Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore.

Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the γ-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs.

Association between microRNA polymorphisms and coronary heart disease : A meta-analysis.

The association between microRNA polymorphisms (miR polymorphisms) and coronary heart disease (CHD) risk has been studied intensively, but the results have been conflicting. Therefore, we conducted the present meta-analysis to obtain a more conclusive answer. We searched for eligible articles in PubMed, MEDLINE, EMBASE, Scopus, and CNKI. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to identify any potential associations. Ten case-control studies including 5,292 CHD patients and 5,446 control subjects were analyzed. The overall meta-analysis results showed that the miR-146a rs2910164 polymorphism, the miR-196a2 rs11614913 polymorphism, and the miR-499 rs3746444 polymorphism were all significantly associated with CHD risk in certain genetic models. Besides, the C allele of the miR-146a rs2910164 and miR-499 rs3746444 polymorphisms conferred increased susceptibility to CHD (C versus G, p < 0.0001, OR = 1.14, 95% CI = 1.07-1.21; p = 0.003, OR = 1.14, 95% CI = 1.05-1.25). Overall, our findings suggest that the miR-146a rs2910164, miR-196a2 rs11614913, and miR-499 rs3746444 polymorphisms may be correlated with the risk of CHD.

G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells.

DNA methylation at imprinting control regions (ICRs) is established in gametes in a sex-specific manner and has to be stably maintained during development and in somatic cells to ensure the correct monoallelic expression of imprinted genes. In addition to DNA methylation, the ICRs are marked by allele-specific histone modifications. Whether these marks are essential for maintenance of genomic imprinting is largely unclear. Here, we show that the histone H3 lysine 9 methylases G9a and GLP are required for stable maintenance of imprinted DNA methylation in embryonic stem cells; however, their catalytic activity and the G9a/GLP-dependent H3K9me2 mark are completely dispensable for imprinting maintenance despite the genome-wide loss of non-imprinted DNA methylation in H3K9me2-depleted cells. We provide additional evidence that the G9a/GLP complex protects imprinted DNA methylation by recruitment of de novo DNA methyltransferases, which antagonize TET dioxygenass-dependent erosion of DNA methylation at ICRs.

Genetic polymorphisms in very important pharmacogenomic (VIP) variants in the Tibetan population.

Genetic polymorphisms of very important pharmacogenomic (VIP) variants are important for personalized medicine. However, these have not been extensively studied in the Tibetan population. In this study, 82 VIP variants were detected in the Tibetan and Han (HAN) populations from northwestern China. Subsequently, we compared the differences between the Tibetan population and ten populations, including the HAN, Japanese in Tokyo (JPT), Mexican ancestry in Los Angeles (MEX), Toscans in Italy (TSI), African ancestry in Southwest USA (ASW), Luhya in California Webuye, Kenya (LWK), Gujarati Indians in Houston, Texas (GIH), Maasai in Kinyawa, Kenya (MKK), Yoruba in Ibadan, Nigeria (YRI), and Utah residents with Northern and Western European ancestry from the CEPH collection (CEU). Using the χ(2) test, we identified differences in the frequency distribution of 4, 4, 7, 10, 11, 11, 13, 15, 19, and 20 loci in the Tibetan population, compared to the HAN, JPT, MEX, TSI, ASW, LWK, GIH, MKK, YRI, and CEU populations, respectively [P < 0.05/(82*10)]. rs2115819, rs9934438, and rs689466, located in the ALOX5 (arachidonate 5-lipoxygenase), VKORC1 (vitamin K epoxide reductase complex, subunit 1) and PTGS2 (prostaglandin-endoperoxide synthase 2) genes, respectively, in the Tibetan population were different from those in most of the populations. Our results complement the information provided by the database of pharmacogenomics on Tibetan people, and provide an avenue for personalized treatment in the Tibetan population.

Dopamine receptor D1 but not D3 essential for morphine-induced conditioned responses.

