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Showing 31-60 of 122 results for "r8508" within Papers
C Grunau et al.
Nucleic acids research, 29(13), E65-E65 (2001-07-04)
Bisulfite genomic sequencing is the method of choice for the generation of methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil by treatment with bisulfite and the sequencing of subsequently generated PCR
Tek N Lamichhane et al.
Molecular and cellular biology, 33(15), 2918-2929 (2013-05-30)
tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N6-isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37
Manuel Neeb et al.
Journal of medicinal chemistry, 57(13), 5554-5565 (2014-06-24)
Drug molecules should remain uncharged while traveling through the body and crossing membranes and should only adopt charged state upon protein binding, particularly if charge-assisted interactions can be established in deeply buried binding pockets. Such strategy requires careful pKa design
Ewa Morawiec et al.
Gene, 526(1), 16-22 (2013-05-10)
Maf1 is a negative regulator of RNA polymerase III (Pol III) in yeast. Maf1-depleted cells manifest elevated tRNA transcription and inability to grow on non-fermentable carbon source, such as glycerol. Using genomic microarray approach, we examined the effect of Maf1
Alexis J Rovner et al.
Nature, 518(7537), 89-93 (2015-01-22)
Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels and chemicals. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs
Structural biology: RNA exerts self-control.
Bhaskar Chetnani et al.
Nature, 500(7462), 279-280 (2013-07-31)
Jungwook Kim et al.
Nature, 498(7452), 123-126 (2013-05-17)
The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and
Md Tauqeer Alam et al.
Gene, 539(1), 44-49 (2014-02-11)
The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a "vulnerable" species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes
Andreas A H Su et al.
Nucleic acids research, 41(12), 6250-6258 (2013-04-27)
The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA
Maria Rosa Garcia-Silva et al.
Gene, 538(2), 379-384 (2014-01-28)
The study of small RNAs and Argonaute proteins in eukaryotes that are deficient in functional RNA interference could provide insights into novel functions of small RNAs. In this study we describe small non-coding RNAs bound to a distinctive Argonaute protein
Alan Hodgkinson et al.
Science (New York, N.Y.), 344(6182), 413-415 (2014-04-26)
Mutations in the mitochondrial genome are associated with multiple diseases and biological processes; however, little is known about the extent of sequence variation in the mitochondrial transcriptome. By ultra-deeply sequencing mitochondrial RNA (>6000×) from the whole blood of ~1000 individuals
Ofer Elhanani et al.
Cell reports, 31(5), 107591-107591 (2020-05-07)
The emerging appreciation of plasticity among pancreatic lineages has created interest in harnessing cellular reprogramming for β cell replacement therapy of diabetes. Current reprogramming methodologies are inefficient, largely because of a limited understanding of the underlying mechanisms. Using an in vitro
Premal Shah et al.
Cell, 153(7), 1589-1601 (2013-06-26)
Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes
Jungwook Kim et al.
BMC structural biology, 13, 5-5 (2013-04-27)
Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the
Leo C K Wan et al.
Nucleic acids research, 41(12), 6332-6346 (2013-04-27)
The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t(6)A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with
Keshab Rijal et al.
Gene, 556(1), 35-50 (2014-12-03)
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system
Rushia Turner et al.
RNA (New York, N.Y.), 19(12), 1857-1863 (2013-10-22)
Estimating the reactivity of 2'-hydroxyl groups along an RNA chain of interest aids in the modeling of the folded RNA structure; flexible loops tend to be reactive, whereas duplex regions are generally not. Among the most useful reagents for probing
Jun-Feng Gao et al.
Gene, 541(2), 92-100 (2014-03-15)
Bunostomum trigonocephalum and Bunostomum phlebotomum are blood-feeding hookworms of sheep and cattle, causing considerable economic losses to the live stock industries. Studying genetic variability within and among hookworm populations is critical to addressing epidemiological and ecological questions. Mitochondrial (mt) DNA
Miao Chen et al.
Genes & development, 28(9), 959-970 (2014-05-03)
tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and
Daniel Castro-Roa et al.
Nature chemical biology, 9(12), 811-817 (2013-10-22)
Fic proteins are ubiquitous in all of the domains of life and have critical roles in multiple cellular processes through AMPylation of (transfer of AMP to) target proteins. Doc from the doc-phd toxin-antitoxin module is a member of the Fic
Lars V Bock et al.
Nature structural & molecular biology, 20(12), 1390-1396 (2013-11-05)
During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM
Timothy M Colussi et al.
Nature, 511(7509), 366-369 (2014-06-10)
RNA is arguably the most functionally diverse biological macromolecule. In some cases a single discrete RNA sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. Such multifunctionality can also be driven or enhanced by the
Martijn J T N Timmermans et al.
Molecular phylogenetics and evolution, 79, 169-178 (2014-06-10)
The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire
Igor Cestari et al.
Molecular and cellular biology, 33(24), 4872-4888 (2013-10-16)
The genes for all cytoplasmic and potentially all mitochondrial aminoacyl-tRNA synthetases (aaRSs) were identified, and all those tested by RNA interference were found to be essential for the growth of Trypanosoma brucei. Some of these enzymes were localized to the
Małgorzata Cieśla et al.
Biochimica et biophysica acta, 1843(6), 1103-1110 (2014-03-01)
Yeast Fba1 (fructose 1,6-bisphosphate aldolase) is a glycolytic enzyme essential for viability. The overproduction of Fba1 enables overcoming of a severe growth defect caused by a missense mutation rpc128-1007 in a gene encoding the C128 protein, the second largest subunit
Fu-Jung Lin et al.
PLoS genetics, 9(5), e1003516-e1003516 (2013-05-30)
Mouse Ikbkap gene encodes IKAP--one of the core subunits of Elongator--and is thought to be involved in transcription. However, the biological function of IKAP, particularly within the context of an animal model, remains poorly characterized. We used a loss-of-function approach
Cem Albayrak et al.
Nucleic acids research, 41(11), 5949-5963 (2013-04-17)
We describe a new cell-free protein synthesis (CFPS) method for site-specific incorporation of non-natural amino acids (nnAAs) into proteins in which the orthogonal tRNA (o-tRNA) and the modified protein (i.e. the protein containing the nnAA) are produced simultaneously. Using this
Xiangyun Wu et al.
Gene, 533(1), 439-446 (2013-10-03)
In contrast to the extreme conservation of nuclear-encoded tRNAs, organization of the mitochondrial (mt) tRNA gene family in invertebrates is highly dynamic and rapidly evolving. While gene duplication and loss, gene isomerism, recruitment, and rearrangements have occurred sporadically in several
David S Tourigny et al.
Science (New York, N.Y.), 340(6140), 1235490-1235490 (2013-07-03)
A key step of translation by the ribosome is translocation, which involves the movement of messenger RNA (mRNA) and transfer RNA (tRNA) with respect to the ribosome. This allows a new round of protein chain elongation by placing the next
Naohiro Terasaka et al.
Nature chemical biology, 10(7), 555-557 (2014-06-09)
The Watson-Crick base pairs between the 3'-terminal end of tRNAs and ribosomal RNA in the peptidyl transferase center are universally conserved. Here, we report that the introduction of compensatory mutations to Escherichia coli RNAs in this site leads to an
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