Webtag: a new web tool providing tags/anchors for RT-PCR experiments with prokaryotes.

BACKGROUND: Webtag is a tool providing oligonucleotide sequences (usually called tags or anchors) that are absent from a specified genome. These tags/anchors can be appended to gene specific primers for reverse transcriptase polymerase chain reaction experiments, circumventing genomic DNA contamination. RESULTS: The use of a relational database, in conjunction with a series of scripts written in PHP and Perl, allows the user to rapidly obtain tags that are: 1) suitable for a specific organism, and 2) compatible with other oligonucleotides to be used in the experimental procedures. CONCLUSION: This new web tool allows scientists to easily and rapidly obtain suitable tags for RT-PCR experiments, and is available at http://www.egs.uu.se/software/webtag/.

Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR.

BACKGROUND: In order to overcome genomic DNA contamination in transcriptional studies, reverse template-specific polymerase chain reaction, a modification of reverse transcriptase polymerase chain reaction, is used. The possibility of using tags whose sequences are not found in the genome further improves reverse specific polymerase chain reaction experiments. Given the absence of software available to produce genome suitable tags, a simple tool to fulfill such need was developed. RESULTS: The program was developed in Perl, with separate use of the basic local alignment search tool, making the tool platform independent (known to run on Windows XP and Linux). In order to test the performance of the generated tags, several molecular experiments were performed. The results show that Tagenerator is capable of generating tags with good priming properties, which will deliberately not result in PCR amplification of genomic DNA. CONCLUSION: The program Tagenerator is capable of generating tag sequences that combine genome absence with good priming properties for RT-PCR based experiments, circumventing the effects of genomic DNA contamination in an RNA sample.

Pancreatic beta-cell lipotoxicity induced by overexpression of hormone-sensitive lipase.

Lipid perturbations associated with triglyceride overstorage in beta-cells impair insulin secretion, a process termed lipotoxicity. To assess the role of hormone-sensitive lipase, which is expressed and enzymatically active in beta-cells, in the development of lipotoxicity, we generated transgenic mice overexpressing hormone-sensitive lipase specifically in beta-cells. Transgenic mice developed glucose intolerance and severely blunted glucose-stimulated insulin secretion when challenged with a high-fat diet. As expected, both lipase activity and forskolin-stimulated lipolysis was increased in transgenic compared with wild-type islets. This was reflected in significantly lower triglycerides levels in transgenic compared with wild-type islets in mice receiving the high-fat diet, whereas no difference in islet triglycerides was found between the two genotypes under low-fat diet conditions. Our results highlight the importance of mobilization of the islet triglyceride pool in the development of beta-cell lipotoxicity. We propose that hormone-sensitive lipase is involved in mediating beta-cell lipotoxicity by providing ligands for peroxisome proliferator-activated receptors and other lipid-activated transcription factors, which in turn alter the expression of critical genes. One such gene might be uncoupling protein-2, which was found to be upregulated in transgenic islets, a change that was accompanied by decreased ATP levels.

An in situ sample environment reaction cell for spatially resolved X-ray absorption spectroscopy studies of powders and small structured reactors.

An easy-to-use sample environment reaction cell for X-ray based in situ studies of powders and small structured samples, e.g., powder, pellet, and monolith catalysts, is described. The design of the cell allows for flexible use of appropriate X-ray transparent windows, shielding the sample from ambient conditions, such that incident X-ray energies as low as 3 keV can be used. Thus, in situ X-ray absorption spectroscopy (XAS) measurements in either transmission or fluorescence mode are facilitated. Total gas flows up to about 500 mln/min can be fed while the sample temperature is accurately controlled (at least) in the range of 25-500 °C. The gas feed is composed by a versatile gas-mixing system and the effluent gas flow composition is monitored with mass spectrometry (MS). These systems are described briefly. Results from simultaneous XAS/MS measurements during oxidation of carbon monoxide over a 4% Pt/Al2O3 powder catalyst are used to illustrate the system performance in terms of transmission XAS. Also, 2.2% Pd/Al2O3 and 2% Ag - Al2O3 powder catalysts have been used to demonstrate X-ray absorption near-edge structure (XANES) spectroscopy in fluorescence mode. Further, a 2% Pt/Al2O3 monolith catalyst was used ex situ for transmission XANES. The reaction cell opens for facile studies of structure-function relationships for model as well as realistic catalysts both in the form of powders, small pellets, and coated or extruded monoliths at near realistic conditions. The applicability of the cell for X-ray diffraction measurements is discussed.

Antitumor reactivity of anti-CD3/anti-CD28 bead-activated lymphoid cells: implications for cell therapy in a murine model.

Ligation of TCR and CD28 expressed on T cells via mAbs results in activation of T cells capable of tumor destruction in adoptive immunotherapy. In a murine model, the authors examined in vitro activation conditions utilizing plate-immobilized and bead-conjugated mAbs that bind to CD3 and CD28. Bead-activated tumor-draining lymph node (TDLN) cells demonstrated superior cytokine (IFN-gamma, GM-CSF, IL-2, and IL-10) secretion and mediated tumor regression more efficiently compared with plate-activated cells. The bead-activated TDLN cells had a significantly higher percentage of CD4+ cells compared with plate-activated cells. On a per-cell basis, positively selected CD4+ cells activated with bead-coupled or plate immobilized mAbs mediated tumor-specific regression equally. Bead-activated CD4+ TDLN cells demonstrated significantly higher levels of tumor specific IL-2 secretion compared with plate-activated CD4+ cells that may provide helper function to CD8+ effector cells. The antitumor reactivity of bead-activated lymphoid cells depended upon their source. TDLN cells after bead activation were more potent than splenocytes from tumor-bearing hosts in mediating tumor regression in vivo. Bead-activated LN cells and splenocytes from nontumor-bearing hosts demonstrated nonspecific cytokine secretion and minimal efficacy in adoptive immunotherapy. At minimal doses of IL-2, the antitumor reactivity of bead-activated TDLN cells was significantly enhanced. Anti-CD3/anti-CD28 bead activation of tumor-primed T cells represents an efficient method to generate effector cells for immunotherapy.