Landscape of transcription in human cells

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific sub-cellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic sub-cellular localizations are also poorly understood. Since RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modifications and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations taken together prompt to a redefinition of the concept of a gene

Grape RNA-Seq analysis pipeline environment

MOTIVATION: The avalanche of data arriving since the development of NGS technologies have prompted the need for developing fast, accurate and easily automated bioinformatic tools capable of dealing with massive datasets. Among the most productive applications of NGS technologies is the sequencing of cellular RNA, known as RNA-Seq. Although RNA-Seq provides similar or superior dynamic range than microarrays at similar or lower cost, the lack of standard and user-friendly pipelines is a bottleneck preventing RNA-Seq from becoming the standard for transcriptome analysis. RESULTS: In this work we present a pipeline for processing and analyzing RNA-Seq data, that we have named Grape (Grape RNA-Seq Analysis Pipeline Environment). Grape supports raw sequencing reads produced by a variety of technologies, either in FASTA or FASTQ format, or as prealigned reads in SAM/BAM format. A minimal Grape configuration consists of the file location of the raw sequencing reads, the genome of the species and the corresponding gene and transcript annotation. Grape first runs a set of quality control steps, and then aligns the reads to the genome, a step that is omitted for prealigned read formats. Grape next estimates gene and transcript expression levels, calculates exon inclusion levels and identifies novel transcripts. Grape can be run on a single computer or in parallel on a computer cluster. It is distributed with specific mapping and quantification tools, but given its modular design, any tool supporting popular data interchange formats can be integrated. AVAILABILITY: Grape can be obtained from the Bioinformatics and Genomics website at: http://big.crg.cat/services/grape.The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 282510. This work has been carried under grants BIO2011-26205 from Ministerio de Economía y Competitividad (Spain) and INB GNV-1 and RETICS RD07/0067/0012 from PN de I+D+i, ISCIII—Subdirección General de Evaluación y Fomento de la Investigación—(Spain) and cofunded by FEDE

Joining of Macroscopic 3D Steel Transition Wire Structures to Steel Sheets: Study on the Mechanical, Microstructural, and Phase Characteristics of Brazed and Glued Joints

With an increased demand for the combination of different material classes in lightweight applications like automobiles, aircraft construction, etc., the need for simple and energy-efficient joining technologies to join these different material classes has been extensively researched over the last decades. One such hybrid material combination is the metal–plastic hybrid structure, which offers the combinational characteristics of high strength and stiffness of the metal part along with characteristic elasticity and low density of the plastic part. In this research work, the focus is laid on generating a graded property transition at the interface of metal–plastic joints by brazing a three-dimensional (3D) macroscopic transition wire structure (TWS) strucwire®, over the metal part before being molded with plastic at a later stage using an injection over-molding process. This helps in providing a mechanical interlocking facility and thereby achieving a higher load transfer at the interface of metal–plastic hybrid joints. The graded steel wire structures with different carbon content were brazed onto the galvanized steel sheets using the hotplate brazing technique. In addition to the Zinc layer on the galvanized steel sheets, electroplated Zinc coatings were fabricated on the wire structures to provide better brazing quality. The microstructural, mechanical, and intermetallic phase characteristics of the resulting brazed joints were evaluated using light microscopy, adhesion tests, and scanning electron microscopy, respectively

Landscape of transcription in human cells

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.This work was supported by the National Human Genome Research Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant/n249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Scienc

Landscape of transcription in human cells

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.This work was supported by the National Human Genome Research Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant/n249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Scienc