RNASim 1.0 - RNA Evolution Model. My Biosoftware. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. Abstract A large proportion of functional sequence within mammalian genomes falls outside protein-coding exons and can be transcribed into long RNAs. However, the roles in mammalian biology of long noncoding RNA (lncRNA) are not well understood.
Few lncRNAs have experimentally determined roles, with some of these being lineage-specific. Determining the extent by which transcription of lncRNA loci is retained or lost across multiple evolutionary lineages is essential if we are to understand their contribution to mammalian biology and to lineage-specific traits. Author Summary The best-understood portion of mammalian genomes contains genes transcribed into RNAs, which are subsequently translated into proteins. Figures Citation: Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, et al. (2012) Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. Editor: David P. Received: January 11, 2012; Accepted: May 30, 2012; Published: July 26, 2012 Introduction Results Figure 1. Sign In. Quest for self-replicating RNA edges closer to life’s possible origin. The discovery of nucleic acid molecules that can catalyze chemical reactions has revolutionized thinking about the origin of life.
These catalytic RNAs, called ribozymes, showed that a single molecule could embody two of the major aspects of life: genetic information and chemical activity. They also raised the intriguing possibility that it might be possible to find an RNA molecule that could copy itself. After all, once you have a single self-duplicating molecule, you would quickly end up with a large collection of self-duplicating molecules competing for resources. Evolution would be off and running. So far, though, efforts to make a self-replicating ribozyme have come up short. Most RNA molecules with this sort of activity have been around 200 bases long and have tended to stall before copying more than a few dozen bases. But now, scientists have produced the first molecule that can copy RNAs longer than itself.
Leclercfl : Daniel Caffrey - Evolution... Twitter. Daniel Caffrey - Evolution of Alu elements in long non coding RNA and mRNA. GenomeBiology : A scenario for the #evolution... Evolution of Foamy Viruses: The Most Ancient of All Retroviruses. Daniel Caffrey - Evolution of Alu elements in long non coding RNA and mRNA. Abstract | Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria. Research article Ida Porcelli, Mark Reuter, Bruce M Pearson, Thomas Wilhelm and Arnoud HM van Vliet* BMC Genomics 2013, 14:616 doi:10.1186/1471-2164-14-616 Published: 12 September 2013 Abstract Background Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels.
Results Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Conclusions close Sign up to receive new article alerts from BMC Genomics.
Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution. Revolution of nephrology research by deep sequencing: ChIP-seq and RNA-seq. New insight into the human genome through the lens of evolution. By comparing the human genome to the genomes of 34 other mammals, Australian scientists have described an unexpectedly high proportion of functional elements conserved through evolution. Less than 1.5% of the human genome is devoted to conventional genes, that is, encodes for proteins. The rest has been considered to be largely junk. However, while other studies have shown that around 5-8% of the genome is conserved at the level of DNA sequence, indicating that it is functional, the new study shows that in addition much more, possibly up to 30%, is also conserved at the level of RNA structure. DNA is a biological blueprint that must be copied into another form before it can be actualised. Through a process known as 'transcription', DNA is copied into RNA, some of which 'encodes' the proteins that carry out the biological tasks within our cells.
"Genomes accumulate mutations over time, some of which don't change the structure of associated RNAs. Sign In. The insect order Hymenoptera encompasses several lineages, including ants, bees, and aculeate wasps, that independently evolved obligate eusociality. Such eusocial lineages are characterized by reproductive division of labor, cooperative brood care, and overlapping generations (Michener 1969).
Ants (Formicidae) represent one of the oldest (∼130 million years) and most successful exclusively eusocial lineages (Cardinal and Danforth 2011). They have colonized every terrestrial habitat except at the highest latitudes, and they have achieved substantial diversity in both individual and colonial traits. The ecological and evolutionary success of the more than 15,000 described extant ant species ( is often attributed to their sociality and ability to engineer environments, e.g., by building elaborate nests, herding aphids for honeydew, or practicing sustainable agriculture (Crozier and Pamilo 1996; Hölldobler and Wilson 2009).
Results Figure 1. Figure 2. BMC Biology | Full text | Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. Enzyme engineering through evolution: Thermostable recombinant group II intron reverse transcriptases provide new tools for RNA research and biotechnology. New insight into the human genome through the lens of evolution — Garvan Institute. By comparing the human genome to the genomes of 34 other mammals, Australian scientists have described an unexpectedly high proportion of functional elements conserved through evolution. Less than 1.5% of the human genome is devoted to conventional genes, that is, encodes for proteins. The rest has been considered to be largely junk. However, while other studies have shown that around 5-8% of the genome is conserved at the level of DNA sequence, indicating that it is functional, the new study shows that in addition much more, possibly up to 30%, is also conserved at the level of RNA structure.
