EMMA—mouse mutant resources for the international scientific community

The laboratory mouse is the premier animal model for studying human disease and thousands of mutants have been identified or produced, most recently through gene-specific mutagenesis approaches. High throughput strategies by the International Knockout Mouse Consortium (IKMC) are producing mutants for all protein coding genes. Generating a knock-out line involves huge monetary and time costs so capture of both the data describing each mutant alongside archiving of the line for distribution to future researchers is critical. The European Mouse Mutant Archive (EMMA) is a leading international network infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resources (FIMRe), EMMA being the European component. Additionally EMMA is one of four repositories involved in the IKMC, and therefore the current figure of 1700 archived lines will rise markedly. The EMMA database gathers and curates extensive data on each line and presents it through a user-friendly website. A BioMart interface allows advanced searching including integrated querying with other resources e.g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org

Computational Identification of Transcriptional Regulators in Human Endotoxemia

One of the great challenges in the post-genomic era is to decipher the underlying principles governing the dynamics of biological responses. As modulating gene expression levels is among the key regulatory responses of an organism to changes in its environment, identifying biologically relevant transcriptional regulators and their putative regulatory interactions with target genes is an essential step towards studying the complex dynamics of transcriptional regulation. We present an analysis that integrates various computational and biological aspects to explore the transcriptional regulation of systemic inflammatory responses through a human endotoxemia model. Given a high-dimensional transcriptional profiling dataset from human blood leukocytes, an elementary set of temporal dynamic responses which capture the essence of a pro-inflammatory phase, a counter-regulatory response and a dysregulation in leukocyte bioenergetics has been extracted. Upon identification of these expression patterns, fourteen inflammation-specific gene batteries that represent groups of hypothetically ‘coregulated’ genes are proposed. Subsequently, statistically significant cis-regulatory modules (CRMs) are identified and decomposed into a list of critical transcription factors (34) that are validated largely on primary literature. Finally, our analysis further allows for the construction of a dynamic representation of the temporal transcriptional regulatory program across the host, deciphering possible combinatorial interactions among factors under which they might be active. Although much remains to be explored, this study has computationally identified key transcription factors and proposed a putative time-dependent transcriptional regulatory program associated with critical transcriptional inflammatory responses. These results provide a solid foundation for future investigations to elucidate the underlying transcriptional regulatory mechanisms under the host inflammatory response. Also, the assumption that coexpressed genes that are functionally relevant are more likely to share some common transcriptional regulatory mechanism seems to be promising, making the proposed framework become essential in unravelling context-specific transcriptional regulatory interactions underlying diverse mammalian biological processes

Evading the anti-tumour immune response - a novel role for Focal Adhesion Kinase

Here I describe a new function of Focal Adhesion Kinase (FAK) in driving anti-tumour immune evasion. The kinase activity of FAK in squamous cancer cells drives the recruitment of regulatory T-cells (Tregs) by transcriptionally regulating chemokine/cytokine and ligand-receptor networks, including the transcription of CCL5 and TGFβ, which are required for enhanced Treg recruitment. In turn, these changes inhibit antigen-primed cytotoxic CD8+ T-cell activity in the tumour microenvironment, permitting survival and growth of FAK-expressing tumours. I show that immune evasion requires FAK’s catalytic activity, and a small molecule FAK kinase inhibitor, VS-4718, which is currently in clinical development, drives depletion of Tregs and permits CD8+ T-cell-mediated tumour clearance. It is therefore likely that FAK inhibitors may trigger immune-mediated tumour regression, providing previously unrecognized therapeutic benefit

En route from artificial to natural: Evaluation of inhibitors of mannose-specific adhesion of E. coli under flow

We investigated the properties of six Escherichia coli adhesion inhibitors under static and under flow conditions. On mannan-covered model substrates and under static conditions, all inhibitors were able to almost completely abolish lectin-mediated E. coli adhesion. On a monolayer of living human microvascular endothelial cells (HMEC-1), the inhibitors reduced adhesion under static conditions as well, but a large fraction of bacteria still managed to adhere even at highest inhibitor concentrations. In contrast, under flow conditions E. coli did not exhibit any adhesion to HMEC-1 not even at inhibitor concentrations where significant adhesion was detected under static conditions. This indicates that the presence of shear stress strongly affects inhibitor properties and must be taken into account when evaluating the potency of bacterial adhesion inhibitors. (C) 2016 Elsevier B.V. All rights reserved

