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Erin heyer

Erin E Heyer, Melissa J Moore
Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remain controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ∼ 590 nt, and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation...
February 11, 2016: Cell
Todd T Eckdahl, A Malcolm Campbell, Laurie J Heyer, Jeffrey L Poet, David N Blauch, Nicole L Snyder, Dustin T Atchley, Erich J Baker, Micah Brown, Elizabeth C Brunner, Sean A Callen, Jesse S Campbell, Caleb J Carr, David R Carr, Spencer A Chadinha, Grace I Chester, Josh Chester, Ben R Clarkson, Kelly E Cochran, Shannon E Doherty, Catherine Doyle, Sarah Dwyer, Linnea M Edlin, Rebecca A Evans, Taylor Fluharty, Janna Frederick, Jonah Galeota-Sprung, Betsy L Gammon, Brandon Grieshaber, Jessica Gronniger, Katelyn Gutteridge, Joel Henningsen, Bradley Isom, Hannah L Itell, Erica C Keffeler, Andrew J Lantz, Jonathan N Lim, Erin P McGuire, Alexander K Moore, Jerrad Morton, Meredith Nakano, Sara A Pearson, Virginia Perkins, Phoebe Parrish, Claire E Pierson, Sachith Polpityaarachchige, Michael J Quaney, Abagael Slattery, Kathryn E Smith, Jackson Spell, Morgan Spencer, Telavive Taye, Kamay Trueblood, Caroline J Vrana, E Tucker Whitesides
Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem...
2015: PloS One
Erin M Fedak, Anup D Patel, Geoffrey L Heyer, Eric G Wood, John R Mytinger
The primary aim of this quality improvement initiative was to increase the number of patients receiving first-line therapy (adrenocorticotropic hormone, corticosteroids, vigabatrin) as the initial treatment for infantile spasms. We implemented a standardized management protocol for infantile spasms based on the best available data and expert consensus. To assess the impact of this intervention, we compared the 3-month remission rates between prestandardization (January 2009 to August 2012) and poststandardization (September 2012 to May 2014) cohorts...
September 2015: Journal of Child Neurology
Erin E Heyer, Hakan Ozadam, Emiliano P Ricci, Can Cenik, Melissa J Moore
Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs...
January 2015: Nucleic Acids Research
Emiliano P Ricci, Alper Kucukural, Can Cenik, Blandine C Mercier, Guramrit Singh, Erin E Heyer, Ami Ashar-Patel, Lingtao Peng, Melissa J Moore
Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3' untranslated regions (UTRs) or in 'strongly distal' 3' UTRs...
January 2014: Nature Structural & Molecular Biology
Erin M Fedak, Nicholas A Zumberge, Geoffrey L Heyer
BACKGROUND: Hemiplegic migraine is a rare form of migraine with aura that includes motor weakness. Diagnosis during the first episode can be difficult to make and costly, especially with the sporadic form. CASES: Our study evaluates the ictal magnetic resonance imaging (MRI) features of four sequential pediatric patients during a first-time, sporadic hemiplegic migraine. Susceptibility-weighted imaging (SWI) revealed cerebral venous prominence and increased magnetic susceptibility affecting brain regions that corresponded with each patient's neurologic deficits...
November 2013: Cephalalgia: An International Journal of Headache
Geoffrey L Heyer, Erin M Fedak, Aggie L LeGros
OBJECTIVE: To identify symptoms that may predict postural tachycardia syndrome (POTS) among adolescent patients with headache and lightheadedness referred for tilt table testing. BACKGROUND: Individuals with POTS can have a variety of symptoms that impair quality of life. The specific symptoms that help to distinguish the POTS patient in an adolescent headache population have not been determined. METHODS: A group of symptoms was compared among 70 adolescent patients with headache and lightheadedness referred to a pediatric headache clinic for tilt table testing...
June 2013: Headache
Erin K Schwartz, William D Wright, Kirk T Ehmsen, James E Evans, Henning Stahlberg, Wolf-Dietrich Heyer
The formation of crossovers is a fundamental genetic process. The XPF-family endonuclease Mus81-Mms4 (Eme1) contributes significantly to crossing over in eukaryotes. A key question is whether Mus81-Mms4 can process Holliday junctions that contain four uninterrupted strands. Holliday junction cleavage requires the coordination of two active sites, necessitating the assembly of two Mus81-Mms4 heterodimers. Contrary to this expectation, we show that Saccharomyces cerevisiae Mus81-Mms4 exists as a single heterodimer both in solution and when bound to DNA substrates in vitro...
August 2012: Molecular and Cellular Biology
Sandra Muñoz-Galván, Cristina Tous, Miguel G Blanco, Erin K Schwartz, Kirk T Ehmsen, Stephen C West, Wolf-Dietrich Heyer, Andrés Aguilera
Most spontaneous DNA double-strand breaks (DSBs) arise during replication and are repaired by homologous recombination (HR) with the sister chromatid. Many proteins participate in HR, but it is often difficult to determine their in vivo functions due to the existence of alternative pathways. Here we take advantage of an in vivo assay to assess repair of a specific replication-born DSB by sister chromatid recombination (SCR). We analyzed the functional relevance of four structure-selective endonucleases (SSEs), Yen1, Mus81-Mms4, Slx1-Slx4, and Rad1, on SCR in Saccharomyces cerevisiae...
May 2012: Molecular and Cellular Biology
Erin K Schwartz, Wolf-Dietrich Heyer
Homologous recombination is required for maintaining genomic integrity by functioning in high-fidelity repair of DNA double-strand breaks and other complex lesions, replication fork support, and meiotic chromosome segregation. Joint DNA molecules are key intermediates in recombination and their differential processing determines whether the genetic outcome is a crossover or non-crossover event. The Holliday model of recombination highlights the resolution of four-way DNA joint molecules, termed Holliday junctions, and the bacterial Holliday junction resolvase RuvC set the paradigm for the mechanism of crossover formation...
April 2011: Chromosoma
David E Wilkes, Nicole Bennardo, Clarence W C Chan, Yu-Loung Chang, Elizabeth O Corpuz, Jennifer DuMond, Jordan A Eboreime, Julianna Erickson, Jonathan Hetzel, Erin E Heyer, Mark J Hubenschmidt, Ekaterina Kniazeva, Hallie Kuhn, Michelle Lum, Andrea Sand, Alicia Schep, Oksana Sergeeva, Natt Supab, Caroline R Townsend, Liesl Van Ryswyk, Hadley E Watson, Alice E Wiedeman, Vidyalakshmi Rajagopalan, David J Asai
We describe the protocol through which we identify and characterize dynein subunit genes in the ciliated protozoan Tetrahymena thermophila. The gene(s) of interest is found by searching the Tetrahymena genome, and it is characterized in silico including the prediction of the open reading frame and identification of likely introns. The gene is then characterized experimentally, including the confirmation of the exon-intron organization of the gene and the measurement of the expression of the gene in nondeciliated and reciliating cells...
2009: Methods in Cell Biology
Karmella A Haynes, Marian L Broderick, Adam D Brown, Trevor L Butner, James O Dickson, W Lance Harden, Lane H Heard, Eric L Jessen, Kelly J Malloy, Brad J Ogden, Sabriya Rosemond, Samantha Simpson, Erin Zwack, A Malcolm Campbell, Todd T Eckdahl, Laurie J Heyer, Jeffrey L Poet
BACKGROUND: We investigated the possibility of executing DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA...
2008: Journal of Biological Engineering
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