DNA is a biological blueprint that must be copied into another form before it can be actualised. Through a process known as ‘transcription’, DNA is copied into RNA, some of which ‘encodes’ the proteins that carry out the biological tasks within our cells. Most RNA molecules do not code for protein, but instead perform regulatory functions, such as determining the ways in which genes are expressed. LincRNAs: Genomics, Evolution, and Mechanisms. LincRNAs: Genomics, Evolution, and Mechanisms. Enzyme engineering through evolution: Thermostable recombinant group II intron reverse transcriptases provide new tools for RNA research and biotechnology. Enzyme engineering through evolution: Thermostable recombinant group II intron reverse transcriptases provide new tools for RNA research and biotechnology. The origin of the RNA world: Co-evolution of genes and metabolism.
Abstract Discoveries demonstrating that RNA can serve genetic, catalytic, structural, and regulatory roles have provided strong support for the existence of an RNA World that preceded the origin of life as we know it. Despite the appeal of this idea, it has been difficult to explain how macromolecular RNAs emerged from small molecules available on the early Earth. We propose here a mechanism by which mutual catalysis in a pre-biotic network initiated a progression of stages characterized by ever larger and more effective catalysts supporting a proto-metabolic network, and the emergence of RNA as the dominant macromolecule due to its ability to both catalyze chemical reactions and to be copied in a template-directed manner.
Graphical abstract Despite the appeal of the RNA world, it has been difficult to explain how macromolecular RNAs emerged from small molecules available on the early Earth. Keywords RNA World; Catalysis; Metabolism; Ribozyme; Pre-biotic chemistry; Evolution. Evolution of fast mutating replicators—RNA viruses and the RNA world.
Volume 371, Issue 1, 1 November 2006, Pages 80–83 IX Latin American Workshop on Nonlinear Phenomena Edited By Pablo M.Gleiser and Marcelo N.Kuperman Abstract In the last two decades, viruses have become the model system to witness evolution in the laboratory. Keywords RNA viruses; Evolutionary dynamics; Molecular quasispecies; RNA world Copyright © 2006 Elsevier B.V. Monte Carlo simulation of early molecular evolution in the RNA World. Abstract The origin of life remains a highly speculative field, mainly due to the shortage of our knowledge on prebiotic chemistry and basic understanding on the essence of life.
In this context, computer simulation is expected to play an important role. For instance, the scenario concerning the genesis of the widely accepted RNA World remains blurry, though we have gathered some circumstantial evidence and fragmented knowledge on several supposed stages, including formation of polynucleotides from a prebiotic nucleotide pool, emergence of RNA replicases (RNA molecules catalyzing their own replication), and evolution of RNA replicases. It is highly valuable to simulate the stages as a continuous process to evaluate the plausibility of the supposition and study the rules involved. Here we construct a computer simulation on the process using Monte Carlo method. Keywords Origin of life; The RNA World; RNA replicase; Molecular evolution; Computer simulation; Monte Carlo method.
The evolution of episodic memory. Natural GMOs Part 169. Co-evolution of genomic parasites and RNA based defences against them have a long, long history. Natural GMOs Part 169. Co-evolution of genomic parasites and RNA based defences against them has a long, long history. Ribosomal RNA genes evolution in Tragopogon: A story of new and old w… The role of mutational robustness in RNA virus evolution. Nobel Laureate Jack Szostak on RNA Evolution, Drug Discovery Chemistry. March 13, 2013 | Jack Szostak has won the Lasker Award and the 2009 Nobel Prize, founded numerous biotech companies including Gilead and more recently Ra Pharmaceuticals, is a Howard Hughes Medical Institute investigator and runs a lab at Mass General Hospital that is an intellectual powerhouse in a broad range of areas from RNA biology to novel chemical structures. And now he’s trying to out-evolve nature. Szostak will be keynoting CHI’s Drug Discovery Chemistry conference in San Diego in April.
In this video interview with Bio-IT World editor Kevin Davies, Szostak discusses his current research interests and entrepreneurial endeavors. “For a long time we’ve had an interest in using the principles of evolution to find new, interesting molecules,” Szostack tells Davies. “What we’re trying to do is basically use evolutionary technology combined with chemistry to make very large populations of [cyclic peptides], and see if we can actually do a little better than nature.” Watch the video. BMC Evolutionary Biology | Full text | Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus. Concerted Evolution in the Ribosomal RNA Cistron. Background Gene conversion is the mechanism proposed to be responsible for the homogenization of multigene families such as the nuclear ribosomal gene clusters.
This concerted evolutionary process prevents individual genes in gene clusters from accumulating mutations. The mechanism responsible for concerted evolution is not well understood but recombination during meiosis has been hypothesized to play a significant role in this homogenization. In this study we tested the hypothesis of unequal crossing over playing a significant role in gene conversion events within the ribosomal RNA cistron during meiosis, mitosis or both life stages in the fungal tree pathogen Ceratocystis manginecans. Methods Ceratocystis manginecans, a haploid ascomycete, reproduces homothallically and was found to have two distinct sequences within the internally transcribed spacer (ITS) region of the ribosomal RNA cistron.
