Increased lymphocyte apoptosis in mouse models of colitis upon ABT-737 treatment is dependent upon BIM expression

Exaggerated activation of lymphocytes contributes to the pathogenesis of inflammatory bowel disease (IBD). Medical therapies are linked to the BCL-2 family-mediated apoptosis. Imbalance in BCL-2 family proteins may cause failure in therapeutic responses. We investigated the role of BCL-2 inhibitor ABT-737 for lymphocyte apoptosis in mice under inflammatory conditions. B.6129P2-interleukin (IL)-10(tm1Cgn) /J (IL-10(-/-) ) weighing 25-30 g with ongoing colitis were used. Fifty mg/kg/day ABT-737 was injected intraperitoneally (i.p.). Haematological analyses were performed with an ADVIA 2120 flow cytometer and mass cytometry with a CyTOF 2. Following i.p. administration, ABT-737 was detected in both spontaneous and acute colitis in peripheral blood (PBL) and colon tissue. Treatment led to lymphopenia. CD4(+) CD44(+) CD62L(+) central memory and CD8(+) , CD44(+) CD62L(-) central memory T cells were decreased in PBL upon ABT-737 compared to vehicle-receiving controls. Increased apoptosis upon ABT-737 was determined in blood lymphocytes, splenocytes and Peyer's patches and was accompanied by a decrease in TNF and IL-1B. ABT-737 positively altered the colonic mucosa and ameliorated inflammation, as shown by colonoscopy, histology and colon length. A decreased BIM/BCL-2 ratio or absence of BIM in both Bim(-) (/) (-) and Il10(-) (/) (-) × Bim(-) (/) (-) impeded the protective effect of ABT-737. The BIM/BCL-2 ratio decreased with age and during the course of treatment. Thus, long-term treatment resulted in adapted TNF levels and macroscopic mucosal damage. ABT-737 was efficacious in diminishing lymphocytes and ameliorating colitis in a BIM-dependent manner. Regulation of inappropriate survival of lymphocytes by ABT-737 may provide a therapeutic strategy in IBD.

Constitutive IDO expression in human cancer is sustained by an autocrine signaling loop involving IL-6, STAT3 and the AHR

Indoleamine-2,3-dioxygenase (IDO) inhibitors have entered clinical trials based on their ability to restore anti-tumor immunity in preclinical studies. However, the mechanisms leading to constitutive expression of IDO in human tumors are largely unknown. Here we analyzed the pathways mediating constitutive IDO expression in human cancer. IDO-positive tumor cells and tissues showed basal phosphorylation and acetylation of STAT3 as evidenced by western blotting and immunoprecipitation. Inhibition of IL-6 or STAT3 using siRNA and/or pharmacological inhibitors reduced IDO mRNA and protein expression as well as kynurenine formation. In turn, IDO enzymatic activity activated the AHR as shown by the induction of AHR target genes. IDO-mediated AHR activation induced IL-6 expression, while inhibition or knockdown of the AHR reduced IL-6 expression. IDO activity thus sustains its own expression via an autocrine AHR–IL-6–STAT3 signaling loop. Inhibition of the AHR–IL-6–STAT3 signaling loop restored T-cell proliferation in mixed leukocyte reactions performed in the presence of IDO-expressing human cancer cells. Identification of the IDO-AHR-IL-6-STAT3 signaling loop maintaining IDO expression in human cancers reveals novel therapeutic targets for the inhibition of this core pathway promoting immunosuppression of human cancers. The relevance of the IDO-AHR-IL-6-STAT3 transcriptional circuit is underscored by the finding that high expression of its members IDO, STAT3 and the AHR target gene CYP1B1 is associated with reduced relapse-free survival in lung cancer patients.

An exploration of sexual desire and sexual activities of women with psychosis

Sexual disturbances in patients with severe mental disorders can be related to medication, to psychological issues such as self-stigma and anhedonia, but also to the social context. This research aims to gain knowledge of desire and sexual practices in women suffering from schizophrenia. Women outpatients suffering from schizophrenia were compared with healthy women. Contrary to previous research, women with schizophrenia featured dyadic and individual desire similar to women of comparable age. Yet, only half of women with psychosis had sexual practice, either alone or with a partner. They were less satisfied with their activity, both in terms of function and psychological issues such as sexual self-esteem. Keeping into account the fact that most clinicians avoid this topic, this finding underscores the stigmatization these women suffer from, which prevents the opportunity of a possible improvement in this important interpersonal domain.

A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity

Background

Many studies of the eukaryotic transcription mechanism and its regulation rely on in vitro assays. Conventional RNA polymerase II transcription assays are based on radioactive labelling of the newly synthesized RNA. Due to the inefficient in vitro transcription, the detection of the RNA involving purification and gel electrophoresis is laborious and not always quantitative.

Results

Herein, we describe a new, non-radioactive, robust and reproducible eukaryotic in vitro transcription assay that has been established in our laboratory. Upon transcription, the newly synthesized RNA is directly detected and quantified using the QuantiGene assay. Alternatively, the RNA can be purified and a primer extension followed by PCR detection or qPCR quantification can be performed. When applied to assess the activity of RNA polymerase II inhibitors, this new method allowed an accurate estimation of their relative potency.

