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This article describes a simple method to perform lock mass corrected accurate mass measurements in tandem mass spectrometry (MS/MS) with a quadrupole time-of-flight (Q-TOF) mass spectrometer. The experimental approach consists of using the protonated molecule of a known compound, which is measured in a MS/MS function using low collision energy (no fragmentation), as mass calibrator. The unknown compound is acquired in MS/MS mode albeit using high collision energy. After the acquisition, the two MS/MS spectra of unknown and mass calibrator are combined, and the fragments of the unknown are lock mass corrected by using the protonated molecule of the mass calibrator. To prove this concept, 10 compounds were analyzed using this approach, the fragments interpreted and, where possible, related to structural data available in the literature. All the unequivocally assigned fragments were accurately mass measured with mass errors within appropriate limits, i.e. for m/z values200 with a mass tolerance of 3 mDa while for m/z200 the mass tolerance is expressed as 10 ppm.

Patients with chronic lymphocytic leukemia (CLL) treated with adenovirus (Ad)-CD154 (CD40L) gene therapy experience reductions in leukemia cell counts and lymph node size associated with induction of the death receptor Fas (CD95). CD4 T cell lines can induce apoptosis of CD40-activated CLL cells via a CD95 ligand (CD95-L)-dependent mechanism. To examine whether CD95-L was sufficient to induce cytolysis of CD40-activated CLL cells, we used Chinese hamster ovary cells transfected with CD95-L as cytotoxic effector cells. CD40-activated CLL cells were initially resistant to CD95-mediated apoptosis despite high-level expression of CD95. However, after 72 h, CLL cells from seven of seven patients became increasingly sensitive to CD95-mediated apoptosis. This sensitivity correlated with a progressive decline in Flice-inhibitory protein (FLIP), which was induced within 24 h of CD40 ligation. Down-regulation of FLIP with an antisense oligonucleotide or a pharmacologic agent, however, was not sufficient to render CLL cells sensitive to CD95-mediated apoptosis in the 24–72 h after CD40 activation. Although the levels of pro-Caspase-8 appeared sufficient, inadequate levels of Fas-associated death domain protein (FADD) and DAP3 may preclude assembly of the death-inducing signaling complex. Seventy-two hours after CD40 ligation, sensitivity to CD95 and a progressive increase in FADD and DAP3 were associated with the acquired ability of FADD and FLIP to coimmunoprecipitate with the death-inducing signaling complex after CD95 ligation. Collectively, these studies reveal that CD40 ligation on CLL B cells induces a programmed series of events in which the cells initially are protected and then sensitized to CD95-mediated apoptosis through shifts in the balance of the anti- and proapoptotic proteins FLIP and FADD.

Laser capture microdissection (LCM) is a unique tool for precise separation of target cells from forensic mixtures. Cells isolated by LCM can subsequently be used for the generation of pure DNA profiles. Although mainly used in sexual assault cases, LCM offers tremendous advantages for many different forensic applications.

International audience; Necrotic enteritis in broiler chickens is associated with netB positive Clostridium perfringens type A strains. It is known that C. perfringens strains isolated from outbreaks of necrotic enteritis are more capable of secreting factors inhibiting growth of other C. perfringens strains than strains isolated from the gut of healthy chickens. This characteristic could lead to extensive and selective presence of a strain that contains the genetic make-up enabling to secrete toxins that cause gut lesions. This report describes the discovery, purification, characterization and recombinant expression of a novel bacteriocin, referred to as perfrin, produced by a necrotic enteritis-associated netB-positive C. perfringens strain. Perfrin is a 11.5 kDa C-terminal fragment of a 22.9 kDa protein and showed no sequence homology to any currently known bacteriocin. The 11.5 kDa fragment can be cloned into Escherichia coli, and expression yielded an active peptide. PCR detection of the gene showed its presence in 10 netB-positive C. perfringens strains of broiler origin, and not in other C. perfringens strains tested (isolated from broilers, cattle, sheep, pigs, and humans). Perfrin and NetB are not located on the same genetic element since NetB is plasmid-encoded and perfrin is not. The bacteriocin has bactericidal activity over a wide pH-range but is thermolabile and sensitive to proteolytic digestion (trypsin, proteinase K). C. perfringens bacteriocins, such as perfrin, can be considered as an additional factor involved in the pathogenesis of necrotic enteritis in broilers.

