Expression analysis of the endogenous Zscan4 locus and its coding proteins in mouse ES cells and preimplantation embryos

Mouse Zinc finger and SCAN domain containing 4 (Zscan4) is encoded in multiple copies of Zscan4 genes, which are expressed in late two-cell stage preimplantation embryos and in 1–5% of the embryonic stem (ES) cell population at a given time. Due to the highly identical nucleotide sequences of multiple copies of Zscan4 paralogs and pseudogenes in the mouse Zscan4 genomic cluster, previous analyses have been done using exogenous transgenes under the regulation of Zscan4c promoter. In this manuscript, we generated knock-in mouse ES cell lines and mouse lines, in which the expression of endogenous Zscan4c, one of the Zscan4 genes, can be specifically monitored with a green fluorescent protein variant, Emerald. Interestingly, we found that only ∼30% of Zscan4-immunopositive ES cells were Emerald positive, suggesting that even when the Zscan4 locus is active, not all Zscan4 genes are expressed synchronously. We also carried out mass spectrometry of protein complexes associated with endogenous Zscan4 proteins. Taken together, our genetic engineering at an endogenous Zscan4c gene provides the first clue for the expression and function of each gene copy of Zscan4 locus in a physiological context

High-resolution upper Maastrichtian carbon isotope stratigraphy of terrestrial organic matter from northern Japan

High-resolution stable carbon isotope stratigraphy of terrestrial organic matter was established for the upper Maastrichtian Senpohshi Formation of the Nemuro Group in eastern Hokkaido, northern Japan. The Senpohshi Formation, approximately 1, 300 m thick, is dominated by hemipelagic mudstone deposited along an active margin in the North Pacific region. Microscopic observations of extracted kerogen samples from the formation revealed the presence of sedimentary organic matter (SOM), predominantly phytoclasts and a minor amount of non-fluorescent amorphous organic matter, indicating material of a terrestrial higher plant origin. The atomic hydrogen/carbon ratios of the kerogen samples indicated a coalification rank at the anthracite stage or below. Therefore, the stable carbon isotope values of the bulk SOM obtained for the Senpohshi Formation represent the unmodified, original values of terrestrial organic matter. The stable carbon isotope profile reconstructed for the formation provides the first high-resolution terrestrial record of the Mid-Maastrichtian Event (MME), which is comparable to high-resolution marine carbon isotope data from other sections. The carbon isotopic signatures defined by the marine records are recognized in the terrestrial data from the formation, especially in middle to upper part of the event. However, the terrestrial record showed a discrepancy from the marine data in the lower part of the MME, suggesting local variation of the hinterland environment in the North Pacific region. This study provides new insight into environmental changes during the late Maastrichtian by establishing a detailed carbon isotope record of terrestrial materials

Prediction of evolutionarily conserved interologs in Mus musculus

<p>Abstract</p> <p>Background</p> <p>Identification of protein-protein interactions is an important first step to understand living systems. High-throughput experimental approaches have accumulated large amount of information on protein-protein interactions in human and other model organisms. Such interaction information has been successfully transferred to other species, in which the experimental data are limited. However, the annotation transfer method could yield false positive interologs due to the lack of conservation of interactions when applied to phylogenetically distant organisms.</p> <p>Results</p> <p>To address this issue, we used phylogenetic profile method to filter false positives in interologs based on the notion that evolutionary conserved interactions show similar patterns of occurrence along the genomes. The approach was applied to <it>Mus musculus</it>, in which the experimentally identified interactions are limited. We first inferred the protein-protein interactions in <it>Mus musculus </it>by using two approaches: i) identifying mouse orthologs of interacting proteins (interologs) based on the experimental protein-protein interaction data from other organisms; and ii) analyzing frequency of mouse ortholog co-occurrence in predicted operons of bacteria. We then filtered possible false-positives in the predicted interactions using the phylogenetic profiles. We found that this filtering method significantly increased the frequency of interacting protein-pairs coexpressed in the same cells/tissues in gene expression omnibus (GEO) database as well as the frequency of interacting protein-pairs shared the similar Gene Ontology (GO) terms for biological processes and cellular localizations. The data supports the notion that phylogenetic profile helps to reduce the number of false positives in interologs.</p> <p>Conclusion</p> <p>We have developed protein-protein interaction database in mouse, which contains 41109 interologs. We have also developed a web interface to facilitate the use of database <url>http://lgsun.grc.nia.nih.gov/mppi/</url>.</p

