and budesonide on the secretion of TNF by human monocytes. Both prednisolone and budesonide inhibited TNF secretion induced by these four stimulating agents in a different degree. Inhibition was strong when TNF secretion was induced by lipopolysaccharide or anti-human IgG antibody. A weaker inhibitory effect was observed when TNF secretion was induced by silica quartz. Only minimal inhibition of phorbol myristate acetate induced TNF secretion was observed, Furthermore, it is shown that inhibition is dependent on the dose of corticosteroid, but not or only minimally on the dose of stimulating agent, indicating that inhibition cannot he overcome by increasing the cell-activating stimulus. Finally, optimal inhibition of TNF secretion by corticosteroids is shown to be dependent on the presence of corticosteroids during the phase of cell stimulation. [ABSTRACT FROM AUTHOR]

Movement disorders are usually of central origin, but sometimes involuntary movements occur after peripheral trauma. Twenty eight patients, 13 women and 15 men, mean age 37 years (range 15-78), were studied with dystonia or tremor in whom the onset of abnormal movements was related, in time and in distribution, to injury of a body part. Among 23 patients with latency of less than one year after injury, focal dystonia of the involved body part was found in 18, nine of whom had associated reflex sympathetic dystrophy (RSD). One of five patients with peripherally induced tremor had RSD. Abnormal electromyography or nerve conduction velocities were found in the affected limb in four patients, but other electrophysiologic techniques provided evidence for disturbed central function. In 15 patients (65%) possible predisposing factors may have contributed to the pathogenesis of the trauma induced abnormal involuntary movements. [ABSTRACT FROM AUTHOR]

The article focuses on the design and construction of the Nieuwe Kerk or New Church in Haarlem, Netherlands. In 1645, the city ordered that a new Calvinist church be built to replace the medieval Sint Annakapel or the Saint Anne's Chapel. The council preferred a design by Jacob van Campen, which preserved Lieven de Key's tower of 1613. Van Campen's design was thought to have inspired by the desire to have the new building harmonize with the existing tower. The architectural form of the church appears to refer to an image current of the Temple of Jerusalem, as showed in Reformed bibles.

Drought sensitivity of potato leads to a reduction in total tuber yield and marketable yield. An investigation of drought effects on tuber yield attributes will facilitate our understanding of how to reduce such huge yield losses. We have evaluated tuber yield, tuber size distribution and marketable yield of a set of 103 European commercial potato cultivars under irrigated and non-irrigated conditions in the field. The multi-year results from two locations, Connantre, France (2013–2015) and Nieuw-Namen in Zeeland, The Netherlands (2013–2014), were analysed. We used Normal and Gamma Distribution models to describe the tuber size distribution of tuber fresh weight and tuber number, respectively. The interactions among parameters of tuber size distribution and total/marketable tuber yield traits were analysed using correlation matrices and biplots. Finally, we used a 14K Infinium SNP marker array to find associations between the parameters or traits and genetic loci on the potato genome. Late foliage maturity facilitated a wider spread of tuber size distribution in favour of larger-sized tubers. Drought effects on total yield were representative of their impact on marketable yield, however, absolute values of total tuber number may not be indicative of marketable number of tubers. We found significant marker-trait associations between a region on chromosome 3 and the spread of tuber number distribution, size class with maximum tuber number and marketable fractions of tuber number and tuber weight. These findings will contribute to improvement and selection for drought tolerance in potato. [ABSTRACT FROM AUTHOR]