Background The medicinal plant Artemisia annua is covered with filamentous trichomes and glandular, artemisinin producing trichomes. A high artemisinin supply is needed at a reduced cost for treating malaria. Artemisinin production in bioreactors can be facilitated if a better insight is obtained in the biosynthesis of artemisinin and other metabolites. Therefore, metabolic activities of glandular and filamentous trichomes were investigated at the transcriptome level. Results By laser pressure catapulting, glandular and filamentous trichomes as well as apical and sub-apical cells from glandular trichomes were collected and their transcriptome was sequenced using Illumina RNA-Seq. A de novo transcriptome was assembled (Trinity) and studied with a differential expression analysis (edgeR). A comparison of the transcriptome from glandular and filamentous trichomes shows that MEP, MVA, most terpene and lipid biosynthesis pathways are significantly upregulated in glandular trichomes. Conversely, some transcripts coding for specific sesquiterpenoid and triterpenoid enzymes such as 8-epi-cedrol synthase and an uncharacterized oxidosqualene cyclase were significantly upregulated in filamentous trichomes. All known artemisinin biosynthesis genes are upregulated in glandular trichomes and were detected in both the apical and sub-apical cells of the glandular trichomes. No significant differential expression could be observed between the apical and sub-apical cells. Conclusions Our results underscore the vast metabolic capacities of A. annua glandular trichomes but nonetheless point to the existence of specific terpene metabolic pathways in the filamentous trichomes. Candidate genes that might be involved in artemisinin biosynthesis are proposed based on their putative function and their differential expression level.

Two methods are commonly used to report on evidence carried by forensic DNA profiles: the "Random Man Not Excluded" (RMNE) approach and the likelihood ratio (LR) approach. Each approach has its advantages and disadvantages. The RMNE approach is much more straightforward to implement, requires less interpretation (which is subject to non-objectivity) and is easier to explain in court. The RNME approach returns a value which is valid, independent of the knowledge of possible contributors. It is often claimed a major advantage of the LR method that drop-out can be assessed probabilistically. We propose new RMNE calculations that likewise account for allelic drop-out in an observed forensic DNA profile. The reported calculations present a non suspect-driven alternative to the poor practice of omitting an inconvenient locus from the standard RMNE calculation when there are loci that require dropped out alleles to allow for a match with the suspect sample. In contrast with the LR approach, the presented RMNE approach does not need error-prone assumptions on the probability P (D) that an allelic drop-out has occurred in the evidence profile. An Excel file with pre-programmed calculations of RMNE probabilities for DNA profiles up to 16 loci and with a maximum of 2 drop-outs is available at: http://www.labfbt.UGent.be/RMNE.php.

The sizing capability of slab gel electrophoresis for short tandem repeat (STR) fragments was compared to the sizing capability of capillary electrophoresis (CE). Both systems used automated laser fluorescence detection to detect four fluorescent dyes, enabling the use of an internal lane standard within each sample. The STR fragments were amplified using a multiplex polymerase chain reaction (PCR) in which the STR fragments Hum CD-4, Hum TH01, Hum D21S11 and Hum SE33 were amplified simultaneously. The reproducibility of the size calling was determined for both systems. The average standard deviation obtained for the slab gel system was 0.2, which was comparable to the standard deviation of 0.12 obtained for the CE system. The CE system produced results comparable to those obtained on the slab gel system, with a level of precision of +/- 1.0 bp (between instruments).

The in vitro adduct formation between phenyl glycidyl ether (PGE) and calf thymus DNA was inves-tigated. Agarose slab gel electrophoresis of DNA incubated with PGE revealed that nearly all high-molecular-weight species were degraded after 10 h of incubation. After DNA precipitation the reaction products present in the supernatant were subjected to a solid-phase extraction on a polystyrene divinylbenzene copolymer, enabling analysis on capillary zone electrophoresis (CZE), using sample stacking. These reaction products were mainly produced during the first 10 h of incubation, indicating that these products result from the DNA degradation. On the other hand, analysis of the adducts present in the enzymatic digest of the DNA pellet revealed that these adducts were formed only after 10 h of incubation. The reaction products present in the DNA supernatant were identified by on-line coupling of CZE to electrospray tandem mass spectrometry. Three major reaction products resulted from phosphate alkylation, as proven by the analysis of the corresponding low-energy CAD product ion mass spectra. This phosphate alkylation results in phosphotriesters which readily hydrolyze, resulting in DNA strand breaks.

