3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

We must : twenty-two notes on the way to self-perfection / by Swami Chinmayananda.

http://www.archive.org/details/wemusttwentytwo00chinuoft

Participation in Self-Collection of Maternal and Infant DNA in a Case-Control Study on Clubfoot

National Institute of Child Health and Human Development (HD051804)

Performance Evaluation of Two-Shadow Speculative Concurrency Control

Speculative Concurrency Control (SCC) [Best92a] is a new concurrency control approach especially suited for real-time database applications. It relies on the use of redundancy to ensure that serializable schedules are discovered and adopted as early as possible, thus increasing the likelihood of the timely commitment of transactions with strict timing constraints. In [Best92b], SCC-nS, a generic algorithm that characterizes a family of SCC-based algorithms was described, and its correctness established by showing that it only admits serializable histories. In this paper, we evaluate the performance of the Two-Shadow SCC algorithm (SCC-2S), a member of the SCC-nS family, which is notable for its minimal use of redundancy. In particular, we show that SCC-2S (as a representative of SCC-based algorithms) provides significant performance gains over the widely used Optimistic Concurrency Control with Broadcast Commit (OCC-BC), under a variety of operating conditions and workloads.

A Self-Organizing Neural Model for Motor Equivalent Phoneme Production

This paper describes a model of speech production called DIVA that highlights issues of self-organization and motor equivalent production of phonological units. The model uses a circular reaction strategy to learn two mappings between three levels of representation. Data on the plasticity of phonemic perceptual boundaries motivates a learned mapping between phoneme representations and vocal tract variables. A second mapping between vocal tract variables and articulator movements is also learned. To achieve the flexible control made possible by the redundancy of this mapping, desired directions in vocal tract configuration space are mapped into articulator velocity commands. Because each vocal tract direction cell learns to activate several articulator velocities during babbling, the model provides a natural account of the formation of coordinative structures. Model simulations show automatic compensation for unexpected constraints despite no previous experience or learning under these constraints.

A Self-Organizing Neural Network Model for Redundant Sensory-Motor Control, Motor Equivalence, and Tool Use

A neural network is introduced which provides a solution of the classical motor equivalence problem, whereby many different joint configurations of a redundant manipulator can all be used to realize a desired trajectory in 3-D space. To do this, the network self-organizes a mapping from motion directions in 3-D space to velocity commands in joint space. Computer simulations demonstrate that, without any additional learning, the network can generate accurate movement commands that compensate for variable tool lengths, clamping of joints, distortions of visual input by a prism, and unexpected limb perturbations. Blind reaches have also been simulated.