Loss of nonsense mediated decay suppresses mutations in Saccharomyces cerevisiae TRA1

<p>Abstract</p> <p>Background</p> <p>Tra1 is an essential protein in <it>Saccharomyces cerevisiae</it>. It was first identified in the SAGA and NuA4 complexes, both with functions in multiple aspects of gene regulation and DNA repair, and recently found in the ASTRA complex. Tra1 belongs to the PIKK family of proteins with a C-terminal PI3K domain followed by a FATC domain. Previously we found that mutation of leucine to alanine at position 3733 in the FATC domain of Tra1 (<it>tra1-L3733A</it>) results in transcriptional changes and slow growth under conditions of stress. To further define the regulatory interactions of Tra1 we isolated extragenic suppressors of the <it>tra1-L3733A </it>allele.</p> <p>Results</p> <p>We screened for suppressors of the ethanol sensitivity caused by <it>tra1-L3733A</it>. Eleven extragenic recessive mutations, belonging to three complementation groups, were identified that partially suppressed a subset of the phenotypes caused by tra<it>1-L3733A</it>. Using whole genome sequencing we identified one of the mutations as an opal mutation at tryptophan 165 of <it>UPF1/NAM7</it>. Partial suppression of the transcriptional defect resulting from <it>tra1-L3733A </it>was observed at <it>GAL10</it>, but not at <it>PHO5</it>. Suppression was due to loss of nonsense mediated decay (NMD) since deletion of any one of the three NMD surveillance components (<it>upf1/nam7, upf2/nmd2</it>, or <it>upf3</it>) mediated the effect. Deletion of <it>upf1 </it>suppressed a second FATC domain mutation, <it>tra1-F3744A</it>, as well as a mutation to the PIK3 domain. In contrast, deletions of SAGA or NuA4 components were not suppressed.</p> <p>Conclusions</p> <p>We have demonstrated a genetic interaction between <it>TRA1 </it>and genes of the NMD pathway. The suppression is specific for mutations in <it>TRA1</it>. Since NMD and Tra1 generally act reciprocally to control gene expression, and the FATC domain mutations do not directly affect NMD, we suggest that suppression occurs as the result of overlap and/or crosstalk in these two broad regulatory networks.</p

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology.

BACKGROUND: A normally developed placenta is integral to a successful pregnancy. Preeclampsia (PE) and intrauterine growth restriction (IUGR) are two common pregnancy related complications that maybe a result of abnormal placental development. Placental microRNAs (miRNAs) have been investigated as potential biomarkers for these complications, as they may play a role in placental development and pathophysiology by influencing gene expression. The purpose of this study is to utilize next-generation sequencing to determine miRNA and gene expression in human placental (chorionic villous) samples from three distinct patient groups with early-onset (EO) PE, IUGR, or PE + IUGR. METHODS: Placental tissues were collected from four patient groups (control [N = 21], EO-PE [N = 20], EO-IUGR [N = 18], and EO-PE + IUGR [N = 20]), and total RNA was used for miRNA and RNA sequencing on the Illumina Hiseq2000 platform. For stringent differential expression analysis multiple analysis programs were used to analyze both expression datasets in each patient group compared to gestational age-matched controls. RESULTS: Analysis revealed miRNAs and genes that are disease-specific, as well as others that were common between disease groups, which suggests common underlying placental pathologies in EO-PE and EO-IUGR. More specifically, 6 miRNAs and 22 genes were identified to be differentially expressed in all three patient groups. In addition, integrative analysis between the miRNA and gene expression datasets revealed candidate gene targets for miRNAs of interest. CONCLUSIONS: Integration of miRNA and RNA profiling in the same three subgroups of pregnancy complications, provides an alternate level of molecular information, in addition it can be used to better understand both unique and common molecular mechanisms involved in the pathophysiology of these diseases

Laparoscopic ventral hernia repair is safe and cost effective

Background: Ventral hernia repair is increasingly performed by laparoscopic means since the introduction of dual-layer meshes. This study aimed to compare the early complications and cost effectiveness of open hernia repair with those associated with laparoscopic repair. Methods: Open ventral hernia repair was performed for 92 consecutive patients using a Vypro mesh, followed by laparoscopic repair for 49 consecutive patients using a Parietene composite mesh. Results: The rate of surgical-site infections was significantly higher with open ventral hernia repair (13 vs 1; p = 0.03). The median length of hospital stay was significantly shorter with laparoscopic surgery (7 vs 6 days; p = 0.02). For laparoscopic repair, the direct operative costs were higher (2,314 vs 2,853 euros; p = 0.03), and the overall hospital costs were lower (9,787 vs 7,654 euros; p = 0.02). Conclusions: Laparoscopic ventral hernia repair leads to fewer surgical-site infections and a shorter hospital stay than open repair. Despite increased operative costs, overall hospital costs are lowered by laparoscopic ventral hernia repai

A Visualization System for Correctness Proofs of Graph Algorithms

In this paper we describe a system for visualizing correctness proofs of graph algorithms. The system has been demonstrated for a greedy algorithm. Prim\u27s algorithm for finding a minimum spanning tree of an undirected, weighted graph. We believe that our system is particularly appropriate for greedy algorithms, though much of what we discuss can guide visualization of proofs in other contexts. While an example is not a proof, our system provides concrete examples to illustrate the operation of the algorithm. These examples can be referred to by the user interactively and alternatively with the visualization of the proof where the general case is portrayed abstractly

Theory of Ferromagnetism in Doped Excitonic Condensates

Nesting in a semimetal can lead to an excitonic insulator state with spontaneous coherence between conduction and valence bands and a gap for charged excitations. In this paper we present a theory of the ferromagnetic state that occurs when the density of electrons in the conduction band and holes in the valence band differ. We find an unexpectedly rich doping-field phase diagram and an unusual collective excitation spectrum that includes two gapless collective modes. We predict regions of doping and external field in which phase-separated condensates of electrons and holes with parallel spins and opposing spins coexist.Comment: 5 pages, 3 postscript file

Microbiome datasets are compositional: and this is not optional

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data. The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis. We briefly introduce compositional data, illustrate the pathologies that occur when compositional data are analyzed inappropriately, and finally give guidance and point to resources and examples for the analysis of microbiome datasets using compositional data analysis.Peer ReviewedPostprint (published version

The microbiota of breast tissue and its association with breast cancer

In the United States, 1 in 8 women will be diagnosed with breast cancer in her lifetime. Along with genetics, the environmentcontributes to disease development, but what these exact environmental factors are remains unknown. We have previouslyshown that breast tissue is not sterile but contains a diverse population of bacteria. We thus believe that the host\u27s local microbiomecould be modulating the risk of breast cancer development. Using 16S rRNA amplicon sequencing, we show that bacterialprofiles differ between normal adjacent tissue from women with breast cancer and tissue from healthy controls. Women withbreast cancer had higher relative abundances of Bacillus, Enterobacteriaceae and Staphylococcus. Escherichia coli (a member ofthe Enterobacteriaceae family) and Staphylococcus epidermidis, isolated from breast cancer patients, were shown to induce DNAdouble-stranded breaks in HeLa cells using the histone-2AX (H2AX) phosphorylation (γ-H2AX) assay. We also found that microbialprofiles are similar between normal adjacent tissue and tissue sampled directly from the tumor. This study raises importantquestions as to what role the breast microbiome plays in disease development or progression and how we can manipulatethis for possible therapeutics or prevention