A number of cis-dichloro[bis(aminocoumarin)]platinum complexes have been synthesized and evaluated for their in vitro cytotoxicity against Caco-2T cells. The complex with 7-amino-4-trifluoromethylcoumarin as ligand has been found to be the most active (IC50 10 mu g/ml) in this study. (C) 1997 Elsevier Science Ltd. Bioorg Med Chem Lett

The objective of this study was to screen a dog population from Belgium, the Netherlands and Germany for the presence of mutant alleles associated with hip dysplasia (HD), degenerative myelopathy (DM), exercise-induced collapse (EIC), neuronal ceroid lipofuscinosis 4A (NCL), centronuclear myopathy (HMLR), mucopolysaccharidosis VII (MPS VII), myotonia congenita (MG), gangliosidosis (GM1) and muscular dystrophy (Duchenne type) (GRMD). Blood samples (K3EDTA) were collected for genotyping with Kompetitive Allele Specific PCR (n = 476). Allele and genotype frequencies were calculated in those breeds with at least 12 samples (n = 8). Hardy-Weinberg equilibrium was tested. Genetic variation was identified for 4 out of 9 disorders: mutant alleles were found in 49, 15, 3 and 2 breeds for HD, DM, EIC and NCL respectively. Additionally, mutant alleles were identified in crossbreeds for both HD and EIC. For HD, DM, EIC and NCL mutant alleles were newly discovered in 43, 13, 2 and 1 breed(s), respectively. In 9, 2 and 1 breed(s) for DM, EIC and NCL respectively, the mutant allele was detected, but the respective disorder has not been reported in those breeds. For 5 disorders (HMLR, MPS VII, MG, GM1, GRMD), the mutant allele could not be identified in our population. For the other 4 disorders (HD, DM, EIC, NCL), prevalence of associated mutant alleles seems strongly breed dependent. Surprisingly, mutant alleles were found in many breeds where the disorder has not been reported to date.

Background Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. Results In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. Conclusions Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.

Correction to: Molecular Psychiatry advance online publication, 14 August 2012; doi:10.1038/mp.2012.85 The name of coauthor LK Davis was omitted from the author line. Dr Davis should have been listed as the tenth author (between ER Gamazon and L Osiecki). Her affiliation is as follows: Department ofMedicine, University of Chicago, Chicago, IL, USA.

Transcriptome analysis through next-generation sequencing technologies allows the generation of detailed gene catalogs for non-model species, at the cost of new challenges with regards to computational requirements and bioinformatics expertise. Here, we present TRAPID, an online tool for the fast and efficient processing of assembled RNA-Seq transcriptome data, developed to mitigate these challenges. TRAPID offers high-throughput open reading frame detection, frameshift correction and includes a functional, comparative and phylogenetic toolbox, making use of 175 reference proteomes. Benchmarking and comparison against state-of-the-art transcript analysis tools reveals the efficiency and unique features of the TRAPID system. TRAPID is freely available at http://bioinformatics.psb.ugent.be/webtools/trapid/., Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 900

The in vitro adduct formation with phenyl glycidyl ethers (PGEs) was studied on 2'-deoxynucleotides and DNA. The modified DNA was hydrolyzed enzymatically, and the mixtures consisting of unmodified 2'-deoxynucleotide adducts were analyzed by capillary zone electrophoresis (CZE), CZE-electrospray mass spectrometry (CZE/ES-MS) and CZE-electrospray tandem mass spectrometry (CZE/ES-MS/MS) using sample stacking. For the CZE analyses, a homemade system was developed in order to enhance the reproducibility of the retention times. This modification enabled the total comparison of the electropherograms obtained for the analysis of 2'deoxynucleotides mixtures with the electropherograms obtained for the DNA hydrolysates both treated with PGEs. The assignment of adducted and nonadducted 2'-deoxynucleotide peaks was unambiguous. Analysis of the CZE/ES-MS data gave the necessary structural information and revealed the presence of mono- and dialkylated 2'-deoxynucleotides. Interpretation of the CZE/ES-MS/MS data of the monoalkylated products allowed differentiation between purine or pyrimidine alkylation and alkylation of the 5-phosphate moiety. Recording of full-scan mass spectra during CZE/ES-MS/MS analysis of 2'-deoxynucleotide reaction mixtures and DNA hydrolysates was possible, using the described CZE sample stacking technique.

