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38 papers found.
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TEMP: a computational method for analyzing transposable element polymorphism in populations

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of...

Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome

Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei. Here, we report the effects of arginine...

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes

M5S 3B2 1 Department of Molecular Genetics, University of Toronto , Toronto, ON , Canada M5S 1A8 2 Present address: Jie Wang, Department of Biochemistry, University at Buffalo, and NY State Center of

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data

Summary: Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non...

The spatial distribution of galactic satellites in the Λ cold dark matter cosmology

We investigate the spatial distribution of galactic satellites in high-resolution simulations of structure formation in the Λ cold dark matter (ΛCDM) model: the Aquarius dark matter simulations of individual haloes and the Millennium-II simulation of a large cosmological volume. To relate the simulations to observations of the Milky Way we use two alternative models to populate...

A systemic study of 14 southern infrared dark clouds with N2H+, HNC, HCO+ and HCN lines

We studied 14 southern infrared dark clouds (IRDCs) using data taken from the Millimetre Astronomy Legacy Team 90 GHz (MALT90) survey and the GLIMPSE and MIPSGAL mid-infrared surveys of the inner Galaxy. The physical and chemical characteristics of the 14 IRDCs were investigated using N2H+(1–0), HNC(1–0), HCO+(1–0) and HCN(1–0) molecular lines. We found that the 14 IRDCs are in...

Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells

We synthesized three 20mer caged circular antisense oligodeoxynucleotides (R20, R20B2 and R20B4) with a photocleavable linker and an amide bond linker between two 10mer oligodeoxynucleotides. With these caged circular antisense oligodeoxynucleotides, RNA-binding affinity and its digestion by ribonuclease H were readily photomodulated. RNA cleavage rates were upregulated ∼43-, 25...

PsRobot: a web-based plant small RNA meta-analysis toolbox

Small RNAs (smRNAs) in plants, mainly microRNAs and small interfering RNAs, play important roles in both transcriptional and post-transcriptional gene regulation. The broad application of high-throughput sequencing technology has made routinely generation of bulk smRNA sequences in laboratories possible, thus has significantly increased the need for batch analysis tools. PsRobot...

Are mergers responsible for universal halo properties?

N-body simulations of cold dark matter (CDM) have shown that, in this hierarchical structure formation model, dark matter halo properties, such as the density profile, the phase-space density profile, the distribution of axial ratio, the distribution of spin parameter and the distribution of internal specific angular momentum, follow ‘universal’ laws or distributions. Here, we...

Plasma membrane receptor-like kinase leaf panicle 2 acts downstream of the DROUGHT AND SALT TOLERANCE transcription factor to regulate drought sensitivity in rice

Drought is a recurring climatic hazard that reduces the crop yields. To avoid the negative effects of drought on crop production, extensive efforts have been devoted to investigating the complex mechanisms of gene expression and signal transduction during drought stress. Receptor-like kinases (RLKs) play important roles in perceiving extracellular stimuli and activating...

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

Gene Ontology (GO) analysis has become a commonly used approach for functional studies of large-scale genomic or transcriptomic data. Although there have been a lot of software with GO-related analysis functions, new tools are still needed to meet the requirements for data generated by newly developed technologies or for advanced analysis purpose. Here, we present a Gene Ontology...

Proteome analysis of Physcomitrella patens exposed to progressive dehydration and rehydration

Physcomitrella patens is an extremely dehydration-tolerant moss. However, the molecular basis of its responses to loss of cellular water remains unclear. A comprehensive proteomic analysis of dehydration- and rehydration-responsive proteins has been conducted using quantitative two-dimensional difference in-gel electrophoresis (2D-DIGE), and traditional 2-D gel electrophoresis (2...

PIM Kinase Inhibitor AZD1208 for Treatment of MYC-Driven Prostate Cancer

Background: PIM1 kinase is coexpressed with c-MYC in human prostate cancers (PCs) and dramatically enhances c-MYC-induced tumorigenicity. Here we examine the effects of a novel oral PIM inhibitor, AZD1208, on prostate tumorigenesis and recurrence.

Photomodulating RNA cleavage using photolabile circular antisense oligodeoxynucleotides

Caged antisense oligodeoxynucleotides (asODNs) are synthesized by linking two ends of linear oligodeoxynucleotides using a photocleavable linker. Two of them (H30 and H40) have hairpin-like structures which show a large difference in thermal stability (ΔTm = 17.5°C and 11.6°C) comparing to uncaged ones. The other three (C20, C30 and C40) without stable secondary structures have...

Discreteness effects in simulations of hot/warm dark matter

In hot/warm dark matter (HDM/WDM) universes the density fluctuations at early times contain very little power below a characteristic wavelength related inversely to the particle mass. We study how discreteness noise influences the growth of non-linear structures smaller than this coherence scale in N-body simulations of cosmic structure formation. It has been known for 20 yr that...

A gemcitabine sensitivity screen identifies a role for NEK9 in the replication stress response

The Replication Stress Response (RSR) is a signaling network that recognizes challenges to DNA replication and coordinates diverse DNA repair and cell-cycle checkpoint pathways. Gemcitabine is a nucleoside analogue that causes cytotoxicity by inducing DNA replication blocks. Using a synthetic lethal screen of a RNAi library of nuclear enzymes to identify genes that when silenced...

Substructure lensing: effects of galaxies, globular clusters and satellite streams

Lensing flux-ratio anomalies have been frequently observed and taken as evidence for the presence of abundant dark matter substructures in lensing galaxies, as predicted by the cold dark matter (CDM) model of cosmogony. In previous work, we examined the cusp–caustic relations of the multiple images of background quasars lensed by galaxy-scale dark matter haloes, using a suite of...

The haloes of bright satellite galaxies in a warm dark matter universe

High-resolution N-body simulations of galactic cold dark matter haloes indicate that we should expect to find a few satellite galaxies around the Milky Way whose haloes have a maximum circular velocity in excess of 40 km s−1. Yet, with the exception of the Magellanic Clouds and the Sagittarius dwarf, which likely reside in subhaloes with significantly larger velocities than this...

The dependence of galaxy formation on cosmological parameters: can we distinguish between the WMAP1 and WMAP3 parameter sets?

Jie Wang Gabriella De Lucia Manfred G. Kitzbichler Simon D. M. White Max-Planck-Institut fur Astrophysik Karl-Schwarzschild-Str. D- Garching Germany A B S T R A C T We combine N-body simulations of

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation...