7196 research outputs found
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Inferring copy number variation from gene expression data: methods, comparisons, and applications to oncology
No full textCopy number variations (CNVs) are genomic events where the number of copies of a particular gene varies from cell to cell. Cancer cells are associated with somatic CNV changes resulting in gene amplifications and gene deletions. However, short of single-cell whole-genome sequencing, it is difficult to detect and quantify CNV events in single cells. In contrast, the rapid development of single-cell RNA sequencing (scRNA-seq) technologies has enabled easy acquisition of single-cell gene expression data. In this work, we employ three methods to infer CNV events from scRNA-seq data and provide a statistical comparison of the methods’ results. In addition, we combine the analysis of scRNA-seq and inferred CNV data to visualize and determine subpopulations and heterogeneity in tumor cell populations
Identification of bile salt export pump inhibitors using machine learning: Predictive safety from an industry perspective
No full textBile salt export pump (BSEP) is a transporter that moves bile salts from hepatocytes into bile canaliculi. BSEP inhibition can result in the toxic accumulation of bile salts in the liver, which has been identified as a risk factor of drug-induced liver injury (DILI). Since DILI is a frequent cause of drug withdrawals from the market or failings in drug development, in vitro BSEP activity is measured with the [3H]taurocholate uptake assay and a half-maximal inhibitory concentration (IC50) higher than 30µM is advised. Herein, a machine learning classification model was developed to accurately detect BSEP inhibitors and help in the prioritization of in vitro testing. The model is currently used for the detection of BSEP liabilities, and prioritization of compounds and chemical series. Moreover, regression models for short-term and long-term predictions were also built and evaluated. This work illustrates how predictive safety can help in the early detection of potential toxicity and support decision making by leveraging Novartis historical experimental data
Basophils promote barrier dysfunction and resolution in the atopic skin
No full textBackground: The type 2 cytokines IL-4 and IL-13 promote not
only atopic dermatitis (AD) but also the resolution of
inflammation. How type 2 cytokines participate in the resolution
of AD is poorly known.
Objective: Our aim was to determine the mechanisms and cell
types governing skin inflammation, barrier dysfunction, and
resolution of inflammation in a model of AD.
Methods: Mice that exhibit expression of IL-4, IL-13, and
MCPT8 or that could be depleted of basophils or eosinophils, be
deficient in IL-4 or MHC class II molecules, or have basophils
lacking macrophage colony-stimulating factor (M-CSF) were
treated with calcipotriol (MC903) as an acute model of AD.
Kinetics of the disease; keratinocyte differentiation; and
leukocyte accumulation, phenotype, function, and cytokine
production were measured by transepidermal water loss,
histopathology, molecular biology, or unbiased analysis of
spectral flow cytometry.
Results: In this model of AD, basophils were activated
systemically and were the initial and main source of IL-4 in the
skin. Basophils and IL-4 promoted epidermal hyperplasia and
skin barrier dysfunction by acting on keratinocyte differentiation
during inflammation. Basophils, IL-4, and basophil-derived
M-CSF inhibited the accumulation of proinflammatory cells in
the skin while promoting the expansion and function of
proresolution M2-like macrophages and the expression of probarrier genes. Basophils kept their proresolution properties
during AD resolution.
Conclusion: Basophils can display both beneficial and
detrimental type 2 functions simultaneously during atopic
inflammation
Refractive Index: The Ultimate Tool for Real-Time Monitoring of Solid-Phase Peptide Synthesis. Greening the Process
No full textPeptides are the basis of many drugs currently in the market and much more entering clinical trials, as well as in preclinical studies. The most part of peptides in both research and industrial modes are synthesized using Solid-Phase Peptide Synthesis (SPPS) processes. A characteristic of this strategy is that the synthetic intermediates are not isolated and not characterized. In this context, the development of a real-time monitoring method would assure an optimal synthetic process. Refractive index (RI) of a liquid has important information about its physical properties and makes it possible to know the composition of any solution. Herein, RI is demonstrated for the first time as a Process Analytical Tool (PAT) that can be used for real-time monitoring of SPPS. The three basic steps involved in this process can be followed up on line: coupling, deprotection and washes. This has consequences for the determination of the end-point of the reactions and the optimization of all synthetic steps. This will impact directly into the consumption of reagents, solvents, and time, making SPPS greener
Optical cryomicroscopy and differential scanning calorimetry of buffer solutions containing cryoprotectants
No full textIn the pharmaceutical industry, cryoprotectants are added to buffer formulations to protect the active pharmaceutical ingredient from freeze- and thaw damage. We investigated the freezing and thawing of aqueous sodium citrate buffer with various cryoprotectants, specifically amino acids (cysteine, histidine, arginine, proline and lysine), disaccharides (trehalose and sucrose), polyhydric alcohols (glycerol and mannitol) and surfactants (polysorbate 20 and polysorbate 80). Hereby, we employed optical cryomicroscopy in combination with differential scanning calorimetry in the temperature range to −80 °C. The effect of cryoprotectants on the morphology of the ice crystals, the glass transition temperature and the initial melting temperature is presented. Some of the cryoprotectants have a significant impact on ice crystal size. Disaccharides restrict ice crystal growth, whereas surfactants and glycerol allow ice crystals to increase in size. Cysteine and mannitol cause dehydration after thawing. Either one or two glass transition temperatures were detected, where arginine, surfactants, glycerol, proline and lysine suppress the second, implying a uniform freeze-concentrated solution. The initial melting temperature of pure buffer solution can be shifted up by adding mannitol, both disaccharides and both surfactants; but down by glycerol, proline and lysine
La chimie verte comme catalyseur de l'innovation !
