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Articles by K. Collins
Total Records ( 3 ) for K. Collins
  M. T Couvillion , S. R Lee , B Hogstad , C. D Malone , L. A Tonkin , R Sachidanandam , G. J Hannon and K. Collins

PAZ/PIWI domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23- to 24-nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether, Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length, while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs.

  J. Petrofsky , H. J. Suh , A. Fish , V. Hernandez , A. Abdo , K. Collins , E. Mendoza and T. -N. Yang
  When electrical stimulation is used on wounds, the electrical current has difficulty penetrating areas where there is necrotic tissue. Further, for an irregularly shaped wound, current distribution is poor in some areas of the wound since conventional two-electrode delivery systems provide the greatest current in a line directly between the electrodes. A new stimulator and electrode system is described which uses three electrodes spaced around a wound to disperse current more evenly. The stimulator senses tissue impedance and then redirects current by altering its Thevenin’s output impedance for each electrode; each of the three electrodes becomes the active one in sequence while the remaining are the sink electrodes. Eight subjects were examined to test the stimulator. Electrical stimulation was applied to the skin above the quadriceps muscle at currents of 15┬ámA in six subjects without wounds and in two subjects with wounds. The relationship between electrode position and current dispersion on the skin was examined with a two-electrode vs. a three-electrode system to set stimulation parameters for the computer. The results showed that the three-electrode system could (1) detect areas of the skin with high impedance; (2) compensate by altering the Thevenin’s output impedance at each of the three electrodes to shift current to high impedance areas; (3) provide uniform current across the skin as assessed by skin current and blood flow measurements with a laser Doppler flow imager.
  S. R Lee , K. B Talsky and K. Collins

Members of the conserved family of eukaryotic RNA-dependent RNA polymerases (Rdrs) synthesize double-stranded RNA (dsRNA) intermediates in diverse pathways of small RNA (sRNA) biogenesis and RNA-mediated silencing. Rdr-dependent pathways of sRNA production are poorly characterized relative to Rdr-independent pathways, and the Rdr enzymes themselves are poorly characterized relative to their viral RNA-dependent RNA polymerase counterparts. We previously described a physical and functional coupling of the Tetrahymena thermophila Rdr, Rdr1, and a Dicer enzyme, Dcr2, in the production of ~24-nucleotide (nt) sRNA in vitro. Here we characterize the endogenous complexes that harbor Rdr1, termed RDRCs. Distinct RDRCs assemble to contain Rdr1 and subsets of the total of four tightly Rdr1-associated proteins. Of particular interest are two RDRC subunits, Rdn1 and Rdn2, which possess noncanonical ribonucleotidyl transferase motifs. We show that the two Rdn proteins are uridine-specific polymerases of separate RDRCs. Two additional RDRC subunits, Rdf1 and Rdf2, are present only in RDRCs containing Rdn1. Rdr1 catalytic activity is retained in RDRCs purified from cell extracts lacking any of the nonessential RDRC subunits (Rdn2, Rdf1, Rdf2) or if the RDRC harbors a catalytically inactive Rdn. However, specific disruption of each RDRC imposes distinct loss-of-function consequences at the cellular level and has a differential impact on the accumulation of specific 23–24-nt sRNA sequences in vivo. The biochemical and biological phenotypes of RDRC subunit disruption reveal a previously unanticipated complexity of Rdr-dependent sRNA biogenesis in vivo.

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