The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes

We synthesized a series of puromycin analogues to probe the chemical specificity of the ribosome in an intact eukaryotic translation system. These studies reveal that both d-enantiomers and β-amino acid analogues can be incorporated into protein, and provide a quantitative means to rank natural and unnatural residues. Modeling of a d-amino acid analogue into the 50S ribosomal subunit indicates that steric clash may provide part of the chiral discrimination. The data presented provide one metric of the chiral and regiospecificity of mammalian ribosomes

Detectability subspaces and observer synthesis for two-dimensional systems

The notions of input-containing and detectability subspaces are developed within the context of observer synthesis for two-dimensional (2-D) Fornasini-Marchesini models. Specifically, the paper considers observers which asymptotically estimate the local state, in the sense that the error tends to zero as the reconstructed local state evolves away from possibly mismatched boundary values, modulo a detectability subspace. Ultimately, the synthesis of such observers in the absence of explicit input information is addressed

Composition codes

In this paper we introduce a special class of 2D convolutional codes, called composition codes, which admit encoders G(d1,d2) that can be decomposed as the product of two 1D encoders, i.e., G(d1,d2)=G2(d2)G1(d1). Taking into account this decomposition, we obtain syndrome formers of the code directly from G1(d1) andG2(d2), in case G1(d1) andG2(d2) are right prime. Moreover we consider 2D state-space realizations by means of a separable Roesser model of the encoders and syndrome formers of a composition code and we investigate the minimality of such realizations. In particular, we obtain minimal realizations for composition codes which admit an encoder G(d1,d2)=G2(d2)G1(d1) withG2(d2) a systematic 1D encoder. Finally, we investigate the minimality of 2D separable Roesser state-space realizations for syndrome formers of these codes.publishe

Both U2 snRNA and U12 snRNA are required for accurate splicing of exon 5 of the rat calcitonin/CGRP gene

Two classes of spliceosome are present in eukaryotic cells. Most introns in nuclear pre-mRNAs are removed by a spliceosome that requires U1, U2, U4, U5, and U6 small nuclear ribonucleoprotein particles (snRNPs). A minor class of introns are removed by a spliceosome containing U11, U12, U5, U4atac, and U6 atac snRNPs. We describe experiments that demonstrate that splicing of exon 5 of the rat calcitonin/CGRP gene requires both U2 snRNA and U12 snRNA. In vitro, splicing to calcitonin/ CGRP exon 5 RNA was dependent on U2 snRNA, as preincubation of nuclear extract with an oligonucleotide complementary to U2 snRNA abolished exon 5 splicing. Addition of an oligonucleotide complementary to U12 snRNA increased splicing at a cryptic splice site in exon 5 from <5% to 50% of total spliced RNA. Point mutations in a candidate U12 branch sequence in calcitonin/CGRP intron 4, predicted to decrease U12-pre-mRNA base-pairing, also significantly increased cryptic splicing in vitro. Calcitonin/CGRP genes containing base changes disrupting the U12 branch sequence expressed significantly decreased CGRP mRNA levels when expressed in cultured cells. Coexpression of U12 snRNAs containing base changes predicted to restore U12-pre-mRNA base pairing increased CGRP mRNA synthesis to the level of the wild-type gene. These observations indicate that accurate, efficient splicing of calcitonin/CGRP exon 5 is dependent upon both U2 and U12 snRNAs