Conclusions

Our novel assay provides a non-radioactive alternative to a standard in vitro transcription assay that allows for sensitive detection and precise quantification of the newly transcribed, unlabelled RNA and is particularly useful for quantification of strong transcriptional inhibitors like α-amanitin. Moreover, the method can be easily adapted to quantify the reaction yield and the transcription efficiency of other eukaryotic in vitro systems, thus providing a complementary tool for the field of transcriptional research.

Signal extraction from movies of honeybee brain activity: the ImageBee plugin for KNIME

Background

In the antennal lobe, a dedicated olfactory center of the honeybee brain, odours are encoded as activity patterns of coding units, the so-called glomeruli. Optical imaging with calcium-sensitive dyes allows us to record these activity patterns and to gain insight into olfactory information processing in the brain.

Method

We introduce ImageBee, a plugin for the data analysis platform KNIME. ImageBee provides a variety of tools for processing optical imaging data. The main algorithm behind ImageBee is a matrix factorisation approach. Motivated by a data-specific, non-negative mixture model, the algorithm aims to select the generating extreme vectors of a convex cone that contains the data. It approximates the movie matrix by non-negative combinations of the extreme vectors. These correspond to pure glomerular signals that are not mixed with neighbour signals.

Results

Evaluation shows that the proposed algorithm can identify the relevant biological signals on imaging data from the honeybee AL, as well as it can recover implanted source signals from artificial data.

Conclusions

ImageBee enables automated data processing and visualisation for optical imaging data from the insect AL. The modular implementation for KNIME offers a flexible platform for data analysis projects, where modules can be rearranged or added depending on the particular application.

Availability

ImageBee can be installed via the KNIME update service. Installation instructions are available at http://tech.knime.org/imagebee-analysing-imaging-data-from-the-honeybee-brain.

Amino acid transporters expression in acinar cells is changed during acute pancreatitis

Pancreatic acinar cells accumulate amino acids against a marked concentration gradient to synthesize digestive enzymes. Thus, the function of acinar cells depends on amino acid uptake mediated by active transport. Despite the importance of this process, pancreatic amino acid transporter expression and cellular localization is still unclear. We screened mouse pancreas for the expression of genes encoding amino acid transporters. We showed that the most highly expressed transporters, namely sodium dependent SNAT3 (Slc38a3) and SNAT5 (Slc38a5) and sodium independent neutral amino acids transporters LAT1 (Slc7a5) and LAT2 (Slc7a8), are expressed in the basolateral membrane of acinar cells. SNAT3 and SNAT5, LAT1 and LAT2 are expressed in acinar cells. Additional evidence that these transporters are expressed in mature acinar cells was gained using acinar cell culture and acute pancreatitis models. In the acute phase of pancreatic injury, when acinar cell loss occurs, and in an acinar cell culture model, which mimics changes occurring during pancreatitis, SNAT3 and SNAT5 are strongly down-regulated. LAT1 and LAT2 were down-regulated only in the in vitro model. At protein level, SNAT3 and SNAT5 expression was also reduced during pancreatitis. Expression of other amino acid transporters was also modified in both models of pancreatitis. The subset of transporters with differential expression patterns during acute pancreatitis might be involved in the injury/regeneration phases. Further expression, localization and functional studies will follow to better understand changes occurring during acute pancreatitis. These findings provide insight into pancreatic amino acid transport in healthy pancreas and during acute pancreatitis injury.

An endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor

Activation of the aryl hydrocarbon receptor (AHR) by environmental xenobiotic toxic chemicals, for instance 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin), has been implicated in a variety of cellular processes such as embryogenesis, transformation, tumorigenesis and inflammation. But the identity of an endogenous ligand activating the AHR under physiological conditions in the absence of environmental toxic chemicals is still unknown. Here we identify the tryptophan (Trp) catabolite kynurenine (Kyn) as an endogenous ligand of the human AHR that is constitutively generated by human tumour cells via tryptophan-2,3-dioxygenase (TDO), a liver- and neuron-derived Trp-degrading enzyme not yet implicated in cancer biology. TDO-derived Kyn suppresses antitumour immune responses and promotes tumour-cell survival and motility through the AHR in an autocrine/paracrine fashion. The TDO-AHR pathway is active in human brain tumours and is associated with malignant progression and poor survival. Because Kyn is produced during cancer progression and inflammation in the local microenvironment in amounts sufficient for activating the human AHR, these results provide evidence for a previously unidentified pathophysiological function of the AHR with profound implications for cancer and immune biology.