Helicobacter (H.) suis is a porcine and human gastric pathogen. Previous studies in mice showed that an H. suis infection does not result in protective immunity, whereas immunization with H. suis whole-cell lysate (lysate) protects against a subsequent experimental infection. Therefore, two-dimensional gel electrophoresis of H. suis proteins was performed followed by immunoblotting with pooled sera from H. suis- infected mice or mice immunized with lysate. Weak reactivity against H. suis proteins was observed in post-infection sera. Sera from lysate-immunized mice, however, showed immunoreactivity against a total of 19 protein spots which were identified using LC-MS/MS. The H. suis urease subunit B (UreB) showed most pronounced reactivity against sera from lysate-immunized mice and was not detected with sera from infected mice. None of the pooled sera detected H. suis neutrophil-activating protein A (NapA). The protective efficacy of intranasal vaccination of BALB/c mice with H. suis UreB and NapA, both recombinantly expressed in Escherichia coli (rUreB and rNapA, respectively), was compared with that of H. suis lysate. All vaccines contained choleratoxin as adjuvant. Immunization of mice with rUreB and lysate induced a significant reduction of H. suis colonization compared to non-vaccinated H. suis-infected controls, whereas rNapA had no significant protective effect. Probably, a combination of local Th1 and Th17 responses, complemented by antibody responses play a role in the protective immunity against H. suis infections.

Ventilator-associated pneumonia (VAP) is a common nosocomial infection in mechanically ventilated patients. Biofilm formation is one of the mechanisms through which the endotracheal tube (ET) facilitates bacterial contamination of the lower airways. In the present study, we analyzed the composition of the ET biofilm flora by means of culture dependent and culture independent (16 S rRNA gene clone libraries and pyrosequencing) approaches. Overall, the microbial diversity was high and members of different phylogenetic lineages were detected (Actinobacteria, beta-Proteobacteria, Candida spp., Clostridia, epsilon-Proteobacteria, Firmicutes, Fusobacteria and gamma-Proteobacteria). Culture dependent analysis, based on the use of selective growth media and conventional microbiological tests, resulted in the identification of typical aerobic nosocomial pathogens which are known to play a role in the development of VAP, e. g. Staphylococcus aureus and Pseudomonas aeruginosa. Other opportunistic pathogens were also identified, including Staphylococcus epidermidis and Kocuria varians. In general, there was little correlation between the results obtained by sequencing 16 S rRNA gene clone libraries and by cultivation. Pyrosequencing of PCR amplified 16 S rRNA genes of four selected samples resulted in the identification of a much wider variety of bacteria. The results from the pyrosequencing analysis suggest that these four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria. A combination of methods is recommended to obtain a complete picture of the microbial diversity of the ET biofilm.

Population frequency data for nine short tandem repeats (STR) (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820) were determined from 280 unrelated Caucasians from the North region of Belgium (Flanders). The data were obtained using the AmpF/STR Profiler kit from Applied Biosystems.