No full textIl ne se passe pas un jour sans que l'on entende des nouvelles alarmantes sur le changement climatique ou sur le rythme insoutenable auquel le monde se développe. Il est de notre responsabilité, à nous scientifiques en particulier, et collectivement au sein de nos organisations respectives, de changer la culture, d'offrir des options perturbatrices pour inverser radicalement les pratiques non durables, et d'encourager des changements ambitieux. Vers la fin de l'année 2010, nous avons, à Novartis, commencé à nous attaquer activement aux problèmes environnementaux. L'utilisation inappropriée de substances toxiques, et plus particulièrement des solvants aprotiques polaires très couramment utilisés et reportés comme reprotoxiques, est alors devenue une priorité. La législation REACH et son volet "substances extrêmement préoccupantes" nous ont particulièrement incités à agir de manière stratégique.[1] Une douzaine de projets de différents niveaux d'ambition ont été lancés. Nous avons étudié le potentiel des milieux supercritiques[2], évalué divers solvants amphotères de manière impartiale (collaboration Fribourg), encouragé le développement d'alternatives plus désirables[3] et plus généralement comme nous le montrerons dans l’article qui suit sur le développement d'une boîte à outils de chimie dans l'eau. Pour cette dernière approche, nous avons évidemment renforcé notre arsenal d'outils biocatalytiques, et complété cet aspect par une nouvelle boîte à outils de chimie à base de tensioactifs
Membrane-tethered mucins and lubricin mediate the interfacial properties of model ocular epithelial surfaces
No full textThe human ocular surface is enriched with endogenously expressed mucins, which are known to contribute to its lubricious character. Reduced biosynthesis or loss of functional mucins has been reported in some dry eye disease (DED) patients, contributing to mechanical alterations during blink cycles that can result in tissue damage and vision-threatening sequelae. While identifying strategies to reduce adhesion and shear stresses at the ocular surface is a promising approach to improve the signs and symptoms of DED, current pre-clinical models generally rely on scarce, heterogeneous tissue samples or model synthetic substrates that do not capture the complex biochemical and biophysical cues present at the ocular surface. Here we developed a mucin-deficient dry eye mimetic cell model and utilized contact angle hysteresis and step-strain rheological tests to investigate the contributions of mucins and mucin-like glycoproteins to the interfacial, rheological, and adhesive properties of ocular epithelial surfaces. This model system was designed with the purpose of providing mechanistic insight into the consequences of ocular surface mucin dysfunction that may inform treatment strategies. The contact angle hysteresis measurements showed that the hydration of the model ocular epithelial surfaces is maintained even in absence of endogenous membrane-tethered mucins. However, stress relaxation behaviors at the interface of model ocular surfaces demonstrated that membrane-tethered mucins are essential for biolubrication at the model interface. Supplementation with recombinant human lubricin, a mucin-like glycoprotein currently undergoing clinical trials for DED treatment, restored the lubrication function induced by the lack of cell surface mucins in a dose-dependent manner. This suggests that lubrication-related dysfunction due to mucin deficiency may be reversible and that recombinant human lubricin might be a promising treatment for DED patients. Together, these results demonstrate that mucin-deficient, biomimetic ocular surfaces serve as a promising platform for drug screening assays and fundamental studies of ocular surface biology
Biosynthetic production and evaluation of knotted peptide topology and characteristics.
No full textKnotted peptides present a wealth of structurally diverse, biologically-active molecules, with the inhibi-tor cystine knot or knottin folds among the most prevalent. Many of these natural products interact with extracellular targets such as voltage-gated ion channels with exquisite selectivity and potency, making them intriguing therapeutic modalities. However, such compounds are often produced by exotic organisms in low concentrations, making structure determination and biological characterization challenging. Heterologous expression in bacterial hosts could potential-ly solve these issues by making scalable production of these compounds accessible - though this methodology would rely on correct in vivo disulfide formation and folding in the absence of native oxidative folding pathways that are pre-sent in the original organisms. We screened expression constructs for a heterologously biosynthesized knotted peptide to determine the most influential parameters for successful disulfide folding using NMR spectroscopic fingerprinting to validate the topological structure of folded products. To better understand this emerging modality of peptides, we performed pharmacokinetic characterization which indicate the interlocking disulfide structure minimizes liabilities of linear peptide sequences and has a profound influence on these molecules’ behavior in vivo. We then developed an assay to study the solution folding of toxin residues in real time, providing a method for studying the complex folding process these molecules undergo during maturation
Dangerous Air: How air pollution affects astrocyte functions
No full textOutdoor air pollution is the largest environmental risk factor that has been associated with cardiovascular, lung, and lately also neurodegenerative diseases. A few studies have been conducted to demonstrate that air pollutant exposure may lead to neuroinflammation, oxidative stress and the appearance of protein aggregates in the brain. It was shown that air pollution can cause not only peripheral effects, but airborne particles can also enter the brain directly through olfactory nerve road or enter the blood circulation. Therefore, there is an unmet need for understanding how different brain cell types are involved in this pathological process. In this study, we aim to decipher how size-segregated urban particulate matter (PM) that was collected from urban air in Nanjing, China affects astrocytes and their functions and to investigate genes that could be targeted to mitigate the adverse effect of PM exposure. Our results demonstrate that both ultrafine (particles with an aerodynamic diameter of 0.1 μm or less) and coarse (size 2.5-10 μm) particles trigger activation of antioxidative stress signalling genes in vitro in astrocytes harvested from the adult mouse brain, indicating activation of the cellular protection system in response to PM. Such robust effects were not observed in primary cortical neurons exposed to the same conditions, indicating the predominant role of glial cell responses to adverse effects of air pollution in the brain. We also detected reduced ApoE expression in both adult and neonatal PM-treated astrocytes in response to PM exposure. These results provide insight into astrocyte responses to air pollutant exposure