Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

<p>Abstract</p> <p>Background</p> <p>Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.</p> <p>Results</p> <p>We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt) not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundant human pre-mRNA sequences has been carried out. Four distinct components of these molecules (5'-UTRs, exons, introns and 3'-UTRs) were considered separately, since they differ in overall nucleotide composition, sequence motifs and periodicities. For each pre-mRNA component, the abundance of strong local SS (< -25 kcal/mol) was a factor of two to ten greater than a random expectation model. The randomization process preserves the short-range inhomogeneity of the corresponding natural sequences, thus, eliminating short-range signals as possible contributors to any observed phenomena.</p> <p>Conclusion</p> <p>We demonstrate that the excess of strong local SS in pre-mRNAs is linked to the little explored phenomenon of genomic mid-range inhomogeneity (MRI). MRI is an interdependence between nucleotide choice and base composition over a distance of 20–1000 nt. Additionally, we have created a public computational resource to support further study of genomic MRI.</p

An efficient and accurate method of estimating substrate noise coupling in heavily doped substrates

This thesis presents a Z-parameter based model to predict the substratenoise coupling between two contacts in a heavily doped substrate for frequenciesless than 2 GHz. The empirical model is scalable with contact size and spacingsbetween the contacts and model parameters can be readily extracted from simu-lated or measured data. The error is within acceptable limits and computationalcosts associated with extraction of substrate parasitics is significantly reduced byusing this model compared to numerical techniques. An application of the modelto analyze the substrate noise coupling between a digital and analog block is alsodemonstrated

Synthesis, Characterization and Biological Activity of Mn2+, Co2+, Ni2+ and Cu2+ Complexes of Benzoic Acid Ligand

Metal complex of Mn(II), Co(II), Ni(II) and Cu(II) with benzoic acid have been prepared and characterized by physiochemical methods. On the basis of electronic spectra and magnetic susceptibility measurement in conjunction with infrared spectra, six coordinated octahedral structure have been proposed to all the complexes. The benzoic acid and their complexes have been tested for their antibacterial activity against the bacteria E. coli, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus. Further, the non electrolytic nature of all the synthesized complexes was identified from conductivity measurements

An Efficient and Accurate Method of Estimating Substrate Noise Coupling in Heavily Doped Substrates

Abstract approved