Results Conclusion Figures Editor: Nicolas Corradi, University of Ottawa, Canada Introduction. Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia. To view the full text, please login as a subscribed user or purchase a subscription. Click here to view the full text on ScienceDirect. Figure 1 Significantly Mutated Genes and Associated Gene Pathways in 160 CLL Samples (A) Mutation significance analysis using the MutSig2.0 and GISTIC2.0 algorithms identifies recurrently mutated genes and recurrent sCNAs in CLL, respectively. (B) The significantly mutated genes fall into seven core signaling pathways, in which the genes play well-established roles. See also Figures S1 , S2 , and Table S2 A. Figure 2 Subclonal and Clonal sSNVs Are Detected in CLL in Varying Quantities Based on Age at Diagnosis, IGHV Mutation Status, and Treatment Status (A) The analysis workflow: “CLL driver events” (red box) were identified by mutation significance analysis using WES and SNP array data collected from matched germline and tumor DNA.
(B) A representative example of the transformations generated by ABSOLUTE (for sample CLL088). Figure 3 Figure 4 Figure 5 Figure 6. Wja.2012. Wasp Transcriptome Analysis Hints at Evolution of Social Behavior. Science Magazine: Sign In. First artificial enzyme created by evolution in a test tube. 3D structure of the evolved enzyme (an RNA ligase), using 10 overlaid snapshots. In the top region, the overlays show the range of bending and folding flexibility in the amino acid chain that forms the molecule. The two gray balls are zinc ions. (Credit: University of Minnesota) There’s a wobbly new biochemical structure in Burckhard Seelig’s lab at the University of Minnesota that may resemble what enzymes looked like billions of years ago, when life on earth began to evolve.
Seelig created the fledgling enzyme by using directed evolution in the laboratory. Working with team members, he subsequently determined its structure.. Seelig speculates the new protein resembles primordial enzymes, before their current structures evolved. Using directed evolution While a handful of groups worldwide are developing artificial enzymes, they use rational design to construct the proteins on computers. Instead, the Seelig lab employs directed evolution. The Evolution of the Cell. The RNA world hypothesis: the worst theory of th... [Biol Direct. Current Opinion in Cell Biology - Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists.
Volume 25, Issue 1, February 2013, Pages 134–141 Cell architecture Edited By Anna Akhmanova and Tim Stearns Microbial eukaryotes encompass the majority of eukaryotic evolutionary and cytoskeletal diversity. The cytoskeletal complexity observed in multicellular organisms appears to be an expansion of components present in genomes of diverse microbial eukaryotes such as the basal lineage of flagellates, the Excavata. Excavate protists have complex and diverse cytoskeletal architectures and life cycles — essentially alternative cytoskeletal ‘landscapes’ — yet still possess conserved microtubule-associated and actin-associated proteins.
Comparative genomic analyses have revealed that a subset of excavates, however, lack many canonical actin-binding proteins central to actin cytoskeleton function in other eukaryotes. Copyright © 2012 Elsevier Ltd. Birth and expression evolution of mammalian microRNA genes. Craig Mello - The role of RNA in evolution - Nobel Week Dialogue. Human genome data would be very difficult to mine unless you had something like RNAi according to Nobel Laureate Craig Mello. He spoke me about his insights into RNAi, new research and what we have yet to discover. This will be the first time that Prof Craig Mello will visit Stockholm during Nobel Week since he brought home the prize to UMass six years ago. Reminiscing about his previous “whirlwind” visit, he said “it was an incredible experience and I’m really looking forward to going back.” Reviewing RNAi Mello was honoured along with Andrew Fire for their discovery of RNA interference, now known an RNAi. Fourteen years after their first paper on RNAi, Mello said “the human genome data, would be very difficult to mine for functional insights unless you had something like RNAi.”
Audio: Here’s a great insight into Craig Mello as a kid and what blew his mind (Length = 1:24). Non-Coding RNA Much of Mello’s latest research has been on the non-coding genome. Role in Evolution Back. Evolution: It's All In How You Splice It. The Institute for Genomic Biology | Where Science Meets Society. Carl R. Woese: 1928 – 2012 | The Institute for Genomic Biology. Medical News Today: Health News. Science Magazine: Sign In. RNA-only genes: The origin of species? Evolution: It's All In How You Splice It.
Craig Mello - The role of RNA in evolution - Nobel Week Dialogue. Nobel Week Dialogue. Epidemiology, Molecular Epidemiology and Evolution of Bovine Respiratory Syncytial Virus. MicroRNAs in opioid addiction: elucidating evolution. Popular press wildly overblows “gene for humanity” Birth and expression evolution of mammalian microRNA genes. Genome Research. Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity.
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Coevolution in RNA Molecules Driven by Selective Constraints: Evidence from 5S rRNA. Evolution and Complexity of Micro RNA in the Human Brain.
Expression of cassini, a murine gamma-satellite sequence conserved in evolution, is regulated in normal and malignant hematopoietic cells. Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system. Evolution of protein synthesi... [Cold Spring Harb Perspect Biol. 2012. Current Opinion in Cell Biology - Small non-coding RNAs mount a silent revolution in gene expression. Abstract | The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others) Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana : Scientific Reports. Service d'authentification de l'Inist-CNRS. Synthetic Genetic Polymers Capable of Heredity and Evolution.
RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. Phylogenomics of Prokaryotic Ribosomal Proteins.