Genotoxic effects of culture media on human pluripotent stem cells

Culture conditions play an important role in regulating the genomic integrity of Human Pluripotent Stem Cells (HPSCs). We report that HPSCs cultured in Essential 8 (E8) and mTeSR, two widely used media for feeder-free culturing of HPSCs, had many fold higher levels of ROS and higher mitochondrial potential than cells cultured in Knockout Serum Replacement containing media (KSR). HPSCs also exhibited increased levels of 8-hydroxyguanosine, phospho-histone-H2a.X and p53, as well as increased sensitivity to γ-irradiation in these two media. HPSCs in E8 and mTeSR had increased incidence of changes in their DNA sequence, indicating genotoxic stress, in addition to changes in nucleolar morphology and number. Addition of antioxidants to E8 and mTeSR provided only partial rescue. Our results suggest that it is essential to determine cellular ROS levels in addition to currently used criteria i.e. pluripotency markers, differentiation into all three germ layers and normal karyotype through multiple passages, in designing culture media

A Method to Identify and Isolate Pluripotent Human Stem Cells and Mouse Epiblast Stem Cells Using Lipid Body-Associated Retinyl Ester Fluorescence.

We describe the use of a characteristic blue fluorescence to identify and isolate pluripotent human embryonic stem cells and human-induced pluripotent stem cells. The blue fluorescence emission (450–500 nm) is readily observed by fluorescence microscopy and correlates with the expression of pluripotency markers (OCT4, SOX2, and NANOG). It allows easy identification and isolation of undifferentiated human pluripotent stem cells, high-throughput fluorescence sorting and subsequent propagation. The fluorescence appears early during somatic reprogramming. We show that the blue fluorescence arises from the sequestration of retinyl esters in cytoplasmic lipid bodies. The retinoid-sequestering lipid bodies are specific to human and mouse pluripotent stem cells of the primed or epiblast-like state and absent in naive mouse embryonic stem cells. Retinol, present in widely used stem cell culture media, is sequestered as retinyl ester specifically by primed pluripotent cells and also can induce the formation of these lipid bodies

Analyzing the HCP Datasets using GPUs: The Anatomy of a Science Engagement

This paper documents the experience improving the performance of a data processing workflow for analysis of the Human Connectome Project's HCP900 data set. It describes how network and compute bottlenecks were discovered and resolved during the course of a science engagement. A series of computational enhancements to the stock FSL BedpostX workflow are described. These enhancements migrated the workflow from a slow serial execution of computations resulting from Slurm scheduler incompatibilities to eventual execution on GPU resources, going from a 21-day execution on a single CPU core to a 2 hour execution on a GPU. This workflow contributed a vital use-case to the build-out of the campus compute cluster with additional GPUs and resulted in enhancements to network bandwidth. It also shares insights on potential improvements to distribution of scientific software to avoid stagnation in site-specific deployment decisions. The discussion highlights the advantages of open licenses and popular code collaboration sites like GitHub.com in feeding contributions upstream.Comment: 6 pages, 3 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

A rare case of a peritoneal cyst arising from the falciform ligament

Peritoneal cysts are rare benign intra-abdominal lesions most commonly found attached to the mesentery of the ileum. They may be asymptomatic, present with abdominal pain, bloating or discovered incidentally. We describe the case of a peritoneal cyst located in an unusual position in a female patient; attached to the falciform ligament

Weak lensing effects in the measurement of the dark energy equation of state with LISA

The Laser Interferometer Space Antenna’s (LISA’s) observation of supermassive binary black holes (SMBBH) could provide a new tool for precision cosmography. Inclusion of subdominant signal harmonics in the inspiral signal allows for high-accuracy sky localization, dramatically improving the chances of finding the host galaxy and obtaining its redshift. A SMBBH merger can potentially have component masses from a wide range (105–108M⊙) over which parameter accuracies vary considerably. We perform an in-depth study in order to understand (i) what fraction of possible SMBBH mergers allow for sky localization, depending on the parameters of the source, and (ii) how accurately w can be measured when the host galaxy can be identified. We also investigate how accuracies on all parameters improve when a knowledge of the sky position can be folded into the estimation of errors. We find that w can be measured to within a few percent in most cases, if the only error in measuring the luminosity distance is due to LISA’s instrumental noise and the confusion background from Galactic binaries. However, weak lensing-induced errors will severely degrade the accuracy with which w can be obtained, emphasizing that methods to mitigate weak lensing effects would be required to take advantage of LISA’s full potential