Recent studies indicate the involvement of dopamine receptors D1 and D3 in the regulation of locomotor stimulant and conditioned responses to morphine in mice. Moreover, expression of brain-derived neurotrophic factor (BDNF) may be modulated by D1 and D3 receptor activities in the nucleus accumbens (NAc) and prefrontal cortex (PFC). However, the underlying interactions between D1 and D3 receptors and BDNF in the expression of behavioral responses controlled by drug-associated cues have not yet been fully elucidated. In this study, we used dopamine receptor mutant mice to explore the roles of the D1 and D3 receptors in locomotion and morphine-induced place preference; furthermore, we investigated the effects of morphine on BDNF expression in the NAc and PFC of the mouse brain. Our results show that D1 receptor but not D3 receptor mutant mice had decreased sensitivity to acute morphine-induced (10 mg/kg) locomotion (D1: 3814.82 ± 319.9 cm vs D3: 8089.64 ± 967.4 cm). Furthermore, D1 receptor mutant mice did not acquire morphine-conditioned place preference (D1: -18.3 ± 59.9, D3: 217.7 ± 64.1) and showed decreased BDNF expression in the NAc (D1: 0.33 ± 0.07 fold, D3: 2.21 ± 0.18 fold) and PFC (D1: 0.74 ± 0.15 fold, D3: 1.68 ± 0.22 fold) compared with wild-type and D3 receptor mutant mice. These findings suggest that the D1 receptor is necessary for the induction of cue-associated morphine seeking and modulates locomotor habituation processes in response to acute morphine. The dopamine receptor D1 but not the D3 is also critical for morphine-induced BDNF expression in the NAc and PFC.

Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression.

Tumourigenic transformation of normal cells into cancer typically involves several steps resulting in acquisition of unlimited growth potential, evasion of apoptosis and non-responsiveness to growth inhibitory signals. Both genetic and epigenetic changes can contribute to cancer development and progression. Given the vast genetic heterogeneity of human cancers and difficulty to monitor cancer-initiating events in vivo, the precise relationship between acquisition of genetic mutations and the temporal progression of epigenetic alterations in transformed cells is largely unclear. Here, we use an in vitro model system to investigate the contribution of cellular immortality and oncogenic transformation of primary human cells to epigenetic reprogramming of DNA methylation and gene expression. Our data demonstrate that extension of replicative life span of the cells is sufficient to induce accumulation of DNA methylation at gene promoters and large-scale changes in gene expression in a time-dependent manner. In contrast, continuous expression of cooperating oncogenes in immortalized cells, although essential for anchorage-independent growth and evasion of apoptosis, does not affect de novo DNA methylation at promoters and induces subtle expression changes. Taken together, these observations imply that cellular immortality promotes epigenetic adaptation to highly proliferative state, whereas transforming oncogenes confer additional properties to transformed human cells.

The sheep genome reference sequence: a work in progress.

Until recently, the construction of a reference genome was performed using Sanger sequencing alone. The emergence of next-generation sequencing platforms now means reference genomes may incorporate sequence data generated from a range of sequencing platforms, each of which have different read length, systematic biases and mate-pair characteristics. The objective of this review is to inform the mammalian genomics community about the experimental strategy being pursued by the International Sheep Genomics Consortium (ISGC) to construct the draft reference genome of sheep (Ovis aries). Component activities such as data generation, sequence assembly and annotation are described, along with information concerning the key researchers performing the work. This aims to foster future participation from across the research community through the coordinated activities of the consortium. The review also serves as a 'marker paper' by providing information concerning the pre-publication release of the reference genome. This ensures the ISGC adheres to the framework for data sharing established at the recent Toronto International Data Release Workshop and provides guidelines for data users.

Scattering measurements on optical disks and their relation to media noise.