Humoral and cellular immune parameters before and during immunosuppressive therapy of a patient with stiff-man syndrome and insulin dependent diabetes mellitus

OBJECTIVES—Humoral and cellular immune reactivity are reported for two neuroendocrine autoantigens—glutamic acid decarboxylase (GAD) and the protein tyrosine phosphatase IA-2—in a patient with the autoimmune type of stiff-man syndrome and insulin dependent diabetes (IDDM).
METHODS—Antibodies and T cell proliferation against GAD and IA-2 and cytokine release of antigen stimulated T cells (IFN-γ) were determined before and several times during immunosuppressive therapy with prednisolone.
RESULTS—Raised GAD antibodies against full length GAD65 or chimeric constructs were detected before therapy and they remained at a high concentration despite a marked clinical improvement during cortisone treatment. Antibodies to IA-2 were undetectable, but weak T cell responses to both GAD and IA-2 were seen before therapy and once on reduction of high cortisone dosages when the patient showed signs of clinical deterioration. Cytokine profiles showed increased IFN-γ production after stimulation with GAD or IA-2 suggesting increased activation of TH1 cells.
CONCLUSION—Immunosuppressive therapy —even with extremely high doses of 500 mg a day—does not lead to the reduction of antibody concentrations in the periphery nor to a switch in epitope recognition of such antibodies despite clinical improvement. The amount of T cell reactivity to various antigens, however, may be a useful marker to monitor the effectiveness of immunotherapy.


Substrate viscosity plays an important role in bacterial adhesion under fluid flow

Many materials used in the medical settings such as catheters and contact lenses as well as most biological tissues are not purely elastic, but rather viscoelastic. While substrate elasticity has been investigated for its influence on bacterial adhesion, the impact of substrate viscosity has not been explored. Here, the importance of considering substrate viscosity is explored by using polydimethylsiloxane (PDMS) as the substrate material, whose mechanical properties can be tuned from predominantly elastic to viscous by varying cross-linking degree. Interfacial rheology and atomic force microscopy analysis prove that PDMS with a low cross-linking degree exhibits both low stiffness and high viscosity. This degree of viscoelasticity confers to PDMS a remarkable stress relaxation, a good capability to deform and an increased adhesive force. Bacterial adhesion assays were conducted under flow conditions to study the impact of substrate viscosity on Escherichia coli adhesion. The viscous PDMS not only enhanced E. coli adhesion but also conferred greater resistance to desorption against shear stress at air/liquid interface, compared to the PDMS with high crosslinking degree. These findings highlight the importance to consider substrate viscosity while studying bacterial adhesion. The current work provides new insights to an improved understanding of how bacteria interact with complex viscoelastic environments.ISSN:0021-9797ISSN:1095-710

Substrate viscosity plays an important role in bacterial adhesion under fluid flow

Many materials used in the medical settings such as catheters and contact lenses as well as most biological tissues are not purely elastic, but rather viscoelastic. While substrate elasticity has been investigated for its influence on bacterial adhesion, the impact of substrate viscosity has not been explored. Here, the importance of considering substrate viscosity is explored by using polydimethylsiloxane (PDMS) as the substrate material, whose mechanical properties can be tuned from predominantly elastic to viscous by varying cross-linking degree. Interfacial rheology and atomic force microscopy analysis prove that PDMS with a low cross-linking degree exhibits both low stiffness and high viscosity. This degree of viscoelasticity confers to PDMS a remarkable stress relaxation, a good capability to deform and an increased adhesive force. Bacterial adhesion assays were conducted under flow conditions to study the impact of substrate viscosity on Escherichia coli adhesion. The viscous PDMS not only enhanced E. coli adhesion but also conferred greater resistance to desorption against shear stress at air/liquid interface, compared to the PDMS with high crosslinking degree. These findings highlight the importance to consider substrate viscosity while studying bacterial adhesion. The current work provides new insights to an improved understanding of how bacteria interact with complex viscoelastic environments. (C) 2019 The Authors. Published by Elsevier Inc