Introduction The transforming growth factor (TGF)-β superfamily consists of a number of molecules that regulate a variety of cellular processes such as growth, differentiation and oncogenesis. Growth differentiation factor 15 is a distant member of this TGF-β family. GDF15 was previously shown to be elevated in serum of rheumatoid arthritis (RA)-patients compared to healthy controls. This study aims to compare GDF15 serum and synovial fluid levels in several inflammatory rheumatic diseases. Methods GDF15 levels were determined by ELISA in two different cohorts. A first group included serum samples from patients with an indication for an arthroscopic procedure for diagnostic purposes. A total of 37 RA patients, 63 spondyloarthritis (SpA) patients and 17 osteoarthritis patients was analysed. Synovial fluid levels in RA and SpA patients from this cohort were determined as well. A second confirmatory cohort constituted of a consecutive cohort of 555 patients visiting the outpatient clinic of the department of Rheumatology at Ghent University Hospital. Results SpA samples show a significant lower serum concentration of GDF15 compared to RA patients. When SpA patients were stratified according to the subdiagnosis (USpA, AS or PsA) no statistically significant differences could be observed between the groups. Interestingly, SpA patients, but not RA-patients, show a significant higher concentration of GDF15 in the synovial fluid compared to serum (serum=516.38 pg/ml ± 71.09 vs syn fluid 803.2167 pg/ml ± 99.14; paired sample t-test, p Analysis the second group consisting of a consecutive cohort of 555 patients confirmed the lower concentration of GDF15 in serum samples of SpA patients compared to RA patients. To estimate the diagnostic potential to discriminate SpA from RA patients, a ROC curve analysis was performed, characterised by a AUC of 0.76. In addition, it was demonstrated that GDF15 levels might have an added value to anti-CCP and rheumatoid factor to discriminate RA and SpA patients. Conclusion GDF15 serum concentrations are significantly lower in SpA patients compared to other inflammatory joint diseases. The serum levels are not directly correlated to inflammatory or known diagnostic parameters and thus may serve as an additional marker for diagnostic purposes in inflammatory joint diseases.

Background: HSP27 (HSPb1) is one of the small heat-shock proteins (sHSP), a protein family characterized by a molecular weight below 30 kDa. Recently, we reported the differential expression of alphaBcrystallin, another sHSP (Lambrecht et al, Arthritis Rheum, 2009). Based on the functional and structural relationship between alphaBcrystallin and HSP27, we further performed differential expression analysis on HSP27 Objectives: We aimed to achieve further insights in the involvement of small heat-shock proteins, more specific HSP27, in the biology of chondrocytes. Methods: Western blot and real-time RT-PCR analysis were performed to determine the expression levels of HSP27 in healthy and OA chondrocytes cultured in alginate beads. RNA-interference mediated gene knock-down was used to explore the role of this small heat shock protein in IL-1b activated pathways by transfecting low concentrations of siRNA in cultured chondrocytes. Upon knock-down of HSP27, cells were stimulated by IL-1b and IL-6 concentrations were determined by ELISA. Results: Western blot of healthy and OA chondrocyte lysates showed a decreased abundance of HSP27 in OA. Moreover, real-time RT-PCR confirmed the differential expression at the mRNA-level between chondrocytes isolated from visually intact and visually damaged zones of OA cartilage. The pro-inflammatory cytokines IL-1beta and TNF-alpha, both down regulated HP27 expression. Transfection of low concentrations siRNA in cultured chondrocytes resulted in an efficient knock down of HSP27 gene expression. This decreased HSP27 expression results in a reduced secretion of IL-6, in response to IL-1b. Conclusion: This study adds to the evidence that small heat-shock proteins may be important mediators in chondrocyte biology during the development of OA. Our study showed the involvement of HSP27 in IL-1b induced IL-6 secretion in human articular chondrocytes.

Introduction: Rheumatoid arthritis (RA) is an inflammatory disease, which results in destruction of the joint. The presence of immune complexes (IC) in serum and synovial fluid of RA patients might contribute to this articular damage through different mechanisms, such as complement activation. Therefore, identification of the antigens from these IC is important to gain more insight into the pathogenesis of RA. Since RA patients have antibodies against citrullinated proteins (ACPA) in their serum and synovial fluid (SF) and since elevated levels of citrullinated proteins are detected in the joints of RA patients, citrullinated antigens are possibly present in IC from RA patients. Methods: IC from serum of healthy persons, serum of RA patients and IC from synovial fluid of RA patients and Spondyloarthropathy (SpA) patients were isolated by immunoprecipitation. Identification of the antigens was performed by SDS-PAGE, mass spectrometry and immunodetection. The presence of citrullinated proteins was evaluated by anti-modified citrulline (AMC) staining. Results: Circulating IC in the serum of RA patients and healthy controls contain fibrinogen beta and fibronectin, both in a non-citrullinated form. Additionally, in IC isolated from RA SF, fibrinogen. and vimentin were identified as well. More importantly, vimentin and a minor portion of fibrinogen beta were found to be citrullinated in the isolated complexes. Moreover these citrullinated antigens were only found in ACPA+ patients. No citrullinated antigens were found in IC from SF of SpA patients. Conclusions: Citrullinated fibrinogen beta and citrullinated vimentin were found in IC from SF of ACPA+ RA patients, while no citrullinated antigens were found in IC from SF of ACPA-RA patients or SpA patients or in IC from serum of RA patients or healthy volunteers. The identification of citrullinated vimentin as a prominent citrullinated antigen in IC from SF of ACPA+ RA patients strengthens the hypothesis that citrullinated vimentin plays an important role in the pathogenesis of RA.

