MUGEN mouse database; Animal models of human immunological diseases

The MUGEN mouse database (MMdb) (www.mugen-noe.org/database/) is a database of murine models of immune processes and immunological diseases. Its aim is to share and publicize information on mouse strain characteristics and availability from participating institutions. MMdb's basic classification of models is based on three major research application categories: Models of Human Disease, Models of Immune Processes and Transgenic Tools. Data on mutant strains includes detailed information on affected gene(s), mutant allele(s) and genetic background (DNA origin, gene targeted, host and backcross strain background). Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress and NCBI's Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI's mammalian phenotypic ontology terms. Availability (e.g. live mice, cryopreserved embryos, sperm and ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and Jax/IMSR hyperlinks where available). MMdb's design offers a user-friendly query interface and provides instant access to the list of mutant strains and genes. Database access is free of charge and there are no registration requirements for data querying

Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Strain relaxation and multidentate anchoring in n-type perovskite transistors and logic circuits

This is the author accepted manuscriptData availability: Source data are provided with this paper. Additional data related to this work are available from the corresponding authors upon request.Code availability statement: All codes (software) used in the calculation and visualization are publicly available and the condition of their usage in the publication is an appropriate citation.The engineering of tin halide perovskites has led to the development of p-type transistors with field-effect mobilities of over 70 cm2 V-1 s-1 . However, due to their background hole doping, these perovskites are not suitable for n-type transistors. Ambipolar lead halide perovskites are potential candidates, but their defective nature limits electron mobilities to around 3-4 cm2 V-1 s-1, which makes the development all-perovskite logical circuits challenging. Here, we report formamidinium lead iodide perovskite n-type transistors with field-effect mobilities of up to 33 cm2 V-1s-1 measured in continuous bias mode. This is achieved through strain relaxation of the perovskite lattice using a methyl ammonium chloride additive, followed by suppression of undercoordinated lead through tetramethyl ammonium fluoride multidentate anchoring. Our approach stabilizes the alpha phase, balances strain, and improves surface morphology, crystallinity, and orientation. It also enables low-defect perovskite–dielectric interfaces. We use 46 the transistors to fabricate unipolar inverters and eleven-stage ring oscillator

Soluble TNF Mediates the Transition from Pulmonary Inflammation to Fibrosis

BACKGROUND: Fibrosis, the replacement of functional tissue with excessive fibrous tissue, can occur in all the main tissues and organ systems, resulting in various pathological disorders. Idiopathic Pulmonary Fibrosis is a prototype fibrotic disease involving abnormal wound healing in response to multiple sites of ongoing alveolar epithelial injury. METHODOLOGY/PRINCIPAL FINDINGS: To decipher the role of TNF and TNF-mediated inflammation in the development of fibrosis, we have utilized the bleomycin-induced animal model of Pulmonary Fibrosis and a series of genetically modified mice lacking components of TNF signaling. Transmembrane TNF expression is shown to be sufficient to elicit an inflammatory response, but inadequate for the transition to the fibrotic phase of the disease. Soluble TNF expression is shown to be crucial for lymphocyte recruitment, a prerequisite for TGF-b1 expression and the development of fibrotic lesions. Moreover, through a series of bone marrow transfers, the necessary TNF expression is shown to originate from the non-hematopoietic compartment further localized in apoptosing epithelial cells. CONCLUSIONS: These results suggest a primary detrimental role of soluble TNF in the pathologic cascade, separating it from the beneficial role of transmembrane TNF, and indicate the importance of assessing the efficacy of soluble TNF antagonists in the treatment of Idiopathic Pulmonary Fibrosis

Genomics and proteomics approaches to the study of cancer-stroma interactions

<p>Abstract</p> <p>Background</p> <p>The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression.</p> <p>Methods</p> <p>The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells.</p> <p>Results</p> <p>We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (<it>ARID4A</it>, <it>CALR</it>, <it>GNB2L1</it>, <it>RNF10</it>, <it>SQSTM1</it>, <it>USP9X</it>) were validated by real time PCR.</p> <p>Conclusions</p> <p>A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.</p

Temperature Dependence of the EPR Spectra of the Nanocrystalline TiN and TiC Dispersed in a Carbon Matrix

Two powder samples: nanocrystalline titanium carbide (TiC) and titanium nitride (TiN) dispersed in a carbon matrix were synthesized by a nonhydrolytic sol-gel process. Both samples were characterized by the X-ray diffraction and transmission electron microscopy. The transmission electron microscopy examination of the TiC and TiN nanoparticles showed that their average crystalline size was about 20 nm. The temperature dependence of the EPR spectra for both samples was measured in 10 K to 200 K temperature range. A similar very narrow (about 0.2 mT) EPR line centered at g≈2 (at room temperature) was recorded in both samples. The EPR line observed in both samples is arising from electron conductivity centers dispersed in the carbon matrix and it was fitted by Dysonian line shape. The temperature dependence of the EPR spectrum showed different behavior of these two samples. It is suggested that in the sample TiC/C multiwall carbon nanotubes are formed while in the sample TiN/C the graphite structure dominates

On the Outage Capacity of Transdermal Optical Wireless Links with Stochastic Spatial Jitter and Skin-Induced Attenuation

The tremendous development of both optical wireless communications (OWC) and implantable medical devices (IMDs) has recently enabled the establishment of transdermal optical wireless (TOW) links that utilize light waves to transfer information inside the living body to the outside world and conversely. Indeed, numerous emerging medical applications such as cortical recording and telemetry with cochlear implants require extremely high data rates along with low power consumption that only this new technology could accommodate. Thus, in this paper, a typical TOW link is investigated in terms of outage capacity which is a critical performance metric that has so far not been evaluated for such wireless systems in the open technical literature. More precisely, an outage capacity analysis is performed considering both skin-induced attenuation and stochastic spatial jitter, i.e., pointing error effects. Analytical expressions and results for the outage capacity are derived for a variety of skin channel conditions along with varying stochastic pointing errors which demonstrate the feasibility of this cross-field cooperation. Lastly, the corresponding simulation outcomes further validate our suggestions

Temperature dependence of the EPR spectra of the nanocrystalline TiN and TiC dispersed in a carbon matrix

Two powder samples: nanocrystalline titanium carbide (TiC) and titanium nitride (TiN) dispersed in a carbon matrix were synthesized by a nonhydrolytic sol-gel process. Both samples were characterized by the X-ray diffraction and transmission electron microscopy. The transmission electron microscopy examination of the TiC and TiN nanoparticles showed that their average crystalline size was about 20 urn. The temperature dependence of the EPR spectra for both samples was measured in 10 K to 200 K temperature range. A similar very narrow (about 0.2 mT) EPR line centered at g approximate to 2 (at room temperature) was recorded in both samples. The EPR line observed in both samples is arising from electron conductivity centers dispersed in the carbon matrix and it was fitted by Dysonian line shape. The temperature dependence of the EPR spectrum showed different behavior of these two samples. It is suggested that in the sample TiC/C multiwall carbon nanotubes are formed while in the sample TiN/C the graphite structure dominates

Microstructure formation phenomena in phase inversion membranes

Most structural studies of polymeric phase inversion membranes have focused on macrovoid formation, while the rich microstructure (size scale &lt; 5 μm) has received little independent attention. We present a classification and qualitative description of possible microstructures on the basis of phase diagram, kinetic, and connectivity considerations. Special attention is given to the microstructural features resulting from a two-stage phase separation. Subsequently, our considerations are extended to the microstructure of the skin and that of the macrofinger boundaries. Finally, the features of actual phase inversion microstructures are described and interpreted