New genetic resources for mammalian developmental biologists

The utilization of homologous recombination in embryonic stem cells as a means to generate mice carrying pre-determined modifications of genomic sequences has revolutionized the study of developmental biology. Recognizing the potential efficiencies that can be obtained by high-throughput production at centralized technology centers, a number of large-scale efforts for generating mice with targeted mutations have been funded. These programs are reaching fruition, and a variety of libraries of embryonic stem cells with defined mutations are now available

Smoothed Complexity Theory

Smoothed analysis is a new way of analyzing algorithms introduced by Spielman and Teng (J. ACM, 2004). Classical methods like worst-case or average-case analysis have accompanying complexity classes, like P and AvgP, respectively. While worst-case or average-case analysis give us a means to talk about the running time of a particular algorithm, complexity classes allows us to talk about the inherent difficulty of problems. Smoothed analysis is a hybrid of worst-case and average-case analysis and compensates some of their drawbacks. Despite its success for the analysis of single algorithms and problems, there is no embedding of smoothed analysis into computational complexity theory, which is necessary to classify problems according to their intrinsic difficulty. We propose a framework for smoothed complexity theory, define the relevant classes, and prove some first hardness results (of bounded halting and tiling) and tractability results (binary optimization problems, graph coloring, satisfiability). Furthermore, we discuss extensions and shortcomings of our model and relate it to semi-random models.Comment: to be presented at MFCS 201

Wolf, Canis lupus, Den Site Selection in the Rocky Mountains

Because mortality of Wolves, Canis lupus, is highest during the first six months of life, den site selection may affect reproductive success of Wolf populations. We studied fine-scale denning habitat selection (within 100 m of den site) by comparing field-measured characteristics of 22 dens in Idaho, Montana, and Alberta with 22 paired random contrast locations within pack home ranges. In order of importance, Wolves denned in areas with greater canopy cover, hiding cover, herbaceous ground cover, and woody debris, and were closer to water than paired random sites. Thus Wolves may select den sites for physical protection and available water. We also studied coarse-scale denning habitat selection by comparing 35 Wolf dens with 35 paired contrast locations in Idaho, Montana, and Wyoming with respect to six remotely-sensed variables (elevation, slope, coniferous forest cover, solar radiation, distance to water, and distance to roads). Although these variables did not differ (univariate P > 0.10) between den and contrast locations, a Mahalanobis-distance model using four remotely-sensed variables (slope, elevation, coniferous forest cover, and solar radiation) suggested > 85% of dens would occur in potential denning habitat occupying < 12% of the Wolf recovery areas in the northern Rocky Mountains. This model may be useful for identifying likely den locations in areas not yet occupied by Wolves. Wolf core use areas, including den areas, showed higher intensity of use throughout the year when compared to the entire territory

Production of a Natural Antibody to the Mouse Polyoma Virus Is a Multigenic Trait

MA/MyJ mice express a natural antibody to the highly oncogenic polyoma virus. C57BR/cdJ mice lack this antibody but mount an adaptive T-cell response to the virus. Analysis of F2 progeny of a cross between these strains reveals a pattern of inheritance of expression of the natural antibody involving two genes in an epistatic relationship

Agouti C57BL/6N embryonic stem cells for mouse genetic resources.

We report the characterization of a highly germline competent C57BL/6N mouse embryonic stem cell line, JM8. To simplify breeding schemes, the dominant agouti coat color gene was restored in JM8 cells by targeted repair of the C57BL/6 nonagouti mutation. These cells provide a robust foundation for large-scale mouse knockout programs that aim to provide a public resource of targeted mutations in the C57BL/6 genetic background

Geochemistry of volcanic glasses from the Louisville Seamount Trail (IODP Expedition 330): Implications for eruption environments and mantle melting

Volcanic glasses recovered from four guyots during drilling along the Louisville Seamount Trail, southwest Pacific, have been analyzed for major, trace, and volatile elements (H2O, CO2, S, and Cl), and oxygen isotopes. Compared to other oceanic island settings, they are geochemically homogeneous, providing no evidence of the tholeiitic stage that characterizes Hawaii. The degrees and depth of partial melting remained constant over 1–3 Ma represented by the drill holes, and along-chain over several million years. The only exception is Hadar Guyot with compositions that suggest small degree preferential melting of an enriched source, possibly because it erupted on the oldest and thickest lithosphere. Incompatible element enriched glass from late-stage volcaniclastics implies lower degrees of melting as the volcanoes moved off the melting anomaly. Volcaniclastic glasses from throughout the igneous basement are degassed suggesting generation during shallow submarine eruptions (<20 mbsl) or as subaerial flows entered the sea. Drill depths may no longer reflect relative age due to postquench downslope movement. Higher volatile contents in late-stage volcaniclastics indicate submarine eruptions at 118–258 mbsl and subsidence of the edifices below sea level by the time they erupted, or generation in flank eruptions. Glass from intrusion margins suggests emplacement ∼100 m below the surface. The required uplift to achieve these paleo-quench depths and the subsequent subsidence to reach their current depths exceeds that expected for normal oceanic lithosphere, consistent with the Louisville melting anomaly being <100°C hotter than normal asthenosphere at 50–70 Ma when the guyots were erupted. Key Points: - Louisville glasses show remarkable temporal geochemical homogeneity - All recovered Louisville glasses are variably degassed - Louisville melting anomaly was <100°C hotter than normal asthenospher