We have conducted measurements of scattered light from bare polycarbonate and glass substrates and from complete optical disks using a He-Ne laser beam in different polarization states and at different angles of incidence. The results are compared with the measured media noise obtained from the same disks on a dynamic tester. Both the scattered light and the media noise originate from the jaggedness and other imperfections of the groove structure, the roughness of the substrate's surface, and the inhomogeneities of the bulk of the substrate. Although some sources of media noise manifest themselves in the scattered light distribution, others cannot be easily detected by this type of measurement.

Crystallization studies on phase-change optical recording media by use of a two-dimensional periodic mark array.

We present the results of crystallization studies in thin-film samples of amorphous and crystalline Ge(x)Sb(y)Te(z). The experiments, conducted at moderately elevated temperatures, are based on measurements of the first-order diffraction efficiency from a two-dimensional periodic array of recorded marks. When the samples are slowly heated above room temperature, changes in the efficiencies of various diffracted orders give information about the on-going crystallization process within the sample. Two different compositions of the GeSbTe alloy are used in these experiments. Measurements on Ge(2)Sb(2.3)Te(5) films show crystallization dominated by nucleation. For the Sb-rich eutectic composition Ge-(SbTe), crystallization is found to be dominated by growth from crystalline boundaries. We also show that crystalline marks written by relatively high-power laser pulses are different in their optical properties from the regions crystallized by slow heating of the sample to moderate temperatures.

Crystallization and amorphization studies of a Ge(2)Sb(2.3)Te(5) thin-film sample under pulsed laser irradiation.

We present the results of crystallization and amorphization studies on a thin-film sample of Ge(2)Sb(2.3)Te(5), encapsulated in a quadrilayer stack as in the media of phase-change optical disk data storage. The study was conducted on a two-laser static tester in which one laser, operating in pulsed mode, writes either amorphous marks on a crystalline film or crystalline marks on an amorphous film. The second laser, operating at low power in the cw mode, simultaneously monitors the progress of mark formation in terms of the variations of reflectivity both during the write pulse and in the subsequent cooling period. In addition to investigating some of the expected features associated with crystallization and amorphization, we noted certain curious phenomena during the mark-formation process. For example, at low-power pulsed illumination, which is insufficient to trigger the phase transition, there is a slight change in the reflectivity of the sample. This is believed to be caused by a reversible change in the complex refractive index of the Ge(2)Sb(2.3)Te(5) film in the course of heating above the ambient temperature. We also observed that the mark-formation process may continue for as long as 1 mus beyond the end of the write laser pulse. This effect is especially pronounced during amorphous mark formation under high-power, long-pulse illumination.

Estimation of thermal conductivity of magneto-optic media.

We describe a method to estimate the thermal conductivity of the substrate, the dielectric layer, and the magneto-optic (MO) layer of MO recording media. The method relies on the disappearance of the polar Kerr rotation above the Curie temperature of the MO layer. We obtain the thermal conductivities by taking into account the differences in the heat diffusion behavior under different sized focused spots. The results are reliable to better than 5% accuracy.

Static tester for characterization of phase-change, dye-polymer, and magneto-optical media for optical data storage.

We have designed and built a static tester around a commercially available polarized light microscope. This device employs two semiconductor laser diodes (at 643- and 680-nm wavelengths) for the purpose of recording small marks on various media for optical data storage and for the simultaneous monitoring of the recording process. We use one of the lasers in the single-pulse mode to write a mark on the sample and operate the other laser in the cw mode to monitor the recording process. The two laser beams are brought to coincident focus on the sample through the objective lens of the microscope. The reflected beams are sent through a polarizing beam splitter and thus divided into two branches, depending on whether they are p or s polarized. In each branch the beam is further divided into two according to the wavelength. The four beams thus produced are sent to four high-speed photodetectors, and the resulting signals are used to monitor the reflectance as well as the polarization state of the beam on reflection from the sample. We provide a comprehensive description of the tester's design and operating principles. We also report preliminary results of measurements of phase-change, dye-polymer, and magneto-optical samples, which are currently of interest in the areas of writable and rewritable optical data storage.