Zscan4 regulates telomere elongation and genomic stability in ES cells

Exceptional genomic stability is one of the hallmarks of mouse embryonic stem (ES) cells. However, the genes contributing to this stability remain obscure. We previously identified Zscan4 as a specific marker for two-cell embryo and ES cells. Here we show that Zscan4 is involved in telomere maintenance and long-term genomic stability in ES cells. Only 5% of ES cells express Zscan4 at a given time, but nearly all ES cells activate Zscan4 at least once during nine passages. The transient Zscan4-positive state is associated with rapid telomere extension by telomere recombination and upregulation of meiosis-specific homologous recombination genes, which encode proteins that are colocalized with ZSCAN4 on telomeres. Furthermore, Zscan4 knockdown shortens telomeres, increases karyotype abnormalities and spontaneous sister chromatid exchange, and slows down cell proliferation until reaching crisis by passage eight. Together, our data show a unique mode of genome maintenance in ES cells. © 2010 Macmillan Publishers Limited. All rights reserved

Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells

Research articl

Measurement of radon emanation and impurity adsorption from argon gas using ultralow radioactive zeolite

The amount of radioactive impurities contaminated in the detector gases is required to be kept at a very low level for rare event particle physics such as dark matter and neutrino observation experiments. Zeolite is a well-known adsorbent material and is one of the possible candidates for removing impurities from these gases. At the same time, the amount of radioactive impurities released from the adsorbent material needs to be sufficiently small. In this paper, a development of a new ultralow radioactive zeolite as a product of the selection of ultralow radioactive materials is reported. Results on the radon emanation and impurity adsorption from argon gas measurements are also described.Comment: 8 pages, 7 figure

Exploring flavor structure of supersymmetry breaking from rare B decays and unitarity triangle

We study effects of supersymmetric particles in various rare B decay processes as well as in the unitarity triangle analysis. We consider three different supersymmetric models, the minimal supergravity, SU(5) SUSY GUT with right-handed neutrinos, and the minimal supersymmetric standard model with U(2) flavor symmetry. In the SU(5) SUSY GUT with right-handed neutrinos, we consider two cases of the mass matrix of the right-handed neutrinos. We calculate direct and mixing-induced CP asymmetries in the b to s gamma decay and CP asymmetry in B_d to phi K_S as well as the B_s--anti-B_s mixing amplitude for the unitarity triangle analysis in these models. We show that large deviations are possible for the SU(5) SUSY GUT and the U(2) model. The pattern and correlations of deviations from the standard model will be useful to discriminate the different SUSY models in future B experiments.Comment: revtex4, 36 pages, 10 figure

Zscan4 transiently reactivates early embryonic genes during the generation of induced pluripotent stem cells

The generation of induced pluripotent stem cells (iPSCs) by the forced expression of defined transcription factors in somatic cells holds great promise for the future of regenerative medicine. However, the initial reprogramming mechanism is still poorly understood. Here we show that Zscan4, expressed transiently in 2-cell embryos and embryonic stem cells (ESCs), efficiently produces iPSCs from mouse embryo fibroblasts when coexpressed with Klf4, Oct4, and Sox2. Interestingly, the forced expression of Zscan4 is required only for the first few days of iPSC formation. Microarray analysis revealed transient and early induction of preimplantation-specific genes in a Zscan4-dependent manner. Our work indicates that Zscan4 is a previously unidentified potent natural factor that facilitates the reprogramming process and reactivates early embryonic genes