A Spontaneous Fatp4/Scl27a4 Splice Site Mutation in a New Murine Model for Congenital Ichthyosis

Congenital ichthyoses are life-threatening conditions in humans. We describe here the identification and molecular characterization of a novel recessive mutation in mice that results in newborn lethality with severe congenital lamellar ichthyosis. Mutant newborns have a taut, shiny, non-expandable epidermis that resembles cornified manifestations of autosomal-recessive congenital ichthyosis in humans. The skin is stretched so tightly that the newborn mice are immobilized. The genetic defect was mapped to a region near the proximal end of chromosome 2 by SNP analysis, suggesting Fatp4/Slc27a4 as a candidate gene. FATP4 mutations in humans cause ichthyosis prematurity syndrome (IPS), and mutations of Fatp4 in mice have previously been found to cause a phenotype that resembles human congenital ichthyoses. Characterization of the Fatp4 cDNA revealed a fusion of exon 8 to exon 10, with deletion of exon 9. Genomic sequencing identified an A to T mutation in the splice donor sequence at the 3′-end of exon 9. Loss of exon 9 results in a frame shift mutation upstream from the conserved very long-chain acyl-CoA synthase (VLACS) domain. Histological studies revealed that the mutant mice have defects in keratinocyte differentiation, along with hyperproliferation of the stratum basale of the epidermis, a hyperkeratotic stratum corneum, and reduced numbers of secondary hair follicles. Since Fatp4 protein is present primarily at the stratum granulosum and the stratum spinosum, the hyperproliferation and the alterations in hair follicle induction suggest that very long chain fatty acids, in addition to being required for normal cornification, may influence signals from the stratum corneum to the basal cells that help to orchestrate normal skin differentiation

p38 MAPK signaling during murine preimplantation development.

Mitogen-activated protein kinase (MAPK) pathways mediate some important cellular processes and are likely to also regulate preimplantation development. The role of p38 MAP kinase signaling during murine preimplantation development was investigated in the present study. p38 MAPK, p38-regulated or -activated kinase (PRAK; MK5), map kinase-activated protein kinase 2 (MK2), and heat shock protein 25 (hsp25) mRNAs and proteins were detected throughout preimplantation development. Two-cell stage embryos cultured in the presence of SB220025 and SB203580 (specific inhibitors of p38 MAPK alpha/beta), progressed to the eight-cell stage with the same frequency as controls; however, treated embryos halted their development at the 8- to 16-cell stage. In addition, embryos treated with p38 MAPK inhibitors displayed a complete loss of MK2 and hsp25 phosphorylation and also a complete loss of filamentous actin as indicated by the absence of rhodamine-phalloidin staining. In these inhibitor-treated groups, the embryos were composed of a mixture of compacting and noncompacting cells, and the embryos were one to two cell divisions behind controls. Treated embryos remained viable as the developmental blockade was rescued by removing embryos from the drug treatment and placing them in drug-free medium until they progressed to the blastocyst stage. This study demonstrates that p38 MAPK activity is required to support development through the murine preimplantation interval

The Arginine Methyltransferase Carm1 is Necessary for Heart Development

To discover genes implicated in human congenital disorders, we performed ENU mutagenesis in the mouse and screened for mutations affecting embryonic development. In this work we report defects of heart development in mice homozygous for a mutation of Coactivator-associated Arginine Methyltransferase 1 (Carm1). While Carm1 has been extensively studied, it has never been previously associated with a role in heart development. Phenotype analysis combining histology and micro-computed tomography (micro-CT) imaging shows a range of cardiac defects. Most notably, many affected mid-gestation embryos appear to have cardiac rupture and hemorrhaging in the thorax. Mice that survive to late gestation show a variety of cardiac defects, including Ventricular Septal Defects (VSDs), Double Outlet Right Ventricle (DORV), and Persistent Truncus Arteriosus (PTA). Transcriptome analyses of the mutant embryos by mRNA-seq reveal the perturbation of several genes involved in cardiac morphogenesis and muscle development and function. In addition, we observe the mis-localization of cardiac neural crest cells at E12.5 in the outflow tract. The cardiac phenotype of Carm1 mutant embryos is similar to that of Pax3 null mutants, and PAX3 is a putative target of CARM1. However, our analysis does not support the hypothesis that developmental defects in Carm1 mutant embryos are primarily due to a functional defect of PAX3