89,432 research outputs found
In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes
No full textBackground: Repeat-induced point mutation (RIP) is a fungal genome defence mechanism guarding against transposon invasion. RIP mutates the sequence of repeated DNA and over time renders the affected regions unrecognisable by similarity search tools such as BLAST.
Results: DeRIP is a new software tool developed to predict the original sequence of a RIP-mutated region prior to the occurrence of RIP. In this study, we apply deRIP to the genome of the wheat pathogen Stagonospora nodorum SN15 and predict the origin of several previously uncharacterised classes of repetitive DNA.
Conclusions: Five new classes of transposon repeats and four classes of endogenous gene repeats were identified after deRIP. The deRIP process is a new tool for fungal genomics that facilitates the identification and understanding of the role and origin of fungal repetitive DNA. DeRIP is open-source and is available as part of the RIPCAL suite at http://www.sourceforge.net/projects/ripcal
Little rip in classical and quantum f(R) cosmology
No full textThe little rip is a cosmological abrupt event predicted by some phantom dark energy models that could describe the future evolution of our Universe. This event can be interpreted as a big rip singularity delayed indefinitely, although in those models bounded structures will be destroyed in a finite cosmic time in the future. In this work, we analyze the little rip cosmology from a classical and quantum point of view within the scheme of alternative metric f(R) theories of gravity. The quantum analysis is performed in the framework of f(R) quantum geometrodynamics by means of the modified Wheeler-DeWitt equation. In this context, we show that the DeWitt criterion can be satisfied. Similar to what happens in general relativity, this result points toward the avoidance of the little rip in f(R) quantum cosmology.Ministerio de Economía y Competitividad (España)European CommissionUniversidad Complutense de MadridBanco de SantanderIkerbasqueEusko JaurlaritzaDepto. de Física TeóricaFac. de Ciencias FísicasInstituto de Física de Partículas y del Cosmos (IPARCOS)TRUEpu
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
No full textBackground
Repeat-induced point mutation (RIP) is a fungal-specific genome defence mechanism that alters the sequences of repetitive DNA, thereby inactivating coding genes. Repeated DNA sequences align between mating and meiosis and both sequences undergo C:G to T:A transitions. In most fungi these transitions preferentially affect CpA di-nucleotides thus altering the frequency of certain di-nucleotides in the affected sequences. The majority of previously published in silico analyses were limited to the comparison of ratios of pre- and post-RIP di-nucleotides in putatively RIP-affected sequences – so-called RIP indices. The analysis of RIP is significantly more informative when comparing sequence alignments of repeated sequences. There is, however, a dearth of bioinformatics tools available to the fungal research community for alignment-based RIP analysis of repeat families.
Results
We present RIPCAL http://www.sourceforge.net/projects/ripcal, a software tool for the automated analysis of RIP in fungal genomic DNA repeats, which performs both RIP index and alignment-based analyses. We demonstrate the ability of RIPCAL to detect RIP within known RIP-affected sequences of Neurospora crassa and other fungi. We also predict and delineate the presence of RIP in the genome of Stagonospora nodorum – a Dothideomycete pathogen of wheat. We show that RIP has affected different members of the S. nodorum rDNA tandem repeat to different extents depending on their genomic contexts.
