Metabolic characterization of directly reprogrammed renal tubular epithelial cells (iRECs)

Fibroblasts can be directly reprogrammed to induced renal tubular epithelial cells (iRECs) using four transcription factors. These engineered cells may be used for disease modeling, cell replacement therapy or drug and toxicity testing. Direct reprogramming induces drastic changes in the transcriptional landscape, protein expression, morphological and functional properties of cells. However, how the metabolome is changed by reprogramming and to what degree it resembles the target cell type remains unknown. Using untargeted gas chromatography-mass spectrometry (GC-MS) and targeted liquid chromatography-MS, we characterized the metabolome of mouse embryonic fibroblasts (MEFs), iRECs, mIMCD-3 cells, and whole kidneys. Metabolic fingerprinting can distinguish each cell type reliably, revealing iRECs are most similar to mIMCD-3 cells and clearly separate from MEFs used for reprogramming. Treatment with the cytotoxic drug cisplatin induced typical changes in the metabolic profile of iRECs commonly occurring in acute renal injury. Interestingly, metabolites in the medium of iRECs, but not of mIMCD-3 cells or fibroblast could distinguish treated and non-treated cells by cluster analysis. In conclusion, direct reprogramming of fibroblasts into renal tubular epithelial cells strongly influences the metabolome of engineered cells, suggesting that metabolic profiling may aid in establishing iRECs as in vitro models for nephrotoxicity testing in the future

A calibration method for broad-bandwidth cavity enhanced absorption spectroscopy performed with supercontinuum radiation

An efficient calibration method has been developed for broad-bandwidth cavity enhanced absorption spectroscopy. The calibration is performed using phase shift cavity ring-down spectroscopy, which is conveniently implemented through use of an acousto-optic tunable filter (AOTF). The AOTF permits a narrowband portion of the SC spectrum to be scanned over the full high-reflectivity bandwidth of the cavity mirrors. After calibration the AOTF is switched off and broad-bandwidth CEAS can be performed with the same light source without any loss of alignment to the set-up. We demonstrate the merits of the method by probing transitions of oxygen molecules O-2 and collisional pairs of oxygen molecules (O-2)(2) in the visible spectral range

Fluid dynamics of R-charged black holes

We construct electrically charged AdS_5 black hole solutions whose charge, mass and boost-parameters vary slowly with the space-time coordinates. From the perspective of the dual theory, these are equivalent to hydrodynamic configurations with varying chemical potential, temperature and velocity fields. We compute the boundary theory transport coefficients associated with a derivative expansion of the energy momentum tensor and R-charge current up to second order. In particular, we find a first order transport coefficient associated with the axial component of the current.Comment: 31 pages, v2: published version; added some references, discussion of the charge-current changed, results unchanged, v3: typo in formula (15) changed, v4: added footnote 3 in order to clarify the relation of our results to those of arXiv:0809.259

Is It Rational to Assume that Infants Imitate Rationally? A Theoretical Analysis and Critique

It has been suggested that preverbal infants evaluate the efficiency of others' actions (by applying a principle of rational action) and that they imitate others' actions rationally. The present contribution presents a conceptual analysis of the claim that preverbal infants imitate rationally. It shows that this ability rests on at least three assumptions: that infants are able to perceive others' action capabilities, that infants reason about and conceptually represent their own bodies, and that infants are able to think counterfactually. It is argued that none of these three abilities is in place during infancy. Furthermore, it is shown that the idea of a principle of rational action suffers from two fallacies. As a consequence, is it suggested that it is not rational to assume that infants imitate rationally. Copyright (C) 2012 S. Karger AG, Base

Tuning the 3D microenvironment of reprogrammed tubule cells enhances biomimetic modeling of polycystic kidney disease

Renal tubular cells frequently lose differentiation markers and physiological properties when propagated in conventional cell culture conditions. Embedding cells in 3D microenvironments or controlling their 3D assembly by bioprinting can enhance their physiological properties, which is beneficial for modeling diseases in vitro. A potential cellular source for modeling renal tubular physiology and kidney diseases in vitro are directly reprogrammed induced renal tubular epithelial cells (iRECs). iRECs were cultured in various biomaterials and as bioprinted tubular structures. They showed high compatibility with the embedding substrates and dispensing methods. The morphology of multicellular aggregates was substantially influenced by the 3D microenvironment. Transcriptomic analyses revealed signatures of differentially expressed genes specific to each of the selected biomaterials. Using a new cellular model for autosomal-dominant polycystic kidney disease, Pkd1(−/−) iRECs showed disrupted morphology in bioprinted tubules and a marked upregulation of the Aldehyde dehydrogenase 1a1 (Aldh1a1). In conclusion, 3D microenvironments strongly influence the morphology and expression profiles of iRECs, help to unmask disease phenotypes, and can be adapted to experimental demands. Combining a direct reprogramming approach with appropriate biomaterials will facilitate construction of biomimetic kidney tubules and disease models at the microscale

