To better understand endogenous parameters that influence pluripotent cell differentiation we used human embryonic stem cells (hESCs) as a model system. We demonstrate that differentiation trajectories in aggregate (embryoid body [EB])-induced differentiation, a common approach to mimic some of the spatial and temporal aspects of in vivo development, are affected by three factors: input hESC composition, input hESC colony size, and EB size. Using a microcontact printing approach, size-specified hESC colonies were formed by plating single-cell suspensions onto micropatterned (MP) extracellular matrix islands. Subsequently, size-controlled EBs were formed by transferring entire colonies into suspension culture enabling the independent investigation of colony and aggregate size effects on differentiation induction. Gene and protein expression analysis of MP-hESC populations revealed that the ratio of Gata6 (endoderm-associated marker) to Pax6 (neural-associated marker) expression increased with decreasing colony size. Moreover, upon forming EBs from these MP-hESCs, we observed that differentiation trajectories were affected by both colony and EB size-influenced parameters. In MPEBs generated from endoderm-biased (high Gata6/Pax6) input hESCs, higher mesoderm and cardiac induction was observed at larger EB sizes. Conversely, neural-biased (low Gata6/Pax6) input hESCs generated MP-EBs that exhibited higher cardiac induction in smaller EBs. Our analysis demonstrates that heterogeneity in hESC colony and aggregate size, typical in most differentiation strategies, produces subsets of appropriate conditions for differentiation into specific cell types. Moreover, our findings suggest that the local microenvironment modulates endogenous parameters that can be used to influence pluripotent cell differentiation trajectories. STEM CELLS

Processes involving self-assembly of monomeric units into organized polymeric arrays are currently the subject of much attention, particularly in the areas of nanotechnology and biomaterials. One biological example of a protein polymer with potential for self-organization is elastin. Elastin is the extracellular matrix protein that imparts the properties of extensibility and elastic recoil to large arteries, lung parenchyma, and other tissues. Tropoelastin, the approximately 70 kDa soluble monomeric form of elastin, is highly nonpolar in character, consisting essentially of 34 alternating hydrophobic and crosslinking domains. Crosslinking domains contain the lysine residues destined to form the covalent intermolecular crosslinks that stabilize the polymer. We and others have suggested that the hydrophobic domains are sites of interactions that contribute to juxtaposition of lysine residues in preparation for crosslink formation. Here, using recombinant polypeptides based on sequences in human elastin, we demonstrate that as few as three hydrophobic domains flanking two crosslinking domains are sufficient to support a self-assembly process that aligns lysines for zero-length crosslinking, resulting in formation of the crosslinks of native elastin. This process allows fabrication of a polymeric matrix with solubility and mechanical properties similar to those of native elastin.

BackgroundIdentification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenotype-associated SNPs in genome-wide association studies (GWAS). The small sample sizes of some previous eQTL studies have limited their statistical power. We conducted an eQTL investigation of microarray-based gene and exon expression levels in whole blood in a cohort of 5257 individuals, exceeding the single cohort size of previous studies by more than a factor of 2.ResultsWe detected over 19,000 independent lead cis-eQTLs and over 6000 independent lead trans-eQTLs, targeting over 10,000 gene targets (eGenes), with a false discovery rate (FDR) < 5%. Of previously published significant GWAS SNPs, 48% are identified to be significant eQTLs in our study. Some trans-eQTLs point toward novel mechanistic explanations for the association of the SNP with the GWAS-related phenotype. We also identify 59 distinct blocks or clusters of trans-eQTLs, each targeting the expression of sets of six to 229 distinct trans-eGenes. Ten of these sets of target genes are significantly enriched for microRNA targets (FDR < 5%). Many of these clusters are associated in GWAS with multiple phenotypes.ConclusionsThese findings provide insights into the molecular regulatory patterns involved in human physiology and pathophysiology. We illustrate the value of our eQTL database in the context of a recent GWAS meta-analysis of coronary artery disease and provide a list of targeted eGenes for 21 of 58 GWAS loci.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1142-6) contains supplementary material, which is available to authorized users.

This paper describes a 25‐year project in which we defined problem solving, identified effective methods for developing students' skill in problem solving, implemented a series of four required courses to develop the skill, and evaluated the effectiveness of the program. Four research projects are summarized in which we identified which teaching methods failed to develop problem solving skill and which methods were successful in developing the skills. We found that students need both comprehension of Chemical Engineering and what we call general problem solving skill to solve problems successfully. We identified 37 general problem solving skills. We use 120 hours of workshops spread over four required courses to develop the skills. Each skill is built (using content‐independent activities), bridged (to apply the skill in the content‐specific domain of Chemical Engineering) and extended (to use the skill in other contexts and contents and in everyday life). The tests and examinations of process skills, TEPS, that assess the degree to which the students can apply the skills are described. We illustrate how self‐assessment was used.

A series of degradable polyurethanes of variable soft segment chemistry and content were synthesized and characterized. An amino acid-based diester chain extender was used to confer degradability and both polycaprolactone diol (PCL) and polyethylene oxide (PEO) were used as soft segments. In addition, the diisocyanate component was a potentially nontoxic diisocyanate (2,6-diisocyanato methyl caproate, LDI). The physicochemical properties of these unique series of polyurethanes were investigated. It was found that the PEO containing polyurethanes were generally weak, tacky amorphous materials. In contrast, the PCL polyurethanes were relatively strong, elastomeric materials which ranged from completely amorphous to semicrystalline as noted by differential scanning calorimetry. The PCL containing polyurethanes exhibited increasing tensile strength, modulus, and ultimate strain with increasing PCL molecular weight because of increasing phase separation and increasing soft segment crystallinity. Fourier transform infrared analysis showed significant hard segment urea and urethane hydrogen bonding which increased with hard segment content, although interphase bonding is believed to be significant for the PCL polyurethanes. Surface characterization carried out by contact angle analysis and X-ray photoelectron spectroscopy indicated soft segment surface enrichment for all of the polyurethanes. The PEO-based polymers were very hydrophilic whereas the PCL-based polymers displayed significantly higher contact angles, indicating greater surface hydrophobicity. The observed diversity in material properties suggests that these polyurethanes may be useful for a wide range of applications.

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Objective To identify transcriptomic biomarkers of coronary heart disease (CHD) in 188 CHD cases and 188 age- and sex-matched controls who were participants in the Framingham Heart Study. Approach and results A total of 35 genes were differentially expressed in CHD cases vs. controls at FDR<0.5 including GZMB, TMEM56 and GUK1. Cluster analysis revealed three gene clusters associated with CHD, two linked to increased erythrocyte production and a third to reduced natural killer (NK) and T cell activity in CHD cases. Exon-level results corroborated and extended the gene-level results. Alternative splicing analysis suggested that GUK1 and 38 other genes were differentially spliced in CHD cases vs. controls. Gene ontology analysis linked ubiquitination and T-cell-related pathways with CHD. Conclusion Two bioinformatically defined groups of genes show consistent associations with CHD. Our findings are consistent with the hypotheses that hematopoesis is up-regulated in CHD, possibly reflecting a compensatory mechanism, and that innate immune activity is disrupted in CHD or altered by its treatment. Transcriptomic signatures may be useful in identifying pathways associated with CHD and point toward novel therapeutic targets for its treatment and prevention.

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