Mouse mesenchymal stem cells suppress antigen-specific TH cell immunity independent of indoleamine 2,3-dioxygenase 1 (IDO1)

Due to their immunosuppressive properties, human mesenchymal stem cells (hMSC) represent a promising tool for cell-based therapies of autoimmune diseases such as multiple sclerosis (MS). Mouse MSC (mMSC) have been used extensively to characterize and optimize route of administration, motility, cellular targets, and immunosuppressive mechanisms in mouse models of autoimmune diseases, such as experimental autoimmune encephalomyelitis (EAE). Tryptophan (trp) catabolism by indolamine-2,3-dioxygenase 1 (IDO1) is a chief endogenous metabolic pathway that tightly regulates unwanted immune responses through depletion of trp and generation of immunosuppressive kynurenines (kyn). IDO1 activity contributes to the immunosuppressive phenotype of hMSC. Here, we demonstrate that although IDO1 is inducible in bone marrow-derived mMSC by proinflammatory stimuli such as interferon-g (IFN-g) and ligands of toll-like receptors (TLR), it does not lead to catabolism of trp in vitro. This failure to catabolize trp is not due to defective TLR signaling as demonstrated by induction of interleukin 6 (IL-6) by TLR activation. While mMSC suppressed the activation of antigen-specific myelin oligodendrocyte glycoprotein (MOG)-reactive T-cell receptor (TCR) transgenic T-helper (TH) cells in co-culture, neither pharmacologic inhibition nor genetic ablation of IDO1 reversed this suppressive effect. Finally, systemic administration of both, IDO1-proficient and phenotypically identical IDO1-deficient mMSC, equally resulted in amelioration of EAE. mMSC, unlike hMSC, do not display IDO1-mediated suppression of antigen-specific T-cell responses.

Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets

Statistical shape analysis techniques have shown to be efficient tools to build population specific models of anatomical variability. Their use is commonplace as prior models for segmentation, in which case the instance from the shape model that best fits the image data is sought. In certain cases, however, it is not just the most likely instance that must be searched, but rather the whole set of shape instances that meet certain criterion. In this paper we develop a method for the assessment of specific anatomical/morphological criteria across the shape variability found in a population. The method is based on a level set segmentation approach, and used on the parametric space of the statistical shape model of the target population, solved via a multi-level narrow-band approach for computational efficiency. Based on this technique, we develop a framework for evidence-based orthopaedic implant design. To date, implants are commonly designed and validated by evaluating implant bone fitting on a limited set of cadaver bones, which not necessarily span the whole variability in the population. Based on our framework, we can virtually fit a proposed implant design to samples drawn from the statistical model, and assess which range of the population is suitable for the implant. The method highlights which patterns of bone variability are more important for implant fitting, allowing and easing implant design improvements, as to fit a maximum of the target population. Results are presented for the optimisation of implant design of proximal human tibia, used for internal fracture fixation.

The Complexity of Circumscription in DLs

As fragments of first-order logic, Description logics (DLs) do not provide nonmonotonic features such as defeasible inheritance and default rules. Since many applications would benefit from the availability of such features, several families of nonmonotonic DLs have been developed that are mostly based on default logic and autoepistemic logic. In this paper, we consider circumscription as an interesting alternative approach to nonmonotonic DLs that, in particular, supports defeasible inheritance in a natural way. We study DLs extended with circumscription under different language restrictions and under different constraints on the sets of minimized, fixed, and varying predicates, and pinpoint the exact computational complexity of reasoning for DLs ranging from ALC to ALCIO and ALCQO. When the minimized and fixed predicates include only concept names but no role names, then reasoning is complete for NExpTime^NP. It becomes complete for NP^NExpTime when the number of minimized and fixed predicates is bounded by a constant. If roles can be minimized or fixed, then complexity ranges from NExpTime^NP to undecidability.

Conjunctive Query Answering for the Description Logic SHIQ

Conjunctive queries play an important role as an expressive query language for Description Logics (DLs). Although modern DLs usually provide for transitive roles, conjunctive query answering over DL knowledge bases is only poorly understood if transitive roles are admitted in the query. In this paper, we consider unions of conjunctive queries over knowledge bases formulated in the prominent DL SHIQ and allow transitive roles in both the query and the knowledge base. We show decidability of query answering in this setting and establish two tight complexity bounds: regarding combined complexity, we prove that there is a deterministic algorithm for query answering that needs time single exponential in the size of the KB and double exponential in the size of the query, which is optimal. Regarding data complexity, we prove containment in co-NP.

Successful salvage treatment of disseminated cutaneous fusariosis with liposomal amphotericin B and terbinafine after allogeneic stem cell transplantation

Fusarium infections are associated with high mortality after allogeneic stem cell transplantation. We report on successful treatment of a disseminated cutaneous Fusarium proliferatum infection using liposomal amphotericin B and terbinafine. In vitro susceptibility tests of antifungal drugs suggest that terbinafine is a potent additional antifungal drug for disseminated cutaneous fusariosis.

Einstein relation generalized to nonequilibrium

The Einstein relation connecting the diffusion constant and the mobility is violated beyond the linear response regime. For a colloidal particle driven along a periodic potential imposed by laser traps, we test the recent theoretical generalization of the Einstein relation to the nonequilibrium regime which involves an integral over measurable velocity correlation functions.