A systems analysis of importin-α–β mediated nuclear protein import

Importin-β (Impβ) is a major transport receptor for Ran-dependent import of nuclear cargo. Impβ can bind cargo directly or through an adaptor such as Importin-α (Impα). Factors involved in nuclear transport have been well studied, but systems analysis can offer further insight into regulatory mechanisms. We used computer simulation and real-time assays in intact cells to examine Impα–β-mediated import. The model reflects experimentally determined rates for cargo import and correctly predicts that import is limited principally by Impα and Ran, but is also sensitive to NTF2. The model predicts that CAS is not limiting for the initial rate of cargo import and, surprisingly, that increased concentrations of Impβ and the exchange factor, RCC1, actually inhibit rather than stimulate import. These unexpected predictions were all validated experimentally. The model revealed that inhibition by RCC1 is caused by sequestration of nuclear Ran. Inhibition by Impβ results from depletion nuclear RanGTP, and, in support of this mechanism, expression of mRFP-Ran reversed the inhibition

Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells

In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient\u27s tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing

Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic Levels

Age is a powerful predictor of survival in glioblastoma multiforme (GBM) yet the biological basis for the difference in clinical outcome is mostly unknown. Discovering genes and pathways that would explain age-specific survival difference could generate opportunities for novel therapeutics for GBM. Here we have integrated gene expression, exon expression, microRNA expression, copy number alteration, SNP, whole exome sequence, and DNA methylation data sets of a cohort of GBM patients in The Cancer Genome Atlas (TCGA) project to discover age-specific signatures at the transcriptional, genetic, and epigenetic levels and validated our findings on the REMBRANDT data set. We found major age-specific signatures at all levels including age-specific hypermethylation in polycomb group protein target genes and the upregulation of angiogenesis-related genes in older GBMs. These age-specific differences in GBM, which are independent of molecular subtypes, may in part explain the preferential effects of anti-angiogenic agents in older GBM and pave the way to a better understanding of the unique biology and clinical behavior of older versus younger GBMs

Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization.

Histone methylation regulates normal stem cell fate decisions through a coordinated interplay between histone methyltransferases and demethylases at lineage specific genes. Malignant transformation is associated with aberrant accumulation of repressive histone modifications, such as polycomb mediated histone 3 lysine 27 (H3K27me3) resulting in a histone methylation mediated block to differentiation. The relevance, however, of histone demethylases in cancer remains less clear. We report that JMJD3, a H3K27me3 demethylase, is induced during differentiation of glioblastoma stem cells (GSCs), where it promotes a differentiation-like phenotype via chromatin dependent (INK4A/ARF locus activation) and chromatin independent (nuclear p53 protein stabilization) mechanisms. Our findings indicate that deregulation of JMJD3 may contribute to gliomagenesis via inhibition of the p53 pathway resulting in a block to terminal differentiation

Biofuel Blending Reduces Aircraft Engine Particle Emissions at Cruise Conditions

Aviation aerosol emissions have a disproportionately large climatic impact because they are emitted high in the relatively pristine upper troposphere where they can form linear contrails and influence cirrus clouds. Research aircraft from NASA, DLR, and NRC Canada made airborne measurements of gaseous and aerosol composition and contrail microphysical properties behind the NASA DC-8 aircraft at cruise altitudes. The DC-8 CFM-56-2C engines burned traditional medium-sulfur Jet A fuel as well as a low-sulfur Jet A fuel and a 50:50 biofuel blend. Substantial, two-to-three-fold emissions reductions are found for both particle number and mass emissions across the range of cruise thrust operating conditions. These observations provide direct and compelling evidence for the beneficial impacts of biojet fuel blending under real-world conditions

Thermodynamics of mixtures with strongly negative deviations from Raoult's law. XV. Permittivities and refractive indices for 1-alkanol + n-hexylamine systems at (293.15–303.15) K. Application of the Kirkwood-Fröhlich model

Relative permittivities at 1 MHz, , and refractive indices at the sodium D-line, , are reported at 0.1 MPa and at (293.15–303.15) K for the binary systems 1-alkanol + n-hexylamine (HxA). Also, their corresponding excess functions are calculated and correlated. Positive values of the excess permittivities, , are encountered for the methanol system, whereas the remaining mixtures show negative values. This reveals that interactions between unlike molecules contribute positively to . This contribution is dominant for the methanol mixture, while those arising from the breaking of interactions between like molecules are prevalent for the remaining mixtures. At (volume fraction) = 0.5, changes in the order: methanol > 1-propanol > 1-butanol > 1-pentanol < 1-heptanol. Similar variation with the chain length of the 1-alkanol is observed for mixtures such as 1-alkanol + heptane, or + cyclohexylamine, and can be explained in terms of the lower and weaker self-association of longer 1-alkanols. The effect of the replacement of HxA by cyclohexylamine, or by aniline, is also shown. Calculations on molar refractions indicate that dispersive interactions in the systems under study increase with the length of the 1-alkanol. The mixtures are studied by means of the application of the Kirkwood-Fröhlich model, and the Kirkwood correlation factors, including the corresponding excess values, are reported.Ministerio de Educación, Cultura y Deporte for the grants FPU14/04104 and FPU15/05456 respectively. The authors gratefully acknowledge the financial support received from the Consejería de Educación y Cultura of Junta de Castilla y León, under Project BU034U16

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

SRA directly interacts with NANOG and is important for reprogramming of iPS cells.

<p>(A) RNA pull down using nuclear extract of human pluripotent stem cells NTERA2, followed by western blot analysis of indicated proteins. (B) NANOG interacts with sense SRA. Recombinant proteins were used for RNA pull down experiment and western blotting. (C) SRA forms a complex with NANOG and p68. Co-IP was performed using recombinant NANOG and p68 in the presence of antisense or sense SRA. All experiments were performed as at least two independent replicates. The inputs were used at 10% of the samples. (D and E) SRA facilitates reprogramming of iPS cells. Human fibroblasts were transfected with a plasmid over-expressing the reprogramming factors OCT4, SOX2, c-MYC and KLF4 without or with <i>SRA</i> silencing. At day 30 cells were stained for alkaline phosphatase (AP) (D) or SSEA3 (E). Data are shown as mean±SD; n = 3. * <i>p</i> < 0.05. <i>p</i> value calculated with two-tailed Student’s <i>t</i> test.</p