247 research outputs found
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
Many Eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications, and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5'-complete cDNA sequencing with an integrated data analysis workflow to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first available developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1,300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes
Random perfect lattices and the sphere packing problem
Motivated by the search for best lattice sphere packings in Euclidean spaces
of large dimensions we study randomly generated perfect lattices in moderately
large dimensions (up to d=19 included). Perfect lattices are relevant in the
solution of the problem of lattice sphere packing, because the best lattice
packing is a perfect lattice and because they can be generated easily by an
algorithm. Their number however grows super-exponentially with the dimension so
to get an idea of their properties we propose to study a randomized version of
the algorithm and to define a random ensemble with an effective temperature in
a way reminiscent of a Monte-Carlo simulation. We therefore study the
distribution of packing fractions and kissing numbers of these ensembles and
show how as the temperature is decreased the best know packers are easily
recovered. We find that, even at infinite temperature, the typical perfect
lattices are considerably denser than known families (like A_d and D_d) and we
propose two hypotheses between which we cannot distinguish in this paper: one
in which they improve Minkowsky's bound phi\sim 2^{-(0.84+-0.06) d}, and a
competitor, in which their packing fraction decreases super-exponentially,
namely phi\sim d^{-a d} but with a very small coefficient a=0.06+-0.04. We also
find properties of the random walk which are suggestive of a glassy system
already for moderately small dimensions. We also analyze local structure of
network of perfect lattices conjecturing that this is a scale-free network in
all dimensions with constant scaling exponent 2.6+-0.1.Comment: 19 pages, 22 figure
ROOOH: A missing piece of the puzzle for OH measurements in low-NO environments?
Abstract. Field campaigns have been carried out with the FAGE (fluorescence assay by
gas expansion) technique in remote biogenic environments in the last decade
to quantify the in situ concentrations of OH, the main oxidant in the
atmosphere. These data have revealed concentrations of OH radicals up to a
factor of 10 higher than predicted by models, whereby the disagreement
increases with decreasing NO concentration. This was interpreted as a major
lack in our understanding of the chemistry of biogenic VOCs (volatile organic
compounds), particularly isoprene, which are dominant in remote pristine
conditions. But interferences in these measurements of unknown origin have
also been discovered for some FAGE instruments: using a pre-injector, all
ambient OH is removed by fast reaction before entering the FAGE cell, and any
remaining OH signal can be attributed to an interference. This technique is
now systematically used for FAGE measurements, allowing the reliable
quantification of ambient OH concentrations along with the signal due to
interference OH. However, the disagreement between modelled and measured high
OH concentrations of earlier field campaigns as well as the origin of the
now-quantifiable background OH is still not understood. We present in this
paper the compelling idea that this interference, and thus the disagreement
between model and measurement in earlier field campaigns, might be at least
partially due to the unexpected decomposition of a new class of molecule,
ROOOH, within the FAGE instruments. This idea is based on experiments,
obtained with the FAGE set-up of the University of Lille, and supported by a
modelling study. Even though the occurrence of this interference will be
highly dependent on the design and measurement conditions of different FAGE
instruments, including ROOOH in atmospheric chemistry models might reflect a
missing piece of the puzzle in our understanding of OH in clean atmospheres.
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ASaiM: A Galaxy-based framework to analyze microbiota data
Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable
The BMV experiment : a novel apparatus to study the propagation of light in a transverse magnetic field
In this paper, we describe in detail the BMV (Bir\'efringence Magn\'etique du
Vide) experiment, a novel apparatus to study the propagation of light in a
transverse magnetic field. It is based on a very high finesse Fabry-Perot
cavity and on pulsed magnets specially designed for this purpose. We justify
our technical choices and we present the current status and perspectives.Comment: To be published in the European Physical Journal
Experimental Evolution of a Plant Pathogen into a Legume Symbiont
Following acquisition of a rhizobial symbiotic plasmid, adaptive mutations in the virulence pathway allowed pathogenic Ralstonia solanacearum to evolve into a legume symbiont under plant selection
Ten simple rules for making training materials FAIR
Author summary: Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, itâs sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: Theyâre often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all
The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis
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