Invariant Natural Killer T (iNKT) cells are characterized by expression of a semi-invariant Vα14-Jα18 TCRα chain and NK lineage markers such as NK1.1. In the thymus, iNKT cell maturation coincides with NK1.1 up-regulation and paradoxically, the retention of the mature NK1.1+ subset. The signals involved in the retention of iNKT cells remain undefined. Here, we report that upregulation of the chemokine receptor CxCR3 on thymic iNKT cells serves to retain them in the thymus of adult mice. Strikingly, genetic deletion or neutralization of CxCR3 results in leakage of thymic iNKT cells into the peripheral circulation. These results suggest an unexpected role for CxCR3 in thymic iNKT cell homing and localization patterns.

We studied the diagnostic performance of the anti-human citrullinated fibrinogen antibody (AhFibA) ELISA for rheumatoid arthritis (RA) in a consecutive cohort (population 1) and evaluated the agreement between the AhFibA ELISA and four other assays for anti-citrullinated protein/peptide antibodies (ACPAs) as well as rheumatoid factor in patients with longstanding RA (population 2). Population 1 consisted of 1024 patients with rheumatic symptoms; serum samples from these patients were sent to our laboratory for ACPA testing within the context of a diagnostic investigation for RA. Ninety-two of these patients were classified as having RA according to the American College of Rheumatology criteria and 463 were classified as non-RA patients. Population 2 consisted of 180 patients with longstanding RA and was used to assess agreement and correlations between five ACPA assays: anti-cyclic citrullinated peptide (CCP)1 and anti-CCP2 antibodies were detected using a commercially available ELISA, AhFibA using ELISA, and anti-PepA and anti-PepB antibodies using line immunoassay. Applying previously proposed cut-offs for AhFibA, we obtained a sensitivity of 60.9% and a specificity of 98.7% in population 1. Receiver operating characteristic curve analysis could not detect a significant difference in diagnostic performance between the AhFibA ELISA and anti-CCP2 assay. Performing a hierarchical nearest neighborhood cluster analysis of the five different ACPA assays in population 2, we identified two clusters: a cluster of anti-pepA, anti-pepB and anti-CCP1, and a cluster of AhFibA and anti-CCP2. In conclusion, we found that AhFibA and anti-CCP2 antibodies had similar diagnostic performance. However, disagreement between ACPA tests may occur.

Selective serotonin reuptake inhibitors, such as fluoxetine, have recently been shown to exert anti-inflammatory and immunosuppressive effects. Although the effects on cytokine secretion, proliferation and viability of T lymphocytes have been extensively characterized, little is known about the mechanism behind these effects. It is well known that Ca(2+) signaling is an important step in the signaling transduction pathway following T cell receptor activation. Therefore, we investigated if fluoxetine interferes with Ca(2+) signaling in Jurkat T lymphocytes. Fluoxetine was found to suppress Ca(2+) signaling in response to T cell receptor activation. Moreover, fluoxetine was found to deplete intracellular Ca(2+) stores, thereby leaving less Ca(2+) available for release upon IP3- and ryanodine-receptor activation. The Ca(2+)-modifying effects of fluoxetine are not related to its capability to block the serotonin transporter, as even a large excess of 5HT did not abolish the effects. In conclusion, these data show that fluoxetine decreases IP3- and ryanodine-receptor mediated Ca(2+) release in Jurkat T lymphocytes, an effect likely to be at the basis of the observed immunosuppression.

