Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

The genome is organized in three-dimensional units called topologically associating domains (TADs), through a process dependent on the cooperative action of cohesin and the DNA-binding factor CTCF. Genomic rearrangements of TADs have been shown to cause gene misexpression and disease, but genome-wide depletion of CTCF has no drastic effects on transcription. Here, we investigate TAD function in vivo in mouse limb buds at the Sox9-Kcnj2 locus. We show that the removal of all major CTCF sites at the boundary and within the TAD resulted in a fusion of neighboring TADs, without major effects on gene expression. Gene misexpression and disease phenotypes, however, were achieved by redirecting regulatory activity through inversions and/or the repositioning of boundaries. Thus, TAD structures provide robustness and precision but are not essential for developmental gene regulation. Aberrant disease-related gene activation is not induced by a mere loss of insulation but requires CTCF-dependent redirection of enhancer-promoter contacts

Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Mouse models are a critical tool for studying human diseases, particularly developmental disorders. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution

Response of human bone marrow stromal cells to a novel ultra-fine-grained and dispersion-strengthened titanium-based material

A novel titanium-based material, containing no toxic or expensive alloying elements, was compared to the established biomaterials: commercially pure titanium (c.p. Ti) and Ti6Al4V. This material (Ti/1.3HMDS) featured similar hardness, yield strength and better wear resistance than Ti6Al4V, as well as better electrochemical properties at physiological pH 7.4 than c.p. Ti grade 1 of our study. These excellent properties were obtained by utilizing an alternative mechanism to produce a microstructure of very fine titanium silicides and carbides (<100 nm) embedded in an ultra-fine-grained Ti matrix (365 nm). The grain refinement was achieved by high-energy ball milling of Ti powder with 1.3 wt.% of hexamethyldisilane (HMDS). The powder was consolidated by spark plasma sintering at moderate temperatures of 700 °C. The microstructure was investigated by optical and scanning electron microscopy (SEM) and correlated to the mechanical properties. Fluorescence microscopy revealed good adhesion of human mesenchymal stem cells on Ti/1.3HMDS comparable to that on c.p. Ti or Ti6Al4V. Biochemical analysis of lactate dehydrogenase and specific alkaline phosphatase activities of osteogenically induced hMSC exhibited equal proliferation and differentiation rates in all three cases. Thus the new material Ti/1.3HMDS represents a promising alternative to the comparatively weak c.p. Ti and toxic elements containing Ti6Al4V

A new homozygous CACNB2 mutation has functional relevance and supports a role for calcium channels in autism spectrum disorder.

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Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

Balanced chromosomal rearrangements such as inversions and translocations can cause congenital disease or cancer by inappropriately rewiring promoter-enhancer contacts1,2. To study the potentially pathogenic consequences of balanced chromosomal rearrangements, we generated a series of genomic inversions by placing an active limb enhancer cluster from the Epha4 regulatory domain at different positions within a neighbouring gene-dense region and investigated their effects on gene regulation in vivo in mice. Expression studies and high-throughput chromosome conformation capture from embryonic limb buds showed that the enhancer cluster activated several genes downstream that are located within asymmetric regions of contact, the so-called architectural stripes3. The ectopic activation of genes led to a limb phenotype that could be rescued by deleting the CCCTC-binding factor (CTCF) anchor of the stripe. Architectural stripes appear to be driven by enhancer activity, because they do not form in mouse embryonic stem cells. Furthermore, we show that architectural stripes are a frequent feature of developmental three-dimensional genome architecture often associated with active enhancers. Therefore, balanced chromosomal rearrangements can induce ectopic gene expression and the formation of asymmetric chromatin contact patterns that are dependent on CTCF anchors and enhancer activity

EERI Earthquake Reconnaissance Team Report: M7.8 Muisne, Ecuador Earthquake on April 16, 2016

In mid-April of 2016, the coastal Ecuadoran province of Manabí suffered a devastating earthquake. Damage was spread up and down the coast, with some towns almost being completely erased. In about a month’s time, EERI sent out a reconnaissance team to study the damage. The team was made up of highly energetic structural engineers from both practice and academia. Deploying the team was a race against time, as the central government of Ecuador was in full swing of demolishing all severely damaged buildings. Even by the time the EERI team reached the field, many of the low rise buildings have already been completely cleared out in some of the towns. This earthquake further strengthens the case that non-ductile, masonry infilled buildings continue to pose a high hazard to lives and buildings in the seismically active areas of the world. For example, most of the hospitals the team visited were inoperative mainly due to the masonry infill and other non-structural damage where in most cases the building structure itself withstood the earthquake. This in turn put more pressure and resources on the response teams to set up temporary emergency hospitals and potentially delayed their ability to take in the injured immediately following the earthquake. The world, and more specifically the developing world, is dictated by economics. It’s always going to be cheaper to fill a wall with locally produced brick masonry over manufactured flexible light-weight building materials. We, the earthquake engineering community, need to find a way of safely using brick masonry where it can be compatible with the building’s structure. This report is filled with images, data and observations. It is part of a growing collection of information the EERI staff, reconnaissance team, and community have developed on the Ecuador earthquake, including an extensive video briefing and a detailed virtual clearinghouse. The people of Ecuador were very helpful and most of all, welcoming during our visit, especially the Ecuadoran Army Corps of Engineers, who generously provided transportation for the team. Our hearts and our encouragement go out to the people of Manabí Province as they try to rebuild after the devastating earthquake