A reference human induced pluripotent stem cell line for large-scale collaborative studies

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field

Access and benefit sharing: Issues related to marine genetic resources

Since the entry into force of the CBD in 1993, countries have struggled to find answers to several questions related to ABS issues and have spent considerable amounts of time, energy and money in understanding how to operationalise these principles. One critical area that is beginning to appear during the discussions under the international regime is the status of marine genetic resources with a particular emphasis emerging on genetic resources available in areas beyond national jurisdiction. This paper presents some key legal and policy issues that negotiators of the international regime on ABS need to consider in relation to marine genetic resources. © 2008, RIS

Effect of Heterogeneity in Coal Ash Chemical Composition on the Onset of Conditions Favorable for Agglomeration in Fluid Beds

Ash agglomeration issues that arise due to the sticking of slag-wetted, colliding particles have been creating operational difficulties and monetary losses for the fluidized bed combustion (FBC) industry. Difficulties have been experienced in the detection of slag-liquid at the low operating temperatures in fluidized bed combustors (FBCs) and predicting the agglomeration behavior of fuel. This study aims to study the effect of heterogeneity in ash composition on the detection of slag-liquid in FBCs. It quantifies the slag-liquid amounts at the particle-level, under oxidizing environments, by dividing the bulk fuel into density classes. FactSage™ thermodynamic simulations of each of the particle classes, along with experimental validation of the trends with thermo-mechanical analysis (TMA) and high temperature X-ray diffraction (HT-XRD) were performed. The results obtained can be used to estimate the stickiness of particles in the development of ash agglomeration models based on particle collisions. The study of these particle classes shows that particle classes with specific minerals can form low temperature eutectics and lead to onset of slag-liquid formation at temperatures below those predicted by bulk analysis alone. Comparison of the differences in slag-liquid formation tendencies under reducing and oxidizing environments is also presented

Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity

Background It is apparent that genomes harbor massive amounts of structural variation, and that this variation has largely gone undetected for technical reasons. In addition to being inherently interesting, structural variation can cause artifacts when short-read sequencing data are mapped to a reference genome. In particular, spurious SNPs (that do not show Mendelian segregation) may result from mapping of reads to duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million heterozygous SNPs (44% of total). Given that Arabidopsis thaliana (A. thaliana) is highly selfing, we hypothesized that these SNPs reflected cryptic copy number variation, and investigated them further. Results The heterozygosity we observed consisted of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. Focusing on such pseudo-heterozygosity in annotated genes, we used GWAS to map the position of the duplicates, identifying 2500 putatively duplicated genes. The results were validated using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that, in fact, transpose together. Finally, we use existing bisulfite sequencing data to demonstrate that cryptic structural variation can produce highly inaccurate estimates of DNA methylation polymorphism. Conclusions Our study confirms that most heterozygous SNPs calls in A. thaliana are artifacts, and suggest that great caution is needed when analyzing SNP data from short-read sequencing. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggest that future analyses based on independently assembled genomes will be very informative

The Churchland birthday data cake

My lab is the best!! They got me this incredible science cake highlighting our latest observations. However, I fear it makes us vulnerable to being scooped! If you want to refer to the figures, may I request that you cite the cake? #labmeeting #birthdaycake Cake by Barbara Cascon

A study of Indian limestones for sulfur capture in FBC plants: Particle size sensitivity of sulfation behavior

India generates about 59% of its electricity from coal (EIA, 2014) [1]. Most of the coal available in India is of low quality, high ash and low calorific value. Fluidized bed combustion is an appropriate technology to utilize these low quality coals. Currently there are no emission regulations for SO2 emissions from power plants. However, SO2 control is becoming a requirement for some projects funded by International agencies to control air emissions. For the first time, five limestone samples from various parts of India that are currently being used in fluidized bed power plants are characterized as sorbents for sulfur capture behavior in a TGA. These limestones were identified as Sorbents A–E, and were characterized for their physical properties (porosity and pore size distribution, surface area), chemical composition analysis, petrographic characteristics, and mineral structural features using XRD. Analytical results indicated that the particle size of the sorbents plays a critical role in the sulfation behavior of the sorbents with some sorbents are more sensitive to particle size than the others. Hot Stage Microscopy observations indicated that this sensitivity was due to the formation of thermally activated fractures (TIFs) at fluidized bed temperatures. BET surface area and BJH pore diameter tests performed on the five sorbents indicated that Sorbent A had the highest surface area of all the limestones and large also the pore diameter.After comparing the BET data with the TGA sulfation data, it appears that Sorbent B might be subjected to the pore-plugging effect due to its small pore diameter. Sorbent C and Sorbent E had low BET surface area and high BJH pore diameter suggesting that although they may not experience much diffusion resistance, due to the low surface area, their sulfur utilization might be limited for coarse particle sizes. The sulfation behavior of these Indian limestones is compared with that of some US limestones with similar physical, chemical and petrographical properties