Deep learning is widely applicable to phenotyping embryonic development and disease

Genome editing simplifies the generation of new animal models for congenital disorders. However, the detailed and unbiased phenotypic assessment of altered embryonic development remains a challenge. Here, we explore how deep learning (U-Net) can automate segmentation tasks in various imaging modalities, and we quantify phenotypes of altered renal, neural and craniofacial development in Xenopus embryos in comparison with normal variability. We demonstrate the utility of this approach in embryos with polycystic kidneys (pkd1 and pkd2) and craniofacial dysmorphia (six1). We highlight how in toto light-sheet microscopy facilitates accurate reconstruction of brain and craniofacial structures within X. tropicalis embryos upon dyrk1a and six1 loss of function or treatment with retinoic acid inhibitors. These tools increase the sensitivity and throughput of evaluating developmental malformations caused by chemical or genetic disruption. Furthermore, we provide a library of pre-trained networks and detailed instructions for applying deep learning to the reader's own datasets. We demonstrate the versatility, precision and scalability of deep neural network phenotyping on embryonic disease models. By combining light-sheet microscopy and deep learning, we provide a framework for higher-throughput characterization of embryonic model organisms. This article has an associated 'The people behind the papers' interview

Anomalous Transport from Kubo Formulae

Chiral anomalies have profound impact on the transport properties of relativistic fluids. In four dimensions there are different types of anomalies, pure gauge and mixed gauge-gravitational anomalies. They give rise to two new non-dissipative transport coefficients, the chiral magnetic conductivity and the chiral vortical conductivity. They can be calculated from the microscopic degrees of freedom with the help of Kubo formulae. We review the calculation of the anomalous transport coefficients via Kubo formulae with a particular emphasis on the contribution of the mixed gauge-gravitational anomaly.Comment: 36 pages, 4 figures, 1 table; to appear in Lect. Notes Phys. "Strongly interacting matter in magnetic fields" (Springer), edited by D. Kharzeev, K. Landsteiner, A. Schmitt, H.-U. Yee; v2 small changes in introduction, added references; v3 corrected eq. (21) and added eq. (77), added reference

Engineering kidney cells: reprogramming and directed differentiation to renal tissues

Growing knowledge of how cell identity is determined at the molecular level has enabled the generation of diverse tissue types, including renal cells from pluripotent or somatic cells. Recently, several in vitro protocols involving either directed differentiation or transcription-factor-based reprogramming to kidney cells have been established. Embryonic stem cells or induced pluripotent stem cells can be guided towards a kidney fate by exposing them to combinations of growth factors or small molecules. Here, renal development is recapitulated in vitro resulting in kidney cells or organoids that show striking similarities to mammalian embryonic nephrons. In addition, culture conditions are also defined that allow the expansion of renal progenitor cells in vitro. Another route towards the generation of kidney cells is direct reprogramming. Key transcription factors are used to directly impose renal cell identity on somatic cells, thus circumventing the pluripotent stage. This complementary approach to stem-cell-based differentiation has been demonstrated to generate renal tubule cells and nephron progenitors. In-vitro-generated renal cells offer new opportunities for modelling inherited and acquired renal diseases on a patient-specific genetic background. These cells represent a potential source for developing novel models for kidney diseases, drug screening and nephrotoxicity testing and might represent the first steps towards kidney cell replacement therapies. In this review, we summarize current approaches for the generation of renal cells in vitro and discuss the advantages of each approach and their potential applications

Fatigue design of welded double-sided T-joints and double-sided cruciform joints in steel marine structures: A total stress concept

Fatigue is a governing design limit state for marine structures. Welded joints are important in that respect. The weld notch stress (intensity) distributions contain essential information and formulations have been established to obtain a total stress fatigue damage criterion and corresponding fatigue resistance curve; a total stress concept. However, the involved weld load carrying stress model does not provide the required estimates and trends for varying geometry dimensions and loading & response combinations. A new one has been developed and performance evaluation for T-joints and cruciform joints in steel marine structures shows that in comparison with the nominal stress, hot spot structural stress and effective notch stress concept based results up to 50% more accurate fatigue design life time estimates can be obtained. Taking advantage of the weld notch stress formulations, the effective notch stress concept performance has improved adopting a stress-averaged criterion rather than a fictitious notch radius-based one.Ship Hydromechanics and StructuresMarine and Transport Technolog