Conclusion
The RIPCAL alignment-based method has considerable advantages over RIP indices for the analysis of whole genomes. We demonstrate its application to the recently published genome assembly of S. nodorum
Behaviours of rip cosmological models in f(Q,C) gravity
No full textIn this study, the Universe's rip cosmology theories have been provided for the f(Q,C) gravity theory, where Q and C stand for the non-metricity scalar and boundary term. We assume f(Q,C)=αQn+βC and analyze the nature of the physical parameters for the Little Rip (LR), Big Rip (BR) and Pseudo Rip (PR) models. In the LR and PR models, the EoS parameter exhibits phantom characteristics but remains closely aligned with the ΛCDM line. The non-metricity term Q has direct effect on the rip models. After investigating the energy conditions, we recognise that our model violates the strong energy constraint. Avoiding singularity situations has been noted in all of these accelerated models. The characteristics of the jerk and snap parameters have been investigated. Our model provides an effective description of the Universe's evolutionary history and fits well with contemporary cosmic data
Inactivation of the Neurospora crassa Gene Encoding the Mitochondrial Protein Import Receptor MOM19 by the Technique of ''Sheltered RIP''
No full textWe have used a technique referred to as ``sheltered RIP'' (repeat induced point mutation) to create mutants of the mom-19 gene of Neurospora crassa, which encodes an import receptor for nuclear encoded mitochondrial precursor proteins. Sheltered RIP permits the isolation of a mutant gene in one nucleus, even if that gene is essential for the survival of the organism, by sheltering the nucleus carrying the mutant gene in a heterokaryon with an unaffected nucleus. Furthermore, the nucleus harboring the RIPed gene contains a selectable marker so that it is possible to shift nuclear ratios in the heterokaryons to a state in which the nucleus containing the RIPed gene predominates in cultures grown under selective conditions. This results in a condition where the target gene product should be present at very suboptimal levels and allows the study of the mutant phenotype. One allele of mom-19 generated by this method contains 44 transitions resulting in 18 amino acid substitutions. When the heterokaryon containing this allele was grown under conditions favoring the RIPed nucleus, no MOM19 protein was detectable in the mitochondria of the strain. Homokaryotic strains containing the RIPed allele exhibit a complex and extremely slow growth phenotype suggesting that the product of the mom-19 gene is important in N. crassa
MACISTE-RIP (Rifiuti-Inquinamento-Pulizia)
No full textRIP-system provides information for the management of environmental clean-up services. Dedicated software MACISTE-RIP, developed in collaboration with SME SEPG, providing multidisciplinary management of clean-up services and their relationship to environmental data
Classical and Quantum <i>f</i>(<i>R</i>) Cosmology: The Big Rip, the Little Rip and the Little Sibling of the Big Rip
No full textThe big rip, the little rip and the little sibling of the big rip are cosmological doomsdays predicted by some phantom dark-energy models that could describe the future evolution of our universe. When the universe evolves towards either of these future cosmic events, all bounded structures and, ultimately, space–time itself are ripped apart. Nevertheless, it is commonly believed that quantum gravity effects may smooth or even avoid these classically predicted singularities. In this review, we discuss the classical and quantum occurrence of these riplike events in the scheme of metric f(R) theories of gravity. The quantum analysis is performed in the framework of f(R) quantum geometrodynamics. In this context, we analyze the fulfilment of the DeWitt criterion for the avoidance of these singular fates. This review contains as well new unpublished work (the analysis of the equation of state for the phantom fluid and a new quantum treatment of the big rip and the little sibling of the big rip events)
f(R) quantum cosmology: avoiding the Big Rip
No full textExtended theories of gravity have gathered a lot of attention over the last years, for they not only provide an excellent framework to describe the inflationary era but also yields an alternative to the elusive and mysterious dark energy. Among the different extended theories of gravity, on this work we focus on metric theories. In addition, it is well known that if the late-time acceleration of the universe is stronger than the one induced by a cosmological constant then some future cosmic singularities might arise, being the Big Rip the most virulent one. Following this reasoning, on this work, we analyse the Big Rip singularity in the framework of quantum geometrodynamics. Invoking the DeWitt criterium, i. e. that the wave function vanishes at the classical singularity, we proof that a class of solutions to the Wheeler-DeWitt equation fulfilling this condition can be found. Therefore, this result hints towards the avoidance of the Big Rip in metric theories of gravity
Tilting at Windmills : BLDSC and the UK Higher Education Community
No full textPurpose - To provide an overview of, the relationship between the British Library and higher education libraries in the 1990s, with particular relation to document supply. It also goes on to explore current developments in scholarly communication. Design/methodology/approach - The author played a role in several of the events described and uses the available literature to enlarge on a personal view of that decade. Findings - The paper shows that the relationship was a strained one caused in part by a mismatch of resources, but is in any case dwarfed by the larger external forces and changing opportunities and technologies for scholarly communication. Originality/value - Provides a record of the period
RIP-Seq data analysis to determine RNA-protein associations
No full textNext-generation sequencing (NGS) technologies have opened new avenues of unprecedented power for research in molecular biology and genetics. In particular, their application to the study of RNA-binding proteins (RBPs), extracted through immunoprecipitation (RIP), permits to sequence and characterize all RNAs that were found to be bound in vivo by a given RBP (RIP-Seq). On the other hand, NGS-based experiments, including RIP-Seq, produce millions of short sequence fragments that have to be processed with suitable bioinformatic tools and methods to recover and/or quantify the original sequence sample. In this chapter we provide a survey of different approaches that can be taken for the analysis of RIP-Seq data and the identification of the RNAs bound by a given RBP
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