Caspase-14 is an important protease in the proper formation of a fully functional skin barrier. Newborn mice that are deficient in caspase-14 exhibit increased transepidermal water loss and are highly sensitive to UVB-induced photodamage. Decreased caspase-14 expression and incomplete caspase-14 processing in lesional psoriatic parakeratotic stratum corneum has been reported previously. In this study, we show that caspase-14-deficient skin frequently displays incompletely cornified cells in the transitional zone between the granular and the cornified layers, pointing to a delay in cornification. We also demonstrate that after challenge of epidermal permeability barrier function by repetitive acetone treatment, a higher incidence of large parakeratotic plaques was observed in caspase-14-deficient skin. Furthermore, caspase-14-deficient mice are more prone than control mice to the development of parakeratosis upon induction of psoriasis-like dermatitis by imiquimod treatment. These results show that lack of caspase-14 expression predisposes to the development of parakeratosis and that caspase-14 has an important role in keratinocyte terminal differentiation and the maintenance of normal stratum corneum, especially in conditions causing epidermal hyperproliferation.

Serotonin reuptake inhibitors (SRIs) are widely used drugs in the treatment of depression and anxiety disorders. Although SRIs are generally regarded as safe drugs with relatively few side effects, literature suggests that high concentrations of SRIs may alter immune function. We investigated whether high-dose treatment with fluoxetine was able to suppress acute graft-versus-host disease (GvHD) in a MHC-matched, minor histocompatibility antigen mismatched murine bone marrow transplantation model. We found that high doses fluoxetine induce a significant reduction of clinical symptoms and increase survival of these animals. The amelioration of clinical GvHD was accompanied by a reduced expansion of alloreactive T cells. We further analyzed the direct in vitro effect of six SRIs on the viability and proliferation of human T cells and found an anti-proliferative and pro-apoptotic effect that was significantly larger in activated than in resting T cells. We discuss these results in the light of potential future exploration of SRIs as a novel class of T cell immunosuppressive drugs.

In sexual assault crimes, differential extraction of spermatozoa from vaginal swab smears is often ineffective, especially when only a few spermatozoa are present in an overwhelming amount of epithelial cells. Laser capture microdissection (LCM) enables the precise separation of spermatozoa and epithelial cells. However, standard sperm-staining techniques are non-specific and rely on sperm morphology for identification. Moreover, manual screening of the microscope slides is time-consuming and labor-intensive. Here, we describe an automated screening method to detect spermatozoa stained with Sperm HY-LITER (TM). Different ratios of spermatozoa and epithelial cells were used to assess the automatic detection method. In addition, real postcoital samples were also screened. Detected spermatozoa were isolated using LCM and DNA analysis was performed. Robust DNA profiles without allelic dropout could be obtained from as little as 30 spermatozoa recovered from postcoital samples, showing that the staining had no significant influence on DNA recovery.

SummaryVariation in the level of mtDNA heteroplasmy in adult tissues is commonly seen in patients with a mixture of wild-type and mutant mtDNA. A mixture of different mtDNA variants may influence such variation and cause mtDNA segregation bias. We analyzed cellular heterogeneity in embryonic stem cells (ESCs) derived from a polymorphic mouse model containing NZB and BALB mtDNA genotypes. In ESCs, inter-colony heterogeneity varied up to 61%, whereas intra-colony heterogeneity varied up to 100%. Three out of five cell lines displayed nearly homoplasmic BALB and NZB mtDNA haplotypes in differentiated single cells. The proportion of NZB mtDNA genotype increased with progressive passaging (0.39%; p = 0.002). These results demonstrate the bimodal segregation of mtDNA haplotypes, indicating the occurrence of tissues with variable levels of heteroplasmies in individuals with mtDNA mutations. Furthermore, proliferation of one mtDNA genotype over another may pose the risk of accumulating mutant mtDNAs during subsequent cell divisions.

Forensic scientists are currently investigating how to transition from capillary electrophoresis (CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing. We present our bioinformatic framework My-Forensic-Loci-queries (MyFLq) for analysis of MPS forensic data. For allele calling, the framework uses a MySQL reference allele database with automatically determined regions of interest (ROIs) by a generic maximal flanking algorithm which makes it possible to use any STR or SNP forensic locus. Python scripts were designed to automatically make allele calls starting from raw MPS data. We also present a method to assess the usefulness and overall performance of a forensic locus with respect to MPS, as well as methods to estimate whether an unknown allele, which sequence is not present in the MySQL database, is in fact a new allele or a sequencing error. The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library, generated from multilocus STR polymerase chain reaction (PCR) on both single contributor samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results show excellent results for most loci. The results show a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Technically, forensic MPS affords great promise for routine implementation in forensic genomics. The method is also applicable to adjacent disciplines such as molecular autopsy in legal medicine and in mitochondrial DNA research.

Emerging evidence suggests that long non-coding RNAs (lncRNAs) are critically involved in a variety of human tumor entities and the identification of cancer-associated lncRNAs might reveal new prognostic biomarkers or novel therapeutic targets for the treatment of human cancer. In this study, we characterized the lncRNA expression signature associated with ETV6/RUNX1-positive pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL), one of the most prevalent genetic subtypes of childhood leukemia. First, we used primary leukemia patient samples to identify an ETV6/RUNX1 specific expression signature consisting of 596 lncRNA transcripts. Besides using primary BCP-ALL patient samples, we also integrated these lncRNA expression data with RNA sequencing results from a panel of human BCP-ALL leukemia cell lines and identified a unique lncRNA expression profile of 16 lncRNAs exclusively associated with the presence of the ETV6/RUNX1 fusion protein. Notably, lnc-SARDH-1 (also known as DBH-AS1) was the only lncRNA from this list for which an oncogenic role has previously been postulated. Given that previous studies revealed putative overlap between lncRNA expression and the presence of regulatory enhancer elements, we also evaluated the distribution of H3K27ac, a histone modification associated with enhancer activity, at the genomic loci of the 16 ETV6/RUNX1 specific lncRNAs mentioned above. Notably, broad H3K27ac binding was identified for lnc-NKX2-3-1, lnc-RTN4R-1, lnc-GIP-1, lnc-LRP8-3, lnc-TCF12-2, lnc- C8orf4-1, lnc-C8orf4-2, lnc-TINAGL1-1 and lnc-LSM11-4 in ETV6/RUNX1-positive REH cells, whereas more discrete H3K27ac peaks were identified at putative promoter regions for lnc-TIMM21-5 and lnc-CPT2-7. Interestingly, coding genes adjacent to some of these lncRNAs showed unique overexpression in ETV6/RUNX1-positive BCP-ALLs, suggesting a possible cis regulatory relationship between these lncRNAs and their nearby protein coding genes. Finally, we applied shRNA-mediated silencing of endogenous ETV6/RUNX1, integrated these expression profiles with the patient and cell line data, to show that lnc-NKX2-3-1, lnc-TIMM21-5, lnc-ASTN1-1 and lnc-RTN4R-1 were the only lncRNAs that were truly regulated by the oncogenic fusion protein. Interestingly, subsequent lncRNA modulation experiments using LNA GapmeR technology revealed that lnc-TIMM21-5 and lnc-ASTN1-1 modulation has no effect on overall transcription, suggesting that these lncRNAs might act at the translational level or/and at various steps of mRNA processing. In contrast, lnc-NKX2-3-1 and lnc-RTN4R-1 perturbations resulted in severe changes in gene expression, suggesting an alternative mechanism of action for these lncRNAs that is more transcriptionally oriented. Most notably, loss of lnc-RTN4R-1expression significantly affected part of the ETV6/RUNX1-specific mRNA expression signature as exemplified by reduced levels of AK7, PTPRKand GBA3. Altogether, our study identified a panel of ETV6/RUNX1 specific lncRNAs that might be implicated in the biology of human BCP-ALL and could serve as novel biomarkers or novel therapeutic targets for the treatment of this prevalent subtype of human leukemia. TLM and PVV are shared last authors Disclosures No relevant conflicts of interest to declare.

1- O -octadecyl-2- O -methylglycero-3-phosphocholine (E T-18-OMe) treated precultured heart fragments (PHF) are resistant toward s invasion by malignant cells. Previous studies demonstrated that this effect was due to alterations of N-linked glycoproteins in PHF after 48 h ET-18-OMe treatment. Moreov er, the observed effect was still present seven days after ET-18-OMe was omitted. T he present study reveals that approximately 13.4% of the administered ET-18-OMe was taken up by PHF and about 75% of the initial uptake remained present after ET-18- OMe was removed. In addition, we found significant changes in sialic acid content and sialyltransferase activities in both conditions. Together, these results clearly dem onstrate that uptake and retention of ET-18-OMe are responsible for resistance towards invasion of malignant cells due to altered sialylation of cell surface glycoproteins in PHF. hal-00132868, version 1 - 22 Feb 2007 Author manuscript, published in "Oncology reports. 17, 2 (2007) 433-439"